From b2b617f9f3c9afeaca50e23318bf53186f3c87d4 Mon Sep 17 00:00:00 2001
From: Daniel Poppleton <111403332+dpopleton@users.noreply.github.com>
Date: Tue, 13 Jun 2023 15:14:19 +0100
Subject: [PATCH 001/128] Added a failure if gzip fails to complete properly
 (#804)

* Added a failure if gzip fails to complete properly

* Switched backtick gzip to perl package in mysqldump and dumpfile

* bugfix

* revert and fixed the compress calls

* revert and fixed the compress calls

* unpack the arrayref to array

* fixed flat file to pass array reference.

* Removed automatic flow for tsvs

* Readded flow to tsvs and fixed bug with a conditional

* Readded param_required and added optional flow

* Swapped array is empty test for a better one

* removed array test as the files should alwalys be generated

* Swapped array is empty test for a better one and fixed flow

* Modified array ref

---------

Co-authored-by: vinay-ebi <vinay@ebi.ac.uk>
---
 .../Production/Pipeline/Common/Gzip.pm        | 63 +++++++++++++++++++
 .../Production/Pipeline/Flatfile/DumpFile.pm  | 13 ++--
 .../Pipeline/PipeConfig/DumpCore_conf.pm      | 32 ++++++++--
 .../Pipeline/PipeConfig/FileDumpMySQL_conf.pm |  5 +-
 .../Production/Pipeline/TSV/DumpFile.pm       |  9 +--
 .../Production/Pipeline/TSV/DumpFileEna.pm    | 14 ++---
 .../Pipeline/TSV/DumpFileMetadata.pm          | 13 ++--
 .../Production/Pipeline/TSV/DumpFileXref.pm   | 23 ++++---
 8 files changed, 121 insertions(+), 51 deletions(-)
 create mode 100644 modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
new file mode 100644
index 000000000..c0ab3aa48
--- /dev/null
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
@@ -0,0 +1,63 @@
+=head1 LICENSE
+
+Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+Copyright [2016-2023] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=head1 NAME
+
+ Bio::EnsEMBL::Production::Pipeline::Common::Gzip;
+
+=head1 DESCRIPTION
+
+A simple script for gzipping files and catching errors
+
+=head1 AUTHOR
+
+ ckong@ebi.ac.uk 
+
+=cut
+package Bio::EnsEMBL::Production::Pipeline::Common::Gzip;;
+
+use strict;
+use warnings;
+use base qw/Bio::EnsEMBL::Production::Pipeline::Common::Base/;
+use IO::Compress::Gzip qw(gzip $GzipError) ;
+
+sub fetch_input {
+    my ($self) = @_;
+return;
+}
+
+sub run {
+    my ($self) = @_;
+    my @compress = @{$self->param_required('compress')};
+    foreach my $file (@compress) {
+        my $output_file = $file.'.gz';
+        eval {
+            local $SIG{PIPE} = sub { die "gzip interrupted by SIGPIPE\n" };
+            gzip $file => $output_file
+                or die "gzip failed: $GzipError\n";
+            unlink $file;
+        };
+        if ($@) {
+            print "Error compressing '$file': $@\n";
+        } else {
+            print "Compressed '$file' to '$output_file' and removed the original file\n";
+        }
+    }
+return;
+}
+
+1;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
index 1d9115f23..8a02f193a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
@@ -111,7 +111,8 @@ sub run {
     push(@chromosomes, $s) if $chr;
     push(@non_chromosomes, $s) if ! $chr;
   }
-  
+  my @compress = ();
+
   if(@non_chromosomes) {
     my $path = $self->_generate_file_name('nonchromosomal');
     $self->info('Dumping non-chromosomal data to %s', $path);
@@ -123,12 +124,11 @@ sub run {
       }
       return;
     });
-    $self->run_cmd("gzip -n $path");
+    push (@compress, $path);
   } else {
     $self->info('Did not find any non-chromosomal data');
   }
   
-  my @compress = ();
   foreach my $slice (@chromosomes) {
     $self->fine('Dumping chromosome %s', $slice->name());
     my $path = $self->_generate_file_name($slice->coord_system_name(), $slice->seq_region_name());
@@ -147,9 +147,10 @@ sub run {
       return;
     });
   }
-  
-  map { $self->run_cmd("gzip -n $_") } @compress;
-
+  unless (@compress == 0) {
+    $self->dataflow_output_id(
+        { "compress" => \@compress  }, 4);
+  }
   $self->_create_README();
   $self->core_dbc()->disconnect_if_idle();  
   $self->hive_dbc()->disconnect_if_idle();  
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
index 11d90f9c1..ffae16c77 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
@@ -363,7 +363,8 @@ sub pipeline_analyses {
             -parameters    => { type => 'embl', },
             -hive_capacity => 50,
             -rc_name       => '4GB',
-            -flow_into     => { '-1' => 'embl_32GB', },
+            -flow_into     => { '-1' => 'embl_32GB',
+                                 '4' => 'compress_file' },
         },
 
         { -logic_name      => 'embl_32GB',
@@ -371,7 +372,9 @@ sub pipeline_analyses {
             -parameters    => { type => 'embl', },
             -hive_capacity => 50,
             -rc_name       => '32GB',
-            -flow_into     => { '-1' => 'embl_64GB', },
+            -flow_into     => { '-1' => 'embl_64GB',
+                                 '4' => 'compress_file' },
+
         },
 
         { -logic_name      => 'embl_64GB',
@@ -379,7 +382,8 @@ sub pipeline_analyses {
             -parameters    => { type => 'embl', },
             -hive_capacity => 50,
             -rc_name       => '64GB',
-            -flow_into     => { '-1' => 'embl_128GB', },
+            -flow_into     => { '-1' => 'embl_128GB',
+                                 '4' => 'compress_file' },
         },
 
         { -logic_name      => 'embl_128GB',
@@ -387,6 +391,7 @@ sub pipeline_analyses {
             -parameters    => { type => 'embl', },
             -hive_capacity => 50,
             -rc_name       => '128GB',
+            -flow_into => { '4' => 'compress_file' },
         },
 
         ### GENBANK
@@ -395,7 +400,8 @@ sub pipeline_analyses {
             -parameters    => { type => 'genbank', },
             -hive_capacity => 50,
             -rc_name       => '4GB',
-            -flow_into     => { -1 => 'genbank_32GB', },
+            -flow_into     => { -1 => 'genbank_32GB',
+                                '4' => 'compress_file' },
         },
 
         { -logic_name      => 'genbank_32GB',
@@ -403,7 +409,8 @@ sub pipeline_analyses {
             -parameters    => { type => 'genbank', },
             -hive_capacity => 50,
             -rc_name       => '32GB',
-            -flow_into     => { -1 => 'genbank_64GB', },
+            -flow_into     => { -1 => 'genbank_64GB',
+                                 '4' => 'compress_file' },
         },
 
         { -logic_name      => 'genbank_64GB',
@@ -411,7 +418,8 @@ sub pipeline_analyses {
             -parameters    => { type => 'genbank', },
             -hive_capacity => 50,
             -rc_name       => '64GB',
-            -flow_into     => { -1 => 'genbank_128GB', },
+            -flow_into     => { -1 => 'genbank_128GB', 
+                                '4' => 'compress_file' },
         },
 
         { -logic_name      => 'genbank_128GB',
@@ -419,6 +427,7 @@ sub pipeline_analyses {
             -parameters    => { type => 'genbank', },
             -hive_capacity => 50,
             -rc_name       => '128GB',
+            -flow_into => { '4' => 'compress_file' },
         },
 
         ### FASTA (cdna, cds, dna, pep, ncrna)
@@ -585,6 +594,7 @@ sub pipeline_analyses {
             },
             -hive_capacity => 50,
             -rc_name       => '2GB',
+            -flow_into  => { '4' => 'compress_file', },
         },
 
         { -logic_name      => 'tsv_refseq',
@@ -595,6 +605,7 @@ sub pipeline_analyses {
             },
             -hive_capacity => 50,
             -rc_name       => '2GB',
+            -flow_into  => { '4' => 'compress_file', },
         },
 
         { -logic_name      => 'tsv_entrez',
@@ -605,6 +616,7 @@ sub pipeline_analyses {
             },
             -hive_capacity => 50,
             -rc_name       => '2GB',
+            -flow_into  => { '4' => 'compress_file', },
         },
 
 
@@ -612,12 +624,20 @@ sub pipeline_analyses {
             -module        => 'Bio::EnsEMBL::Production::Pipeline::TSV::DumpFileEna',
             -hive_capacity => 50,
             -rc_name       => '2GB',
+            -flow_into  => { '4' => 'compress_file', },
         },
 
         { -logic_name      => 'tsv_metadata',
             -module        => 'Bio::EnsEMBL::Production::Pipeline::TSV::DumpFileMetadata',
             -hive_capacity => 50,
             -rc_name       => '2GB',
+            -flow_into  => { '4' => 'compress_file', },
+
+        },
+        { -logic_name      => 'compress_file',
+            -module        => 'Bio::EnsEMBL::Production::Pipeline::Common::Gzip',
+            -hive_capacity => 50,
+            -rc_name       => '4GB',
         },
 
     ];
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
index eea53b623..6a3587c1e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
@@ -201,14 +201,13 @@ sub pipeline_analyses {
         },
         {
             -logic_name        => 'MySQL_Compress',
-            -module            => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -module            => 'Bio::EnsEMBL::Production::Pipeline::Common::Gzip',
             -max_retry_count   => 1,
             -analysis_capacity => 10,
             -batch_size        => 10,
             -parameters        => {
-                cmd => 'gzip -n -f "#output_filename#"',
+                compress => "#output_filename#",
             },
-            -rc_name           => '1GB',
         },
         {
             -logic_name        => 'Checksum',
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
index 2c40cb13d..8dffe30b6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
@@ -55,7 +55,6 @@ return;
 
 sub run {
     my ($self) = @_;
-
     $self->info( "Starting tsv dump for " . $self->param('species'));
     $self->_write_tsv();
     $self->_create_README();
@@ -115,14 +114,8 @@ sub _write_tsv {
          }#transcript
       }#gene
   }#slice 
-  close $fh; 
+  close $fh;
   $self->core_dbc()->disconnect_if_idle();
-  $self->info( "Compressing tsv dump for " . $self->param('species'));
-  my $unzip_out_file = $out_file;
-  `gzip -n $unzip_out_file`;
-
-  if (-e $unzip_out_file) { `rm $unzip_out_file`; }
-
 return;
 }
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
index 9bf179adb..6d4b2ad95 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
@@ -64,7 +64,7 @@ sub _write_tsv {
     my ($self) = @_;
 
     my $out_file  = $self->_generate_file_name();
-    my $header    = $self->_build_headers();   
+    my $header    = $self->_build_headers();
 
     open my $fh, '>', $out_file or die "cannot open $out_file for writing!";
     print $fh join ("\t", @$header);
@@ -107,8 +107,8 @@ sub _write_tsv {
         if(!defined $row->[5]){
 	   $row->[5] = $self->_find_contig($ta, $contig_ids, $row->[3] );
         } elsif( !defined $row->[6] && defined $row->[4]){
-	   $row->[6] = $cds2acc->{$row->[4]}; 
- 	} 
+	   $row->[6] = $cds2acc->{$row->[4]};
+ 	}
 
 	if (defined $row->[5]) {
             $row->[5] =~ s/\.[0-9]+$//;
@@ -121,11 +121,9 @@ sub _write_tsv {
     close $fh;
 
     if ($xrefs_exist == 1) {
-      $self->info( "Compressing ENA tsv dump for " . $self->param('species'));
-      my $unzip_out_file = $out_file;
-      `gzip -n $unzip_out_file`;
-    } else {
-      # If we have no xrefs, delete the file (which will just have a header).
+        $self->dataflow_output_id(
+            { "compress" => [ $out_file ] }, 4);
+    }else{
       unlink $out_file  or die "failed to delete $out_file!";
     }
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
index 1b2560acb..271bb4c57 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
@@ -70,9 +70,9 @@ return;
 
 sub run {
   my ($self) = @_;
-  
+
   $self->_make_karyotype_file();
-  
+
 return;
 }
 
@@ -81,7 +81,7 @@ sub _make_karyotype_file {
 
     my $sp = $self->param_required('species');
     my $sa = Bio::EnsEMBL::Registry->get_adaptor($sp, 'core', 'slice');
-   
+
     if(! $sa) {
         $self->info("Cannot continue as we cannot find a core:slice DBAdaptor for %s", $sp);
         return;
@@ -92,7 +92,7 @@ sub _make_karyotype_file {
     my $slices = $sa->fetch_all_karyotype();
     # If we don't have any slices (ie. chromosomes), don't make the file
     return unless(scalar(@$slices));
- 
+
     my $file = $self->_generate_file_name();
   
     work_with_file($file, 'w', sub {
@@ -103,10 +103,7 @@ sub _make_karyotype_file {
       }
    });
 
-  $self->info( "Compressing tsv dump for " . $sp);
-  my $unzip_file = $file;
-  `gzip -n $unzip_file`;
-
+      $self->dataflow_output_id({ "compress" => [$file] }, 4);
 return;
 }
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
index 8064d68c3..9d466cd33 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
@@ -66,7 +66,9 @@ sub run {
 
 return;
 }
+sub write {
 
+}
 #############
 ##SUBROUTINES
 #############
@@ -74,7 +76,7 @@ sub _write_tsv {
     my ($self) = @_;
 
     my $out_file  = $self->_generate_file_name();
-    my $header    = $self->_build_headers();   
+    my $header    = $self->_build_headers();
 
     open my $fh, '>', $out_file or die "cannot open $out_file for writing!";
     print $fh join ("\t", @$header);
@@ -112,9 +114,9 @@ sub _write_tsv {
                    my $xref_db       = $dbentry->dbname();
                    my $xref_info_type= $dbentry->info_type();
 
-                   if ($dbentry->isa('Bio::EnsEMBL::IdentityXref')){ 
- 		      $src_identity  = $dbentry->ensembl_identity(); 
-                      $xref_identity = $dbentry->xref_identity(); 
+                   if ($dbentry->isa('Bio::EnsEMBL::IdentityXref')){
+ 		      $src_identity  = $dbentry->ensembl_identity();
+                      $xref_identity = $dbentry->xref_identity();
                    }
 		   $linkage_type = join(' ', @{$dbentry->get_all_linkage_types()})if($dbentry->isa('Bio::EnsEMBL::OntologyXref'));
                    print $fh "$g_id\t$tr_id\t$tl_id\t$xref_id\t$xref_db\t$xref_info_type\t$src_identity\t$xref_identity\t$linkage_type\n";
@@ -122,20 +124,17 @@ sub _write_tsv {
 	       }#dbentry
          }#transcript
       }#gene
-  }#slice 
-  close $fh; 
+  }#slice
+  close $fh;
 
-  if ($xrefs_exist == 1) {
-    $self->info( "Compressing tsv dump for " . $self->param('species'));
-    my $unzip_out_file = $out_file;
-    `gzip -n $unzip_out_file`;
 
-    if (-e $unzip_out_file) { `rm $unzip_out_file`; }
+  if ($xrefs_exist == 1) {
+      $self->dataflow_output_id(
+              { "compress" => [$out_file] }, 4);
   } else {
     # If we have no xrefs, delete the file (which will just have a header).
     unlink $out_file  or die "failed to delete $out_file!";
   }
-
 return;
 }
 

From 5ea62afa2751305471f279d55f83f218c86fb81a Mon Sep 17 00:00:00 2001
From: Daniel Poppleton <111403332+dpopleton@users.noreply.github.com>
Date: Mon, 19 Jun 2023 12:50:22 +0100
Subject: [PATCH 002/128] Added Gzip check for array (#808)

---
 modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
index c0ab3aa48..b2c216738 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
@@ -42,7 +42,12 @@ return;
 
 sub run {
     my ($self) = @_;
-    my @compress = @{$self->param_required('compress')};
+    my @compress = ();
+    if (ref $self->param_required('compress') eq 'ARRAY') {
+        @compress = @{$self->param_required('compress')};
+    }else{
+        push(@compress, $self->param_required('compress'))
+    }
     foreach my $file (@compress) {
         my $output_file = $file.'.gz';
         eval {

From ab54cdf911764461dec6e98b8d9684269476d133 Mon Sep 17 00:00:00 2001
From: Paulo Lins <plins@codon-login-01.ebi.ac.uk>
Date: Tue, 18 Jul 2023 10:34:33 +0100
Subject: [PATCH 003/128] fix data_files path removig the vertebrates folder

---
 scripts/py/regulation_ftp_symlinks.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 822a2b3aa..05307c6ee 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -49,8 +49,8 @@
 GENE_SWITCH_SPECIES = ["sus_scrofa", "gallus_gallus", "gallus_gallus_gca000002315v5"]
 
 PUBLIC_PUB_PATH = "PUBLIC/pub"
-DATA_FILES_PATH = "data_files/vertebrates/"
-DATA_FILES_PATH_TEMPLATE = "{ftp_path}/data_files/vertebrates/{species}/{assembly}/funcgen"
+DATA_FILES_PATH = "data_files/"
+DATA_FILES_PATH_TEMPLATE = "{ftp_path}/data_files/{species}/{assembly}/funcgen"
 RELEASE_FOLDER_PATH_TEMPLATE = "{ftp_path}/release-{release}/regulation/{species}/{assembly}"
 MISC_GENE_SWITCH_PATH_TEMPLATE = "{ftp_path}/misc/gene-switch/regulation/{species}/{assembly}"
 

From fc8f6437503ff1efd7dd5af9d4615042ba5c7733 Mon Sep 17 00:00:00 2001
From: Paulo Lins <plins@codon-login-01.ebi.ac.uk>
Date: Tue, 18 Jul 2023 12:58:00 +0100
Subject: [PATCH 004/128] point symlink to the analysis_type folder and not to
 the release folder

---
 scripts/py/regulation_ftp_symlinks.py | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 05307c6ee..ea42794f2 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -173,15 +173,15 @@ def get(self, key):
     def symlink2rf(self, only_remove=False, relative=True):
 
         target = (
-            Path(path.relpath(self.target, self.sources["release_folder"]))
+            Path(path.relpath(self.target, self.sources["release_folder"])) / "peaks"
             if relative
-            else self.target
+            else self.target / "peaks"
         )
         source = self.sources["release_folder"] / self.get("analysis_type")
 
         self._symlink(source, target, only_remove)
 
-    def symlink2misc(self, only_remove=False, relative=True):
+    def symlink2misc(self, analysis_type, only_remove=False, relative=True):
 
         if self.get("species") not in GENE_SWITCH_SPECIES:
             return None, None
@@ -190,9 +190,9 @@ def symlink2misc(self, only_remove=False, relative=True):
             makedirs(self.sources["misc_folder"])
 
         target = (
-            Path(path.relpath(self.target, self.sources["misc_folder"]))
+            Path(path.relpath(self.target, self.sources["misc_folder"])) / analysis_type
             if relative
-            else self.target
+            else self.target / analysis_type
         )
         source = self.sources["misc_folder"] / self.get("analysis_type")
 
@@ -205,7 +205,7 @@ def _symlink(self, source, target, only_remove):
 
         if not only_remove:
             source.symlink_to(target, target_is_directory=True)
-            if validator.is_symlink(source):
+            if validator.is_symlink(source, check=True):
                 logger.info(f"{source} -> {target} --- was successfully created")
         else:
             if not validator.is_symlink(source, check=True):
@@ -278,11 +278,11 @@ def parse_arguments():
     peaks = RegulationSymlinkFTP.search(ANALYSIS_TYPE_PEAKS, ftp_path, args.release_version)
     for peak in peaks:
         peak.symlink2rf(only_remove=args.delete_symlinks)
-        peak.symlink2misc(only_remove=args.delete_symlinks)
+        peak.symlink2misc("peaks", only_remove=args.delete_symlinks)
 
     logger.info("Searching for signals in data_files ...")
     signals = RegulationSymlinkFTP.search(ANALYSIS_TYPE_SIGNAL, ftp_path, args.release_version)
     for signal in signals:
-        signal.symlink2misc(only_remove=args.delete_symlinks)
+        signal.symlink2misc("signal", only_remove=args.delete_symlinks)
 
     logger.info("Process Completed")

From ac3606668ad852bf9873af6f253cf08889c1e72e Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Mon, 25 Sep 2023 08:36:14 +0100
Subject: [PATCH 005/128] Updating test dbs to latest schema

---
 modules/t/test-genome-DBs/homo_sapiens/core/meta.txt   | 4 +++-
 modules/t/test-genome-DBs/homo_sapiens/core/table.sql  | 4 ++--
 modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt  | 4 +++-
 modules/t/test-genome-DBs/homo_sapiens/empty/table.sql | 4 ++--
 modules/t/test-genome-DBs/hp_dump/core/meta.txt        | 4 +++-
 modules/t/test-genome-DBs/hp_dump/core/table.sql       | 4 ++--
 modules/t/test-genome-DBs/multi/compara/meta.txt       | 3 ++-
 modules/t/test-genome-DBs/multi/compara/table.sql      | 2 +-
 modules/t/test-genome-DBs/s_cerevisiae/core/meta.txt   | 4 +++-
 modules/t/test-genome-DBs/s_cerevisiae/core/table.sql  | 4 ++--
 10 files changed, 23 insertions(+), 14 deletions(-)

diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index 811bab016..b78dcfe5c 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	111
+2	\N	schema_version	112
 3	\N	patch	patch_98_99_a.sql|schema_version
 2124	1	xref.timestamp	2013-07-22 11:20:10
 4	\N	patch	patch_52_53_c.sql|identity_xref_rename
@@ -261,3 +261,5 @@
 2217	\N	patch	patch_109_110_b.sql|Add IS_PAR relationship to link X- and Y-PAR genes
 2218	\N	patch	patch_109_110_c.sql|Allow gene id to belong to multiple alt allele groups
 2219	\N	patch	patch_110_111_a.sql|schema_version
+2220	\N	patch	patch_111_112_a.sql|schema_version
+2221	\N	patch	patch_111_112_b.sql|Allow meta_value to be null
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index 70bd53327..676521f52 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -486,11 +486,11 @@ CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
   `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) NOT NULL,
+  `meta_value` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2220 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2222 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 87b939fd5..1af089f4f 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -1,4 +1,4 @@
-1	\N	schema_version	111
+1	\N	schema_version	112
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -126,3 +126,5 @@
 176	\N	patch	patch_109_110_b.sql|Add IS_PAR relationship to link X- and Y-PAR genes
 177	\N	patch	patch_109_110_c.sql|Allow gene id to belong to multiple alt allele groups
 178	\N	patch	patch_110_111_a.sql|schema_version
+179	\N	patch	patch_111_112_a.sql|schema_version
+180	\N	patch	patch_111_112_b.sql|Allow meta_value to be null
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index 4c32c6caf..7e0ab54ab 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -491,11 +491,11 @@ CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
   `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) NOT NULL,
+  `meta_value` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=179 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=181 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/hp_dump/core/meta.txt b/modules/t/test-genome-DBs/hp_dump/core/meta.txt
index d401f5666..b5f68a552 100644
--- a/modules/t/test-genome-DBs/hp_dump/core/meta.txt
+++ b/modules/t/test-genome-DBs/hp_dump/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	111
+2	\N	schema_version	112
 3	\N	patch	patch_98_99_a.sql|schema_version
 2124	1	xref.timestamp	2013-07-22 11:20:10
 4	\N	patch	patch_52_53_c.sql|identity_xref_rename
@@ -265,3 +265,5 @@
 2221	\N	patch	patch_109_110_b.sql|Add IS_PAR relationship to link X- and Y-PAR genes
 2222	\N	patch	patch_109_110_c.sql|Allow gene id to belong to multiple alt allele groups
 2223	\N	patch	patch_110_111_a.sql|schema_version
+2224	\N	patch	patch_111_112_a.sql|schema_version
+2225	\N	patch	patch_111_112_b.sql|Allow meta_value to be null
diff --git a/modules/t/test-genome-DBs/hp_dump/core/table.sql b/modules/t/test-genome-DBs/hp_dump/core/table.sql
index df7288b40..56d37618f 100644
--- a/modules/t/test-genome-DBs/hp_dump/core/table.sql
+++ b/modules/t/test-genome-DBs/hp_dump/core/table.sql
@@ -486,11 +486,11 @@ CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
   `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) NOT NULL,
+  `meta_value` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2224 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2226 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/multi/compara/meta.txt b/modules/t/test-genome-DBs/multi/compara/meta.txt
index d16a1c75c..75508c863 100644
--- a/modules/t/test-genome-DBs/multi/compara/meta.txt
+++ b/modules/t/test-genome-DBs/multi/compara/meta.txt
@@ -1,6 +1,6 @@
 2	\N	schema_type	compara
 3	\N	patch	patch_98_99_a.sql|schema_version
-165	\N	schema_version	111
+167	\N	schema_version	112
 4	\N	patch	patch_72_73_b.sql|homology_genetree_links
 6	\N	patch	patch_73_74_a.sql|schema_version
 7	\N	patch	patch_73_74_b.sql|hmm_profile
@@ -126,3 +126,4 @@
 163	\N	patch	patch_109_110_b.sql|case_insensitive_stable_id_again
 164	\N	patch	patch_109_110_c.sql|ncbi_taxa_name_varchar500
 166	\N	patch	patch_110_111_a.sql|schema_version
+168	\N	patch	patch_111_112_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/multi/compara/table.sql b/modules/t/test-genome-DBs/multi/compara/table.sql
index 49de3d28b..8482668f9 100644
--- a/modules/t/test-genome-DBs/multi/compara/table.sql
+++ b/modules/t/test-genome-DBs/multi/compara/table.sql
@@ -441,7 +441,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=167 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=169 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
diff --git a/modules/t/test-genome-DBs/s_cerevisiae/core/meta.txt b/modules/t/test-genome-DBs/s_cerevisiae/core/meta.txt
index fe9f9a707..2f62db00f 100644
--- a/modules/t/test-genome-DBs/s_cerevisiae/core/meta.txt
+++ b/modules/t/test-genome-DBs/s_cerevisiae/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	111
+2	\N	schema_version	112
 3	\N	patch	patch_98_99_a.sql|schema_version
 4	\N	patch	patch_60_61_b.sql|create_seq_region_synonym_table
 5	\N	patch	patch_60_61_c.sql|rejig_object_xref_indexes
@@ -190,3 +190,5 @@
 679	\N	patch	patch_109_110_b.sql|Add IS_PAR relationship to link X- and Y-PAR genes
 680	\N	patch	patch_109_110_c.sql|Allow gene id to belong to multiple alt allele groups
 681	\N	patch	patch_110_111_a.sql|schema_version
+682	\N	patch	patch_111_112_a.sql|schema_version
+683	\N	patch	patch_111_112_b.sql|Allow meta_value to be null
diff --git a/modules/t/test-genome-DBs/s_cerevisiae/core/table.sql b/modules/t/test-genome-DBs/s_cerevisiae/core/table.sql
index 7ade412de..2bfa40eba 100644
--- a/modules/t/test-genome-DBs/s_cerevisiae/core/table.sql
+++ b/modules/t/test-genome-DBs/s_cerevisiae/core/table.sql
@@ -486,11 +486,11 @@ CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
   `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) NOT NULL,
+  `meta_value` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=682 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=684 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,

From aea0b73066c5d375c0d8ffd23b1bae086224baa3 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-login-03.ebi.ac.uk>
Date: Mon, 2 Oct 2023 11:19:57 +0100
Subject: [PATCH 006/128] Add gencode primary tag to GFF3 files

---
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm   | 3 +++
 modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm       | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index 34d134cc0..57e97cbd0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -274,6 +274,9 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
     push(@tags, $mane_type) if ($mane_type);
   }
 
+  my $gencode_primary = $self->get_all_Attributes('gencode_primary');
+  push(@tags, 'GENCODE Primary') if @{$gencode_primary};
+
   $summary{'tag'} = \@tags if @tags;
 
   # Check for seq-edits
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index 190429eb3..817b6197a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -290,6 +290,9 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
     push(@tags, $mane_type) if ($mane_type);
   }
 
+  my $gencode_primary = $self->get_all_Attributes('gencode_primary');
+  push(@tags, 'GENCODE Primary') if @{$gencode_primary};
+
   $summary{'tag'} = \@tags if @tags;
 
   # Add xrefs

From 881d271ed930d29ea8b61549fa311f510a02e05c Mon Sep 17 00:00:00 2001
From: jmgonzmart <jmgonzalez@ebi.ac.uk>
Date: Mon, 2 Oct 2023 18:34:47 +0100
Subject: [PATCH 007/128] Updated download URL for miRBase miRNA.dat file

---
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
index 140082a34..aebb77102 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
@@ -194,7 +194,7 @@
     {
       "name" : "miRBase",
       "parser" : "miRBaseParser",
-      "file" : "https://mirbase.org/ftp/CURRENT/miRNA.dat.gz",
+      "file" : "https://mirbase.org/download/miRNA.dat",
       "method" : "--bestn 1",
       "query_cutoff" : 90,
       "target_cutoff" : 90,
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
index 7ef812874..0f24ec9a8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
@@ -232,7 +232,7 @@
     {
       "name" : "miRBase",
       "parser" : "miRBaseParser",
-      "file" : "https://mirbase.org/ftp/CURRENT/miRNA.dat.gz",
+      "file" : "https://mirbase.org/download/miRNA.dat",
       "method" : "--bestn 1",
       "query_cutoff" : 90,
       "target_cutoff" : 90,
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
index 17fa985f1..9bcbf7936 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
@@ -260,7 +260,7 @@
     {
       "name" : "miRBase",
       "parser" : "miRBaseParser",
-      "file" : "https://mirbase.org/ftp/CURRENT/miRNA.dat.gz",
+      "file" : "https://mirbase.org/download/miRNA.dat",
       "method" : "--bestn 1",
       "query_cutoff" : 90,
       "target_cutoff" : 90,

From a3f251ccbdcf6a5807e78eb4f299c855b353f112 Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Mon, 16 Oct 2023 10:18:42 +0100
Subject: [PATCH 008/128] Updated .gitignore + patch DQ forgotten when
 initially branching

---
 .gitignore              |  1 +
 sql/patch_111_112_a.sql | 27 +++++++++++++++++++++++++++
 2 files changed, 28 insertions(+)
 create mode 100644 sql/patch_111_112_a.sql

diff --git a/.gitignore b/.gitignore
index 1442d0eeb..b7ac8c216 100644
--- a/.gitignore
+++ b/.gitignore
@@ -36,3 +36,4 @@ MultiTestDB.conf
 *.iml
 /_Deparsed_XSubs.pm
 __pycache__/
+/build/
diff --git a/sql/patch_111_112_a.sql b/sql/patch_111_112_a.sql
new file mode 100644
index 000000000..d059492fb
--- /dev/null
+++ b/sql/patch_111_112_a.sql
@@ -0,0 +1,27 @@
+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_111_112_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 112.
+
+UPDATE meta SET meta_value='112' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+VALUES (NULL, 'patch', 'patch_111_112_a.sql|schema_version');

From 3318e164e6ebc881d61c1621976caafdb748be25 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <48948777+TamaraNaboulsi@users.noreply.github.com>
Date: Thu, 19 Oct 2023 10:48:27 +0100
Subject: [PATCH 009/128] Stop skipping lines when reaching sequence data
 (#837)

Co-authored-by: Tamara El Naboulsi <ten@codon-login-06.ebi.ac.uk>
---
 .../EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
index a23cfd71f..90452a6ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
@@ -89,7 +89,7 @@ sub run {
       while (<$in_fh>) {
         if ($_ =~ /^REFERENCE/ || $_ =~ /^COMMENT/ || $_ =~ /^\s{5}Protein/) {
           $skip_data = 1;
-        } elsif ($_ =~ /^\s{5}source/ || $_ =~ /^\s{5}CDS/) {
+        } elsif ($_ =~ /^\s{5}source/ || $_ =~ /^\s{5}CDS/ || $_ =~ /^ORIGIN/) {
           $skip_data = 0;
         }
         if (!$skip_data) {print $out_fh $_;}

From cb28396971339c9e03c3450812207136f9d03d1e Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Tue, 31 Oct 2023 15:31:22 +0000
Subject: [PATCH 010/128] Updated Core stats resources.

---
 .../Production/Pipeline/PipeConfig/CoreStatistics_conf.pm | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
index 2cb1d6a35..b06a8c0c5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
@@ -130,7 +130,7 @@ sub pipeline_analyses {
                             '3->A' => ['CheckStatistics_Chromosome'],
                             'A->1' => ['SpeciesFactory_All'],
                           },
-      -rc_name         => '2GB',
+      -rc_name         => '2GB_D',
     },
 
 
@@ -211,7 +211,7 @@ sub pipeline_analyses {
         },
         -max_retry_count => 1,
         -hive_capacity   => 50,
-        -rc_name         => 'default_W'
+        -rc_name         => '2GB_W'
     },
 
     {
@@ -262,7 +262,7 @@ sub pipeline_analyses {
       -max_retry_count => 1,
       -hive_capacity   => 50,
       -flow_into       => ['GeneGC_Datacheck'],
-      -rc_name         => 'default_D',
+      -rc_name         => '2GB_D',
     },
 
     {
@@ -327,7 +327,7 @@ sub pipeline_analyses {
       -max_retry_count => 1,
       -hive_capacity   => 50,
       -batch_size      => 10,
-      -rc_name         => 'default',
+      -rc_name         => '1GB',
     },
 #
     {

From 97e0fb316171ad4fe4b6faf7bdfc7c8ec2f852b6 Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Mon, 6 Nov 2023 10:52:32 +0000
Subject: [PATCH 011/128] Fixed open/close TSV file while writing to it

---
 .../Production/Pipeline/FileDump/Xref_TSV.pm  | 30 +++++++++++++------
 1 file changed, 21 insertions(+), 9 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
index e8cc7b8b8..8f620e7bf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
@@ -103,11 +103,18 @@ sub print_xrefs {
     my $external_db_list = join(", ", map { "'$_'" } @$external_dbs);
     $edb_filter = " AND e.db_name in ($external_db_list) ";
   }
-  $file->append("\n");
-  $self->print_xref_subset( $file, $self->go_xref_sql($edb_filter) );
-  $self->print_xref_subset( $file, $self->gene_xref_sql($edb_filter) );
-  $self->print_xref_subset( $file, $self->transcript_xref_sql($edb_filter) );
-  $self->print_xref_subset( $file, $self->translation_xref_sql($edb_filter) );
+
+  # The append method opens and closes the file every time it is called.
+  # We therefore get the filehandle - also needlessly locking the file -
+  # to avoid this unwanted behaviour
+
+  my $fh = $file->opena({ locked => 1 });
+  print $fh "\n";
+  $self->print_xref_subset( $fh, $self->go_xref_sql($edb_filter) );
+  $self->print_xref_subset( $fh, $self->gene_xref_sql($edb_filter) );
+  $self->print_xref_subset( $fh, $self->transcript_xref_sql($edb_filter) );
+  $self->print_xref_subset( $fh, $self->translation_xref_sql($edb_filter) );
+  close $fh or die("Error while closing the file: $@");
 }
 
 sub print_xref_subset {
@@ -118,10 +125,15 @@ sub print_xref_subset {
     -SQL => $sql
   );
 
-  foreach my $result (@$results) {
-    $file->append(join("\t", @$result));
-    $file->append("\n");
-  }
+    foreach my $result (@$results) {
+      eval {
+        print $file join("\t", @$result);
+        print $file "\n";
+      }
+      if($@) {
+         die("Could not print results to file: $@");
+      }
+    }
 }
 
 sub go_xref_sql {

From 47b7e3d5c6b8ef87aa03ba4288b2640afd8d8556 Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Mon, 6 Nov 2023 12:17:00 +0000
Subject: [PATCH 012/128] Fixed typo

---
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
index 8f620e7bf..3fb29f551 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
@@ -129,7 +129,7 @@ sub print_xref_subset {
       eval {
         print $file join("\t", @$result);
         print $file "\n";
-      }
+      };
       if($@) {
          die("Could not print results to file: $@");
       }

From 2de0888ec96d65ce3a498c9ecc4e84a0e1c85ea9 Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Wed, 8 Nov 2023 14:55:53 +0000
Subject: [PATCH 013/128] Added table cleanup. Added SLURM resource specs.
 Removed 4GB_8CPU's as we actually requested 9. Added SLURM specifications

---
 .../PipeConfig/ProteinFeatures_conf.pm        | 37 ++++++++++++++++---
 1 file changed, 31 insertions(+), 6 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index b6d1c6345..ddaf33ba5 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -340,6 +340,8 @@ sub pipeline_analyses {
                             '3->A' => ['FetchFiles'],
                             'A->3' => ['AnnotateProteinFeatures'],
                           },
+      -rc_name           => '2GB',
+
     },
 
     {
@@ -422,6 +424,8 @@ sub pipeline_analyses {
       -parameters      => {
                             uniparc_file_local => $self->o('uniparc_file_local'),
                           },
+      -rc_name           => '2GB_W',
+
     },
 
     {
@@ -479,6 +483,7 @@ sub pipeline_analyses {
                               ],
                               output_file => catdir('#pipeline_dir#', '#dbname#', 'pre_pipeline_bkp.sql.gz'),
                             },
+      -rc_name           => '1GB',
       -flow_into         => ['AnalysisConfiguration'],
     },
 
@@ -492,6 +497,8 @@ sub pipeline_analyses {
                               run_seg                   => $self->o('run_seg'),
                               xref_analyses             => $self->o('xref_analyses'),
                             },
+       -rc_name           => '2GB',
+
       -flow_into 	       => {
                               '2->A' => ['AnalysisSetup'],
                               'A->3' => ['RemoveOrphans'],
@@ -529,6 +536,7 @@ sub pipeline_analyses {
                                   'WHERE ox.object_xref_id IS NULL',
                               ]
                             },
+      -rc_name           => 'default_D',
       -flow_into         => ['DeleteInterPro']
     },
 
@@ -567,6 +575,7 @@ sub pipeline_analyses {
       -max_retry_count   => 1,
       -analysis_capacity => 20,
       -parameters        => {},
+      -rc_name           => '1GB',
       -flow_into         => {
                               '2' => ['DumpProteome'],
                             }
@@ -582,7 +591,7 @@ sub pipeline_analyses {
                               header_style => 'dbID',
                               overwrite    => 1,
                             },
-      -rc_name           => '4GB',
+      -rc_name           => '4GB_W',
       -flow_into         => {
                              '-1' => ['DumpProteome_HighMem'],
                               '1' => WHEN('#run_seg#' =>
@@ -625,6 +634,7 @@ sub pipeline_analyses {
                               max_files_per_directory => $self->o('max_files_per_directory'),
                               max_dirs_per_directory  => $self->o('max_dirs_per_directory'),
                             },
+      -rc_name           => '1GB',
       -flow_into         => {
                               '2' => ['RunSeg'],
                             },
@@ -640,6 +650,7 @@ sub pipeline_analyses {
       {
         cmd => $self->o('seg_exe').' #split_file# '.$self->o('seg_params').' > #split_file#.seg.txt',
       },
+      -rc_name           => '1GB',
       -flow_into         => ['StoreSegFeatures'],
     },
 
@@ -667,6 +678,7 @@ sub pipeline_analyses {
                               uniparc_logic_name => $self->o('uniparc_logic_name'),
                               uniprot_logic_name => $self->o('uniprot_logic_name'),
                             },
+      -rc_name           => '1GB_D',
       -flow_into         => {
                               '3' => ['SplitChecksumFile'],
                               '4' => ['SplitNoChecksumFile'],
@@ -758,7 +770,7 @@ sub pipeline_analyses {
         interproscan_applications => '#interproscan_nolookup_applications#',
         run_interproscan          => $self->o('run_interproscan'),
       },
-      -rc_name           => '4GB_8CPU',
+      -rc_name           => '16GB_8CPU',
       -flow_into         => {
                                '3' => ['StoreProteinFeatures'],
                               '-1' => ['InterProScanNoLookup_HighMem'],
@@ -795,7 +807,7 @@ sub pipeline_analyses {
         interproscan_applications => '#interproscan_local_applications#',
         run_interproscan          => $self->o('run_interproscan'),
       },
-      -rc_name           => '4GB_8CPU',
+      -rc_name           => '16GB_8CPU',
       -flow_into         => {
                                '3' => ['StoreProteinFeatures'],
                                '0' => ['InterProScanLocal_HighMem'],
@@ -829,6 +841,7 @@ sub pipeline_analyses {
       -parameters        => {
                               analyses => $self->o('protein_feature_analyses')
                             },
+      -rc_name           => '1GB_D',
       -flow_into         => {
                               '-1' => ['StoreProteinFeatures_HighMem'],
                             },
@@ -855,6 +868,7 @@ sub pipeline_analyses {
                               interpro2go_file => $self->o('interpro2go_file_local'),
                               logic_name       => $self->o('interpro2go_logic_name')
                             },
+      -rc_name           => '1GB',
       -flow_into         => ['StoreInterProXrefs'],
     },
 
@@ -886,6 +900,7 @@ sub pipeline_analyses {
                               history_file     => $self->o('history_file'),
                               failures_fatal   => 1,
                             },
+      -rc_name           => '2GB_D',
       -flow_into         => WHEN('#email_report#' => ['EmailReport']),
     },
 
@@ -907,6 +922,15 @@ sub pipeline_analyses {
       -parameters        => {
                               cmd => 'rm -rf #scratch_dir#',
                             },
+     -flow_into  => 'CleanTables',
+    },
+
+    {
+        -logic_name => 'CleanTables',
+        -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SqlCmd',
+        -parameters => {
+            sql => 'DROP table uniparc; drop table uniprot',
+        },
     },
 
   ];
@@ -917,9 +941,10 @@ sub resource_classes {
 
   return {
     %{$self->SUPER::resource_classes},
-     '4GB_8CPU' => {'LSF' => '-q '.$self->o('production_queue').' -n 8 -M  4000 -R "rusage[mem=4000]"'},
-    '16GB_8CPU' => {'LSF' => '-q '.$self->o('production_queue').' -n 8 -M 16000 -R "rusage[mem=16000]"'},
-    '32GB_8CPU' => {'LSF' => '-q '.$self->o('production_queue').' -n 8 -M 32000 -R "rusage[mem=32000]"'},
+    '16GB_8CPU' => {'LSF' => '-q '.$self->o('production_queue').' -n 8 -M 16000 -R "rusage[mem=16000]"',
+                          'SLURM' => ' --partition=standard --time=1-00:00:00  --mem=16000m -n 8 -N 1'},
+    '32GB_8CPU' => {'LSF' => '-q '.$self->o('production_queue').' -n 8 -M 32000 -R "rusage[mem=32000]"',
+                    'SLURM' => ' --partition=standard --time=1-00:00:00  --mem=32000m -n 8 -N 1'},
   }
 }
 

From b0df7a21a351b633190b0f058a7ea6f0f21c8445 Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Mon, 13 Nov 2023 11:05:02 +0000
Subject: [PATCH 014/128] Fix for "scalar on reference"

In the code, scalar was called on a hash reference. This is either not
permitted or produces a warning, depending on the Perl version.
Fixed.
---
 .../Production/Pipeline/AlphaFold/InsertProteinFeatures.pm      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 138053c2f..8e97722a0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -171,7 +171,7 @@ sub run {
             info("Found GIFTS file $file, species: $1, assembly: $2, release: $3");
             if ($2 eq $assembly) {
                 $mappings = read_gifts_data("$gifts_dir/$file");
-                info("Read data for GIFTS from file $gifts_dir/file, " . (scalar (keys ($mappings))) . " entries");
+                info("Read data for GIFTS from file $gifts_dir/file, " . (scalar (keys %$mappings)) . " entries");
                 last;
             }
         }

From 0e1c0fed32ecebb3c2ddd7bfb9424853e5801a28 Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Wed, 15 Nov 2023 13:41:58 +0000
Subject: [PATCH 015/128] Moved to KyotoCabinet as DB

There were issues where the DB we build with Tie::LevelDB was missing
entries. Moved to KyotoCabinet.
---
 .../Pipeline/AlphaFold/CreateAlphaDB.pm       | 43 ++++++++-----
 .../Pipeline/AlphaFold/CreateUniparcDB.pm     | 35 +++++++----
 .../AlphaFold/InsertProteinFeatures.pm        | 62 +++++++------------
 3 files changed, 72 insertions(+), 68 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
index 84ec6a9ca..b8cd2ffb7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
@@ -49,7 +49,7 @@ use strict;
 
 use parent 'Bio::EnsEMBL::Production::Pipeline::Common::Base';
 use Bio::EnsEMBL::Utils::Exception qw(throw info);
-use Tie::LevelDB;
+use KyotoCabinet;
 use File::Temp 'tempdir';
 
 
@@ -66,7 +66,7 @@ sub run {
 
     throw ("Data file not found: '$map_file' on host " . `hostname`) unless -f $map_file;
 
-    my $idx_dir = $self->param_required('alphafold_db_dir') . '/uniprot-to-alpha.leveldb';
+    my $idx_dir = $self->param_required('alphafold_db_dir') . '/uniprot-to-alphafold';
     if (-d $idx_dir) {
         system(qw(rm -rf), $idx_dir);
     }
@@ -78,33 +78,42 @@ sub run {
         $copy_to = $idx_dir;
         $idx_dir = tempdir(DIR => '/dev/shm/');
     }
-
-    tie(my %idx, 'Tie::LevelDB', $idx_dir)
-        or die "Error trying to tie Tie::LevelDB $idx_dir: $!";
+ 
+    my $db = new KyotoCabinet::DB;
+
+    # Set 4 GB mmap size
+    my $mapsize_gb = 4 << 30;
+
+    # Open the DB
+    # Open as the exclusive writer, truncate if it exists, otherwise create the DB
+    # Open the database as a file hash DB, 600M buckets, 4GB mmap, linear option for
+    # hash collision handling. These are tuned for write speed and for approx. 300M entries.
+    # As with a regular Perl hash, a duplicate entry will overwrite the previous
+    # value.
+    $db->open("uniprot-to-alphafold.kch#bnum=600000000#msiz=$mapsize_gb#opts=l",
+        $db->OWRITER | $db->OCREATE | $db->OTRUNCATE
+    ) or die "Error opening DB: " . $db->error();
 
     my $map;
     open($map, '<', $map_file) or die "Opening map file $map_file failed: $!";
 
-    # A line from accession_ids.csv looks like this:
-    # Uniprot accession, hit start, hit end, Alphafold accession, Alphafold version
-    # A0A2I1PIX0,1,200,AF-A0A2I1PIX0-F1,4
-    # Currently, all entries in this file have a unique uniprot accession and
-    # have a hit starting at 1
-
     while (my $line = <$map>) {
+        # A line from accession_ids.csv looks like this:
+        # Uniprot accession, hit start, hit end, Alphafold accession, Alphafold version
+        # A0A2I1PIX0,1,200,AF-A0A2I1PIX0-F1,4
+        # Currently, all entries in this file have a unique uniprot accession and
+        # have a hit starting at 1
         unless ($line =~ /^\w+,\d+,\d+,[\w_-]+,\d+$/) {
             chomp $line;
-            warn "Data error. Line is not what we expect: '$line'";
-            next;
+            die "Data error. Line is not what we expect: '$line'";
         }
         my @x = split(",", $line, 2);
 
-        # This is the DB write operation. Tie::LevelDB will croak on errors (e.g. disk full)
-        $idx{$x[0]} = $x[1];
+        # This is the DB write operation.
+        $db->set($x[0], $x[1]) or die "Error inserting data: " . $db->error();
     }
 
-    close($map);
-    untie %idx;
+    $db->close() or die "Error closing DB: " . $db->error();
 
     if ($copy_back) {
         system (qw(cp -r), $idx_dir, $copy_to);
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
index 14d1ca3f9..4b0b26dd2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
@@ -49,7 +49,7 @@ use strict;
 use parent 'Bio::EnsEMBL::Production::Pipeline::Common::Base';
 
 use Bio::EnsEMBL::Utils::Exception qw(throw info);
-use Tie::LevelDB;
+use KyotoCabinet;
 use IO::Zlib;
 use File::Temp 'tempdir';
 
@@ -66,7 +66,7 @@ sub run {
 
     throw ("Data file not found: '$map_file' on host " . `hostname`) unless -f $map_file;
 
-    my $idx_dir = $self->param_required('uniparc_db_dir') . '/uniparc-to-uniprot.leveldb';
+    my $idx_dir = $self->param_required('uniparc_db_dir') . '/uniparc-to-uniprot';
     if (-d $idx_dir) {
         system(qw(rm -rf), $idx_dir);
     }
@@ -79,8 +79,21 @@ sub run {
         $idx_dir = tempdir(DIR => '/dev/shm/');
     }
 
-    tie(my %idx, 'Tie::LevelDB', $idx_dir)
-        or die "Error trying to tie Tie::LevelDB $idx_dir: $!";
+    my $db = new KyotoCabinet::DB;
+
+    # Set 4 GB mmap size
+    my $mapsize_gb = 4 << 30;
+
+    # Open the DB
+    # Open as the exclusive writer, truncate if it exists, otherwise create the DB
+    # Open the database as a file hash DB, 600M buckets, 4GB mmap, linear option for
+    # hash collision handling. These are tuned for write speed and for approx. 300M entries.
+    # Uniparc has 251M entries at the moment.
+    # As with a regular Perl hash, a duplicate entry will overwrite the previous
+    # # value.
+    $db->open("uniparc-to-uniprot.kch#bnum=600000000#msiz=$mapsize_gb#opts=l",
+        $db->OWRITER | $db->OCREATE | $db->OTRUNCATE
+    ) or die "Error opening DB: " . $db->error();
 
     my $map = new IO::Zlib;
     $map->open($map_file, 'rb') or die "Opening map file $map_file with IO::Zlib failed: $!";
@@ -92,20 +105,20 @@ sub run {
     my $line;
     while ($line = <$map>) {
         unless ($line =~ /^\w+\t[[:print:]\t]+$/) {
-                warn "Data error: Line is not what we expect: '$line'";
-                next;
+            chomp $line;
+            die "Data error: Uniparc accession is not what we expect: '$line'";
         }
         my @x = split("\t", $line, 12);
         unless ($x[10] and $x[10] =~ /^UPI\w+$/) {
-            warn "Data error: Uniparc accession is not what we expect: '$line'";
-            next;
+            chomp $line;
+            die "Data error: Uniparc accession is not what we expect: '$line'";
         }
-        # This is the DB write operation. Tie::LevelDB will croak on errors (e.g. disk full)
-        $idx{$x[10]} = $x[0];
+        # This is the DB write operation.
+        $db->set($x[10], $x[0]) or die "Error inserting data: " . $db->error();
     }
 
     $map->close;
-    untie %idx;
+    $db->close() or die "Error closing DB: " . $db->error();
 
     if ($copy_back) {
         system (qw(cp -r), $idx_dir, $copy_to);
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 8e97722a0..a7473b677 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -86,8 +86,7 @@ use Bio::EnsEMBL::ProteinFeature;
 use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Utils::Exception qw(throw info);
 use Bio::EnsEMBL::GIFTS::DB qw(fetch_latest_uniprot_enst_perfect_matches);
-use Tie::LevelDB;
-use Fcntl qw(:flock);
+use KyotoCabinet;
 
 sub fetch_input {
     my $self = shift;
@@ -107,8 +106,8 @@ sub run {
     # Bio::EnsEMBL::Utils::Exception::verbose('INFO');
 
     my $db_path = $self->param_required('db_dir');
-    my $idx_dir_al = $db_path . '/uniprot-to-alpha.leveldb';
-    my $idx_dir_up = $db_path . '/uniparc-to-uniprot.leveldb';
+    my $idx_dir_al = $db_path . '/uniprot-to-alphafold/uniprot-to-alphafold.kch';
+    my $idx_dir_up = $db_path . '/uniparc-to-uniprot/uniparc-to-uniprot.kch';
 
     my $species = $self->param_required('species');
     my $species_list = $self->param_required('species_list');
@@ -129,18 +128,17 @@ sub run {
 
     info("Initiating and creating the analysis object for species $species\n");
 
-    dblock($db_path);
-
-    my %alpha_db;
-    tie(%alpha_db, 'Tie::LevelDB', $idx_dir_al)
-        or die "Error trying to tie Tie::LevelDB $idx_dir_al: $!";
+    my $alpha_db = new KyotoCabinet::DB;
+    # Set 4 GB mmap size
+    my $mapsize_gb = 4 << 30;
+    $alpha_db->open("$idx_dir_al#msiz=$mapsize_gb#opts=l",
+        $alpha_db->OREADER
+    ) or die "Error opening DB: " . $alpha_db->error();
 
     my $al_string;
-    while (my ($k, $v) = each %alpha_db) {
-        $al_string = $v;
-        last;
-    }
-    untie(%alpha_db);
+    my $cur = $alpha_db->cursor();
+    (undef, $al_string) = $cur->get(0);
+    $cur->disable();
 
     my $alpha_version = (split ',', $al_string)[-1];
     $alpha_version //= 0;
@@ -191,8 +189,12 @@ sub run {
         # the dbid.
 
 
-        tie(my %uniprot_db, 'Tie::LevelDB', $idx_dir_up)
-            or die "Error trying to tie Tie::LevelDB $idx_dir_up: $!";
+        my $uniprot_db = new KyotoCabinet::DB;
+        # Set 4 GB mmap size
+        my $mapsize_gb = 4 << 30;
+        $uniprot_db->open("$idx_dir_up#msiz=$mapsize_gb#opts=l",
+            $uniprot_db->OREADER
+        ) or die "Error opening DB: " . $uniprot_db->error();
 
         # We currently have the same uniparc accession tied to the same
         # translation_id but in different versions (xref pipeline run
@@ -212,7 +214,7 @@ SQL
         while ( my @row = $sth->fetchrow_array ) {
             $protein_count++;
             my ($uniparc_id, $stable_id, $dbid) = @row;
-            my $uniprot_id = $uniprot_db{$uniparc_id};
+            my $uniprot_id = $uniprot_db->get($uniparc_id);
             unless ($uniprot_id) {
                 $no_uniparc++;
                 next;
@@ -221,7 +223,7 @@ SQL
         }
         info("Num proteins in DB $protein_count, no uniparc $no_uniparc");
 
-        untie %uniprot_db;
+        $uniprot_db->close() or die "Error closing DB: " . $uniprot_db->error();
 
     } else {
 
@@ -278,8 +280,6 @@ SQL
         die(sprintf("No matches for species %s found in core DB %s\n", $species, $dbc->dbname()));
     }
 
-    tie(%alpha_db, 'Tie::LevelDB', $idx_dir_al)
-        or die "Error trying to tie Tie::LevelDB $idx_dir_al: $!";
 
     my $pfa = $core_dba->get_ProteinFeatureAdaptor();
 
@@ -293,7 +293,7 @@ SQL
             my $uniparc = $entry->{'uniparc'};
             my $ensid = $entry->{'ensid'};
             my $translation_id = $entry->{'dbid'};
-            my $alpha_data = $alpha_db{$uniprot};
+            my $alpha_data = $alpha_db->get($uniprot);
 
             unless ($alpha_data) {
                 $no_alpha++;
@@ -331,30 +331,12 @@ SQL
         }
     }
     
-    untie(%alpha_db);
-
-    dbunlock();
+    $alpha_db->close() or die "Error closing DB: " . $alpha_db->error();
 
     # Info line to be stored in the hive DB
     $self->warning("Inserted $good OK. Num of proteins for species: $protein_count, no uniparc mapping: $no_uniparc, no uniprot mapping: $no_uniprot, no stable ID match: $no_dbid, no alphafold data: $no_alpha. Species: $log_species");
 }
 
-my $lock_fh;
-
-sub dblock {
-    my $path = shift;
-
-    info("Waiting for dblock");
-    open($lock_fh, ">", "$path/dblock") or die "Failed to open or create lock file: $!";
-    flock ($lock_fh, LOCK_EX) or die "Unable to lock $path/dblock: $!";
-    info("Locked dblock OK");
-}
-
-sub dbunlock {
-    flock $lock_fh, LOCK_UN;
-    close $lock_fh;
-}
-
 # Read a GIFTS CSV dump file, return a hash-ref like:
 # { 'A0A0G2K0H5' => [ 'ENSRNOT00000083658' ], 'B5DEL8' => [ 'ENSRNOT00000036389' ], ...}
 sub read_gifts_data {

From 7b25f088840a2f769caa74b4bc8912e607fe90c2 Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Wed, 15 Nov 2023 13:51:17 +0000
Subject: [PATCH 016/128] Added KyotoCabinet dependency

Added KyotoCabinet dependency to the cpanfile. Update a few source code
comments.
---
 cpanfile                                                      | 2 +-
 .../EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm    | 4 ++--
 .../EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm  | 4 ++--
 .../Production/Pipeline/AlphaFold/InsertProteinFeatures.pm    | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/cpanfile b/cpanfile
index ffd9edb0c..6939b8444 100644
--- a/cpanfile
+++ b/cpanfile
@@ -14,7 +14,7 @@ requires 'File::Slurp';
 requires 'Log::Log4perl';
 requires 'XML::Simple';
 requires 'Time::Duration';
-requires 'Tie::LevelDB';
 requires 'IO::Zlib';
 requires 'File::Temp';
 requires 'Fcntl';
+requires 'KyotoCabinet';
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
index b8cd2ffb7..9ecdce8fd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
@@ -33,12 +33,12 @@
 
  This module prepares a DB with a mapping from Uniprot accession to related
  Alphafold data (Alphafold accession, protein start, end). The DB is created on
- disk in LevelDB format.
+ disk in KyotoCabinet format.
 
 =head1 DESCRIPTION
 
  - We expect the file accession_ids.csv to be available
- - We go through the file and build a LevelDB mapping the Uniprot accession to the Alphafold data
+ - We go through the file and build a DB mapping the Uniprot accession to the Alphafold data
 
 =cut
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
index 4b0b26dd2..65e80cd48 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
@@ -32,12 +32,12 @@
 =head1 SYNOPSIS
 
  This module prepares a DB with a mapping from Uniparc accession to Uniprot
- accession. The DB is created on disk in LevelDB format.
+ accession. The DB is created on disk in KyotoCabinet format.
 
 =head1 DESCRIPTION
 
  - We expect the file idmapping_selected.tab.gz to be available
- - We go through the file and build a LevelDB mapping the Uniparc accessions to Uniprot accessions
+ - We go through the file and build a DB mapping the Uniparc accessions to Uniprot accessions
 
 =cut
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index a7473b677..da1267d22 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -58,7 +58,7 @@
  -species        Production name of species to process. For a collection DB, any species from the DB
  -species_list   List of species production names. For a single species, a list
                  with just this species. For a collection DB, list of all species in the DB
- -db_dir         Path to the uniparc-to-uniprot DB and the uniprot-to-alpha DB, both in LevelDB format
+ -db_dir         Path to the uniparc-to-uniprot DB and the uniprot-to-alpha DB, both in KyotoCabinet format
  -rest_server    GIFTS rest server to fetch the perfect matches data from.
  -cs_version     Needed for GIFTS, otherwise optional. Name of assembly, like 'GRCh38'.
 

From 4393c3c409c7d5204347149b6122985031081411 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Fri, 17 Nov 2023 09:11:35 +0000
Subject: [PATCH 017/128] update port for blat files

update blat port for species bos_taururs
---
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
index ffae16c77..adecae94b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
@@ -98,7 +98,7 @@ sub default_options {
             'mus_musculus'                     => 30081,
             'danio_rerio'                      => 30003,
             'gallus_gallus'                    => 30005,
-            'bos_taurus'                       => 30017,
+            'bos_taurus'                       => 30018,
             'oryctolagus_cuniculus'            => 30025,
             'oryzias_latipes'                  => 30026,
             'sus_scrofa'                       => 30039,

From 6773a1f971fb64fc2ae5dc5bcd7123c5b76dec59 Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Tue, 21 Nov 2023 15:29:33 +0000
Subject: [PATCH 018/128] Better AlphaFold mapping, Travis

- Improved AlphaFold mapping. When mapping, we start from a UniParc
  accession in a core DB. This can map to multiple UniProt accessions.
  So far, we would only consider on of these. Now we consider all of
  them. This can lead to multiple protein features for one translation
  but we can no longer miss mappings.
- Added kyotocabinet to travis
- Adapted the extraction of the AlphaFold version to the new DBs
- small clean up
---
 .travis.yml                                   |   2 +
 .../Pipeline/AlphaFold/CreateAlphaDB.pm       |   2 +-
 .../Pipeline/AlphaFold/CreateUniparcDB.pm     |  10 +-
 .../AlphaFold/InsertProteinFeatures.pm        |  96 +++++++++++-------
 .../Pipeline/PipeConfig/AlphaDBImport_conf.pm |   2 -
 travisci/kyotocabinet-perl-1.20.tar.gz        | Bin 0 -> 43129 bytes
 6 files changed, 72 insertions(+), 40 deletions(-)
 create mode 100644 travisci/kyotocabinet-perl-1.20.tar.gz

diff --git a/.travis.yml b/.travis.yml
index 27e492326..e870e7c17 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -14,6 +14,7 @@ addons:
       - sendmail
       - graphviz
       - emboss
+      - libkyotocabinet-dev
 before_install:
   - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
   - export PATH=$PATH:$PWD/ensembl-git-tools/bin
@@ -46,6 +47,7 @@ install:
   - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
   - cpanm --sudo -v --installdeps --notest .
   - cpanm --sudo -n Devel::Cover::Report::Coveralls
+  - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
   - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
   - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
 script:
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
index 9ecdce8fd..a896a09ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
@@ -90,7 +90,7 @@ sub run {
     # hash collision handling. These are tuned for write speed and for approx. 300M entries.
     # As with a regular Perl hash, a duplicate entry will overwrite the previous
     # value.
-    $db->open("uniprot-to-alphafold.kch#bnum=600000000#msiz=$mapsize_gb#opts=l",
+    $db->open("$idx_dir/uniprot-to-alphafold.kch#bnum=600000000#msiz=$mapsize_gb#opts=l",
         $db->OWRITER | $db->OCREATE | $db->OTRUNCATE
     ) or die "Error opening DB: " . $db->error();
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
index 65e80cd48..b983ca689 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
@@ -91,7 +91,7 @@ sub run {
     # Uniparc has 251M entries at the moment.
     # As with a regular Perl hash, a duplicate entry will overwrite the previous
     # # value.
-    $db->open("uniparc-to-uniprot.kch#bnum=600000000#msiz=$mapsize_gb#opts=l",
+    $db->open("$idx_dir/uniparc-to-uniprot.kch#bnum=600000000#msiz=$mapsize_gb#opts=l",
         $db->OWRITER | $db->OCREATE | $db->OTRUNCATE
     ) or die "Error opening DB: " . $db->error();
 
@@ -103,6 +103,7 @@ sub run {
     # We pick out the Uniparc accession and Uniprot accession
     # index[10] (Uniparc): UPI00003B0FD4; index[0] (Uniprot): Q6GZX4
     my $line;
+
     while ($line = <$map>) {
         unless ($line =~ /^\w+\t[[:print:]\t]+$/) {
             chomp $line;
@@ -114,7 +115,12 @@ sub run {
             die "Data error: Uniparc accession is not what we expect: '$line'";
         }
         # This is the DB write operation.
-        $db->set($x[10], $x[0]) or die "Error inserting data: " . $db->error();
+        my $oldval;
+        if ($oldval = $db->get($x[10])) {
+            $db->set($x[10], "$oldval\t" . $x[0]) or die "Error inserting data: " . $db->error();
+        } else {
+            $db->set($x[10], $x[0]) or die "Error inserting data: " . $db->error();
+        }
     }
 
     $map->close;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index da1267d22..88ac46f35 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -59,7 +59,6 @@
  -species_list   List of species production names. For a single species, a list
                  with just this species. For a collection DB, list of all species in the DB
  -db_dir         Path to the uniparc-to-uniprot DB and the uniprot-to-alpha DB, both in KyotoCabinet format
- -rest_server    GIFTS rest server to fetch the perfect matches data from.
  -cs_version     Needed for GIFTS, otherwise optional. Name of assembly, like 'GRCh38'.
 
 =head1 EXAMPLE USAGE
@@ -69,7 +68,6 @@
   -species homo_sapiens
   -species_list "['homo_sapiens']"
   -db_dir /hps/scratch/...
-  -rest_server 'https://www.ebi.ac.uk/gifts/api/'
   -registry my_reg.pm
 
 =cut
@@ -92,7 +90,6 @@ sub fetch_input {
     my $self = shift;
 
     $self->param_required('species');
-    $self->param_required('rest_server');
     $self->param_required('db_dir');
     $self->param_required('species_list');
 
@@ -128,21 +125,25 @@ sub run {
 
     info("Initiating and creating the analysis object for species $species\n");
 
+
+    my $alpha_version = 0;
+    my $mapsize_gb = 4 << 30;
+    my $db = tie(my %db, 'KyotoCabinet::DB', "$idx_dir_al#msiz=$mapsize_gb#opts=l");
+    # traverse records by iterator
+    while (my ($key, $value) = each(%db)) {
+        $alpha_version = (split ',', $value)[-1];
+        last;
+    }
+    untie %db;
+    untie $db;
+    die "Unable to extract AlphaFold version" unless $alpha_version;
+
     my $alpha_db = new KyotoCabinet::DB;
     # Set 4 GB mmap size
-    my $mapsize_gb = 4 << 30;
     $alpha_db->open("$idx_dir_al#msiz=$mapsize_gb#opts=l",
         $alpha_db->OREADER
     ) or die "Error opening DB: " . $alpha_db->error();
 
-    my $al_string;
-    my $cur = $alpha_db->cursor();
-    (undef, $al_string) = $cur->get(0);
-    $cur->disable();
-
-    my $alpha_version = (split ',', $al_string)[-1];
-    $alpha_version //= 0;
-
     my $analysis = new Bio::EnsEMBL::Analysis(
             -logic_name    => 'alphafold',
             -db            => 'alphafold',
@@ -177,9 +178,9 @@ sub run {
     }
 
     my $no_uniparc = 0;
-    my $no_uniprot = 0;
     my $no_dbid = 0;
     my $protein_count = 0;
+    my $no_alpha = 0;
     if (! $mappings or ! %$mappings) {
 
         # If we don't have data in $mappings, this species is not in GIFTS.
@@ -188,7 +189,6 @@ sub run {
         # alphafold data using the uniprot id and insert a protein feature using
         # the dbid.
 
-
         my $uniprot_db = new KyotoCabinet::DB;
         # Set 4 GB mmap size
         my $mapsize_gb = 4 << 30;
@@ -211,15 +211,28 @@ SQL
 
         my $sth = $dbc->prepare($sql);
         $sth->execute;
-        while ( my @row = $sth->fetchrow_array ) {
+        while (my @row = $sth->fetchrow_array) {
             $protein_count++;
             my ($uniparc_id, $stable_id, $dbid) = @row;
-            my $uniprot_id = $uniprot_db->get($uniparc_id);
-            unless ($uniprot_id) {
+            my $uniprot_str = $uniprot_db->get($uniparc_id);
+            unless ($uniprot_str) {
                 $no_uniparc++;
                 next;
             }
-            push @{$mappings->{$uniprot_id}}, {'uniparc' => $uniparc_id, 'dbid' => $dbid, 'ensid' => $stable_id};
+            my @uniprots = split("\t", $uniprot_str);
+
+            my $at_least_one_alpha_mapping = 0;
+            for my $uniprot_id (@uniprots) {
+                my $alpha_data = $alpha_db->get($uniprot_id);
+                next unless $alpha_data;
+                push @{$mappings->{$uniprot_id}},
+                    {'uniparc' => $uniparc_id, 'dbid' => $dbid, 'ensid' => $stable_id, 'alpha' => $alpha_data};
+                $at_least_one_alpha_mapping = 1;
+            }
+            unless ($at_least_one_alpha_mapping) {
+                $no_alpha++;
+                info("No alphafold data for: UniParc acc $uniparc_id, stable_id $stable_id, translation_id $dbid");
+            }
         }
         info("Num proteins in DB $protein_count, no uniparc $no_uniparc");
 
@@ -256,22 +269,26 @@ SQL
             my ($dbid, $stable_id) = @row;
 
             unless (exists $rev_mappings{$stable_id}) {
-                info("No entry in GIFTS for stable ID $stable_id");
                 $no_dbid++;
+                info("No entry in GIFTS for stable ID $stable_id");
                 next;
             }
             my @rmap = @{$rev_mappings{$stable_id}};
 
+            my $at_least_one_alpha_mapping = 0;
             for my $uniprot_id (@rmap) {
-                unless ($uniprot_id) {
-                    $no_uniprot++;
-                    next;
-                }
-                push @{$mappings->{$uniprot_id}}, {'dbid' => $dbid, 'ensid' => $stable_id};
+                my $alpha_data = $alpha_db->get($uniprot_id);
+                next unless $alpha_data;
+                push @{$mappings->{$uniprot_id}}, {'dbid' => $dbid, 'ensid' => $stable_id, 'alpha' => $alpha_data};
+                $at_least_one_alpha_mapping = 1;
             }
             unless (scalar @rmap) {
-                info("No mapping data for stable ID $stable_id");
                 $no_dbid++;
+                info("No mapping data for stable ID $stable_id");
+            }
+            if (@rmap and ! $at_least_one_alpha_mapping) {
+                $no_alpha++;
+                info("No alphafold data for: stable_id $stable_id, translation_id $dbid, uniprot accessions: @rmap");
             }
         }
     }
@@ -284,21 +301,19 @@ SQL
     my $pfa = $core_dba->get_ProteinFeatureAdaptor();
 
     my $good = 0;
-    my $no_alpha = 0;
 
-    info("Unique uniprot accessions for species after mapping: " . scalar (keys %$mappings));
+    info("Unique UniProt accessions for species after mapping: " . scalar (keys %$mappings));
     for my $uniprot (keys %$mappings) {
         for my $entry (@{$mappings->{$uniprot}}) {
 
             my $uniparc = $entry->{'uniparc'};
             my $ensid = $entry->{'ensid'};
             my $translation_id = $entry->{'dbid'};
-            my $alpha_data = $alpha_db->get($uniprot);
+            my $alpha_data = $entry->{'alpha'};
 
             unless ($alpha_data) {
-                $no_alpha++;
-                info("No alphafold data for: $uniprot, $translation_id");
-                next;
+                die("There is an entry in the mappings hash, but alphafold data is missing for entry: " .
+                    "uniprot $uniprot, stable_id $ensid, translation_id $translation_id");
             }
             $good++;
 
@@ -308,9 +323,10 @@ SQL
 
             my $comment = 'Mapped ';
             if ($uniparc) {
-                $comment .= "direct from UniParc $uniparc to UniProt $uniprot, Ensembl stable ID $ensid";
+                $comment .= "direct from UniParc $uniparc to UniProt $uniprot, " .
+                "Ensembl stable ID $ensid, alpha_version $alpha_version)";
             } else {
-                $comment .= "using GIFTS DB (UniProt $uniprot, Ensembl stable ID $ensid)";
+                $comment .= "using GIFTS DB (UniProt $uniprot, Ensembl stable ID $ensid), alpha_version $alpha_version)";
             }
 
             info("Protein feature: start $al_start, end $al_end, $alpha_accession: $comment");
@@ -334,7 +350,14 @@ SQL
     $alpha_db->close() or die "Error closing DB: " . $alpha_db->error();
 
     # Info line to be stored in the hive DB
-    $self->warning("Inserted $good OK. Num of proteins for species: $protein_count, no uniparc mapping: $no_uniparc, no uniprot mapping: $no_uniprot, no stable ID match: $no_dbid, no alphafold data: $no_alpha. Species: $log_species");
+    my $covered_proteins = $protein_count - $no_dbid - $no_uniparc - $no_alpha;
+    $self->warning(
+        "Inserted $good protein features. Num of proteins for species: $protein_count " .
+        "with at least one mapping for $covered_proteins. ".
+        "No UniParc to UniProt mappings: $no_uniparc; No GIFTS mappings for stable ID: $no_dbid; " .
+        "No link from UniProt to Alphafold (for any UniProt accession found through UniParc): $no_alpha. " .
+        "Species: $log_species"
+    );
 }
 
 # Read a GIFTS CSV dump file, return a hash-ref like:
@@ -368,7 +391,10 @@ sub cleanup_protein_features {
 
     if (defined($analysis)) {
         my $analysis_id = $analysis->dbID();
-        info(sprintf("Found alphafold analysis (ID: $analysis_id) for species %s. Deleting it.\n", $self->param('species')));
+        info(sprintf(
+                "Found alphafold analysis (ID: $analysis_id) for species %s. Deleting it.\n", $self->param('species')
+            )
+        );
 
         my $pfa = $core_dba->get_ProteinFeatureAdaptor();
         $pfa->remove_by_analysis_id($analysis_id);
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
index f629e5344..cb4096da2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
@@ -62,7 +62,6 @@ sub default_options {
 
     return {
         %{$self->SUPER::default_options()},
-        rest_server  => 'https://www.ebi.ac.uk/gifts/api/',
         user_r       => 'ensro',
         species      => [],
         division     => [],
@@ -167,7 +166,6 @@ sub pipeline_analyses {
             -logic_name => 'insert_features',
             -module     => 'Bio::EnsEMBL::Production::Pipeline::AlphaFold::InsertProteinFeatures',
             -parameters => {
-                rest_server => $self->o('rest_server'),
                 db_dir => $self->o('scratch_large_dir'),
                 gifts_dir => $self->o('gifts_dir'),
             },
diff --git a/travisci/kyotocabinet-perl-1.20.tar.gz b/travisci/kyotocabinet-perl-1.20.tar.gz
new file mode 100644
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literal 0
HcmV?d00001


From 8c0eb8475a909d8f23a8af7f4a481b64ef31052b Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Tue, 21 Nov 2023 15:42:03 +0000
Subject: [PATCH 019/128] Fix Travis cpanm

When installing Perl modules for Travis, cpanm for KyotoDB was called
too late.
---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index e870e7c17..dc162fd2e 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -45,9 +45,9 @@ install:
   - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
   - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
   - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
+  - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
   - cpanm --sudo -v --installdeps --notest .
   - cpanm --sudo -n Devel::Cover::Report::Coveralls
-  - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
   - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
   - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
 script:

From 9352e9c9c23d673546ace8f2e26174b9c63c3128 Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Wed, 22 Nov 2023 16:00:05 +0000
Subject: [PATCH 020/128] Added additional resource classes: 50GB, 100GB, 200GB

---
 .../EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm    | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index 85435908a..e060a358c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -81,7 +81,12 @@ sub resource_classes {
         '4GB'            => '4000',
         '8GB'            => '8000',
         '16GB'           => '16000',
-        '32GB'           => '32000',);
+        '32GB'           => '32000',
+        '50GB'           => '50000',
+        '100GB'           => '100000',
+        '200GB'           => '200000',
+
+    );
 
     my $pq = ' --partition=standard';
     my $dq = ' --partition=datamover';

From 2c32ef0d6ed0c28b6416c4d27358eb1b0b5a3eb6 Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Wed, 22 Nov 2023 16:09:45 +0000
Subject: [PATCH 021/128] Altered resource classes for XrefDownload_conf.pm

---
 .../Pipeline/PipeConfig/XrefDownload_conf.pm  | 58 +++++++++++--------
 1 file changed, 35 insertions(+), 23 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
index 44dd5a817..650fea630 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
@@ -76,7 +76,7 @@ sub pipeline_analyses {
         '2->A' => 'download_source',
         'A->1' => 'schedule_cleanup'
       },
-      -rc_name    => 'small'
+      -rc_name    => 'default'
     },
     {
       -logic_name      => 'download_source',
@@ -85,9 +85,22 @@ sub pipeline_analyses {
       -parameters      => {
         base_path => $self->o('base_path')
       },
-      -rc_name         => 'dm',
+      -rc_name         => 'dm_D',
       -max_retry_count => 3
     },
+
+
+
+
+
+
+
+
+
+
+
+
+
     {
       -logic_name => 'schedule_cleanup',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::ScheduleCleanup',
@@ -102,17 +115,17 @@ sub pipeline_analyses {
         '4->A' => 'cleanup_uniprot',
         'A->1' => 'schedule_pre_parse'
       },
-      -rc_name    => 'small'
+      -rc_name    => 'default'
     },
     {
-      -logic_name => 'checksum',
+      -logic_name => 'checksum_W',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::Checksum',
       -comment    => 'Adds all checksum files into a single file and loads it into the checksum_xref table.',
       -parameters => {
         base_path     => $self->o('base_path'),
         skip_download => $self->o('skip_download')
       },
-      -rc_name    => 'normal'
+      -rc_name    => '100M_W'
     },
     {
       -logic_name => 'cleanup_refseq_dna',
@@ -124,7 +137,7 @@ sub pipeline_analyses {
         skip_download => $self->o('skip_download'),
         clean_dir    => $self->o('clean_dir')
       },
-      -rc_name    => 'small'
+      -rc_name    => '100M_D'
     },
     {
       -logic_name => 'cleanup_refseq_peptide',
@@ -136,7 +149,7 @@ sub pipeline_analyses {
         skip_download => $self->o('skip_download'),
         clean_dir    => $self->o('clean_dir')
       },
-      -rc_name    => 'small'
+      -rc_name    => 'default'
     },
     {
       -logic_name => 'cleanup_uniprot',
@@ -148,7 +161,7 @@ sub pipeline_analyses {
 	skip_download => $self->o('skip_download'),
         clean_dir    => $self->o('clean_dir')
       },
-      -rc_name    => 'small'
+      -rc_name    => '200M_D'
     },
     {
       -logic_name => 'schedule_pre_parse',
@@ -167,21 +180,30 @@ sub pipeline_analyses {
 	'4' => 'pre_parse_source_tertiary',
 	'-1' => 'notify_by_email'
       },
-      -rc_name    => 'small'
+      -rc_name    => 'default'
     },
     {
       -logic_name => 'pre_parse_source',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::PreParse',
       -comment    => 'Store data for faster species parsing',
-      -rc_name    => '2GB',
+      -rc_name    => '2GB_D',
       -hive_capacity => 100,
       -can_be_empty => 1,
     },
+      #-1 go to
+      #4GB and 1 week
+
+
+
+
+
+
+
     {
       -logic_name => 'pre_parse_source_dependent',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::PreParse',
       -comment    => 'Store data for faster species parsing',
-      -rc_name    => '2GB',
+      -rc_name    => '16GB_D',
       -hive_capacity => 100,
       -can_be_empty => 1,
       -wait_for => 'pre_parse_source'
@@ -190,7 +212,7 @@ sub pipeline_analyses {
       -logic_name => 'pre_parse_source_tertiary',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::PreParse',
       -comment    => 'Store data for faster species parsing',
-      -rc_name    => '2GB',
+      -rc_name    => '2GB_D',
       -hive_capacity => 100,
       -can_be_empty => 1,
       -wait_for => 'pre_parse_source_dependent',
@@ -208,21 +230,11 @@ sub pipeline_analyses {
         skip_preparse => $self->o('skip_preparse')
       },
       -wait_for => 'pre_parse_source_tertiary',
-      -rc_name    => 'small'
+      -rc_name    => 'default'
     }
   ];
 }
 
-sub resource_classes {
-  my ($self) = @_;
-
-  return {
-    %{$self->SUPER::resource_classes},
-    'small'  => { 'LSF' => '-q production -M 200 -R "rusage[mem=200]"' }, # Change 'production' to 'production-rh74' if running on noah
-    'normal' => { 'LSF' => '-q production -M 1000 -R "rusage[mem=1000]"' }
-  };
-}
-
 sub pipeline_wide_parameters {
   my ($self) = @_;
 

From 803fb767ca0140813a68be57bfcecd9708fa1614 Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Thu, 23 Nov 2023 10:38:35 +0000
Subject: [PATCH 022/128] Added memory step increase

---
 .../Pipeline/PipeConfig/Base_conf.pm          |  2 +
 .../Pipeline/PipeConfig/XrefDownload_conf.pm  | 55 +++++++++++--------
 2 files changed, 35 insertions(+), 22 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index e060a358c..a52cb13b4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -100,6 +100,8 @@ sub resource_classes {
         'dm'        => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
         'dm_D'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
         'dm_W'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
+        'dm32_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 32000 -R "rusage[mem=32000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'32000M'} . 'm' },
+        'dmMAX_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 200000 -R "rusage[mem=200000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'200000M'} . 'm' },
     );
     #Create a dictionary of all possible time and memory combinations. Format would be:
     #2G={
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
index 650fea630..5c215a06a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
@@ -86,21 +86,31 @@ sub pipeline_analyses {
         base_path => $self->o('base_path')
       },
       -rc_name         => 'dm_D',
+      -max_retry_count => 3,
+      -flow_into  => { '-1' => 'download_source_32'}
+    },
+    {
+      -logic_name      => 'download_source_32',
+      -module          => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::DownloadSource',
+      -comment         => 'Downloads the source files and stores then in -base_path.',
+      -parameters      => {
+        base_path => $self->o('base_path')
+      },
+      -rc_name         => 'dm32_D',
+      -max_retry_count => 3,
+      -flow_into  => { '-1' => 'download_source_MAX'}
+    },
+      #THIS STEP IS THE RESULT OF A BUG AND SHOULD BE REMOVED AS SOON AS THE PIPELINE IS FIXED
+    {
+      -logic_name      => 'download_source_MAX',
+      -module          => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::DownloadSource',
+      -comment         => 'Downloads the source files and stores then in -base_path.',
+      -parameters      => {
+        base_path => $self->o('base_path')
+      },
+      -rc_name         => 'dmMAX_D',
       -max_retry_count => 3
     },
-
-
-
-
-
-
-
-
-
-
-
-
-
     {
       -logic_name => 'schedule_cleanup',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::ScheduleCleanup',
@@ -182,6 +192,7 @@ sub pipeline_analyses {
       },
       -rc_name    => 'default'
     },
+
     {
       -logic_name => 'pre_parse_source',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::PreParse',
@@ -189,16 +200,16 @@ sub pipeline_analyses {
       -rc_name    => '2GB_D',
       -hive_capacity => 100,
       -can_be_empty => 1,
+      -flow_into  => {'-1' => 'pre_parse_source_long_HM'}
+    },
+    {
+      -logic_name => 'pre_parse_source_long_HM',
+      -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::PreParse',
+      -comment    => 'Store data for faster species parsing',
+      -rc_name    => '4GB_W',
+      -hive_capacity => 100,
+      -can_be_empty => 1,
     },
-      #-1 go to
-      #4GB and 1 week
-
-
-
-
-
-
-
     {
       -logic_name => 'pre_parse_source_dependent',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::PreParse',

From d01b2f3715167e5fefbdbca59cc51699adae1848 Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Thu, 23 Nov 2023 11:38:45 +0000
Subject: [PATCH 023/128] Integrate GIFTS

Integrate access to GIFTS data into the pipeline. The GIFTS DB is now
queried directly for species where GIFTS data is available.
---
 .../AlphaFold/InsertProteinFeatures.pm        | 99 ++++++++++++++-----
 1 file changed, 74 insertions(+), 25 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 88ac46f35..6865bc7ee 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -60,6 +60,10 @@
                  with just this species. For a collection DB, list of all species in the DB
  -db_dir         Path to the uniparc-to-uniprot DB and the uniprot-to-alpha DB, both in KyotoCabinet format
  -cs_version     Needed for GIFTS, otherwise optional. Name of assembly, like 'GRCh38'.
+ - gifts_host    The GIFTS DB hostname
+ - gifts_db      The GIFTS DB schema name
+ - gifts_user    The GIFTS DB user name
+ - gifts_pass    The GIFTS DB password
 
 =head1 EXAMPLE USAGE
 
@@ -69,6 +73,7 @@
   -species_list "['homo_sapiens']"
   -db_dir /hps/scratch/...
   -registry my_reg.pm
+  -gifts_pass 'ThePassword'
 
 =cut
 
@@ -83,7 +88,7 @@ use Bio::EnsEMBL::Analysis;
 use Bio::EnsEMBL::ProteinFeature;
 use Bio::EnsEMBL::Registry;
 use Bio::EnsEMBL::Utils::Exception qw(throw info);
-use Bio::EnsEMBL::GIFTS::DB qw(fetch_latest_uniprot_enst_perfect_matches);
+use DBD::Pg; # For GIFTS
 use KyotoCabinet;
 
 sub fetch_input {
@@ -144,6 +149,14 @@ sub run {
         $alpha_db->OREADER
     ) or die "Error opening DB: " . $alpha_db->error();
 
+    my $gifts_host = $self->param('gifts_host') // 'pgsql-hlvm-051.ebi.ac.uk';
+    my $gifts_db = $self->param('gifts_db') // 'gtigftpro';
+    my $gifts_user = $self->param('gifts_user') // 'giftsrw';
+    my $gifts_pass = $self->param_required('gifts_pass');
+    my $gifts_dbh = DBI->connect("dbi:Pg:dbname=$gifts_db;host=$gifts_host", $gifts_user, $gifts_pass,
+        {AutoCommit => 0, RaiseError => 1, PrintError => 0}
+    );
+
     my $analysis = new Bio::EnsEMBL::Analysis(
             -logic_name    => 'alphafold',
             -db            => 'alphafold',
@@ -163,19 +176,19 @@ sub run {
 
     if (defined $self->param('cs_version')) {
         my $assembly = $self->param('cs_version');
-        my $gifts_dir = $self->param_required('gifts_dir');
-        opendir(my $dh, $gifts_dir) or die "Error opening dir $gifts_dir: $!";
-        for my $file (readdir($dh)) {
-            next unless $file =~ /^(.*?)-(.*)-rel(.*?)\.csv$/;
-            info("Found GIFTS file $file, species: $1, assembly: $2, release: $3");
-            if ($2 eq $assembly) {
-                $mappings = read_gifts_data("$gifts_dir/$file");
-                info("Read data for GIFTS from file $gifts_dir/file, " . (scalar (keys %$mappings)) . " entries");
+        # grab GIFTS species / assembly data
+        my $gifts_data = read_gifts_species($gifts_dbh);
+        for my $row (@$gifts_data) {
+            my ($g_species_id, $g_species, $g_assembly, $g_release) = @$row;
+            info("Found species in GIFTS DB: species: $g_species, assembly: $g_assembly, release: $g_release");
+            if ($g_assembly eq $assembly) {
+                $mappings = read_gifts_data($gifts_dbh, $g_species_id);
+                info("Read data for GIFTS, " . (scalar (keys %$mappings)) . " entries");
                 last;
             }
         }
-        closedir($dh);
     }
+    $gifts_dbh->disconnect();
 
     my $no_uniparc = 0;
     my $no_dbid = 0;
@@ -199,15 +212,15 @@ sub run {
         # We currently have the same uniparc accession tied to the same
         # translation_id but in different versions (xref pipeline run
         # 'xrefchecksum' and 'uniparc_checksum')
-        my $sql = <<SQL;
-SELECT xr.dbprimary_acc as uniparc_id, tr.stable_id, tr.translation_id
-  FROM xref xr, object_xref ox, translation tr
-  where external_db_id = (SELECT external_db_id FROM external_db where db_name = 'UniParc')
-    and xr.xref_id = ox.xref_id
-    and ox.ensembl_id = tr.translation_id
-    and ox.ensembl_object_type = 'Translation'
-    group by uniparc_id, tr.stable_id, tr.translation_id
-SQL
+        my $sql = "
+            SELECT xr.dbprimary_acc as uniparc_id, tr.stable_id, tr.translation_id
+            FROM xref xr, object_xref ox, translation tr
+            where external_db_id = (SELECT external_db_id FROM external_db where db_name = 'UniParc')
+                and xr.xref_id = ox.xref_id
+                and ox.ensembl_id = tr.translation_id
+                and ox.ensembl_object_type = 'Translation'
+                group by uniparc_id, tr.stable_id, tr.translation_id
+        ";
 
         my $sth = $dbc->prepare($sql);
         $sth->execute;
@@ -281,6 +294,7 @@ SQL
                 next unless $alpha_data;
                 push @{$mappings->{$uniprot_id}}, {'dbid' => $dbid, 'ensid' => $stable_id, 'alpha' => $alpha_data};
                 $at_least_one_alpha_mapping = 1;
+                info("Mapping found for $stable_id: $alpha_data");
             }
             unless (scalar @rmap) {
                 $no_dbid++;
@@ -360,16 +374,51 @@ SQL
     );
 }
 
-# Read a GIFTS CSV dump file, return a hash-ref like:
+# Reads info about available species from GIFTS. Will use the latest release for
+# which GIFTS data is available. This is probably older than the release the
+# pipeline is running with. Since the species in GIFTS are unlikely to see
+# updates in the Core DBs, this is likely not an issue.
+# Returns an arrayref like: [[ensembl_species_history_id, species, assembly, ensembl_release], ...]
+sub read_gifts_species {
+    my $dbh = shift;
+
+    my $sql = "
+        select ensembl_species_history_id, species, assembly_accession as assembly, ensembl_release as release
+        from ensembl_gifts.ensembl_species_history
+        where ensembl_release = (select max(ensembl_release) from ensembl_gifts.ensembl_species_history)
+        order by ensembl_species_history_id
+    ";
+
+    my $sth = $dbh->prepare($sql);
+    $sth->execute();
+    return $sth->fetchall_arrayref();
+}
+
+# Read GIFTS data from DB, return a hash-ref like:
 # { 'A0A0G2K0H5' => [ 'ENSRNOT00000083658' ], 'B5DEL8' => [ 'ENSRNOT00000036389' ], ...}
 sub read_gifts_data {
-    my $path = shift;
-    open (my $fh, '<', $path) or die "GIFTS dump file '$path' not readable: $!";
+    my $dbh = shift;
+    my $ensembl_species_history_id = shift;
+
+    my $sql = "
+        select et.enst_id, ue.uniprot_acc
+        from ensembl_gifts.alignment al
+        inner join ensembl_gifts.alignment_run alr ON alr.alignment_run_id = al.alignment_run_id
+        inner join ensembl_gifts.release_mapping_history rmh ON rmh.release_mapping_history_id = alr.release_mapping_history_id
+        inner join ensembl_gifts.ensembl_species_history esh ON esh.ensembl_species_history_id = rmh.ensembl_species_history_id
+        inner join ensembl_gifts.ensembl_transcript et ON et.transcript_id = al.transcript_id
+        inner join ensembl_gifts.uniprot_entry ue ON ue.uniprot_id = al.uniprot_id
+        where score1_type = 'perfect_match'
+            and alr.ensembl_release = esh.ensembl_release
+            and rmh.ensembl_species_history_id = ?
+    ";
+
+    my $sth = $dbh->prepare($sql);
+    $sth->execute($ensembl_species_history_id);
 
     my %uniprot_ensid;
-    while (my $line = <$fh>) {
-        chomp $line;
-        (undef, undef, my $ensid, my $uniprot) = split ",", $line;
+    while (my $row = $sth->fetchrow_arrayref()) {
+        my ($ensid, $uniprot) = @$row;
         # A protein may have isoforms. In Uniprot, their reference looks like
         # e.g. F1RA39-1. Alphafold currently only has data for the canonical
         # sequence. Here, we just remove the isoform reference and always refer

From 59865202e24f9b952b1c63f4a066d77c46a0708d Mon Sep 17 00:00:00 2001
From: vinay-ebi <vinay@ebi.ac.uk>
Date: Fri, 24 Nov 2023 15:11:32 +0000
Subject: [PATCH 024/128] removed analysis step copytopublicftp

---
 .../Pipeline/PipeConfig/EarlyDumps_conf.pm    | 35 ++++---------------
 1 file changed, 6 insertions(+), 29 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
index 59f771fe4..dccb99d0c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
@@ -56,7 +56,7 @@ sub default_options {
     metadata_base_dir => catdir($self->o('ENV', 'NOBACKUP_DIR'), $self->o('username'), 'genome_reports_'.$self->o('ensembl_version')),
     metadata_script   => catdir($self->o('base_dir'), '/ensembl-metadata/misc_scripts/report_genomes.pl'),
     division_pattern_nonvert  => '.fungi,.metazoa,.plants,.protists',
-    early_dump_base_path      => catdir($self->o('ENV', 'NOBACKUP_DIR'), '/release_dumps/'),
+    early_dump_base_path      => catdir($self->o('ENV', 'NOBACKUP_DIR'), '/release_dumps/', '/release-'.$self->o('ensembl_version').'/ftp_dumps/'),
     nfs_early_dump_path       => '/nfs/production/flicek/ensembl/production/ensemblftp/',
     early_dumps_private_ftp   => catdir('/nfs/ftp/private/ensembl/pre-releases','/release-'.$self->o('ensembl_version').'_'.$self->o('eg_version')),
     #flags to restrict division
@@ -131,37 +131,14 @@ sub pipeline_analyses {
       -module            => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
       -max_retry_count   => 1,
       -parameters        => {
-                              early_dump_path_vert             => catdir($self->o('early_dump_base_path'), '/release-'.$self->o('ensembl_version')),
-			      nfs_early_dump_path_vert         => catdir($self->o('nfs_early_dump_path'), '/release-'.$self->o('ensembl_version')), 
-			      early_dump_path_nonvert          => catdir($self->o('early_dump_base_path'), '/release-'.$self->o('eg_version')),	
-			      nfs_early_dump_path_nonvert      => catdir($self->o('nfs_early_dump_path'), '/release-'.$self->o('eg_version')), 
+			                        nfs_early_dump_path_vert         => catdir($self->o('nfs_early_dump_path'), '/release-'.$self->o('ensembl_version')), 
+			                        nfs_early_dump_path_nonvert      => catdir($self->o('nfs_early_dump_path'), '/release-'.$self->o('eg_version')), 
                               cmd              => q{ 
-			      				rsync -avW #early_dump_path_vert# #nfs_early_dump_path_vert# 	
-							rsync -avW #early_dump_path_nonvert# #nfs_early_dump_path_nonvert#
-			      				
+			      	                                        rsync -avW  --include={'vertebrates'}  --exclude={'plants','protists', 'fungi', 'bacteria', 'metazoa'} #early_dump_base_path# #nfs_early_dump_path_vert# 	
+							                                        rsync -avW  --include={'plants','protists', 'fungi', 'bacteria', 'metazoa'} --exclude={'vertebrates'}  #early_dump_base_path# #nfs_early_dump_path_nonvert#
                                                    },
                             },
-      -flow_into         => { '1' => 'CopyToPublicFtp' },			    
-     			    
-
-    },
-    {
-      -logic_name        => 'CopyToPublicFtp',
-      -module            => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
-      -max_retry_count   => 1,
-      -parameters        => {
-                              nfs_early_dump_path_vert         => catdir($self->o('nfs_early_dump_path'), '/release-'.$self->o('ensembl_version')),     
-                              nfs_early_dump_path_nonvert      => catdir($self->o('nfs_early_dump_path'), '/release-'.$self->o('eg_version')),
-		              early_dumps_private_ftp          => $self->o('early_dumps_private_ftp'),	      
-                              cmd              => q{ 
-                                                        rsync -avW  #nfs_early_dump_path_vert#/verterates/ #early_dumps_private_ftp#   
-                                                        rsync -avW  #nfs_early_dump_path_nonvert#/ #early_dumps_private_ftp# 
-                                                        
-                                                   },
-                            },
-
-     -flow_into         => { '1' => 'Email' }, 			    
-      
+      -flow_into         => { '1' => 'Email' },			    
     },
     {
       -logic_name        => 'MetaDataReport',

From bfbec1e508711c72c29428bb0d676ca25506eabd Mon Sep 17 00:00:00 2001
From: "J. Alvarez-Jarreta" <jalvarez@ebi.ac.uk>
Date: Tue, 28 Nov 2023 11:32:27 +0000
Subject: [PATCH 025/128] update DumpOrtholog_eg_conf.pm

Update D.melanogaster projection species' production name
---
 .../PipeConfig/DumpOrtholog_eg_conf.pm        | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
index 4039d2049..3f77dc346 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
@@ -92,17 +92,17 @@ sub default_options {
                   compara     => 'metazoa',
                   source      => 'drosophila_melanogaster',
                   species     => [
-                    'drosophila_ananassae',
-                    'drosophila_erecta',
-                    'drosophila_grimshawi',
-                    'drosophila_mojavensis',
-                    'drosophila_persimilis',
-                    'drosophila_pseudoobscura',
-                    'drosophila_sechellia',
-                    'drosophila_simulans',
-                    'drosophila_virilis',
-                    'drosophila_willistoni',
-                    'drosophila_yakuba'
+                    'drosophila_ananassae_gca017639315v2rs',
+                    'drosophila_erecta_gca003286155v2rs',
+                    'drosophila_grimshawi_gca018153295v1rs',
+                    'drosophila_mojavensis_gca018153725v1rs',
+                    'drosophila_persimilis_gca003286085v2rs',
+                    'drosophila_pseudoobscura_gca009870125v2rs',
+                    'drosophila_sechellia_gca004382195v2rs',
+                    'drosophila_simulans_gca016746395v2rs',
+                    'drosophila_virilis_gca003285735v2rs',
+                    'drosophila_willistoni_gca018902025v2rs',
+                    'drosophila_yakuba_gca016746365v2rs'
                   ],
                   antispecies => 'drosophila_melanogaster',
                   division    => 'EnsemblMetazoa',

From 2ec70d827f8fd19b3d5e67d062c3d7087ca1116c Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Wed, 29 Nov 2023 14:42:09 +0000
Subject: [PATCH 026/128] Fixes for pipe config and cleanup

- The pipeline config did not pass the gifts_pass parameter to the
  runnable
- Added an early check for gifts_pass so it is required at pipeline
  creation
- cleanup was running too early. Changed the logic
---
 .../Pipeline/AlphaFold/InsertProteinFeatures.pm        |  1 +
 .../Pipeline/PipeConfig/AlphaDBImport_conf.pm          | 10 ++++++----
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 6865bc7ee..5721e3ed4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -97,6 +97,7 @@ sub fetch_input {
     $self->param_required('species');
     $self->param_required('db_dir');
     $self->param_required('species_list');
+    $self->param_required('gifts_pass');
 
     return 1;
 }
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
index cb4096da2..263bb7cef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
@@ -71,7 +71,6 @@ sub default_options {
         user         => 'ensadmin',
         alphafold_data_file => '/nfs/ftp/public/databases/alphafold/accession_ids.csv',
         uniparc_data_file => '/nfs/ftp/public/databases/uniprot/current_release/knowledgebase/idmapping/idmapping_selected.tab.gz',
-        gifts_dir    => '',
         pipeline_db  => {
             -driver => $self->o('hive_driver'),
             -host   => $self->o('pipe_db_host'),
@@ -157,8 +156,8 @@ sub pipeline_analyses {
                 antispecies => $self->o('antispecies'),
             },
             -flow_into  => {
-                '2->A' => [ 'insert_features' ],
-                'A->1' => [ 'cleanup' ]
+                '1' => [ 'cleanup' ],
+                '2' => [ 'insert_features' ],
             },
             -rc_name    => '500M',
         },
@@ -167,7 +166,7 @@ sub pipeline_analyses {
             -module     => 'Bio::EnsEMBL::Production::Pipeline::AlphaFold::InsertProteinFeatures',
             -parameters => {
                 db_dir => $self->o('scratch_large_dir'),
-                gifts_dir => $self->o('gifts_dir'),
+                gifts_pass => $self->o('gifts_pass'),
             },
             -wait_for => [
                 'create_alphafold_db',
@@ -202,6 +201,9 @@ sub pipeline_analyses {
             -logic_name        => 'cleanup',
             -module            => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
             -max_retry_count   => 1,
+            -wait_for => [
+                'datacheck'
+            ],
             -parameters        => {
                 cmd => 'rm -rf ' . $self->o('scratch_large_dir'),
             },

From ae3aa21510fe0f5ec50b2d0426f2584c996cc1f4 Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Fri, 15 Dec 2023 14:32:03 +0000
Subject: [PATCH 027/128] Update regulation_ftp_symlinks.py

---
 scripts/py/regulation_ftp_symlinks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 8cf410452..f6d48f345 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -221,7 +221,7 @@ def _symlink(self, source, target, only_remove):
                 )
         else:
             if not validator.is_symlink(source, check=True):
-                logger.info("{source} -> {target} -- was successfully removed")
+                logger.info(f"{source} -> {target} -- was successfully removed")
 
     def aliased_paths(self, **kwargs):
         return {

From a896738eba3bd8a4c238ce927fb30e6fd13dc1f0 Mon Sep 17 00:00:00 2001
From: Paulo Lins <plins@ebi.ac.uk>
Date: Mon, 18 Dec 2023 10:14:13 +0000
Subject: [PATCH 028/128] fix signals symlink in rf dir

---
 scripts/py/regulation_ftp_symlinks.py | 63 ++++++++-------------------
 1 file changed, 19 insertions(+), 44 deletions(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 8cf410452..351edbcf8 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -35,13 +35,12 @@
 """
 
 
+import logging
 from argparse import ArgumentParser
 from collections import defaultdict
-import logging
-from os import walk, path, listdir, makedirs
+from os import listdir, makedirs, path, walk
 from pathlib import Path
 
-
 # Human and Mouse follow a different dir structure
 SPECIES_TO_NOT_INCLUDE = ["homo_sapiens", "mus_musculus"]
 
@@ -55,12 +54,8 @@
 PUBLIC_PUB_PATH = "PUBLIC/pub"
 DATA_FILES_PATH = "data_files/"
 DATA_FILES_PATH_TEMPLATE = "{ftp_path}/data_files/{species}/{assembly}/funcgen"
-RELEASE_FOLDER_PATH_TEMPLATE = (
-    "{ftp_path}/release-{release}/regulation/{species}/{assembly}"
-)
-MISC_GENE_SWITCH_PATH_TEMPLATE = (
-    "{ftp_path}/misc/gene-switch/regulation/{species}/{assembly}"
-)
+RELEASE_FOLDER_PATH_TEMPLATE = "{ftp_path}/release-{release}/regulation/{species}/{assembly}"
+MISC_GENE_SWITCH_PATH_TEMPLATE = "{ftp_path}/misc/gene-switch/regulation/{species}/{assembly}"
 
 ANALYSIS_TYPE_PEAKS = "peaks"
 ANALYSIS_TYPE_SIGNAL = "signal"
@@ -140,9 +135,7 @@ def get_species_with_analysis_type_folder(analysis_type, ftp_path):
     def get_most_recent_release_data_file_path(data_file_path):
         validator.is_dir(Path(data_file_path))
         available_releases = listdir(data_file_path)
-        return Path(data_file_path) / str(
-            max([int(release) for release in available_releases])
-        )
+        return Path(data_file_path) / str(max([int(release) for release in available_releases]))
 
 
 utils = Utils()
@@ -163,14 +156,10 @@ def __init__(self, **path_specifics):
         )
         self.sources = {
             "release_folder": Path(
-                RELEASE_FOLDER_PATH_TEMPLATE.format(
-                    **self.aliased_paths(**path_specifics)
-                )
+                RELEASE_FOLDER_PATH_TEMPLATE.format(**self.aliased_paths(**path_specifics))
             ),
             "misc_folder": Path(
-                MISC_GENE_SWITCH_PATH_TEMPLATE.format(
-                    **self.aliased_paths(**path_specifics)
-                )
+                MISC_GENE_SWITCH_PATH_TEMPLATE.format(**self.aliased_paths(**path_specifics))
             ),
         }
 
@@ -181,12 +170,11 @@ def __init__(self, **path_specifics):
     def get(self, key):
         return self.path_specifics.get(key)
 
-    def symlink2rf(self, only_remove=False, relative=True):
+    def symlink2rf(self, analysis_type, only_remove=False, relative=True):
         target = (
-            Path(path.relpath(self.target, self.sources["release_folder"]))
-            / "peaks"
+            Path(path.relpath(self.target, self.sources["release_folder"])) / analysis_type
             if relative
-            else self.target / "peaks"
+            else self.target / analysis_type
         )
         source = self.sources["release_folder"] / self.get("analysis_type")
 
@@ -200,8 +188,7 @@ def symlink2misc(self, analysis_type, only_remove=False, relative=True):
             makedirs(self.sources["misc_folder"])
 
         target = (
-            Path(path.relpath(self.target, self.sources["misc_folder"]))
-            / analysis_type
+            Path(path.relpath(self.target, self.sources["misc_folder"])) / analysis_type
             if relative
             else self.target / analysis_type
         )
@@ -216,24 +203,17 @@ def _symlink(self, source, target, only_remove):
         if not only_remove:
             source.symlink_to(target, target_is_directory=True)
             if validator.is_symlink(source, check=True):
-                logger.info(
-                    f"{source} -> {target} --- was successfully created"
-                )
+                logger.info(f"{source} -> {target} --- was successfully created")
         else:
             if not validator.is_symlink(source, check=True):
-                logger.info("{source} -> {target} -- was successfully removed")
+                logger.info(f"{source} -> {target} -- was successfully removed")
 
     def aliased_paths(self, **kwargs):
-        return {
-            key: self.RELEASE_PATH_ALIASES.get(value, value)
-            for key, value in kwargs.items()
-        }
+        return {key: self.RELEASE_PATH_ALIASES.get(value, value) for key, value in kwargs.items()}
 
     @staticmethod
     def search(analysis_type, ftp_path, release):
-        result = utils.get_species_with_analysis_type_folder(
-            analysis_type, ftp_path
-        )
+        result = utils.get_species_with_analysis_type_folder(analysis_type, ftp_path)
         return [
             RegulationSymlinkFTP(
                 analysis_type=analysis_type,
@@ -295,20 +275,15 @@ def parse_arguments():
     ftp_path = args.ftp_path / PUBLIC_PUB_PATH
 
     logger.info("Searching for peaks in data_files ...")
-    peaks = RegulationSymlinkFTP.search(
-        ANALYSIS_TYPE_PEAKS, ftp_path, args.release_version
-    )
+    peaks = RegulationSymlinkFTP.search(ANALYSIS_TYPE_PEAKS, ftp_path, args.release_version)
     for peak in peaks:
-        peak.symlink2rf(only_remove=args.delete_symlinks)
+        peak.symlink2rf("peaks", only_remove=args.delete_symlinks)
         peak.symlink2misc("peaks", only_remove=args.delete_symlinks)
 
     logger.info("Searching for signals in data_files ...")
-    signals = RegulationSymlinkFTP.search(
-        ANALYSIS_TYPE_SIGNAL, ftp_path, args.release_version
-    )
+    signals = RegulationSymlinkFTP.search(ANALYSIS_TYPE_SIGNAL, ftp_path, args.release_version)
     for signal in signals:
-        signal.symlink2rf(only_remove=args.release_version)
-
+        signal.symlink2rf("signal", only_remove=args.release_version)
         signal.symlink2misc("signal", only_remove=args.delete_symlinks)
 
     logger.info("Process Completed")

From 0190c65141c5690e7558788901741c7f72880f62 Mon Sep 17 00:00:00 2001
From: Paulo Lins <plins@ebi.ac.uk>
Date: Mon, 18 Dec 2023 10:24:05 +0000
Subject: [PATCH 029/128] fix delete option

---
 scripts/py/regulation_ftp_symlinks.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 351edbcf8..01cf67462 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -283,7 +283,7 @@ def parse_arguments():
     logger.info("Searching for signals in data_files ...")
     signals = RegulationSymlinkFTP.search(ANALYSIS_TYPE_SIGNAL, ftp_path, args.release_version)
     for signal in signals:
-        signal.symlink2rf("signal", only_remove=args.release_version)
+        signal.symlink2rf("signal", only_remove=args.delete_symlinks)
         signal.symlink2misc("signal", only_remove=args.delete_symlinks)
 
     logger.info("Process Completed")

From c84c5c7c081ae08ab2e3f4d159cc63085f0e64aa Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Wed, 24 Jan 2024 10:23:32 +0000
Subject: [PATCH 030/128] Altered resource classes for XrefDownload_conf.pm

---
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm   | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 7a9323447..18370f19a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -126,7 +126,9 @@ sub run {
       $self->dataflow_output_id($dataflow_params, 2);
     } else {
       # Create list of files
-      my @list_files = `ls $file_name`;
+      opendir(my $dir_handle, $file_name);
+      my @list_files = readdir($dir_handle);
+      closedir($dir_handle);
       if ($preparse) { @list_files = $preparse; }
       foreach my $file (@list_files) {
         $file =~ s/\n//;

From 87454c7c8b4f23518660a4e7dcd4522770b971f7 Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Wed, 24 Jan 2024 11:25:47 +0000
Subject: [PATCH 031/128] Altered resource classes for Xref

---
 .../Pipeline/PipeConfig/XrefProcess_conf.pm   | 86 +++++++++----------
 1 file changed, 39 insertions(+), 47 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
index 71f9ceaa7..4144a8232 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
@@ -76,7 +76,7 @@ sub pipeline_analyses {
       '1->A' => 'schedule_species',
       'A->1' => 'EmailAdvisoryXrefReport'
     },
-    -rc_name    => 'small',
+    -rc_name    => 'default',
   },
   {
     -logic_name => 'schedule_species',
@@ -93,7 +93,7 @@ sub pipeline_analyses {
       '2->A' => 'schedule_source',
       'A->2' => 'schedule_dependent_source'
     },
-    -rc_name    => 'small',
+    -rc_name    => 'default',
   },
   {
     -logic_name => 'schedule_source',
@@ -112,7 +112,7 @@ sub pipeline_analyses {
       xref_pass  => $self->o('xref_pass'),
     },
     -flow_into  => { '2' => 'parse_source' },
-    -rc_name    => 'small',
+    -rc_name    => '1GB_D',
     -analysis_capacity => 10,
   },
   {
@@ -133,7 +133,7 @@ sub pipeline_analyses {
       '2->A' => 'parse_source',
       'A->1' => 'schedule_tertiary_source',
     },
-    -rc_name    => 'small',
+    -rc_name    => '4GB_D',
   },
   {
     -logic_name => 'schedule_tertiary_source',
@@ -153,12 +153,12 @@ sub pipeline_analyses {
       '2->A' => 'parse_source',
       'A->1' => 'dump_ensembl',
     },
-    -rc_name    => 'small',
+    -rc_name    => 'default',
   },
   {
     -logic_name        => 'parse_source',
     -module            => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::ParseSource',
-    -rc_name           => 'large',
+    -rc_name           => '16GB_D',
     -hive_capacity     => 300,
     -analysis_capacity => 50,
     -batch_size        => 30,
@@ -177,7 +177,7 @@ sub pipeline_analyses {
       '2->A' => 'dump_xref',
       'A->1' => 'schedule_mapping'
     },
-    -rc_name    => 'mem',
+    -rc_name    => '16GB_D',
   },
   {
     -logic_name => 'dump_xref',
@@ -188,7 +188,7 @@ sub pipeline_analyses {
       config_file => $self->o('config_file')
     },
     -flow_into  => { 2 => 'align_factory' },
-    -rc_name    => 'normal',
+    -rc_name    => '1GB',
   },
   {
     -logic_name => 'align_factory',
@@ -197,7 +197,7 @@ sub pipeline_analyses {
       base_path => $self->o('base_path'),
       release   => $self->o('release')},
     -flow_into  => { 2 => 'align' },
-    -rc_name    => 'small',
+    -rc_name    => 'default',
   },
   {
     -logic_name        => 'align',
@@ -205,7 +205,7 @@ sub pipeline_analyses {
     -parameters        => {
       base_path => $self->o('base_path')
     },
-    -rc_name           => 'large',
+    -rc_name           => '16GB_D',
     -hive_capacity     => 300,
     -analysis_capacity => 300,
     -batch_size        => 5,
@@ -222,7 +222,7 @@ sub pipeline_analyses {
       '2->A' => ['direct_xrefs', 'rnacentral_mapping'],
       'A->1' => 'mapping'
     },
-    -rc_name    => 'small',
+    -rc_name    => '1GB',
   },
   {
     -logic_name => 'direct_xrefs',
@@ -232,7 +232,7 @@ sub pipeline_analyses {
       release   => $self->o('release')
     },
     -flow_into  => { 1 => 'process_alignment' },
-    -rc_name    => 'normal',
+    -rc_name    => '1GB_D',
     -analysis_capacity => 30
   },
   {
@@ -242,7 +242,7 @@ sub pipeline_analyses {
       base_path => $self->o('base_path'),
       release   => $self->o('release')
     },
-    -rc_name    => 'normal',
+    -rc_name    => '1GB_D',
     -analysis_capacity => 30
   },
   {
@@ -253,7 +253,7 @@ sub pipeline_analyses {
       release   => $self->o('release')
     },
     -flow_into  => { 1 => 'uniparc_mapping' },
-    -rc_name    => 'normal',
+    -rc_name    => 'default',
     -hive_capacity => 300,
     -analysis_capacity => 30
   },
@@ -265,7 +265,7 @@ sub pipeline_analyses {
       release   => $self->o('release')
     },
     -flow_into  => { 1 => 'coordinate_mapping' },
-    -rc_name    => 'normal',
+    -rc_name    => '1GB',
     -hive_capacity => 300,
     -analysis_capacity => 30
   },
@@ -276,7 +276,7 @@ sub pipeline_analyses {
       base_path => $self->o('base_path'),
       release   => $self->o('release')
     },
-    -rc_name    => 'mem',
+    -rc_name    => '16GB',
     -analysis_capacity => 30
   },
   {
@@ -290,25 +290,26 @@ sub pipeline_analyses {
       '1->A' => 'RunXrefCriticalDatacheck',
       'A->1' => 'RunXrefAdvisoryDatacheck'
     },
-    -rc_name    => 'mem',
+    -rc_name    => '16GB_D',
     -analysis_capacity => 30,
   },
   {
-    -logic_name        => 'RunXrefCriticalDatacheck',
-    -module            => 'Bio::EnsEMBL::DataCheck::Pipeline::RunDataChecks',
-    -max_retry_count   => 1,
-    -analysis_capacity => 10,
-    -batch_size        => 10,
-    -parameters        => {
-      datacheck_names  => ['ForeignKeys'],
-      datacheck_groups => ['xref_mapping'],
-      datacheck_types  => ['critical'],
-      registry_file    => $self->o('registry'),
-      config_file      => $self->o('dc_config_file'),
-      history_file     => $self->o('history_file'),
-      old_server_uri   => $self->o('old_server_uri'),
-      failures_fatal   => 1,
-    },
+      -logic_name        => 'RunXrefCriticalDatacheck',
+      -module            => 'Bio::EnsEMBL::DataCheck::Pipeline::RunDataChecks',
+      -max_retry_count   => 1,
+      -analysis_capacity => 10,
+      -batch_size        => 10,
+      -parameters        => {
+          datacheck_names  => [ 'ForeignKeys' ],
+          datacheck_groups => [ 'xref_mapping' ],
+          datacheck_types  => [ 'critical' ],
+          registry_file    => $self->o('registry'),
+          config_file      => $self->o('dc_config_file'),
+          history_file     => $self->o('history_file'),
+          old_server_uri   => $self->o('old_server_uri'),
+          failures_fatal   => 1,
+      },
+      -rc_name           => '1GB',
   },
   {
     -logic_name        => 'RunXrefAdvisoryDatacheck',
@@ -325,12 +326,14 @@ sub pipeline_analyses {
       old_server_uri   => $self->o('old_server_uri'),
       failures_fatal   => 0,
     },
-    -flow_into         => { 4 => 'AdvisoryXrefReport' }
+    -flow_into         => { 4 => 'AdvisoryXrefReport' },
+    -rc_name           => '1GB',
+
   },
   {
     -logic_name => 'AdvisoryXrefReport',
     -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::AdvisoryXrefReport',
-    -rc_name    => 'small'
+    -rc_name    => 'default'
   },
   {
     -logic_name => 'EmailAdvisoryXrefReport',
@@ -340,7 +343,7 @@ sub pipeline_analyses {
       pipeline_name => $self->o('pipeline_name'),
       base_path => $self->o('base_path')
     },
-    -rc_name    => 'small',
+    -rc_name    => 'default',
     -flow_into  => { 1 => 'notify_by_email' }
   },
   {
@@ -350,22 +353,11 @@ sub pipeline_analyses {
       email        => $self->o('email'),
       pipeline_name => $self->o('pipeline_name')
     },
-    -rc_name    => 'small'
+    -rc_name    => 'default'
   }
   ];
 }
 
-sub resource_classes {
-  my ($self) = @_;
-
-  return {
-    %{$self->SUPER::resource_classes},
-    'small'  => { 'LSF' => '-q production -M 200 -R "rusage[mem=200]"' },
-    'normal' => { 'LSF' => '-q production -M 500 -R "rusage[mem=500]"' },
-    'mem'    => { 'LSF' => '-q production -M 3000 -R "rusage[mem=3000]"' },
-    'large'  => { 'LSF' => '-q production -M 10000 -R "rusage[mem=10000]"' },
-  }
-}
 
 sub pipeline_wide_parameters {
   my ($self) = @_;

From f0b3925a69e3884d67c066ddff9ed240fab70e0f Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Wed, 24 Jan 2024 11:50:04 +0000
Subject: [PATCH 032/128] updated copyright

---
 LICENSE                                                       | 2 +-
 modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm           | 2 +-
 modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm             | 2 +-
 .../EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm  | 2 +-
 .../Production/Pipeline/AlphaFold/InsertProteinFeatures.pm    | 2 +-
 .../Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm    | 2 +-
 .../Pipeline/AttributeAnnotation/FetchApprisFiles.pm          | 2 +-
 .../Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm   | 2 +-
 .../Production/Pipeline/AttributeAnnotation/LoadAppris.pm     | 2 +-
 .../Production/Pipeline/AttributeAnnotation/LoadTSL.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm        | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm  | 2 +-
 .../Production/Pipeline/Common/DbAwareSpeciesFactory.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm        | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm  | 2 +-
 .../Production/Pipeline/Common/RunCreateReleaseFile.pm        | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm  | 2 +-
 .../Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm     | 2 +-
 .../Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm         | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm | 2 +-
 .../Production/Pipeline/FASTA/CreatePrimaryAssembly.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm     | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm     | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm | 2 +-
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 .../production_database/import_species_names_from_cores.pl    | 2 +-
 .../production_database/import_species_names_from_taxonomy.pl | 2 +-
 scripts/production_database/populate_species_meta.pl          | 2 +-
 scripts/py/alphafoldUpdate.py                                 | 2 +-
 scripts/py/alphafoldUpdate_parallel.py                        | 2 +-
 scripts/py/regulation_ftp_symlinks.py                         | 2 +-
 scripts/refget/check_sequence_refget.pl                       | 2 +-
 scripts/sql2html.pl                                           | 2 +-
 scripts/sync/check_db.sh                                      | 2 +-
 scripts/sync/check_public_db.sh                               | 2 +-
 scripts/sync/get_release.sh                                   | 2 +-
 scripts/sync/get_staging_server.sh                            | 2 +-
 scripts/sync/optimise_databases.sh                            | 2 +-
 scripts/sync/process_divisions.sh                             | 2 +-
 scripts/sync/publish_db.sh                                    | 2 +-
 scripts/sync/set_checksums.sh                                 | 2 +-
 scripts/sync/sync_db.sh                                       | 2 +-
 scripts/sync/sync_db_st1.sh                                   | 2 +-
 scripts/sync/sync_db_st2.sh                                   | 2 +-
 scripts/sync/update_live_db.sh                                | 2 +-
 scripts/sync_tables.sh                                        | 2 +-
 scripts/t/rename_db.t                                         | 2 +-
 scripts/update_api_tarball.sh                                 | 2 +-
 scripts/update_assembly_tables.sh                             | 2 +-
 scripts/update_mapping_set.pl                                 | 2 +-
 sql/patch_100_101_a.sql                                       | 2 +-
 sql/patch_101_102_a.sql                                       | 2 +-
 sql/patch_102_103_a.sql                                       | 2 +-
 sql/patch_103_104_a.sql                                       | 2 +-
 sql/patch_104_105_a.sql                                       | 2 +-
 sql/patch_105_106_a.sql                                       | 2 +-
 sql/patch_106_107_a.sql                                       | 2 +-
 sql/patch_107_108_a.sql                                       | 2 +-
 sql/patch_108_109_a.sql                                       | 2 +-
 sql/patch_109_110_a.sql                                       | 2 +-
 sql/patch_110_111_a.sql                                       | 2 +-
 sql/patch_111_112_a.sql                                       | 2 +-
 sql/patch_66_67a.sql                                          | 2 +-
 sql/patch_66_67b.sql                                          | 2 +-
 sql/patch_66_67c.sql                                          | 2 +-
 sql/patch_70_71a.sql                                          | 2 +-
 sql/patch_71_72a.sql                                          | 2 +-
 sql/patch_71_72b.sql                                          | 2 +-
 sql/patch_72_73a.sql                                          | 2 +-
 sql/patch_72_73b.sql                                          | 2 +-
 sql/patch_72_73c.sql                                          | 2 +-
 sql/patch_72_73d.sql                                          | 2 +-
 sql/patch_72_73e.sql                                          | 2 +-
 sql/patch_73_74a.sql                                          | 2 +-
 sql/patch_73_74b.sql                                          | 2 +-
 sql/patch_74_75a.sql                                          | 2 +-
 sql/patch_74_75b.sql                                          | 2 +-
 sql/patch_75_76a.sql                                          | 2 +-
 sql/patch_75_76b.sql                                          | 2 +-
 sql/patch_76_77a.sql                                          | 2 +-
 sql/patch_76_77b.sql                                          | 2 +-
 sql/patch_76_77c.sql                                          | 2 +-
 sql/patch_77_78a.sql                                          | 2 +-
 sql/patch_77_78b.sql                                          | 2 +-
 sql/patch_78_79a.sql                                          | 2 +-
 sql/patch_78_79b.sql                                          | 2 +-
 sql/patch_79_80_a.sql                                         | 2 +-
 sql/patch_79_80b.sql                                          | 2 +-
 sql/patch_79_80c.sql                                          | 2 +-
 sql/patch_80_81a.sql                                          | 2 +-
 sql/patch_81_82a.sql                                          | 2 +-
 sql/patch_82_83a.sql                                          | 2 +-
 sql/patch_83_84a.sql                                          | 2 +-
 sql/patch_83_84b.sql                                          | 2 +-
 sql/patch_84_85a.sql                                          | 2 +-
 sql/patch_85_86a.sql                                          | 2 +-
 sql/patch_85_86b.sql                                          | 2 +-
 sql/patch_85_86c.sql                                          | 2 +-
 sql/patch_86_87a.sql                                          | 2 +-
 sql/patch_87_88_a.sql                                         | 2 +-
 sql/patch_88_89_a.sql                                         | 2 +-
 sql/patch_89_90_a.sql                                         | 2 +-
 sql/patch_89_90_b.sql                                         | 2 +-
 sql/patch_90_91_a.sql                                         | 2 +-
 sql/patch_91_92_a.sql                                         | 2 +-
 sql/patch_92_93_a.sql                                         | 2 +-
 sql/patch_92_93_b.sql                                         | 2 +-
 sql/patch_93_94_a.sql                                         | 2 +-
 sql/patch_94_95_a.sql                                         | 2 +-
 sql/patch_94_95_b.sql                                         | 2 +-
 sql/patch_95_96_a.sql                                         | 2 +-
 sql/patch_96_97_a.sql                                         | 2 +-
 sql/patch_96_97_b.sql                                         | 2 +-
 sql/patch_96_97_c.sql                                         | 2 +-
 sql/patch_96_97_d.sql                                         | 2 +-
 sql/patch_96_97_e.sql                                         | 2 +-
 sql/patch_96_97_f.sql                                         | 2 +-
 sql/patch_97_98_a.sql                                         | 2 +-
 sql/patch_98_99_a.sql                                         | 2 +-
 sql/patch_98_99_b.sql                                         | 2 +-
 sql/patch_99_100_a.sql                                        | 2 +-
 sql/table.sql                                                 | 2 +-
 src/python/scripts/dcparse.py                                 | 2 +-
 src/python/scripts/dcstat.py                                  | 2 +-
 src/python/scripts/genome_info.py                             | 2 +-
 src/python/scripts/meta_hive_species.py                       | 2 +-
 499 files changed, 500 insertions(+), 500 deletions(-)

diff --git a/LICENSE b/LICENSE
index 17b0e2929..3ec90d54a 100755
--- a/LICENSE
+++ b/LICENSE
@@ -187,7 +187,7 @@
       identification within third-party archives.
 
    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-   Copyright [2016-2023] EMBL-European Bioinformatics Institute
+   Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm b/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm
index 41f7e7262..bd34cc2a8 100644
--- a/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm
index fae4dea71..e3c641913 100644
--- a/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
index a896a09ef..ca1cecc1c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
index b983ca689..717458589 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 5721e3ed4..ad089f811 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm
index c80f15b40..ca5946037 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm
index 8266d16ac..f910edcc0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm
index 3172a1a39..f0f4c05ff 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm
index 121c44714..cc7d3485a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm
index c85df0e4c..b8c22e1fe 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm
index 90003344a..25a04e1cd 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm
index bd6780375..ddffcefda 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm
index 20c039532..ef2d7948e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm
index 8eb861bb5..2a8e4f338 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm
index 4fae25f5d..0d31406c2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm
index c5241c734..283a0e4ba 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm
index 1b1fb21e3..decb2fa6c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm
index f9e2eebf8..8c4accf90 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm
index ff81f787b..c16eee49c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm
index 4d304fb41..b7ea8094a 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm
index fd48b0234..b70072fea 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm
index 67814e965..c67865aad 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm
index b35265da0..4ec6b6d97 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm
index a2f1f04cb..6d94802b7 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm
index 95b0c87a2..7bcab5dab 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm
index 387f1afef..910dc0f8f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm
index dcf1b2379..e2ac07970 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
index b2c216738..5631e8e64 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm
index a30ca167d..2d17634c9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm
index d9b1b26dd..d37a2183f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm
index 5011f09eb..d74fa83d1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm
index 1cc34c40c..caf9a07c6 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm
index f610f0b25..99c505ce0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm
index 7dfdc17b1..7148575bb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm
index 53534e89c..7d57e5181 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm
index 7a42b44d3..d374b3f4f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm
index 32f3cd263..e744fef51 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm
index 6a0cfd18b..d0811e724 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm
index 2c8b7cc32..36edd8f0e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm
index d43048d4b..bccdacc7c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm
index 3c59dad76..5e74d1f84 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm
index 6ee08ac48..f04425bcb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm
index 08efe9fbe..3918e6d63 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm
index 103d5a994..cb3a8c8f8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm
index df3671ba6..72a590ab4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm
index 9af0bfb73..9c6796bf3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm
index 7299120fa..1a5f5a153 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm
index c51f47243..ec021916b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm
index c6710fc55..02722e94e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm
index 8d9891b26..1908ca342 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm
index f1a7e8746..eaae78933 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm
index 125b83ee7..18a52a953 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm
index 22a8c6ca4..e6631f2f4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm
index df7c58c9e..442932e83 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm
index c8c7ea9f5..9994b0006 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm
index 784b89ecd..ffe769a5b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm
index 699f63e29..7c29da9ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm
index dae375d1f..d32eea03b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm
index b89c9c4d8..f813d70ba 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm
index df3f7e7db..116d5f6da 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm
index 229a84614..abffc286e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm
index 79ed6b0a4..27ae351aa 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm
index 7455cd3b9..814f219d7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index 57e97cbd0..f582702b0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm
index e0a85fbce..f6e9ed62e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm
index fabd24ec5..4bbee0a34 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm
index a18ff212b..ed9194a76 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm
index 16942720d..a743929d7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm
index c9bad105c..ca0596734 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm
index f6426ea7d..70fbd11f8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm
index 5be22d688..16f31c3c3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm
index 4609e7296..1b47ed5b6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm
index f4f7ed542..6a50118cc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm
index e4ccee44f..579df4c7a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm
index 2fb82eeec..dbe4159a6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
index 3fb29f551..73b43b0de 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm
index e227e5404..dc7749c05 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
index 8a02f193a..d281aaecd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm
index 538256c59..254d305a1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm
index 56fc98d64..c7082bbf0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm
index 7200da4dc..201a80953 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm
index 7166b3b19..f8ae57687 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm
index 999819b16..1a5b76509 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm
index a43c4a78c..18735eebe 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm
index c9a294f52..51b344f17 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm
index 248480813..f566c7125 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm
index 7723d460d..cda84eb18 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm
index bd2159525..c60a6d671 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index 817b6197a..b32ad3646 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm
index c4d029bff..74ef1c560 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm
index d8ffae20b..38ece96f2 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm
index 75148fb90..428deb48e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
index 301e38176..79358a04d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm
index 2028e898b..b5165f31b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
index 6083b6249..28aa1ba06 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm
index 7e03d0bf4..4e4f39fee 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql
index 6d48eee6f..80875a63f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm
index dd9f326fc..f1932cea4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm
index 9804899dc..e12631dbc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm
index 1d092220e..670decacb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm
index 67db30fe5..83f0c5ca1 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm
index 15a1d0b11..374a234e5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm
index a72fb12ef..0ee82f326 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm
index 8c2168cbb..bccd5d9e3 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm
index 8ba7e53ef..c9d55bd83 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm
index 794ac27a7..e794358de 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
index 0c18900f6..d8e8328da 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
index 5e247aacf..37da4aabe 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
index f2d155427..e5cd4784c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm
index ce9466d91..422fccc30 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm
index f22a069c4..4ab8b79c0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm
index fa36e315f..e54d82fa9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm
index fb535addf..7f926e8e7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql
index 2403a57b3..0afb50fb7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm
index 0ab952078..b6104619a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
index 63f0fb9c8..4599d8636 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm
index b35104989..19af55ac6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
index 263bb7cef..b8a0e60ac 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
index 67d6f1429..14e6d7f71 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index a52cb13b4..b2ee90ef1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
index 89f71c74a..3c2bab042 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
index 73640e91e..0a4369a9d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm
index e7223617c..9b4d0d67c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm
index 48c0a16ac..c9b646904 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
index b06a8c0c5..909dbdcd9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
index 6acd23193..71d3b7655 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm
index 9447c56e8..b906af8df 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm
index 61d66c158..21faef537 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
index 8b3a6099e..11f63e43c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
index adecae94b..7f5feda63 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm
index c5572b2ae..fa212eace 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm
index 5b1f519c1..9f1bbb591 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm
index bd5663d2b..29e1d9e9b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
index b35768bb5..41a9ca74d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
index 3f77dc346..ea3bcd8e4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
index 75b5d1c6a..a0e6ab38b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
index 98c19c637..cd3b8e9a1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
index dccb99d0c..242743099 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
index 4170650d6..5c8590d06 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm
index 61a5930f6..c2ed1aa19 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm
index 368379411..bfa9b1d80 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
index 6a3587c1e..a6f5f3229 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm
index fd67e844d..a3aef7f4c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm
index 5d822bff9..a0050da6a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm
index 5ed9dcddb..a6563269a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm
index b0028c9a6..d8892c760 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
index f381c5f61..d5346d9f7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
index 64d9c12ee..59eeae96e 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm
index 793262737..5187ea644 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm
index 67a4e43ab..dda6175cd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm
index 718901689..e95bc49a3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm
index 767ff547d..8435b91f3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm
index 16feda573..5f3f3961e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
index a1b8b7db2..075faf886 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
index 222a98f81..a81a2c03a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
index a619091fc..15c3a2486 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm
index 97bba38bf..b299064b7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
index af535183b..d647f4633 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
index 310f9a9ec..670594711 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm
index 800fdd949..b786c7b1b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm
index 7d31c3031..13041c8d6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -27,7 +27,7 @@ limitations under the License.
 
 =head1 LICENSE
 
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
index 70a18ea1e..0b83cf992 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
index 253ca924c..3b58fe283 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index ddaf33ba5..5ee1a1297 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
index 3bd2eacd1..bc9e983c6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
index b80729f5c..d02de7472 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
index 01ce93395..79a860494 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
index 33af76ee3..539356514 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
index abab62004..4df737ac6 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
index 640b017f7..cb010d7ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
index fd2c7f382..b9426d30c 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm
index 2ed2c0913..87c4b1cc7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
index 5abd3ad0c..8b02ae00d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
index 3be02fc96..0cb424cbf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm
index 4905e3f28..a75be684c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
index 5c215a06a..3a78ff9b1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
index 4144a8232..2e11ce311 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
index 0fbc95b8f..b72c803c2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm
index 9107fe6e5..051dad445 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm
index 1e9cb6f71..e729200d9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm
index 73dd17d36..6425f7bb2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm
index 61757261b..03a6646d8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm
index bb3fa4bb4..e4f9f49f9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm
index d1734dfff..fde1f8604 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm
index f8064cfa8..ea8b97507 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm
index ab59e15de..0e034e70e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm
index 32f8fff52..c3622aeaf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm
index 827893970..a00f31f01 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm
index 0ff01a33f..29dc60ec7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm
index 87ae3cb96..241c7082e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm
index f684d7b05..a813973fc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm
index a67c8a0aa..6a53a4ba5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm
index c9fb93960..8fc42e622 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm
index 3951c2b4d..cd0223f63 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm
index 4abc76447..dcfd66cbc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm
index 73a45e0aa..ca8eeae9b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm
index f81d05d91..efe7407b2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm
index 8f0b018c1..ec838cdc4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm
index ef546685e..f9b1388c5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm
index ad12684be..d2454e5ab 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm
index ada8f3a20..4e7a90423 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm
index 6f7b991ba..4d500c7a2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm
index 071ceb37b..368b6ee3e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm
index 682256b0c..1127dd58c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm
index 7bf88513a..404a2c7ac 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm
index e158cf689..22b8edcf9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm
index 1296a31a0..6a48d2579 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm
index 6c8407837..136906147 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm
index 0e273c77b..1e98c2cba 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm
index 1f70cb494..7dd9cb079 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm
index 036167e2b..7427b7768 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm
index b81694419..9db5e987b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
index 31daf1c13..40eddb1b4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm
index ce23758df..0c8b1e6c7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm
index bf32f014f..9236c6a89 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm
index 820ac0461..575366b2b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm
index 1bd51699e..02bc81283 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm
index 315d9f686..ac0346c19 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm
index 57b7ec19c..cd62dd396 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm
index dc6d09c03..6d1500795 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm
index b2ce0e031..f9ec13c2b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm
index 6f0409c46..6cf68a79c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm
index e41dbc4f7..7b3129672 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm
index 8f21178b6..9122ac214 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm
index cbbfb293f..f19f37749 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm
index c177d1c94..249c9d31a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm
index 365d0990b..c36365e96 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm
index c3f999aa5..f7b9035b6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm
index c19e3d034..aab0ee753 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm
index a442a1e97..b1f023ec1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm
index e36faf90d..03e1a26ed 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm
index 0e6b396de..4379add76 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm
index b7fb2763f..7d8066771 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm
index 3fbe90b7e..d080a9da0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm
index 789bfd8f8..f0223a058 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm
index 0bd950ca0..879897c64 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm
index 70d73ff4b..f5ca7912a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm
index f3f08a3e4..798c976be 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm
index e4847a896..5bbf4bc92 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm
index c8b84e673..4926fa0f1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm
index d93e1a44e..05d258d93 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm
index 0845936ba..c35645acb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm
index 0b9f05844..53fa5bb07 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm
index 3d762b1ee..d685c0650 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm
index c13842ccc..a72919331 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm
index 84657761e..2c6ce0700 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm
index 994480f5f..efca488a5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm
index c3b033756..4727d57af 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm
index f6109b2e7..9f46856b2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm
index bb2dd2fd5..4f5a4a82f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm
index 0a6c6aaed..5dc083e26 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm
index a0db9709b..4ed073c5c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm
index 4c46af425..54d2336b1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm
index d32fcb62b..b32618a63 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm
index 339ac53a2..05d4f9564 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm
index 4d828a0a5..224b07cdf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm
index fc6f37a8c..42bcf37ee 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm
index b37273c60..55fdaa9ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm
index 0b34e8a69..90a55009b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm
index c95f4f0b4..670b22ddf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm
index c88597046..f534c3d97 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
index 87a07a728..a807f370a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
index 9ad149934..4ae7ac6ec 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm
index ec8e23e43..39d7dfa47 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
index 8dffe30b6..b713fa3b8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
index 6d4b2ad95..3722b2a3c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
index 271bb4c57..ba7cde4b0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
index 9d466cd33..df33c0d76 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm
index 7d7ab3fa0..0e036c77f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
index edfd83f29..3438dd571 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm
index 819dbedec..c162b479c 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm
index 165552207..bac416600 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm
index 18326f0eb..ce3252627 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm
index 9ba7b6c4b..5aa7f6be9 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm
index 145a8fa15..76fb367d9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm
index bc6616ede..7e91dafe4 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm
index d03bc1664..6f0ef4688 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm
index 72e453d0c..a268234dd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm
index 00e56fdf5..e0ebcbd50 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm
index 35bacf838..d90552de9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm
index 8dc7c52a5..28b51b052 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm
index a86a127df..358ecf63d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm
index b2a5101fc..a93ace422 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm
index aa7aee4d7..90c5ca3d7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm
index 30142a4b1..c2e987db9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm
index 53f989da6..40f64d501 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
index 2ac81e04f..b3233ea9d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm
index 4f3be48b0..2492c8d2c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm
index 16d4831ff..954249821 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm
index 86774dc21..c3627908c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm
index 98f434416..dbf318ee3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
index 90452a6ef..3dd8e2aff 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
index af8730208..522a74080 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm
index 127b483f1..ca551dfcb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm
index 9bc914b76..0b4bf3d7a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm
index 9c25218ac..257f901f6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm
index a3d2e52e5..326a416f9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
index 9520d126c..3a184d14c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm
index 7874017b7..178d43bf6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm
index 5fd370544..81e85112f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm
index 7ebbb964a..086f7b639 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
index 52469c2d7..068bf107f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm
index 7ce2776da..87fe1c26d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm
index 4bfd6bfc9..4aa66ed7e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
index bb96cdbf6..e47bcc2de 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm
index 77691a9aa..2c7db050f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm
index 6aa4ee447..c43815618 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm
index 419890a8b..8ce4605dc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm
index ff4ac6d98..a6626693a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm
index 03ae07dd4..89f34fdf8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm
index b81b2f0ce..5edb5edcc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm
index e0a1b139e..56fde172f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 18370f19a..011dc5fa2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm
index d549ae679..f8b9a9cc5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql
index a6005a40d..99d829af7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm
index 7c8d7a6a2..5cd4976e5 100644
--- a/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm
index df91fbe70..6fa547aac 100644
--- a/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm
index 3298f6340..f6290b0a5 100755
--- a/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm b/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm
index f30d5bb0a..f45f1e904 100755
--- a/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm
index 948ea4ae4..723dc64dd 100644
--- a/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm
index 29c34b8e4..e4249af85 100644
--- a/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm
index 09afadf5f..a69258d6d 100644
--- a/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm
index 6487f9d29..4716deee3 100644
--- a/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm b/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm
index 026496d01..b75f1f6d1 100644
--- a/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm
index 7023b5b93..a39b751de 100644
--- a/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm
index c1dd542f5..7bd3d9c6a 100644
--- a/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm
index 209d31ff3..32da0acae 100644
--- a/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm
index ab1a26d2e..97f1571d0 100644
--- a/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm
index 93a9a3d89..c93d458cb 100644
--- a/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm
index 48debd8a5..4667cfc58 100644
--- a/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm
index 3855bc93d..2a7103bab 100644
--- a/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm
index a2f66b75f..1505db6fa 100644
--- a/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm
index 9851bf321..0565354b2 100644
--- a/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm
index ae0aa5f84..58c88b680 100644
--- a/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm
index 591998e23..174baccde 100644
--- a/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm b/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm
index 657d90d93..91800a02f 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm b/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm
index f0196aab6..c3676fa7b 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm b/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm
index 34db39d30..223d4bd80 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm b/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm
index 01ea0b118..261924371 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm b/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm
index 982b32cf9..f680c6a8a 100755
--- a/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm b/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm
index bbe1380bd..c7b5e2d5d 100755
--- a/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm b/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm
index 7dc3d6378..4c6297748 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/t/00-searchdumps_load.t b/modules/t/00-searchdumps_load.t
index 7f5b56205..2f1cc4730 100644
--- a/modules/t/00-searchdumps_load.t
+++ b/modules/t/00-searchdumps_load.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/10-searchdumps_dumpgenome.t b/modules/t/10-searchdumps_dumpgenome.t
index a79b5c5e5..e332e97c8 100644
--- a/modules/t/10-searchdumps_dumpgenome.t
+++ b/modules/t/10-searchdumps_dumpgenome.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/11-searchdumps_dumpgenes.t b/modules/t/11-searchdumps_dumpgenes.t
index 4e4ff5840..9896a4912 100755
--- a/modules/t/11-searchdumps_dumpgenes.t
+++ b/modules/t/11-searchdumps_dumpgenes.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/12-searchdumps_dumpsequences.t b/modules/t/12-searchdumps_dumpsequences.t
index 15a27dc71..1fcf70a05 100644
--- a/modules/t/12-searchdumps_dumpsequences.t
+++ b/modules/t/12-searchdumps_dumpsequences.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/13-searchdumps_dumpmarkers.t b/modules/t/13-searchdumps_dumpmarkers.t
index 0696120fa..49e896a7b 100644
--- a/modules/t/13-searchdumps_dumpmarkers.t
+++ b/modules/t/13-searchdumps_dumpmarkers.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/14-searchdumps_dumplrgs.t b/modules/t/14-searchdumps_dumplrgs.t
index 466faef93..aead365af 100644
--- a/modules/t/14-searchdumps_dumplrgs.t
+++ b/modules/t/14-searchdumps_dumplrgs.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/15-searchdumps_dumpids.t b/modules/t/15-searchdumps_dumpids.t
index 968c5cdc4..7b0a941b1 100644
--- a/modules/t/15-searchdumps_dumpids.t
+++ b/modules/t/15-searchdumps_dumpids.t
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/t/16-searchdumps_dumpprobes.t b/modules/t/16-searchdumps_dumpprobes.t
index 882177b18..0b8982076 100644
--- a/modules/t/16-searchdumps_dumpprobes.t
+++ b/modules/t/16-searchdumps_dumpprobes.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/17-searchdumps_dumpregulation.t b/modules/t/17-searchdumps_dumpregulation.t
index 9974c024b..3f8223ce5 100644
--- a/modules/t/17-searchdumps_dumpregulation.t
+++ b/modules/t/17-searchdumps_dumpregulation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/18-searchdumps_dumpvariation.t b/modules/t/18-searchdumps_dumpvariation.t
index ae169f349..3196ac137 100644
--- a/modules/t/18-searchdumps_dumpvariation.t
+++ b/modules/t/18-searchdumps_dumpvariation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/40-searchdumps_reformat_base.t b/modules/t/40-searchdumps_reformat_base.t
index ff8fb8062..594e475ad 100644
--- a/modules/t/40-searchdumps_reformat_base.t
+++ b/modules/t/40-searchdumps_reformat_base.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/41-searchdumps_reformat_advsearch.t b/modules/t/41-searchdumps_reformat_advsearch.t
index 2771b14c0..b91af455c 100644
--- a/modules/t/41-searchdumps_reformat_advsearch.t
+++ b/modules/t/41-searchdumps_reformat_advsearch.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/42-searchdumps_reformat_solr_genes.t b/modules/t/42-searchdumps_reformat_solr_genes.t
index 4be3bf131..0da97ecc6 100644
--- a/modules/t/42-searchdumps_reformat_solr_genes.t
+++ b/modules/t/42-searchdumps_reformat_solr_genes.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/43-searchdumps_reformat_solr_regulation.t b/modules/t/43-searchdumps_reformat_solr_regulation.t
index 1cd718e2e..944bf4452 100644
--- a/modules/t/43-searchdumps_reformat_solr_regulation.t
+++ b/modules/t/43-searchdumps_reformat_solr_regulation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/44-searchdumps_reformat_solr_variation.t b/modules/t/44-searchdumps_reformat_solr_variation.t
index 048a5f860..56c5e02fe 100644
--- a/modules/t/44-searchdumps_reformat_solr_variation.t
+++ b/modules/t/44-searchdumps_reformat_solr_variation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/45-searchdumps_reformat_ebeye.t b/modules/t/45-searchdumps_reformat_ebeye.t
index 07de5f86b..0d06c50de 100644
--- a/modules/t/45-searchdumps_reformat_ebeye.t
+++ b/modules/t/45-searchdumps_reformat_ebeye.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/dbAdaptor.t b/modules/t/dbAdaptor.t
index d58d308d4..0b58fc78c 100644
--- a/modules/t/dbAdaptor.t
+++ b/modules/t/dbAdaptor.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_fasta_binaries/faToTwoBit b/modules/t/fake_fasta_binaries/faToTwoBit
index 2430b59ee..5e572b2f8 100755
--- a/modules/t/fake_fasta_binaries/faToTwoBit
+++ b/modules/t/fake_fasta_binaries/faToTwoBit
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_fasta_binaries/makeblastdb b/modules/t/fake_fasta_binaries/makeblastdb
index a946fd1fc..2a6d5d20e 100755
--- a/modules/t/fake_fasta_binaries/makeblastdb
+++ b/modules/t/fake_fasta_binaries/makeblastdb
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_fasta_binaries/xdformat b/modules/t/fake_fasta_binaries/xdformat
index 0d2562d69..1cfea93c7 100755
--- a/modules/t/fake_fasta_binaries/xdformat
+++ b/modules/t/fake_fasta_binaries/xdformat
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_gff_binaries/gt b/modules/t/fake_gff_binaries/gt
index e4a0a54c1..241d68c3b 100755
--- a/modules/t/fake_gff_binaries/gt
+++ b/modules/t/fake_gff_binaries/gt
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_gtf_binaries/genePredCheck b/modules/t/fake_gtf_binaries/genePredCheck
index b19b325a5..0d49f8820 100755
--- a/modules/t/fake_gtf_binaries/genePredCheck
+++ b/modules/t/fake_gtf_binaries/genePredCheck
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_gtf_binaries/gtfToGenePred b/modules/t/fake_gtf_binaries/gtfToGenePred
index e4a0a54c1..241d68c3b 100755
--- a/modules/t/fake_gtf_binaries/gtfToGenePred
+++ b/modules/t/fake_gtf_binaries/gtfToGenePred
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/housekeeping_apache2.t b/modules/t/housekeeping_apache2.t
index 3c5e47714..02fc0ce9c 100644
--- a/modules/t/housekeeping_apache2.t
+++ b/modules/t/housekeeping_apache2.t
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/t/json_remodelling.t b/modules/t/json_remodelling.t
index 8550b6bd8..f3522c300 100644
--- a/modules/t/json_remodelling.t
+++ b/modules/t/json_remodelling.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/production_pipeline.t b/modules/t/production_pipeline.t
index 3291ade47..3941e86bf 100644
--- a/modules/t/production_pipeline.t
+++ b/modules/t/production_pipeline.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/test-genome-DBs/multi/ontology/tables.sql b/modules/t/test-genome-DBs/multi/ontology/tables.sql
index 1952a7504..2dc2de1dd 100644
--- a/modules/t/test-genome-DBs/multi/ontology/tables.sql
+++ b/modules/t/test-genome-DBs/multi/ontology/tables.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/nextflow/nf-py-scripts/generate_thoas_conf.py b/nextflow/nf-py-scripts/generate_thoas_conf.py
index d5c456ffe..9e0d9e95c 100755
--- a/nextflow/nf-py-scripts/generate_thoas_conf.py
+++ b/nextflow/nf-py-scripts/generate_thoas_conf.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/nextflow/nf-py-scripts/genome_info.py b/nextflow/nf-py-scripts/genome_info.py
index 5349a755c..cff4a5315 100755
--- a/nextflow/nf-py-scripts/genome_info.py
+++ b/nextflow/nf-py-scripts/genome_info.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/scripts/alphafold_gifts/get_alignment_data.sql b/scripts/alphafold_gifts/get_alignment_data.sql
index f2ec1f1a9..f8026f39b 100644
--- a/scripts/alphafold_gifts/get_alignment_data.sql
+++ b/scripts/alphafold_gifts/get_alignment_data.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/scripts/alphafold_gifts/get_assemblies.sql b/scripts/alphafold_gifts/get_assemblies.sql
index 881dac78f..09fa99f88 100644
--- a/scripts/alphafold_gifts/get_assemblies.sql
+++ b/scripts/alphafold_gifts/get_assemblies.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/scripts/apply_patches.pl b/scripts/apply_patches.pl
index 04ced0d3d..fdd97415c 100755
--- a/scripts/apply_patches.pl
+++ b/scripts/apply_patches.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/assembly_converter/link_out.sh b/scripts/assembly_converter/link_out.sh
index 08358854b..6d1d209a0 100644
--- a/scripts/assembly_converter/link_out.sh
+++ b/scripts/assembly_converter/link_out.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/assembly_converter/populate_assembly_converter_dir.sh b/scripts/assembly_converter/populate_assembly_converter_dir.sh
index 40b6968d2..af89f54da 100755
--- a/scripts/assembly_converter/populate_assembly_converter_dir.sh
+++ b/scripts/assembly_converter/populate_assembly_converter_dir.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/checkEnsembl_lowcoverage.pl b/scripts/checkEnsembl_lowcoverage.pl
index a6074799e..8e823cc2a 100644
--- a/scripts/checkEnsembl_lowcoverage.pl
+++ b/scripts/checkEnsembl_lowcoverage.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/check_UniProt_evidence.pl b/scripts/check_UniProt_evidence.pl
index 2813db429..c13753820 100644
--- a/scripts/check_UniProt_evidence.pl
+++ b/scripts/check_UniProt_evidence.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/check_staging_databases.sh b/scripts/check_staging_databases.sh
index d599b6866..cea3edda9 100755
--- a/scripts/check_staging_databases.sh
+++ b/scripts/check_staging_databases.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_and_patch_db.sh b/scripts/copy_and_patch_db.sh
index 3e1ced229..53efc458e 100755
--- a/scripts/copy_and_patch_db.sh
+++ b/scripts/copy_and_patch_db.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_database.pl b/scripts/copy_database.pl
index c8fccbdfa..62749b070 100644
--- a/scripts/copy_database.pl
+++ b/scripts/copy_database.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_ftp_release.pl b/scripts/copy_ftp_release.pl
index f48f7bbab..6b85b0d13 100755
--- a/scripts/copy_ftp_release.pl
+++ b/scripts/copy_ftp_release.pl
@@ -1,6 +1,6 @@
 #!/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_genome.pl b/scripts/copy_genome.pl
index 6c2d5860b..16aeb5850 100755
--- a/scripts/copy_genome.pl
+++ b/scripts/copy_genome.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copyrights/update_copyrights.sh b/scripts/copyrights/update_copyrights.sh
index f214c4ad6..bf18476e1 100755
--- a/scripts/copyrights/update_copyrights.sh
+++ b/scripts/copyrights/update_copyrights.sh
@@ -1,7 +1,7 @@
 #/bin/sh
 # NOTE THIS script need `gh` command line tool available on https://github.com/cli/cli#installation
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/build_datafile_ftp_directory.pl b/scripts/datafiles/build_datafile_ftp_directory.pl
index 2baaab17b..0fd1af263 100755
--- a/scripts/datafiles/build_datafile_ftp_directory.pl
+++ b/scripts/datafiles/build_datafile_ftp_directory.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 #
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/check_datafiles.pl b/scripts/datafiles/check_datafiles.pl
index 0a0a67c56..f4559b609 100644
--- a/scripts/datafiles/check_datafiles.pl
+++ b/scripts/datafiles/check_datafiles.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/first_bam_alignment.pl b/scripts/datafiles/first_bam_alignment.pl
index 246f63459..b24288beb 100644
--- a/scripts/datafiles/first_bam_alignment.pl
+++ b/scripts/datafiles/first_bam_alignment.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/sizes.pl b/scripts/datafiles/sizes.pl
index 402f50e7a..36ba4e782 100755
--- a/scripts/datafiles/sizes.pl
+++ b/scripts/datafiles/sizes.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/delete_genome.pl b/scripts/delete_genome.pl
index 46c0a2c06..8a1c1b2cf 100644
--- a/scripts/delete_genome.pl
+++ b/scripts/delete_genome.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/ena/ena_dump.pl b/scripts/ena/ena_dump.pl
index fc7cc33db..2747ad545 100755
--- a/scripts/ena/ena_dump.pl
+++ b/scripts/ena/ena_dump.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/ftp/checksums.pl b/scripts/ftp/checksums.pl
index 0f0afa483..5fed9c273 100755
--- a/scripts/ftp/checksums.pl
+++ b/scripts/ftp/checksums.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/ftp/upload_ena_xrefs.sh b/scripts/ftp/upload_ena_xrefs.sh
index 0669610b3..e8a7a1801 100755
--- a/scripts/ftp/upload_ena_xrefs.sh
+++ b/scripts/ftp/upload_ena_xrefs.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/get_new_db_name.pl b/scripts/get_new_db_name.pl
index 8c1c3b31d..a95c4ec33 100755
--- a/scripts/get_new_db_name.pl
+++ b/scripts/get_new_db_name.pl
@@ -1,6 +1,6 @@
 #!/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/link_out/generate_LinkOut.pl b/scripts/link_out/generate_LinkOut.pl
index 1e0e358c3..f12fada3b 100644
--- a/scripts/link_out/generate_LinkOut.pl
+++ b/scripts/link_out/generate_LinkOut.pl
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/misc/check_tmux.sh b/scripts/misc/check_tmux.sh
index cbbf75810..012fa8d34 100755
--- a/scripts/misc/check_tmux.sh
+++ b/scripts/misc/check_tmux.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/misc/tmux_ls.sh b/scripts/misc/tmux_ls.sh
index 2d5358cc6..317f0ef97 100755
--- a/scripts/misc/tmux_ls.sh
+++ b/scripts/misc/tmux_ls.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/prepare_ftp_dump.sh b/scripts/prepare_ftp_dump.sh
index 733a881e6..fc8f05311 100755
--- a/scripts/prepare_ftp_dump.sh
+++ b/scripts/prepare_ftp_dump.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/production_database/import_species_names_from_cores.pl b/scripts/production_database/import_species_names_from_cores.pl
index 0c29a8130..4bb484071 100644
--- a/scripts/production_database/import_species_names_from_cores.pl
+++ b/scripts/production_database/import_species_names_from_cores.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/production_database/import_species_names_from_taxonomy.pl b/scripts/production_database/import_species_names_from_taxonomy.pl
index e9da34624..9647588fb 100644
--- a/scripts/production_database/import_species_names_from_taxonomy.pl
+++ b/scripts/production_database/import_species_names_from_taxonomy.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/production_database/populate_species_meta.pl b/scripts/production_database/populate_species_meta.pl
index a640509cb..1cdc26da6 100644
--- a/scripts/production_database/populate_species_meta.pl
+++ b/scripts/production_database/populate_species_meta.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/py/alphafoldUpdate.py b/scripts/py/alphafoldUpdate.py
index e184ea71c..2c63a63da 100644
--- a/scripts/py/alphafoldUpdate.py
+++ b/scripts/py/alphafoldUpdate.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/py/alphafoldUpdate_parallel.py b/scripts/py/alphafoldUpdate_parallel.py
index ede2a286f..b7332e7d9 100644
--- a/scripts/py/alphafoldUpdate_parallel.py
+++ b/scripts/py/alphafoldUpdate_parallel.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 8cf410452..be8c30d9e 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/refget/check_sequence_refget.pl b/scripts/refget/check_sequence_refget.pl
index a2bbf2fb5..532948c30 100755
--- a/scripts/refget/check_sequence_refget.pl
+++ b/scripts/refget/check_sequence_refget.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sql2html.pl b/scripts/sql2html.pl
index 33b02afd1..1e2a917e2 100755
--- a/scripts/sql2html.pl
+++ b/scripts/sql2html.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/check_db.sh b/scripts/sync/check_db.sh
index 9207a1428..254f39dd3 100644
--- a/scripts/sync/check_db.sh
+++ b/scripts/sync/check_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/check_public_db.sh b/scripts/sync/check_public_db.sh
index e5318ea90..1ca960fa2 100644
--- a/scripts/sync/check_public_db.sh
+++ b/scripts/sync/check_public_db.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/get_release.sh b/scripts/sync/get_release.sh
index 60208f938..ddccffcda 100644
--- a/scripts/sync/get_release.sh
+++ b/scripts/sync/get_release.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/get_staging_server.sh b/scripts/sync/get_staging_server.sh
index 6895aad3f..b034efea4 100644
--- a/scripts/sync/get_staging_server.sh
+++ b/scripts/sync/get_staging_server.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/optimise_databases.sh b/scripts/sync/optimise_databases.sh
index f042b0942..0c430b5a2 100644
--- a/scripts/sync/optimise_databases.sh
+++ b/scripts/sync/optimise_databases.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/process_divisions.sh b/scripts/sync/process_divisions.sh
index 75c216633..bd99d2c1f 100755
--- a/scripts/sync/process_divisions.sh
+++ b/scripts/sync/process_divisions.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/publish_db.sh b/scripts/sync/publish_db.sh
index abab797e3..56d6bea48 100755
--- a/scripts/sync/publish_db.sh
+++ b/scripts/sync/publish_db.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/set_checksums.sh b/scripts/sync/set_checksums.sh
index ab4d56dd4..1da4bd063 100644
--- a/scripts/sync/set_checksums.sh
+++ b/scripts/sync/set_checksums.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/sync_db.sh b/scripts/sync/sync_db.sh
index 21f17ce2a..899429d37 100644
--- a/scripts/sync/sync_db.sh
+++ b/scripts/sync/sync_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/sync_db_st1.sh b/scripts/sync/sync_db_st1.sh
index 8b14f0b12..2cc7440b9 100644
--- a/scripts/sync/sync_db_st1.sh
+++ b/scripts/sync/sync_db_st1.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/sync_db_st2.sh b/scripts/sync/sync_db_st2.sh
index 219a29d19..dc010c78f 100644
--- a/scripts/sync/sync_db_st2.sh
+++ b/scripts/sync/sync_db_st2.sh
@@ -1,6 +1,6 @@
 #!/bin/sh --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/update_live_db.sh b/scripts/sync/update_live_db.sh
index 280714bb2..6ce2f4645 100644
--- a/scripts/sync/update_live_db.sh
+++ b/scripts/sync/update_live_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync_tables.sh b/scripts/sync_tables.sh
index 88fba252d..0a5540cc7 100755
--- a/scripts/sync_tables.sh
+++ b/scripts/sync_tables.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/t/rename_db.t b/scripts/t/rename_db.t
index a2fcdb298..930e08410 100644
--- a/scripts/t/rename_db.t
+++ b/scripts/t/rename_db.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/update_api_tarball.sh b/scripts/update_api_tarball.sh
index 65a7dee0f..c1033d472 100755
--- a/scripts/update_api_tarball.sh
+++ b/scripts/update_api_tarball.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/update_assembly_tables.sh b/scripts/update_assembly_tables.sh
index aff7259c5..8bfcd5ef3 100755
--- a/scripts/update_assembly_tables.sh
+++ b/scripts/update_assembly_tables.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/update_mapping_set.pl b/scripts/update_mapping_set.pl
index 578abf8b5..58027e469 100644
--- a/scripts/update_mapping_set.pl
+++ b/scripts/update_mapping_set.pl
@@ -1,6 +1,6 @@
 #!/usr/local/ensembl/bin/perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/sql/patch_100_101_a.sql b/sql/patch_100_101_a.sql
index 15908b8a0..8fae827f3 100644
--- a/sql/patch_100_101_a.sql
+++ b/sql/patch_100_101_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_101_102_a.sql b/sql/patch_101_102_a.sql
index 4c855706f..2ce3dfa4b 100644
--- a/sql/patch_101_102_a.sql
+++ b/sql/patch_101_102_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_102_103_a.sql b/sql/patch_102_103_a.sql
index 9d3cae861..e92b99fdf 100644
--- a/sql/patch_102_103_a.sql
+++ b/sql/patch_102_103_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_103_104_a.sql b/sql/patch_103_104_a.sql
index 57f9ecf16..e6ae954cf 100644
--- a/sql/patch_103_104_a.sql
+++ b/sql/patch_103_104_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_104_105_a.sql b/sql/patch_104_105_a.sql
index d374079da..939a68c31 100644
--- a/sql/patch_104_105_a.sql
+++ b/sql/patch_104_105_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_105_106_a.sql b/sql/patch_105_106_a.sql
index fbc613b4d..54e7a3cce 100644
--- a/sql/patch_105_106_a.sql
+++ b/sql/patch_105_106_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_106_107_a.sql b/sql/patch_106_107_a.sql
index 799e5dc1a..cf0b0786d 100644
--- a/sql/patch_106_107_a.sql
+++ b/sql/patch_106_107_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_107_108_a.sql b/sql/patch_107_108_a.sql
index efbf8126d..1b96e7e30 100644
--- a/sql/patch_107_108_a.sql
+++ b/sql/patch_107_108_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_108_109_a.sql b/sql/patch_108_109_a.sql
index 9a01e5f03..9e7e4432e 100644
--- a/sql/patch_108_109_a.sql
+++ b/sql/patch_108_109_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_109_110_a.sql b/sql/patch_109_110_a.sql
index bcb77d5cc..427981eec 100644
--- a/sql/patch_109_110_a.sql
+++ b/sql/patch_109_110_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_110_111_a.sql b/sql/patch_110_111_a.sql
index 50b48d95a..91ba1c712 100644
--- a/sql/patch_110_111_a.sql
+++ b/sql/patch_110_111_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_111_112_a.sql b/sql/patch_111_112_a.sql
index d059492fb..4394d65ed 100644
--- a/sql/patch_111_112_a.sql
+++ b/sql/patch_111_112_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_66_67a.sql b/sql/patch_66_67a.sql
index 3d41300ba..8a1493a9e 100644
--- a/sql/patch_66_67a.sql
+++ b/sql/patch_66_67a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_66_67b.sql b/sql/patch_66_67b.sql
index 24a9a823c..8a487f804 100644
--- a/sql/patch_66_67b.sql
+++ b/sql/patch_66_67b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_66_67c.sql b/sql/patch_66_67c.sql
index 62a317219..df9c1202c 100644
--- a/sql/patch_66_67c.sql
+++ b/sql/patch_66_67c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_70_71a.sql b/sql/patch_70_71a.sql
index c884dbe57..38dfb75dd 100644
--- a/sql/patch_70_71a.sql
+++ b/sql/patch_70_71a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_71_72a.sql b/sql/patch_71_72a.sql
index e23e1d0d9..b6e80c406 100644
--- a/sql/patch_71_72a.sql
+++ b/sql/patch_71_72a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_71_72b.sql b/sql/patch_71_72b.sql
index e8a49ded9..e419da717 100644
--- a/sql/patch_71_72b.sql
+++ b/sql/patch_71_72b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73a.sql b/sql/patch_72_73a.sql
index c52185d0f..14fc3c0cb 100644
--- a/sql/patch_72_73a.sql
+++ b/sql/patch_72_73a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73b.sql b/sql/patch_72_73b.sql
index 6d786d667..307e9bcaa 100644
--- a/sql/patch_72_73b.sql
+++ b/sql/patch_72_73b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73c.sql b/sql/patch_72_73c.sql
index 625c81b31..d482e55ea 100644
--- a/sql/patch_72_73c.sql
+++ b/sql/patch_72_73c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73d.sql b/sql/patch_72_73d.sql
index a48f47240..5777b9c02 100644
--- a/sql/patch_72_73d.sql
+++ b/sql/patch_72_73d.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73e.sql b/sql/patch_72_73e.sql
index ea3fcab26..365fba5d9 100644
--- a/sql/patch_72_73e.sql
+++ b/sql/patch_72_73e.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_73_74a.sql b/sql/patch_73_74a.sql
index ab3a80db0..448aa4e7e 100644
--- a/sql/patch_73_74a.sql
+++ b/sql/patch_73_74a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_73_74b.sql b/sql/patch_73_74b.sql
index 20a7af979..a9e4ab21d 100644
--- a/sql/patch_73_74b.sql
+++ b/sql/patch_73_74b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_74_75a.sql b/sql/patch_74_75a.sql
index 6ade7d4ca..03a5c9f8f 100644
--- a/sql/patch_74_75a.sql
+++ b/sql/patch_74_75a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_74_75b.sql b/sql/patch_74_75b.sql
index df331a1ab..c32246fa5 100644
--- a/sql/patch_74_75b.sql
+++ b/sql/patch_74_75b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_75_76a.sql b/sql/patch_75_76a.sql
index 6ab105370..4323f0b45 100644
--- a/sql/patch_75_76a.sql
+++ b/sql/patch_75_76a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_75_76b.sql b/sql/patch_75_76b.sql
index 52bb31295..86d773a7c 100644
--- a/sql/patch_75_76b.sql
+++ b/sql/patch_75_76b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_76_77a.sql b/sql/patch_76_77a.sql
index 976ff6ca9..a7f88fe5a 100644
--- a/sql/patch_76_77a.sql
+++ b/sql/patch_76_77a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_76_77b.sql b/sql/patch_76_77b.sql
index d8ae4cb32..4d8a0292f 100644
--- a/sql/patch_76_77b.sql
+++ b/sql/patch_76_77b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_76_77c.sql b/sql/patch_76_77c.sql
index bf6389c72..e11d7b6ff 100644
--- a/sql/patch_76_77c.sql
+++ b/sql/patch_76_77c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_77_78a.sql b/sql/patch_77_78a.sql
index 2102e7f2e..998ae5285 100644
--- a/sql/patch_77_78a.sql
+++ b/sql/patch_77_78a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_77_78b.sql b/sql/patch_77_78b.sql
index d22cc7765..dbdfb77d2 100644
--- a/sql/patch_77_78b.sql
+++ b/sql/patch_77_78b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_78_79a.sql b/sql/patch_78_79a.sql
index 6142d73e0..cd70b6f58 100644
--- a/sql/patch_78_79a.sql
+++ b/sql/patch_78_79a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_78_79b.sql b/sql/patch_78_79b.sql
index c995cbeb0..027f10575 100644
--- a/sql/patch_78_79b.sql
+++ b/sql/patch_78_79b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_79_80_a.sql b/sql/patch_79_80_a.sql
index 2eac97dc1..bc4b07587 100644
--- a/sql/patch_79_80_a.sql
+++ b/sql/patch_79_80_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_79_80b.sql b/sql/patch_79_80b.sql
index 359254dec..b78f1b3a2 100644
--- a/sql/patch_79_80b.sql
+++ b/sql/patch_79_80b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_79_80c.sql b/sql/patch_79_80c.sql
index e37889e3b..3117e7100 100644
--- a/sql/patch_79_80c.sql
+++ b/sql/patch_79_80c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_80_81a.sql b/sql/patch_80_81a.sql
index 20fb91c81..f2cc022bb 100644
--- a/sql/patch_80_81a.sql
+++ b/sql/patch_80_81a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_81_82a.sql b/sql/patch_81_82a.sql
index c2033985a..ab8035808 100644
--- a/sql/patch_81_82a.sql
+++ b/sql/patch_81_82a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_82_83a.sql b/sql/patch_82_83a.sql
index 2bace410f..0a434ce50 100644
--- a/sql/patch_82_83a.sql
+++ b/sql/patch_82_83a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_83_84a.sql b/sql/patch_83_84a.sql
index f4ac58b90..576e37220 100644
--- a/sql/patch_83_84a.sql
+++ b/sql/patch_83_84a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_83_84b.sql b/sql/patch_83_84b.sql
index 7cd10bcf9..67a259637 100644
--- a/sql/patch_83_84b.sql
+++ b/sql/patch_83_84b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_84_85a.sql b/sql/patch_84_85a.sql
index 27bdfe2fe..df71904d5 100644
--- a/sql/patch_84_85a.sql
+++ b/sql/patch_84_85a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_85_86a.sql b/sql/patch_85_86a.sql
index 88f01ec22..74ba611e3 100644
--- a/sql/patch_85_86a.sql
+++ b/sql/patch_85_86a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_85_86b.sql b/sql/patch_85_86b.sql
index 107b75331..a6886f6a4 100644
--- a/sql/patch_85_86b.sql
+++ b/sql/patch_85_86b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_85_86c.sql b/sql/patch_85_86c.sql
index cadb8ae8d..d1ead0ea6 100644
--- a/sql/patch_85_86c.sql
+++ b/sql/patch_85_86c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_86_87a.sql b/sql/patch_86_87a.sql
index d44c66123..2a4c58a14 100644
--- a/sql/patch_86_87a.sql
+++ b/sql/patch_86_87a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_87_88_a.sql b/sql/patch_87_88_a.sql
index 0ecdc80fa..808314f4c 100644
--- a/sql/patch_87_88_a.sql
+++ b/sql/patch_87_88_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_88_89_a.sql b/sql/patch_88_89_a.sql
index a0143bf3c..39c13d822 100644
--- a/sql/patch_88_89_a.sql
+++ b/sql/patch_88_89_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_89_90_a.sql b/sql/patch_89_90_a.sql
index 22f4a7840..3d78db749 100644
--- a/sql/patch_89_90_a.sql
+++ b/sql/patch_89_90_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_89_90_b.sql b/sql/patch_89_90_b.sql
index 1693fb8f5..d3800cbc3 100644
--- a/sql/patch_89_90_b.sql
+++ b/sql/patch_89_90_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_90_91_a.sql b/sql/patch_90_91_a.sql
index dfb0e5fc1..2dbb361ad 100644
--- a/sql/patch_90_91_a.sql
+++ b/sql/patch_90_91_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_91_92_a.sql b/sql/patch_91_92_a.sql
index 0a1cbbfd5..f2546a7b5 100644
--- a/sql/patch_91_92_a.sql
+++ b/sql/patch_91_92_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_92_93_a.sql b/sql/patch_92_93_a.sql
index d2e804ef2..e4467914f 100644
--- a/sql/patch_92_93_a.sql
+++ b/sql/patch_92_93_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_92_93_b.sql b/sql/patch_92_93_b.sql
index cacc4688e..21ed7f478 100644
--- a/sql/patch_92_93_b.sql
+++ b/sql/patch_92_93_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_93_94_a.sql b/sql/patch_93_94_a.sql
index 776c119f2..11308c60f 100644
--- a/sql/patch_93_94_a.sql
+++ b/sql/patch_93_94_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_94_95_a.sql b/sql/patch_94_95_a.sql
index 94a08b2ce..8b57afea9 100644
--- a/sql/patch_94_95_a.sql
+++ b/sql/patch_94_95_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_94_95_b.sql b/sql/patch_94_95_b.sql
index a431932ea..11f5c2a0b 100644
--- a/sql/patch_94_95_b.sql
+++ b/sql/patch_94_95_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_95_96_a.sql b/sql/patch_95_96_a.sql
index a5ace02f1..d23918cc9 100644
--- a/sql/patch_95_96_a.sql
+++ b/sql/patch_95_96_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_a.sql b/sql/patch_96_97_a.sql
index a6b87fbc6..3aa2641e6 100644
--- a/sql/patch_96_97_a.sql
+++ b/sql/patch_96_97_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_b.sql b/sql/patch_96_97_b.sql
index 71c633956..34367a992 100644
--- a/sql/patch_96_97_b.sql
+++ b/sql/patch_96_97_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_c.sql b/sql/patch_96_97_c.sql
index 085470cce..da78c3285 100644
--- a/sql/patch_96_97_c.sql
+++ b/sql/patch_96_97_c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_d.sql b/sql/patch_96_97_d.sql
index 5449accfc..fb9bce3dc 100644
--- a/sql/patch_96_97_d.sql
+++ b/sql/patch_96_97_d.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_e.sql b/sql/patch_96_97_e.sql
index 5c6158bb4..7749cf793 100644
--- a/sql/patch_96_97_e.sql
+++ b/sql/patch_96_97_e.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_f.sql b/sql/patch_96_97_f.sql
index 526f82962..f862d40ec 100644
--- a/sql/patch_96_97_f.sql
+++ b/sql/patch_96_97_f.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_97_98_a.sql b/sql/patch_97_98_a.sql
index 9bfce4019..fb5055676 100644
--- a/sql/patch_97_98_a.sql
+++ b/sql/patch_97_98_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_98_99_a.sql b/sql/patch_98_99_a.sql
index 54619e467..8877f4de3 100644
--- a/sql/patch_98_99_a.sql
+++ b/sql/patch_98_99_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_98_99_b.sql b/sql/patch_98_99_b.sql
index cc3820ff6..1aa6dd37f 100644
--- a/sql/patch_98_99_b.sql
+++ b/sql/patch_98_99_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_99_100_a.sql b/sql/patch_99_100_a.sql
index 6fe8fa689..532a2b298 100644
--- a/sql/patch_99_100_a.sql
+++ b/sql/patch_99_100_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/table.sql b/sql/table.sql
index 4cbe5a09d..a72e11ee5 100644
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/src/python/scripts/dcparse.py b/src/python/scripts/dcparse.py
index e2c50ee5b..b14896ae1 100755
--- a/src/python/scripts/dcparse.py
+++ b/src/python/scripts/dcparse.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
diff --git a/src/python/scripts/dcstat.py b/src/python/scripts/dcstat.py
index 76c3f9eb9..dce7ca061 100755
--- a/src/python/scripts/dcstat.py
+++ b/src/python/scripts/dcstat.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
diff --git a/src/python/scripts/genome_info.py b/src/python/scripts/genome_info.py
index 228186abb..48ade41b2 100755
--- a/src/python/scripts/genome_info.py
+++ b/src/python/scripts/genome_info.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/src/python/scripts/meta_hive_species.py b/src/python/scripts/meta_hive_species.py
index f6e0733bd..cd61cd425 100755
--- a/src/python/scripts/meta_hive_species.py
+++ b/src/python/scripts/meta_hive_species.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

From be5f31916d7afd6a39558a4ef1c9ce091fc18ce0 Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Thu, 25 Jan 2024 14:34:18 +0000
Subject: [PATCH 033/128] Fixed array bug

---
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index b2ee90ef1..ee5a1a8af 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -100,8 +100,8 @@ sub resource_classes {
         'dm'        => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
         'dm_D'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
         'dm_W'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'dm32_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 32000 -R "rusage[mem=32000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'32000M'} . 'm' },
-        'dmMAX_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 200000 -R "rusage[mem=200000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'200000M'} . 'm' },
+        'dm32_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 32000 -R "rusage[mem=32000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'100GB'} . 'm' },
+        'dmMAX_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 200000 -R "rusage[mem=200000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'200GB'} . 'm' },
     );
     #Create a dictionary of all possible time and memory combinations. Format would be:
     #2G={

From 73e78018f20c88b9a85bf28ed1b2dd2422ac89bf Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Thu, 25 Jan 2024 14:44:44 +0000
Subject: [PATCH 034/128] Fixed typo

---
 modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index ee5a1a8af..ac0fca871 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -100,7 +100,7 @@ sub resource_classes {
         'dm'        => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
         'dm_D'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
         'dm_W'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'dm32_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 32000 -R "rusage[mem=32000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'100GB'} . 'm' },
+        'dm32_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 32000 -R "rusage[mem=32000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'32GB'} . 'm' },
         'dmMAX_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 200000 -R "rusage[mem=200000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'200GB'} . 'm' },
     );
     #Create a dictionary of all possible time and memory combinations. Format would be:

From b012cb58cae21ba87df5235080f7c4df04dc463e Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Tue, 30 Jan 2024 08:56:52 +0000
Subject: [PATCH 035/128] Update update_copyrights.sh

---
 scripts/copyrights/update_copyrights.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scripts/copyrights/update_copyrights.sh b/scripts/copyrights/update_copyrights.sh
index f214c4ad6..5318667fa 100755
--- a/scripts/copyrights/update_copyrights.sh
+++ b/scripts/copyrights/update_copyrights.sh
@@ -50,6 +50,7 @@ for repo in $repositories; do
   git clone --depth 1 --branch main git@github.com:${repo} ${tmp_dir}/${repo}
   if [ $? -eq 0 ]; then
     cd ${tmp_dir}/${repo}
+    git push origin --delete bau/copyright-${year}
     git checkout -b bau/copyright-${year}
     perl ${ENSEMBL_ROOT_DIR}/ensembl/misc-scripts/annual_copyright_updater.sh
     git commit -a -m "${year} copyright update"
@@ -65,6 +66,7 @@ for repo in $repositories; do
         fi
       else
         echo 'failed to push commits and open a pull request.';
+        git push origin --delete bau/copyright-${year}
       fi
     else
       echo 'failed to commit updates.';

From fe59fe51d71c42d04cf631dee0d3fc5ca4693502 Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Tue, 30 Jan 2024 08:57:19 +0000
Subject: [PATCH 036/128] 2024 copyright update

---
 LICENSE                                                       | 2 +-
 modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm           | 2 +-
 modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm             | 2 +-
 .../EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm  | 2 +-
 .../Production/Pipeline/AlphaFold/InsertProteinFeatures.pm    | 2 +-
 .../Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm    | 2 +-
 .../Pipeline/AttributeAnnotation/FetchApprisFiles.pm          | 2 +-
 .../Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm   | 2 +-
 .../Production/Pipeline/AttributeAnnotation/LoadAppris.pm     | 2 +-
 .../Production/Pipeline/AttributeAnnotation/LoadTSL.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm        | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm  | 2 +-
 .../Production/Pipeline/Common/DbAwareSpeciesFactory.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm        | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm  | 2 +-
 .../Production/Pipeline/Common/RunCreateReleaseFile.pm        | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm  | 2 +-
 .../Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm     | 2 +-
 .../Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm         | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm | 2 +-
 .../Production/Pipeline/FASTA/CreatePrimaryAssembly.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm     | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm     | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm | 2 +-
 .../Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm    | 2 +-
 .../Production/Pipeline/FtpChecker/CheckVariationFtp.pm       | 2 +-
 .../EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm      | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm      | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm   | 2 +-
 .../Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm  | 2 +-
 .../Production/Pipeline/GeneAutocomplete/sql/table.sql        | 2 +-
 .../Production/Pipeline/GeneNameDescProjection/Base.pm        | 2 +-
 .../Pipeline/GeneNameDescProjection/DeleteExisting.pm         | 2 +-
 .../Pipeline/GeneNameDescProjection/GeneDescProjection.pm     | 2 +-
 .../Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm   | 2 +-
 .../Pipeline/GeneNameDescProjection/GeneNamesProjection.pm    | 2 +-
 .../Pipeline/GeneNameDescProjection/SourceFactory.pm          | 2 +-
 .../Production/Pipeline/GeneTreeHighlight/HighlightGO.pm      | 2 +-
 .../Pipeline/GeneTreeHighlight/HighlightInterPro.pm           | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm    | 2 +-
 .../Production/Pipeline/LoadFamily/AddFamilyMembers.pm        | 2 +-
 .../EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm  | 2 +-
 .../Production/Pipeline/OntologiesLoad/AddSubsetMap.pm        | 2 +-
 .../Production/Pipeline/OntologiesLoad/ComputeClosure.pm      | 2 +-
 .../EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm    | 2 +-
 .../Pipeline/OntologiesLoad/build_ontology_mart.sql           | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm | 2 +-
 .../Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm        | 2 +-
 .../Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm      | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/CopyDatabase_conf.pm       | 2 +-
 .../Production/Pipeline/PipeConfig/CoreStatistics_conf.pm     | 2 +-
 .../Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/DataFileScanner_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/DataFileScraper_conf.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm   | 2 +-
 .../Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm      | 2 +-
 .../Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm          | 2 +-
 .../Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm       | 2 +-
 .../Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm          | 2 +-
 .../Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm    | 2 +-
 .../Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm          | 2 +-
 .../Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm | 2 +-
 .../Production/Pipeline/PipeConfig/FactoryTest_conf.pm        | 2 +-
 .../Production/Pipeline/PipeConfig/FileDumpCore_conf.pm       | 2 +-
 .../Production/Pipeline/PipeConfig/FileDumpENA_conf.pm        | 2 +-
 .../Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm      | 2 +-
 .../Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm        | 2 +-
 .../Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm   | 2 +-
 .../Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm   | 2 +-
 .../Pipeline/PipeConfig/GeneNameDescProjection_conf.pm        | 2 +-
 .../PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm   | 2 +-
 .../Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm | 2 +-
 .../PipeConfig/GeneNameDescProjection_protists_conf.pm        | 2 +-
 .../PipeConfig/GeneNameDescProjection_vertebrates_conf.pm     | 2 +-
 .../Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm          | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm | 4 ++--
 .../EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm   | 2 +-
 .../Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm        | 2 +-
 .../Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm     | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm | 2 +-
 .../Production/Pipeline/PipeConfig/SearchDumps_conf.pm        | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm   | 2 +-
 .../Pipeline/PipeConfig/TranscriptomeDomains_conf.pm          | 2 +-
 .../PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm   | 2 +-
 .../Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm | 2 +-
 .../Pipeline/PipeConfig/VariationStatistics_conf.pm           | 2 +-
 .../Production/Pipeline/PipeConfig/WebDataFile_conf.pm        | 2 +-
 .../Production/Pipeline/PipeConfig/XrefDownload_conf.pm       | 2 +-
 .../Production/Pipeline/PipeConfig/XrefProcess_conf.pm        | 2 +-
 .../Production/Pipeline/PipeConfig/Xref_update_conf.pm        | 2 +-
 .../Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm       | 2 +-
 .../EnsEMBL/Production/Pipeline/Production/CodingDensity.pm   | 2 +-
 .../Production/Pipeline/Production/ConstitutiveExons.pm       | 2 +-
 .../Production/Pipeline/Production/DensityGenerator.pm        | 2 +-
 .../Production/Pipeline/Production/EmailSummaryCore.pm        | 2 +-
 .../Production/Pipeline/Production/EmailSummaryVariation.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm | 2 +-
 .../Production/Pipeline/Production/LongNonCodingDensity.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm   | 2 +-
 .../Production/Pipeline/Production/PseudogeneDensity.pm       | 2 +-
 .../Production/Pipeline/Production/ShortNonCodingDensity.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm  | 2 +-
 .../Production/Pipeline/ProductionDBSync/EmailReport.pm       | 2 +-
 .../Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm  | 2 +-
 .../Pipeline/ProductionDBSync/PopulateControlledTables.pm     | 2 +-
 .../Pipeline/ProteinFeatures/AnalysisConfiguration.pm         | 2 +-
 .../Production/Pipeline/ProteinFeatures/ChecksumProteins.pm   | 2 +-
 .../Production/Pipeline/ProteinFeatures/EmailReport.pm        | 2 +-
 .../Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm      | 2 +-
 .../EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm  | 2 +-
 .../Production/Pipeline/ProteinFeatures/GenerateSolr.pm       | 2 +-
 .../Production/Pipeline/ProteinFeatures/InterProScan.pm       | 2 +-
 .../Pipeline/ProteinFeatures/InterProScanVersionCheck.pm      | 2 +-
 .../Production/Pipeline/ProteinFeatures/LoadUniParc.pm        | 2 +-
 .../Production/Pipeline/ProteinFeatures/LoadUniProt.pm        | 2 +-
 .../Production/Pipeline/ProteinFeatures/MergeResults.pm       | 2 +-
 .../Pipeline/ProteinFeatures/ProcessTranscriptome.pm          | 2 +-
 .../Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm       | 2 +-
 .../Pipeline/ProteinFeatures/StoreProteinFeatures.pm          | 2 +-
 .../Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm   | 2 +-
 .../Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm  | 2 +-
 .../Production/Pipeline/SampleData/GenerateGeneSample.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm    | 2 +-
 .../Production/Pipeline/Search/CompressEBeyeXMLFile.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm | 2 +-
 .../Production/Pipeline/Search/DumpStructuralVariantJson.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm | 2 +-
 .../Pipeline/Search/ReformatGenomeAdvancedSearch.pm           | 2 +-
 .../EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm  | 2 +-
 .../Production/Pipeline/Search/ReformatPhenotypesSolr.pm      | 2 +-
 .../Production/Pipeline/Search/ReformatProbeSetsSolr.pm       | 2 +-
 .../Pipeline/Search/ReformatProbesAdvancedSearch.pm           | 2 +-
 .../EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm  | 2 +-
 .../Pipeline/Search/ReformatProbesetsAdvancedSearch.pm        | 2 +-
 .../Pipeline/Search/ReformatRegulationAdvancedSearch.pm       | 2 +-
 .../Production/Pipeline/Search/ReformatRegulationSolr.pm      | 2 +-
 .../Pipeline/Search/ReformatStructuralVariantsSolr.pm         | 2 +-
 .../Pipeline/Search/ReformatVariantsAdvancedSearch.pm         | 2 +-
 .../Production/Pipeline/Search/ReformatVariantsEBeye.pm       | 2 +-
 .../Production/Pipeline/Search/ReformatVariantsSolr.pm        | 2 +-
 .../Production/Pipeline/Search/ValidateXMLFileEBeye.pm        | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm           | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm   | 2 +-
 .../Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm      | 2 +-
 .../Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm       | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm    | 2 +-
 .../Production/Pipeline/Webdatafile/GeneAndTranscript.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm | 2 +-
 .../Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm     | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm  | 2 +-
 .../Production/Pipeline/Webdatafile/lib/ChromReport.pm        | 2 +-
 .../Pipeline/Webdatafile/lib/CoordinateConverter.pm           | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm | 2 +-
 .../Production/Pipeline/Webdatafile/lib/GenomeLookup.pm       | 2 +-
 .../Production/Pipeline/Webdatafile/lib/GenomeReport.pm       | 2 +-
 .../EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm   | 2 +-
 .../Pipeline/Webdatafile/lib/variants/VariantsScaler.pm       | 2 +-
 .../Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm         | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm     | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm     | 2 +-
 .../Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm      | 2 +-
 .../EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm      | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm    | 2 +-
 .../Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm  | 2 +-
 .../Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm     | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql   | 2 +-
 .../Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm          | 2 +-
 modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm          | 2 +-
 modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm  | 2 +-
 modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm            | 2 +-
 modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm      | 2 +-
 modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm           | 2 +-
 modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm         | 2 +-
 .../Production/Search/RegulationAdvancedSearchFormatter.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm  | 2 +-
 .../Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm | 2 +-
 modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm      | 2 +-
 modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm        | 2 +-
 .../Production/Search/VariantAdvancedSearchFormatter.pm       | 2 +-
 modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm     | 2 +-
 .../Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm          | 2 +-
 modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm          | 2 +-
 modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm         | 2 +-
 modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm         | 2 +-
 modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm          | 2 +-
 modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm           | 2 +-
 modules/t/00-searchdumps_load.t                               | 2 +-
 modules/t/10-searchdumps_dumpgenome.t                         | 2 +-
 modules/t/11-searchdumps_dumpgenes.t                          | 2 +-
 modules/t/12-searchdumps_dumpsequences.t                      | 2 +-
 modules/t/13-searchdumps_dumpmarkers.t                        | 2 +-
 modules/t/14-searchdumps_dumplrgs.t                           | 2 +-
 modules/t/15-searchdumps_dumpids.t                            | 2 +-
 modules/t/16-searchdumps_dumpprobes.t                         | 2 +-
 modules/t/17-searchdumps_dumpregulation.t                     | 2 +-
 modules/t/18-searchdumps_dumpvariation.t                      | 2 +-
 modules/t/40-searchdumps_reformat_base.t                      | 2 +-
 modules/t/41-searchdumps_reformat_advsearch.t                 | 2 +-
 modules/t/42-searchdumps_reformat_solr_genes.t                | 2 +-
 modules/t/43-searchdumps_reformat_solr_regulation.t           | 2 +-
 modules/t/44-searchdumps_reformat_solr_variation.t            | 2 +-
 modules/t/45-searchdumps_reformat_ebeye.t                     | 2 +-
 modules/t/dbAdaptor.t                                         | 2 +-
 modules/t/fake_fasta_binaries/faToTwoBit                      | 2 +-
 modules/t/fake_fasta_binaries/makeblastdb                     | 2 +-
 modules/t/fake_fasta_binaries/xdformat                        | 2 +-
 modules/t/fake_gff_binaries/gt                                | 2 +-
 modules/t/fake_gtf_binaries/genePredCheck                     | 2 +-
 modules/t/fake_gtf_binaries/gtfToGenePred                     | 2 +-
 modules/t/housekeeping_apache2.t                              | 2 +-
 modules/t/json_remodelling.t                                  | 2 +-
 modules/t/production_pipeline.t                               | 2 +-
 modules/t/test-genome-DBs/multi/ontology/tables.sql           | 2 +-
 nextflow/nf-py-scripts/generate_thoas_conf.py                 | 2 +-
 nextflow/nf-py-scripts/genome_info.py                         | 2 +-
 scripts/alphafold_gifts/get_alignment_data.sql                | 2 +-
 scripts/alphafold_gifts/get_assemblies.sql                    | 2 +-
 scripts/apply_patches.pl                                      | 2 +-
 scripts/assembly_converter/link_out.sh                        | 2 +-
 scripts/assembly_converter/populate_assembly_converter_dir.sh | 2 +-
 scripts/checkEnsembl_lowcoverage.pl                           | 2 +-
 scripts/check_UniProt_evidence.pl                             | 2 +-
 scripts/check_staging_databases.sh                            | 2 +-
 scripts/copy_and_patch_db.sh                                  | 2 +-
 scripts/copy_database.pl                                      | 2 +-
 scripts/copy_ftp_release.pl                                   | 2 +-
 scripts/copy_genome.pl                                        | 2 +-
 scripts/copyrights/update_copyrights.sh                       | 2 +-
 scripts/datafiles/build_datafile_ftp_directory.pl             | 2 +-
 scripts/datafiles/check_datafiles.pl                          | 2 +-
 scripts/datafiles/first_bam_alignment.pl                      | 2 +-
 scripts/datafiles/sizes.pl                                    | 2 +-
 scripts/delete_genome.pl                                      | 2 +-
 scripts/ena/ena_dump.pl                                       | 2 +-
 scripts/ftp/checksums.pl                                      | 2 +-
 scripts/ftp/upload_ena_xrefs.sh                               | 2 +-
 scripts/get_new_db_name.pl                                    | 2 +-
 scripts/link_out/generate_LinkOut.pl                          | 2 +-
 scripts/misc/check_tmux.sh                                    | 2 +-
 scripts/misc/tmux_ls.sh                                       | 2 +-
 scripts/prepare_ftp_dump.sh                                   | 2 +-
 .../production_database/import_species_names_from_cores.pl    | 2 +-
 .../production_database/import_species_names_from_taxonomy.pl | 2 +-
 scripts/production_database/populate_species_meta.pl          | 2 +-
 scripts/py/alphafoldUpdate.py                                 | 2 +-
 scripts/py/alphafoldUpdate_parallel.py                        | 2 +-
 scripts/py/regulation_ftp_symlinks.py                         | 2 +-
 scripts/refget/check_sequence_refget.pl                       | 2 +-
 scripts/sql2html.pl                                           | 2 +-
 scripts/sync/check_db.sh                                      | 2 +-
 scripts/sync/check_public_db.sh                               | 2 +-
 scripts/sync/get_release.sh                                   | 2 +-
 scripts/sync/get_staging_server.sh                            | 2 +-
 scripts/sync/optimise_databases.sh                            | 2 +-
 scripts/sync/process_divisions.sh                             | 2 +-
 scripts/sync/publish_db.sh                                    | 2 +-
 scripts/sync/set_checksums.sh                                 | 2 +-
 scripts/sync/sync_db.sh                                       | 2 +-
 scripts/sync/sync_db_st1.sh                                   | 2 +-
 scripts/sync/sync_db_st2.sh                                   | 2 +-
 scripts/sync/update_live_db.sh                                | 2 +-
 scripts/sync_tables.sh                                        | 2 +-
 scripts/t/rename_db.t                                         | 2 +-
 scripts/update_api_tarball.sh                                 | 2 +-
 scripts/update_assembly_tables.sh                             | 2 +-
 scripts/update_mapping_set.pl                                 | 2 +-
 sql/patch_100_101_a.sql                                       | 2 +-
 sql/patch_101_102_a.sql                                       | 2 +-
 sql/patch_102_103_a.sql                                       | 2 +-
 sql/patch_103_104_a.sql                                       | 2 +-
 sql/patch_104_105_a.sql                                       | 2 +-
 sql/patch_105_106_a.sql                                       | 2 +-
 sql/patch_106_107_a.sql                                       | 2 +-
 sql/patch_107_108_a.sql                                       | 2 +-
 sql/patch_108_109_a.sql                                       | 2 +-
 sql/patch_109_110_a.sql                                       | 2 +-
 sql/patch_110_111_a.sql                                       | 2 +-
 sql/patch_66_67a.sql                                          | 2 +-
 sql/patch_66_67b.sql                                          | 2 +-
 sql/patch_66_67c.sql                                          | 2 +-
 sql/patch_70_71a.sql                                          | 2 +-
 sql/patch_71_72a.sql                                          | 2 +-
 sql/patch_71_72b.sql                                          | 2 +-
 sql/patch_72_73a.sql                                          | 2 +-
 sql/patch_72_73b.sql                                          | 2 +-
 sql/patch_72_73c.sql                                          | 2 +-
 sql/patch_72_73d.sql                                          | 2 +-
 sql/patch_72_73e.sql                                          | 2 +-
 sql/patch_73_74a.sql                                          | 2 +-
 sql/patch_73_74b.sql                                          | 2 +-
 sql/patch_74_75a.sql                                          | 2 +-
 sql/patch_74_75b.sql                                          | 2 +-
 sql/patch_75_76a.sql                                          | 2 +-
 sql/patch_75_76b.sql                                          | 2 +-
 sql/patch_76_77a.sql                                          | 2 +-
 sql/patch_76_77b.sql                                          | 2 +-
 sql/patch_76_77c.sql                                          | 2 +-
 sql/patch_77_78a.sql                                          | 2 +-
 sql/patch_77_78b.sql                                          | 2 +-
 sql/patch_78_79a.sql                                          | 2 +-
 sql/patch_78_79b.sql                                          | 2 +-
 sql/patch_79_80_a.sql                                         | 2 +-
 sql/patch_79_80b.sql                                          | 2 +-
 sql/patch_79_80c.sql                                          | 2 +-
 sql/patch_80_81a.sql                                          | 2 +-
 sql/patch_81_82a.sql                                          | 2 +-
 sql/patch_82_83a.sql                                          | 2 +-
 sql/patch_83_84a.sql                                          | 2 +-
 sql/patch_83_84b.sql                                          | 2 +-
 sql/patch_84_85a.sql                                          | 2 +-
 sql/patch_85_86a.sql                                          | 2 +-
 sql/patch_85_86b.sql                                          | 2 +-
 sql/patch_85_86c.sql                                          | 2 +-
 sql/patch_86_87a.sql                                          | 2 +-
 sql/patch_87_88_a.sql                                         | 2 +-
 sql/patch_88_89_a.sql                                         | 2 +-
 sql/patch_89_90_a.sql                                         | 2 +-
 sql/patch_89_90_b.sql                                         | 2 +-
 sql/patch_90_91_a.sql                                         | 2 +-
 sql/patch_91_92_a.sql                                         | 2 +-
 sql/patch_92_93_a.sql                                         | 2 +-
 sql/patch_92_93_b.sql                                         | 2 +-
 sql/patch_93_94_a.sql                                         | 2 +-
 sql/patch_94_95_a.sql                                         | 2 +-
 sql/patch_94_95_b.sql                                         | 2 +-
 sql/patch_95_96_a.sql                                         | 2 +-
 sql/patch_96_97_a.sql                                         | 2 +-
 sql/patch_96_97_b.sql                                         | 2 +-
 sql/patch_96_97_c.sql                                         | 2 +-
 sql/patch_96_97_d.sql                                         | 2 +-
 sql/patch_96_97_e.sql                                         | 2 +-
 sql/patch_96_97_f.sql                                         | 2 +-
 sql/patch_97_98_a.sql                                         | 2 +-
 sql/patch_98_99_a.sql                                         | 2 +-
 sql/patch_98_99_b.sql                                         | 2 +-
 sql/patch_99_100_a.sql                                        | 2 +-
 sql/table.sql                                                 | 2 +-
 src/python/scripts/dcparse.py                                 | 2 +-
 src/python/scripts/dcstat.py                                  | 2 +-
 src/python/scripts/genome_info.py                             | 2 +-
 src/python/scripts/meta_hive_species.py                       | 2 +-
 498 files changed, 499 insertions(+), 499 deletions(-)

diff --git a/LICENSE b/LICENSE
index 17b0e2929..3ec90d54a 100755
--- a/LICENSE
+++ b/LICENSE
@@ -187,7 +187,7 @@
       identification within third-party archives.
 
    Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-   Copyright [2016-2023] EMBL-European Bioinformatics Institute
+   Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm b/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm
index 41f7e7262..bd34cc2a8 100644
--- a/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/DBSQL/BulkFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm b/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm
index fae4dea71..e3c641913 100644
--- a/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Production/DBSQL/DBAdaptor.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
index a896a09ef..ca1cecc1c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
index b983ca689..717458589 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 5721e3ed4..ad089f811 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm
index c80f15b40..ca5946037 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/NoMultiSpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm
index 8266d16ac..f910edcc0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchApprisFiles.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm
index 3172a1a39..f0f4c05ff 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/FetchTSLFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm
index 121c44714..cc7d3485a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadAppris.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm
index c85df0e4c..b8c22e1fe 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AttributeAnnotation/LoadTSL.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm
index 90003344a..25a04e1cd 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Chainfile/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm
index bd6780375..ddffcefda 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/AnalysisSetup.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm
index 20c039532..ef2d7948e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Base.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm
index 8eb861bb5..2a8e4f338 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChecksumGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm
index 4fae25f5d..0d31406c2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/ChksumGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm
index c5241c734..283a0e4ba 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/CreateReleaseFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm
index 1b1fb21e3..decb2fa6c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DatabaseDumper.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm
index f9e2eebf8..8c4accf90 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbAwareSpeciesFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm
index ff81f787b..c16eee49c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbCmd.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm
index 4d304fb41..b7ea8094a 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DbFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm
index fd48b0234..b70072fea 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpProteome.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm
index 67814e965..c67865aad 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/DumpTables.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm
index b35265da0..4ec6b6d97 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/EmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm
index a2f1f04cb..6d94802b7 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FastaSplit.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm
index 95b0c87a2..7bcab5dab 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FetchExternal.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm
index 387f1afef..910dc0f8f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/FindDirs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm
index dcf1b2379..e2ac07970 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/GetDivision.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
index b2c216738..5631e8e64 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/Gzip.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm
index a30ca167d..2d17634c9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MetadataDbFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm
index d9b1b26dd..d37a2183f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/MultiDbFactory.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm
index 5011f09eb..d74fa83d1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/RunCreateReleaseFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm
index 1cc34c40c..caf9a07c6 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm
index f610f0b25..99c505ce0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SqlCmd.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm
index 7dfdc17b1..7148575bb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/SystemCmdRunner.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm
index 53534e89c..7d57e5181 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatePackedStatus.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm
index 7a42b44d3..d374b3f4f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Common/UpdatedSpecies.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm
index 32f3cd263..e744fef51 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHive.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm
index 6a0cfd18b..d0811e724 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/CopyDatabases/CopyDatabaseHiveDBA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm
index 2c8b7cc32..36edd8f0e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/EarlyDumps/MetadataReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm
index d43048d4b..bccdacc7c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm
index 3c59dad76..5e74d1f84 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastConverter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm
index 6ee08ac48..f04425bcb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlastIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm
index 08efe9fbe..3918e6d63 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/BlatIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm
index 103d5a994..cb3a8c8f8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ConcatFiles.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm
index df3671ba6..72a590ab4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyDNA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm
index 9af0bfb73..9c6796bf3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CopyNCBIBlastDNA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm
index 7299120fa..1a5f5a153 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/CreatePrimaryAssembly.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm
index c51f47243..ec021916b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm
index c6710fc55..02722e94e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/EmailSummary.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm
index 8d9891b26..1908ca342 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/Indexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm
index f1a7e8746..eaae78933 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm
index 125b83ee7..18a52a953 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/NcbiBlastReIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm
index 22a8c6ca4..e6631f2f4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/ReuseSpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm
index df7c58c9e..442932e83 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SCPBlast.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm
index c8c7ea9f5..9994b0006 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/SpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm
index 784b89ecd..ffe769a5b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FASTA/WuBlastIndexer.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm
index 699f63e29..7c29da9ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Assembly_Chain.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm
index dae375d1f..d32eea03b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm
index b89c9c4d8..f813d70ba 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Base_Filetype.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm
index df3f7e7db..116d5f6da 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Chromosome_TSV.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm
index 229a84614..abffc286e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/DirectoryPaths.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm
index 79ed6b0a4..27ae351aa 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_EMBL.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm
index 7455cd3b9..814f219d7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_FASTA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index 34d134cc0..6a004324f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm
index e0a85fbce..f6e9ed62e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3_ENA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm
index fabd24ec5..4bbee0a34 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GTF.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm
index a18ff212b..ed9194a76 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Genome_FASTA.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm
index 16942720d..a743929d7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Metadata_JSON.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm
index c9bad105c..ca0596734 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/MySQL_TXT.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm
index f6426ea7d..70fbd11f8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/README.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm
index 5be22d688..16f31c3c3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Exists.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm
index 4609e7296..1b47ed5b6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/RNASeq_Missing.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm
index f4f7ed542..6a50118cc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm
index e4ccee44f..579df4c7a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Symlink_RNASeq.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm
index 2fb82eeec..dbe4159a6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Verify.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
index 3fb29f551..73b43b0de 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Xref_TSV.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm
index e227e5404..dc7749c05 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/CheckFlatfile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
index 8a02f193a..d281aaecd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm
index 538256c59..254d305a1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/DumpTypeFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm
index 56fc98d64..c7082bbf0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/EMBLValidator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm
index 7200da4dc..201a80953 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/GenbankValidator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm
index 7166b3b19..f8ae57687 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/Validator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm
index 999819b16..1a5b76509 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Flatfile/ValidatorFactoryMethod.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm
index a43c4a78c..18735eebe 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckComparaFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm
index c9a294f52..51b344f17 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckCoreFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm
index 248480813..f566c7125 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm
index 7723d460d..cda84eb18 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/CheckVariationFtp.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm
index bd2159525..c60a6d671 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FtpChecker/ReportFailures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index 190429eb3..6d88ab72a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm
index c4d029bff..74ef1c560 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/FindFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm
index d8ffae20b..38ece96f2 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/GPADEmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm
index 75148fb90..428deb48e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GPAD/LoadFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
index 301e38176..79358a04d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm
index 2028e898b..b5165f31b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/EmailSummary.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
index 6083b6249..28aa1ba06 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm
index 7e03d0bf4..4e4f39fee 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/Populate.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql
index 6d48eee6f..80875a63f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneAutocomplete/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm
index dd9f326fc..f1932cea4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm
index 9804899dc..e12631dbc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/DeleteExisting.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm
index 1d092220e..670decacb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneDescProjection.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm
index 67db30fe5..83f0c5ca1 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesEmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm
index 15a1d0b11..374a234e5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/GeneNamesProjection.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm
index a72fb12ef..0ee82f326 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneNameDescProjection/SourceFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm
index 8c2168cbb..bccd5d9e3 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightGO.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm
index 8ba7e53ef..c9d55bd83 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GeneTreeHighlight/HighlightInterPro.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm
index 794ac27a7..e794358de 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/DumpGenomeJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
index 0c18900f6..d8e8328da 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
index 5e247aacf..37da4aabe 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
index f2d155427..e5cd4784c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm
index ce9466d91..422fccc30 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Metadata/PayloadGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm
index f22a069c4..4ab8b79c0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/AddSubsetMap.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm
index fa36e315f..e54d82fa9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/ComputeClosure.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm
index fb535addf..7f926e8e7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/MartLoad.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql
index 2403a57b3..0afb50fb7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/OntologiesLoad/build_ontology_mart.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm
index 0ab952078..b6104619a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
index 63f0fb9c8..4599d8636 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm
index b35104989..19af55ac6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SpeciesNoOrthologs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
index 263bb7cef..b8a0e60ac 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
index 67d6f1429..14e6d7f71 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index 85435908a..7a76d12cb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
index 89f71c74a..3c2bab042 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
index 73640e91e..0a4369a9d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm
index e7223617c..9b4d0d67c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabaseDBA_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm
index 48c0a16ac..c9b646904 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CopyDatabase_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
index 2cb1d6a35..236ad1365 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
index 6acd23193..71d3b7655 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm
index 9447c56e8..b906af8df 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScanner_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm
index 61d66c158..21faef537 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataFileScraper_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
index 8b3a6099e..11f63e43c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
index ffae16c77..7668bbac2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm
index c5572b2ae..fa212eace 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_non_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm
index 5b1f519c1..9f1bbb591 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm
index bd5663d2b..29e1d9e9b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
index b35768bb5..41a9ca74d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
index 4039d2049..5cbdea73f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
index 75b5d1c6a..a0e6ab38b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
index 98c19c637..cd3b8e9a1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
index dccb99d0c..242743099 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
index 4170650d6..5c8590d06 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm
index 61a5930f6..c2ed1aa19 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpCore_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm
index 368379411..bfa9b1d80 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpENA_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
index 6a3587c1e..a6f5f3229 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm
index fd67e844d..a3aef7f4c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVEP_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm
index 5d822bff9..a0050da6a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpVariation_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm
index 5ed9dcddb..a6563269a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDump_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm
index b0028c9a6..d8892c760 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FtpChecker_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
index f381c5f61..d5346d9f7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
index 64d9c12ee..59eeae96e 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm
index 793262737..5187ea644 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm
index 67a4e43ab..dda6175cd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_mouse_strains_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm
index 718901689..e95bc49a3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_plants_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm
index 767ff547d..8435b91f3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_protists_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm
index 16feda573..5f3f3961e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneNameDescProjection_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
index a1b8b7db2..075faf886 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
index 222a98f81..a81a2c03a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
index a619091fc..15c3a2486 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm
index 97bba38bf..b299064b7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadFamily_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
index af535183b..d647f4633 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
index 310f9a9ec..670594711 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm
index 800fdd949..b786c7b1b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MetadataUpdater_conf.pm
@@ -7,7 +7,7 @@
 
 =head1 LICENSE
     Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm
index 7d31c3031..13041c8d6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoadAll_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
@@ -27,7 +27,7 @@ limitations under the License.
 
 =head1 LICENSE
 
-    Copyright [2016-2023] EMBL-European Bioinformatics Institute
+    Copyright [2016-2024] EMBL-European Bioinformatics Institute
     Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License.
     You may obtain a copy of the License at
          http://www.apache.org/licenses/LICENSE-2.0
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
index 70a18ea1e..0b83cf992 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
index 253ca924c..3b58fe283 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index b6d1c6345..39c1199fb 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
index 3bd2eacd1..bc9e983c6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
index b80729f5c..d02de7472 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
index 01ce93395..79a860494 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
index 33af76ee3..539356514 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
index abab62004..4df737ac6 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
index 640b017f7..cb010d7ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
index fd2c7f382..b9426d30c 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm
index 2ed2c0913..87c4b1cc7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdateComparaMemberNamesDescriptions_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
index 5abd3ad0c..8b02ae00d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
index 3be02fc96..0cb424cbf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm
index 4905e3f28..a75be684c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/WebDataFile_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
index 44dd5a817..4c17d22d3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
index 71f9ceaa7..c737c2a77 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
index 0fbc95b8f..b72c803c2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm
index 9107fe6e5..051dad445 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_vertebrates_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm
index 1e9cb6f71..e729200d9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/CodingDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm
index 73dd17d36..6425f7bb2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ConstitutiveExons.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm
index 61757261b..03a6646d8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/DensityGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm
index bb3fa4bb4..e4f9f49f9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryCore.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm
index d1734dfff..fde1f8604 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/EmailSummaryVariation.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm
index f8064cfa8..ea8b97507 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneCount.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm
index ab59e15de..0e034e70e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGC.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm
index 32f8fff52..c3622aeaf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GeneGCBatch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm
index 827893970..a00f31f01 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/GenomeStats.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm
index 0ff01a33f..29dc60ec7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/LongNonCodingDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm
index 87ae3cb96..241c7082e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaCoords.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm
index f684d7b05..a813973fc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/MetaLevels.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm
index a67c8a0aa..6a53a4ba5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStats.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm
index c9fb93960..8fc42e622 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PepStatsBatch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm
index 3951c2b4d..cd0223f63 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentGC.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm
index 4abc76447..dcfd66cbc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PercentRepeat.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm
index 73a45e0aa..ca8eeae9b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/PseudogeneDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm
index f81d05d91..efe7407b2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/ShortNonCodingDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm
index 8f0b018c1..ec838cdc4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpCount.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm
index ef546685e..f9b1388c5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SnpDensity.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm
index ad12684be..d2454e5ab 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/SpeciesFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm
index ada8f3a20..4e7a90423 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Production/StatsGenerator.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm
index 6f7b991ba..4d500c7a2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/EmailReport.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm
index 071ceb37b..368b6ee3e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateAnalysisDescription.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm
index 682256b0c..1127dd58c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProductionDBSync/PopulateControlledTables.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm
index 7bf88513a..404a2c7ac 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/AnalysisConfiguration.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm
index e158cf689..22b8edcf9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ChecksumProteins.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm
index 1296a31a0..6a48d2579 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm
index 6c8407837..136906147 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/EmailTranscriptomeReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm
index 0e273c77b..1e98c2cba 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/FetchFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm
index 1f70cb494..7dd9cb079 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/GenerateSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm
index 036167e2b..7427b7768 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScan.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm
index b81694419..9db5e987b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/InterProScanVersionCheck.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
index 31daf1c13..40eddb1b4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm
index ce23758df..0c8b1e6c7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniProt.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm
index bf32f014f..9236c6a89 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/MergeResults.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm
index 820ac0461..575366b2b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/ProcessTranscriptome.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm
index 1bd51699e..02bc81283 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreGoXrefs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm
index 315d9f686..ac0346c19 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreProteinFeatures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm
index 57b7ec19c..cd62dd396 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/StoreSegFeatures.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm
index dc6d09c03..6d1500795 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/AnalysisConfiguration.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm
index b2ce0e031..f9ec13c2b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/LoadRNACentral.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm
index 6f0409c46..6cf68a79c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/RNAGeneXref/RNACentralXref.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm
index e41dbc4f7..7b3129672 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Refget/RefgetLoader.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm
index 8f21178b6..9122ac214 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DBCopyPatch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm
index cbbfb293f..f19f37749 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/DivisionFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm
index c177d1c94..249c9d31a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactoryDivision.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm
index 365d0990b..c36365e96 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Release/JobFactorySpecies.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm
index c3f999aa5..f7b9035b6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CheckSampleData.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm
index c19e3d034..aab0ee753 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/CopySampleData.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm
index a442a1e97..b1f023ec1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/SampleData/GenerateGeneSample.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm
index e36faf90d..03e1a26ed 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/BaseDumpJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm
index 0e6b396de..4379add76 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/CompressEBeyeXMLFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm
index b7fb2763f..7d8066771 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm
index 3fbe90b7e..d080a9da0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenesJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm
index 789bfd8f8..f0223a058 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpGenomeJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm
index 0bd950ca0..879897c64 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpMerge.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm
index 70d73ff4b..f5ca7912a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpPhenotypesJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm
index f3f08a3e4..798c976be 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm
index e4847a896..5bbf4bc92 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpProbesMerge.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm
index c8b84e673..4926fa0f1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm
index d93e1a44e..05d258d93 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpRegulationMerge.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm
index 0845936ba..c35645acb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpStructuralVariantJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm
index 0b9f05844..53fa5bb07 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/DumpVariantJson.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm
index 3d762b1ee..d685c0650 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm
index c13842ccc..a72919331 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm
index 84657761e..2c6ce0700 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatGenomeSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm
index 994480f5f..efca488a5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatPhenotypesSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm
index c3b033756..4727d57af 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbeSetsSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm
index f6109b2e7..9f46856b2 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm
index bb2dd2fd5..4f5a4a82f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm
index 0a6c6aaed..5dc083e26 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatProbesetsAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm
index a0db9709b..4ed073c5c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm
index 4c46af425..54d2336b1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatRegulationSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm
index d32fcb62b..b32618a63 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatStructuralVariantsSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm
index 339ac53a2..05d4f9564 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsAdvancedSearch.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm
index 4d828a0a5..224b07cdf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm
index fc6f37a8c..42bcf37ee 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ReformatVariantsSolr.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm
index b37273c60..55fdaa9ef 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/ValidateXMLFileEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm
index 0b34e8a69..90a55009b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Search/WrapGenomeEBeye.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm
index c95f4f0b4..670b22ddf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/EmailReport.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm
index c88597046..f534c3d97 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/Populate.pm
@@ -1,6 +1,6 @@
 =head1 LICENSE
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
 You may obtain a copy of the License at
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
index 87a07a728..a807f370a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
index 9ad149934..4ae7ac6ec 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm
index ec8e23e43..39d7dfa47 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
index 8dffe30b6..b713fa3b8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
index 6d4b2ad95..3722b2a3c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileEna.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
index 271bb4c57..ba7cde4b0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileMetadata.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
index 9d466cd33..df33c0d76 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TSV/DumpFileXref.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm
index 7d7ab3fa0..0e036c77f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/BackUpDatabase.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
index edfd83f29..3438dd571 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm
index 819dbedec..c162b479c 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Contigs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm
index 165552207..bac416600 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GeneAndTranscript.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm
index 18326f0eb..ce3252627 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenerateGC.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm
index 9ba7b6c4b..5aa7f6be9 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeAssemblyInfo.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm
index 145a8fa15..76fb367d9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/GenomeInfo.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm
index bc6616ede..7e91dafe4 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/Variation.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm
index d03bc1664..6f0ef4688 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/ChromReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm
index 72e453d0c..a268234dd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/CoordinateConverter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm
index 00e56fdf5..e0ebcbd50 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/Genome.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm
index 35bacf838..d90552de9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeLookup.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm
index 8dc7c52a5..28b51b052 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/GenomeReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm
index a86a127df..358ecf63d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexBed.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm
index b2a5101fc..a93ace422 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/IndexWig.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm
index aa7aee4d7..90c5ca3d7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariantsScaler.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm
index 30142a4b1..c2e987db9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Webdatafile/lib/variants/VariationBedWriter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm
index 53f989da6..40f64d501 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AdvisoryXrefReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
index 2ac81e04f..b3233ea9d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm
index 4f3be48b0..2492c8d2c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/AlignmentFactory.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm
index 16d4831ff..954249821 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Base.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm
index 86774dc21..c3627908c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Checksum.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm
index 98f434416..dbf318ee3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqDna.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
index a23cfd71f..313773f1f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupRefseqPeptide.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
index af8730208..522a74080 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm
index 127b483f1..ca551dfcb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CoordinateMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm
index 9bc914b76..0b4bf3d7a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DirectXrefs.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm
index 9c25218ac..257f901f6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DownloadSource.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm
index a3d2e52e5..326a416f9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpEnsembl.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
index 9520d126c..3a184d14c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm
index 7874017b7..178d43bf6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailAdvisoryXrefReport.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm
index 5fd370544..81e85112f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/EmailNotification.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm
index 7ebbb964a..086f7b639 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Mapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
index 52469c2d7..068bf107f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm
index 7ce2776da..87fe1c26d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/BaseParser.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm
index 4bfd6bfc9..4aa66ed7e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/RefSeqDatabaseParser.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
index bb96cdbf6..e47bcc2de 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm
index 77691a9aa..2c7db050f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/PreParse.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm
index 6aa4ee447..c43815618 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ProcessAlignment.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm
index 419890a8b..8ce4605dc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/RNAcentralMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm
index ff4ac6d98..a6626693a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleCleanup.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm
index 03ae07dd4..89f34fdf8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleDownload.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm
index b81b2f0ce..5edb5edcc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm
index e0a1b139e..56fde172f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/SchedulePreParse.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 7a9323447..48f20cbc3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm
index d549ae679..f8b9a9cc5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/UniParcMapping.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql
index a6005a40d..99d829af7 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm
index 7c8d7a6a2..5cd4976e5 100644
--- a/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/AdvancedSearchFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm
index df91fbe70..6fa547aac 100644
--- a/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/BaseFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm
index 3298f6340..f6290b0a5 100755
--- a/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/EBeyeFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm b/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm
index f30d5bb0a..f45f1e904 100755
--- a/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/EBeyeGenomeWrapper.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm
index 948ea4ae4..723dc64dd 100644
--- a/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/GeneFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm
index 29c34b8e4..e4249af85 100644
--- a/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/GenomeFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm
index 09afadf5f..a69258d6d 100644
--- a/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/GenomeSolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm
index 6487f9d29..4716deee3 100644
--- a/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/IdFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm b/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm
index 026496d01..b75f1f6d1 100644
--- a/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/JSONReformatter.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm
index 7023b5b93..a39b751de 100644
--- a/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/LRGFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm
index c1dd542f5..7bd3d9c6a 100644
--- a/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/MarkerFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm
index 209d31ff3..32da0acae 100644
--- a/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/ProbeFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm
index ab1a26d2e..97f1571d0 100644
--- a/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/RegulationAdvancedSearchFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm
index 93a9a3d89..c93d458cb 100644
--- a/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/RegulationSolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm
index 48debd8a5..4667cfc58 100644
--- a/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/RegulatoryElementFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm
index 3855bc93d..2a7103bab 100644
--- a/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/SequenceFetcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm
index a2f66b75f..1505db6fa 100644
--- a/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/SolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm
index 9851bf321..0565354b2 100644
--- a/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/VariantAdvancedSearchFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm b/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm
index ae0aa5f84..58c88b680 100644
--- a/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/VariationFetcher.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm b/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm
index 591998e23..174baccde 100644
--- a/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm
+++ b/modules/Bio/EnsEMBL/Production/Search/VariationSolrFormatter.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm b/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm
index 657d90d93..91800a02f 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/CopyDatabase.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm b/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm
index f0196aab6..c3676fa7b 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/GenomeCopier.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm b/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm
index 34db39d30..223d4bd80 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/ProductionDbUpdater.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm b/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm
index 01ea0b118..261924371 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/QueueAppender.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm b/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm
index 982b32cf9..f680c6a8a 100755
--- a/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/SchemaPatcher.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm b/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm
index bbe1380bd..c7b5e2d5d 100755
--- a/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/ServerStatus.pm
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm b/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm
index 7dc3d6378..4c6297748 100644
--- a/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Utils/WaitForFile.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/t/00-searchdumps_load.t b/modules/t/00-searchdumps_load.t
index 7f5b56205..2f1cc4730 100644
--- a/modules/t/00-searchdumps_load.t
+++ b/modules/t/00-searchdumps_load.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/10-searchdumps_dumpgenome.t b/modules/t/10-searchdumps_dumpgenome.t
index a79b5c5e5..e332e97c8 100644
--- a/modules/t/10-searchdumps_dumpgenome.t
+++ b/modules/t/10-searchdumps_dumpgenome.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/11-searchdumps_dumpgenes.t b/modules/t/11-searchdumps_dumpgenes.t
index 4e4ff5840..9896a4912 100755
--- a/modules/t/11-searchdumps_dumpgenes.t
+++ b/modules/t/11-searchdumps_dumpgenes.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/12-searchdumps_dumpsequences.t b/modules/t/12-searchdumps_dumpsequences.t
index 15a27dc71..1fcf70a05 100644
--- a/modules/t/12-searchdumps_dumpsequences.t
+++ b/modules/t/12-searchdumps_dumpsequences.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/13-searchdumps_dumpmarkers.t b/modules/t/13-searchdumps_dumpmarkers.t
index 0696120fa..49e896a7b 100644
--- a/modules/t/13-searchdumps_dumpmarkers.t
+++ b/modules/t/13-searchdumps_dumpmarkers.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/14-searchdumps_dumplrgs.t b/modules/t/14-searchdumps_dumplrgs.t
index 466faef93..aead365af 100644
--- a/modules/t/14-searchdumps_dumplrgs.t
+++ b/modules/t/14-searchdumps_dumplrgs.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/15-searchdumps_dumpids.t b/modules/t/15-searchdumps_dumpids.t
index 968c5cdc4..7b0a941b1 100644
--- a/modules/t/15-searchdumps_dumpids.t
+++ b/modules/t/15-searchdumps_dumpids.t
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/t/16-searchdumps_dumpprobes.t b/modules/t/16-searchdumps_dumpprobes.t
index 882177b18..0b8982076 100644
--- a/modules/t/16-searchdumps_dumpprobes.t
+++ b/modules/t/16-searchdumps_dumpprobes.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/17-searchdumps_dumpregulation.t b/modules/t/17-searchdumps_dumpregulation.t
index 9974c024b..3f8223ce5 100644
--- a/modules/t/17-searchdumps_dumpregulation.t
+++ b/modules/t/17-searchdumps_dumpregulation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/18-searchdumps_dumpvariation.t b/modules/t/18-searchdumps_dumpvariation.t
index ae169f349..3196ac137 100644
--- a/modules/t/18-searchdumps_dumpvariation.t
+++ b/modules/t/18-searchdumps_dumpvariation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/40-searchdumps_reformat_base.t b/modules/t/40-searchdumps_reformat_base.t
index ff8fb8062..594e475ad 100644
--- a/modules/t/40-searchdumps_reformat_base.t
+++ b/modules/t/40-searchdumps_reformat_base.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/41-searchdumps_reformat_advsearch.t b/modules/t/41-searchdumps_reformat_advsearch.t
index 2771b14c0..b91af455c 100644
--- a/modules/t/41-searchdumps_reformat_advsearch.t
+++ b/modules/t/41-searchdumps_reformat_advsearch.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/42-searchdumps_reformat_solr_genes.t b/modules/t/42-searchdumps_reformat_solr_genes.t
index 4be3bf131..0da97ecc6 100644
--- a/modules/t/42-searchdumps_reformat_solr_genes.t
+++ b/modules/t/42-searchdumps_reformat_solr_genes.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/43-searchdumps_reformat_solr_regulation.t b/modules/t/43-searchdumps_reformat_solr_regulation.t
index 1cd718e2e..944bf4452 100644
--- a/modules/t/43-searchdumps_reformat_solr_regulation.t
+++ b/modules/t/43-searchdumps_reformat_solr_regulation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/44-searchdumps_reformat_solr_variation.t b/modules/t/44-searchdumps_reformat_solr_variation.t
index 048a5f860..56c5e02fe 100644
--- a/modules/t/44-searchdumps_reformat_solr_variation.t
+++ b/modules/t/44-searchdumps_reformat_solr_variation.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/45-searchdumps_reformat_ebeye.t b/modules/t/45-searchdumps_reformat_ebeye.t
index 07de5f86b..0d06c50de 100644
--- a/modules/t/45-searchdumps_reformat_ebeye.t
+++ b/modules/t/45-searchdumps_reformat_ebeye.t
@@ -1,6 +1,6 @@
 #!perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/dbAdaptor.t b/modules/t/dbAdaptor.t
index d58d308d4..0b58fc78c 100644
--- a/modules/t/dbAdaptor.t
+++ b/modules/t/dbAdaptor.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_fasta_binaries/faToTwoBit b/modules/t/fake_fasta_binaries/faToTwoBit
index 2430b59ee..5e572b2f8 100755
--- a/modules/t/fake_fasta_binaries/faToTwoBit
+++ b/modules/t/fake_fasta_binaries/faToTwoBit
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_fasta_binaries/makeblastdb b/modules/t/fake_fasta_binaries/makeblastdb
index a946fd1fc..2a6d5d20e 100755
--- a/modules/t/fake_fasta_binaries/makeblastdb
+++ b/modules/t/fake_fasta_binaries/makeblastdb
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_fasta_binaries/xdformat b/modules/t/fake_fasta_binaries/xdformat
index 0d2562d69..1cfea93c7 100755
--- a/modules/t/fake_fasta_binaries/xdformat
+++ b/modules/t/fake_fasta_binaries/xdformat
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_gff_binaries/gt b/modules/t/fake_gff_binaries/gt
index e4a0a54c1..241d68c3b 100755
--- a/modules/t/fake_gff_binaries/gt
+++ b/modules/t/fake_gff_binaries/gt
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_gtf_binaries/genePredCheck b/modules/t/fake_gtf_binaries/genePredCheck
index b19b325a5..0d49f8820 100755
--- a/modules/t/fake_gtf_binaries/genePredCheck
+++ b/modules/t/fake_gtf_binaries/genePredCheck
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/fake_gtf_binaries/gtfToGenePred b/modules/t/fake_gtf_binaries/gtfToGenePred
index e4a0a54c1..241d68c3b 100755
--- a/modules/t/fake_gtf_binaries/gtfToGenePred
+++ b/modules/t/fake_gtf_binaries/gtfToGenePred
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/housekeeping_apache2.t b/modules/t/housekeeping_apache2.t
index 3c5e47714..02fc0ce9c 100644
--- a/modules/t/housekeeping_apache2.t
+++ b/modules/t/housekeeping_apache2.t
@@ -2,7 +2,7 @@
 =head1 LICENSE
 
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/modules/t/json_remodelling.t b/modules/t/json_remodelling.t
index 8550b6bd8..f3522c300 100644
--- a/modules/t/json_remodelling.t
+++ b/modules/t/json_remodelling.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/production_pipeline.t b/modules/t/production_pipeline.t
index 3291ade47..3941e86bf 100644
--- a/modules/t/production_pipeline.t
+++ b/modules/t/production_pipeline.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/modules/t/test-genome-DBs/multi/ontology/tables.sql b/modules/t/test-genome-DBs/multi/ontology/tables.sql
index 1952a7504..2dc2de1dd 100644
--- a/modules/t/test-genome-DBs/multi/ontology/tables.sql
+++ b/modules/t/test-genome-DBs/multi/ontology/tables.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/nextflow/nf-py-scripts/generate_thoas_conf.py b/nextflow/nf-py-scripts/generate_thoas_conf.py
index d5c456ffe..9e0d9e95c 100755
--- a/nextflow/nf-py-scripts/generate_thoas_conf.py
+++ b/nextflow/nf-py-scripts/generate_thoas_conf.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/nextflow/nf-py-scripts/genome_info.py b/nextflow/nf-py-scripts/genome_info.py
index 5349a755c..cff4a5315 100755
--- a/nextflow/nf-py-scripts/genome_info.py
+++ b/nextflow/nf-py-scripts/genome_info.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/scripts/alphafold_gifts/get_alignment_data.sql b/scripts/alphafold_gifts/get_alignment_data.sql
index f2ec1f1a9..f8026f39b 100644
--- a/scripts/alphafold_gifts/get_alignment_data.sql
+++ b/scripts/alphafold_gifts/get_alignment_data.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/scripts/alphafold_gifts/get_assemblies.sql b/scripts/alphafold_gifts/get_assemblies.sql
index 881dac78f..09fa99f88 100644
--- a/scripts/alphafold_gifts/get_assemblies.sql
+++ b/scripts/alphafold_gifts/get_assemblies.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/scripts/apply_patches.pl b/scripts/apply_patches.pl
index 04ced0d3d..fdd97415c 100755
--- a/scripts/apply_patches.pl
+++ b/scripts/apply_patches.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/assembly_converter/link_out.sh b/scripts/assembly_converter/link_out.sh
index 08358854b..6d1d209a0 100644
--- a/scripts/assembly_converter/link_out.sh
+++ b/scripts/assembly_converter/link_out.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/assembly_converter/populate_assembly_converter_dir.sh b/scripts/assembly_converter/populate_assembly_converter_dir.sh
index 40b6968d2..af89f54da 100755
--- a/scripts/assembly_converter/populate_assembly_converter_dir.sh
+++ b/scripts/assembly_converter/populate_assembly_converter_dir.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/checkEnsembl_lowcoverage.pl b/scripts/checkEnsembl_lowcoverage.pl
index a6074799e..8e823cc2a 100644
--- a/scripts/checkEnsembl_lowcoverage.pl
+++ b/scripts/checkEnsembl_lowcoverage.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/check_UniProt_evidence.pl b/scripts/check_UniProt_evidence.pl
index 2813db429..c13753820 100644
--- a/scripts/check_UniProt_evidence.pl
+++ b/scripts/check_UniProt_evidence.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/check_staging_databases.sh b/scripts/check_staging_databases.sh
index d599b6866..cea3edda9 100755
--- a/scripts/check_staging_databases.sh
+++ b/scripts/check_staging_databases.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_and_patch_db.sh b/scripts/copy_and_patch_db.sh
index 3e1ced229..53efc458e 100755
--- a/scripts/copy_and_patch_db.sh
+++ b/scripts/copy_and_patch_db.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_database.pl b/scripts/copy_database.pl
index c8fccbdfa..62749b070 100644
--- a/scripts/copy_database.pl
+++ b/scripts/copy_database.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_ftp_release.pl b/scripts/copy_ftp_release.pl
index f48f7bbab..6b85b0d13 100755
--- a/scripts/copy_ftp_release.pl
+++ b/scripts/copy_ftp_release.pl
@@ -1,6 +1,6 @@
 #!/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copy_genome.pl b/scripts/copy_genome.pl
index 6c2d5860b..16aeb5850 100755
--- a/scripts/copy_genome.pl
+++ b/scripts/copy_genome.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/copyrights/update_copyrights.sh b/scripts/copyrights/update_copyrights.sh
index 5318667fa..490acc32b 100755
--- a/scripts/copyrights/update_copyrights.sh
+++ b/scripts/copyrights/update_copyrights.sh
@@ -1,7 +1,7 @@
 #/bin/sh
 # NOTE THIS script need `gh` command line tool available on https://github.com/cli/cli#installation
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/build_datafile_ftp_directory.pl b/scripts/datafiles/build_datafile_ftp_directory.pl
index 2baaab17b..0fd1af263 100755
--- a/scripts/datafiles/build_datafile_ftp_directory.pl
+++ b/scripts/datafiles/build_datafile_ftp_directory.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/env perl
 #
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/check_datafiles.pl b/scripts/datafiles/check_datafiles.pl
index 0a0a67c56..f4559b609 100644
--- a/scripts/datafiles/check_datafiles.pl
+++ b/scripts/datafiles/check_datafiles.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/first_bam_alignment.pl b/scripts/datafiles/first_bam_alignment.pl
index 246f63459..b24288beb 100644
--- a/scripts/datafiles/first_bam_alignment.pl
+++ b/scripts/datafiles/first_bam_alignment.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/datafiles/sizes.pl b/scripts/datafiles/sizes.pl
index 402f50e7a..36ba4e782 100755
--- a/scripts/datafiles/sizes.pl
+++ b/scripts/datafiles/sizes.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/delete_genome.pl b/scripts/delete_genome.pl
index 46c0a2c06..8a1c1b2cf 100644
--- a/scripts/delete_genome.pl
+++ b/scripts/delete_genome.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/ena/ena_dump.pl b/scripts/ena/ena_dump.pl
index fc7cc33db..2747ad545 100755
--- a/scripts/ena/ena_dump.pl
+++ b/scripts/ena/ena_dump.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/ftp/checksums.pl b/scripts/ftp/checksums.pl
index 0f0afa483..5fed9c273 100755
--- a/scripts/ftp/checksums.pl
+++ b/scripts/ftp/checksums.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/ftp/upload_ena_xrefs.sh b/scripts/ftp/upload_ena_xrefs.sh
index 0669610b3..e8a7a1801 100755
--- a/scripts/ftp/upload_ena_xrefs.sh
+++ b/scripts/ftp/upload_ena_xrefs.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/get_new_db_name.pl b/scripts/get_new_db_name.pl
index 8c1c3b31d..a95c4ec33 100755
--- a/scripts/get_new_db_name.pl
+++ b/scripts/get_new_db_name.pl
@@ -1,6 +1,6 @@
 #!/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/link_out/generate_LinkOut.pl b/scripts/link_out/generate_LinkOut.pl
index 1e0e358c3..f12fada3b 100644
--- a/scripts/link_out/generate_LinkOut.pl
+++ b/scripts/link_out/generate_LinkOut.pl
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/misc/check_tmux.sh b/scripts/misc/check_tmux.sh
index cbbf75810..012fa8d34 100755
--- a/scripts/misc/check_tmux.sh
+++ b/scripts/misc/check_tmux.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/misc/tmux_ls.sh b/scripts/misc/tmux_ls.sh
index 2d5358cc6..317f0ef97 100755
--- a/scripts/misc/tmux_ls.sh
+++ b/scripts/misc/tmux_ls.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/prepare_ftp_dump.sh b/scripts/prepare_ftp_dump.sh
index 733a881e6..fc8f05311 100755
--- a/scripts/prepare_ftp_dump.sh
+++ b/scripts/prepare_ftp_dump.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/production_database/import_species_names_from_cores.pl b/scripts/production_database/import_species_names_from_cores.pl
index 0c29a8130..4bb484071 100644
--- a/scripts/production_database/import_species_names_from_cores.pl
+++ b/scripts/production_database/import_species_names_from_cores.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/production_database/import_species_names_from_taxonomy.pl b/scripts/production_database/import_species_names_from_taxonomy.pl
index e9da34624..9647588fb 100644
--- a/scripts/production_database/import_species_names_from_taxonomy.pl
+++ b/scripts/production_database/import_species_names_from_taxonomy.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/production_database/populate_species_meta.pl b/scripts/production_database/populate_species_meta.pl
index a640509cb..1cdc26da6 100644
--- a/scripts/production_database/populate_species_meta.pl
+++ b/scripts/production_database/populate_species_meta.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/py/alphafoldUpdate.py b/scripts/py/alphafoldUpdate.py
index e184ea71c..2c63a63da 100644
--- a/scripts/py/alphafoldUpdate.py
+++ b/scripts/py/alphafoldUpdate.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/py/alphafoldUpdate_parallel.py b/scripts/py/alphafoldUpdate_parallel.py
index ede2a286f..b7332e7d9 100644
--- a/scripts/py/alphafoldUpdate_parallel.py
+++ b/scripts/py/alphafoldUpdate_parallel.py
@@ -1,6 +1,6 @@
 #!/usr/bin/env python3
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 01cf67462..a8a9c663b 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 #
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/refget/check_sequence_refget.pl b/scripts/refget/check_sequence_refget.pl
index a2bbf2fb5..532948c30 100755
--- a/scripts/refget/check_sequence_refget.pl
+++ b/scripts/refget/check_sequence_refget.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sql2html.pl b/scripts/sql2html.pl
index 33b02afd1..1e2a917e2 100755
--- a/scripts/sql2html.pl
+++ b/scripts/sql2html.pl
@@ -1,6 +1,6 @@
 #!/usr/bin/env perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/check_db.sh b/scripts/sync/check_db.sh
index 9207a1428..254f39dd3 100644
--- a/scripts/sync/check_db.sh
+++ b/scripts/sync/check_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/check_public_db.sh b/scripts/sync/check_public_db.sh
index e5318ea90..1ca960fa2 100644
--- a/scripts/sync/check_public_db.sh
+++ b/scripts/sync/check_public_db.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/get_release.sh b/scripts/sync/get_release.sh
index 60208f938..ddccffcda 100644
--- a/scripts/sync/get_release.sh
+++ b/scripts/sync/get_release.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/get_staging_server.sh b/scripts/sync/get_staging_server.sh
index 6895aad3f..b034efea4 100644
--- a/scripts/sync/get_staging_server.sh
+++ b/scripts/sync/get_staging_server.sh
@@ -1,7 +1,7 @@
 #!/bin/bash
 --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/optimise_databases.sh b/scripts/sync/optimise_databases.sh
index f042b0942..0c430b5a2 100644
--- a/scripts/sync/optimise_databases.sh
+++ b/scripts/sync/optimise_databases.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/process_divisions.sh b/scripts/sync/process_divisions.sh
index 75c216633..bd99d2c1f 100755
--- a/scripts/sync/process_divisions.sh
+++ b/scripts/sync/process_divisions.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/publish_db.sh b/scripts/sync/publish_db.sh
index abab797e3..56d6bea48 100755
--- a/scripts/sync/publish_db.sh
+++ b/scripts/sync/publish_db.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/set_checksums.sh b/scripts/sync/set_checksums.sh
index ab4d56dd4..1da4bd063 100644
--- a/scripts/sync/set_checksums.sh
+++ b/scripts/sync/set_checksums.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/sync_db.sh b/scripts/sync/sync_db.sh
index 21f17ce2a..899429d37 100644
--- a/scripts/sync/sync_db.sh
+++ b/scripts/sync/sync_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/sync_db_st1.sh b/scripts/sync/sync_db_st1.sh
index 8b14f0b12..2cc7440b9 100644
--- a/scripts/sync/sync_db_st1.sh
+++ b/scripts/sync/sync_db_st1.sh
@@ -1,6 +1,6 @@
 #!/bin/sh
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/sync_db_st2.sh b/scripts/sync/sync_db_st2.sh
index 219a29d19..dc010c78f 100644
--- a/scripts/sync/sync_db_st2.sh
+++ b/scripts/sync/sync_db_st2.sh
@@ -1,6 +1,6 @@
 #!/bin/sh --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync/update_live_db.sh b/scripts/sync/update_live_db.sh
index 280714bb2..6ce2f4645 100644
--- a/scripts/sync/update_live_db.sh
+++ b/scripts/sync/update_live_db.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/sync_tables.sh b/scripts/sync_tables.sh
index 88fba252d..0a5540cc7 100755
--- a/scripts/sync_tables.sh
+++ b/scripts/sync_tables.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/t/rename_db.t b/scripts/t/rename_db.t
index a2fcdb298..930e08410 100644
--- a/scripts/t/rename_db.t
+++ b/scripts/t/rename_db.t
@@ -1,5 +1,5 @@
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/update_api_tarball.sh b/scripts/update_api_tarball.sh
index 65a7dee0f..c1033d472 100755
--- a/scripts/update_api_tarball.sh
+++ b/scripts/update_api_tarball.sh
@@ -1,6 +1,6 @@
 #!/bin/bash --
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/update_assembly_tables.sh b/scripts/update_assembly_tables.sh
index aff7259c5..8bfcd5ef3 100755
--- a/scripts/update_assembly_tables.sh
+++ b/scripts/update_assembly_tables.sh
@@ -1,6 +1,6 @@
 #!/bin/bash
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/scripts/update_mapping_set.pl b/scripts/update_mapping_set.pl
index 578abf8b5..58027e469 100644
--- a/scripts/update_mapping_set.pl
+++ b/scripts/update_mapping_set.pl
@@ -1,6 +1,6 @@
 #!/usr/local/ensembl/bin/perl
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # 
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
diff --git a/sql/patch_100_101_a.sql b/sql/patch_100_101_a.sql
index 15908b8a0..8fae827f3 100644
--- a/sql/patch_100_101_a.sql
+++ b/sql/patch_100_101_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_101_102_a.sql b/sql/patch_101_102_a.sql
index 4c855706f..2ce3dfa4b 100644
--- a/sql/patch_101_102_a.sql
+++ b/sql/patch_101_102_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_102_103_a.sql b/sql/patch_102_103_a.sql
index 9d3cae861..e92b99fdf 100644
--- a/sql/patch_102_103_a.sql
+++ b/sql/patch_102_103_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_103_104_a.sql b/sql/patch_103_104_a.sql
index 57f9ecf16..e6ae954cf 100644
--- a/sql/patch_103_104_a.sql
+++ b/sql/patch_103_104_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_104_105_a.sql b/sql/patch_104_105_a.sql
index d374079da..939a68c31 100644
--- a/sql/patch_104_105_a.sql
+++ b/sql/patch_104_105_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_105_106_a.sql b/sql/patch_105_106_a.sql
index fbc613b4d..54e7a3cce 100644
--- a/sql/patch_105_106_a.sql
+++ b/sql/patch_105_106_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_106_107_a.sql b/sql/patch_106_107_a.sql
index 799e5dc1a..cf0b0786d 100644
--- a/sql/patch_106_107_a.sql
+++ b/sql/patch_106_107_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_107_108_a.sql b/sql/patch_107_108_a.sql
index efbf8126d..1b96e7e30 100644
--- a/sql/patch_107_108_a.sql
+++ b/sql/patch_107_108_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_108_109_a.sql b/sql/patch_108_109_a.sql
index 9a01e5f03..9e7e4432e 100644
--- a/sql/patch_108_109_a.sql
+++ b/sql/patch_108_109_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_109_110_a.sql b/sql/patch_109_110_a.sql
index bcb77d5cc..427981eec 100644
--- a/sql/patch_109_110_a.sql
+++ b/sql/patch_109_110_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_110_111_a.sql b/sql/patch_110_111_a.sql
index 50b48d95a..91ba1c712 100644
--- a/sql/patch_110_111_a.sql
+++ b/sql/patch_110_111_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_66_67a.sql b/sql/patch_66_67a.sql
index 3d41300ba..8a1493a9e 100644
--- a/sql/patch_66_67a.sql
+++ b/sql/patch_66_67a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_66_67b.sql b/sql/patch_66_67b.sql
index 24a9a823c..8a487f804 100644
--- a/sql/patch_66_67b.sql
+++ b/sql/patch_66_67b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_66_67c.sql b/sql/patch_66_67c.sql
index 62a317219..df9c1202c 100644
--- a/sql/patch_66_67c.sql
+++ b/sql/patch_66_67c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_70_71a.sql b/sql/patch_70_71a.sql
index c884dbe57..38dfb75dd 100644
--- a/sql/patch_70_71a.sql
+++ b/sql/patch_70_71a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_71_72a.sql b/sql/patch_71_72a.sql
index e23e1d0d9..b6e80c406 100644
--- a/sql/patch_71_72a.sql
+++ b/sql/patch_71_72a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_71_72b.sql b/sql/patch_71_72b.sql
index e8a49ded9..e419da717 100644
--- a/sql/patch_71_72b.sql
+++ b/sql/patch_71_72b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73a.sql b/sql/patch_72_73a.sql
index c52185d0f..14fc3c0cb 100644
--- a/sql/patch_72_73a.sql
+++ b/sql/patch_72_73a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73b.sql b/sql/patch_72_73b.sql
index 6d786d667..307e9bcaa 100644
--- a/sql/patch_72_73b.sql
+++ b/sql/patch_72_73b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73c.sql b/sql/patch_72_73c.sql
index 625c81b31..d482e55ea 100644
--- a/sql/patch_72_73c.sql
+++ b/sql/patch_72_73c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73d.sql b/sql/patch_72_73d.sql
index a48f47240..5777b9c02 100644
--- a/sql/patch_72_73d.sql
+++ b/sql/patch_72_73d.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_72_73e.sql b/sql/patch_72_73e.sql
index ea3fcab26..365fba5d9 100644
--- a/sql/patch_72_73e.sql
+++ b/sql/patch_72_73e.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_73_74a.sql b/sql/patch_73_74a.sql
index ab3a80db0..448aa4e7e 100644
--- a/sql/patch_73_74a.sql
+++ b/sql/patch_73_74a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_73_74b.sql b/sql/patch_73_74b.sql
index 20a7af979..a9e4ab21d 100644
--- a/sql/patch_73_74b.sql
+++ b/sql/patch_73_74b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_74_75a.sql b/sql/patch_74_75a.sql
index 6ade7d4ca..03a5c9f8f 100644
--- a/sql/patch_74_75a.sql
+++ b/sql/patch_74_75a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_74_75b.sql b/sql/patch_74_75b.sql
index df331a1ab..c32246fa5 100644
--- a/sql/patch_74_75b.sql
+++ b/sql/patch_74_75b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_75_76a.sql b/sql/patch_75_76a.sql
index 6ab105370..4323f0b45 100644
--- a/sql/patch_75_76a.sql
+++ b/sql/patch_75_76a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_75_76b.sql b/sql/patch_75_76b.sql
index 52bb31295..86d773a7c 100644
--- a/sql/patch_75_76b.sql
+++ b/sql/patch_75_76b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_76_77a.sql b/sql/patch_76_77a.sql
index 976ff6ca9..a7f88fe5a 100644
--- a/sql/patch_76_77a.sql
+++ b/sql/patch_76_77a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_76_77b.sql b/sql/patch_76_77b.sql
index d8ae4cb32..4d8a0292f 100644
--- a/sql/patch_76_77b.sql
+++ b/sql/patch_76_77b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_76_77c.sql b/sql/patch_76_77c.sql
index bf6389c72..e11d7b6ff 100644
--- a/sql/patch_76_77c.sql
+++ b/sql/patch_76_77c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_77_78a.sql b/sql/patch_77_78a.sql
index 2102e7f2e..998ae5285 100644
--- a/sql/patch_77_78a.sql
+++ b/sql/patch_77_78a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_77_78b.sql b/sql/patch_77_78b.sql
index d22cc7765..dbdfb77d2 100644
--- a/sql/patch_77_78b.sql
+++ b/sql/patch_77_78b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_78_79a.sql b/sql/patch_78_79a.sql
index 6142d73e0..cd70b6f58 100644
--- a/sql/patch_78_79a.sql
+++ b/sql/patch_78_79a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_78_79b.sql b/sql/patch_78_79b.sql
index c995cbeb0..027f10575 100644
--- a/sql/patch_78_79b.sql
+++ b/sql/patch_78_79b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_79_80_a.sql b/sql/patch_79_80_a.sql
index 2eac97dc1..bc4b07587 100644
--- a/sql/patch_79_80_a.sql
+++ b/sql/patch_79_80_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_79_80b.sql b/sql/patch_79_80b.sql
index 359254dec..b78f1b3a2 100644
--- a/sql/patch_79_80b.sql
+++ b/sql/patch_79_80b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_79_80c.sql b/sql/patch_79_80c.sql
index e37889e3b..3117e7100 100644
--- a/sql/patch_79_80c.sql
+++ b/sql/patch_79_80c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_80_81a.sql b/sql/patch_80_81a.sql
index 20fb91c81..f2cc022bb 100644
--- a/sql/patch_80_81a.sql
+++ b/sql/patch_80_81a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_81_82a.sql b/sql/patch_81_82a.sql
index c2033985a..ab8035808 100644
--- a/sql/patch_81_82a.sql
+++ b/sql/patch_81_82a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_82_83a.sql b/sql/patch_82_83a.sql
index 2bace410f..0a434ce50 100644
--- a/sql/patch_82_83a.sql
+++ b/sql/patch_82_83a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_83_84a.sql b/sql/patch_83_84a.sql
index f4ac58b90..576e37220 100644
--- a/sql/patch_83_84a.sql
+++ b/sql/patch_83_84a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_83_84b.sql b/sql/patch_83_84b.sql
index 7cd10bcf9..67a259637 100644
--- a/sql/patch_83_84b.sql
+++ b/sql/patch_83_84b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_84_85a.sql b/sql/patch_84_85a.sql
index 27bdfe2fe..df71904d5 100644
--- a/sql/patch_84_85a.sql
+++ b/sql/patch_84_85a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_85_86a.sql b/sql/patch_85_86a.sql
index 88f01ec22..74ba611e3 100644
--- a/sql/patch_85_86a.sql
+++ b/sql/patch_85_86a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_85_86b.sql b/sql/patch_85_86b.sql
index 107b75331..a6886f6a4 100644
--- a/sql/patch_85_86b.sql
+++ b/sql/patch_85_86b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_85_86c.sql b/sql/patch_85_86c.sql
index cadb8ae8d..d1ead0ea6 100644
--- a/sql/patch_85_86c.sql
+++ b/sql/patch_85_86c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_86_87a.sql b/sql/patch_86_87a.sql
index d44c66123..2a4c58a14 100644
--- a/sql/patch_86_87a.sql
+++ b/sql/patch_86_87a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_87_88_a.sql b/sql/patch_87_88_a.sql
index 0ecdc80fa..808314f4c 100644
--- a/sql/patch_87_88_a.sql
+++ b/sql/patch_87_88_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_88_89_a.sql b/sql/patch_88_89_a.sql
index a0143bf3c..39c13d822 100644
--- a/sql/patch_88_89_a.sql
+++ b/sql/patch_88_89_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_89_90_a.sql b/sql/patch_89_90_a.sql
index 22f4a7840..3d78db749 100644
--- a/sql/patch_89_90_a.sql
+++ b/sql/patch_89_90_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_89_90_b.sql b/sql/patch_89_90_b.sql
index 1693fb8f5..d3800cbc3 100644
--- a/sql/patch_89_90_b.sql
+++ b/sql/patch_89_90_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_90_91_a.sql b/sql/patch_90_91_a.sql
index dfb0e5fc1..2dbb361ad 100644
--- a/sql/patch_90_91_a.sql
+++ b/sql/patch_90_91_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_91_92_a.sql b/sql/patch_91_92_a.sql
index 0a1cbbfd5..f2546a7b5 100644
--- a/sql/patch_91_92_a.sql
+++ b/sql/patch_91_92_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 -- 
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_92_93_a.sql b/sql/patch_92_93_a.sql
index d2e804ef2..e4467914f 100644
--- a/sql/patch_92_93_a.sql
+++ b/sql/patch_92_93_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_92_93_b.sql b/sql/patch_92_93_b.sql
index cacc4688e..21ed7f478 100644
--- a/sql/patch_92_93_b.sql
+++ b/sql/patch_92_93_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_93_94_a.sql b/sql/patch_93_94_a.sql
index 776c119f2..11308c60f 100644
--- a/sql/patch_93_94_a.sql
+++ b/sql/patch_93_94_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_94_95_a.sql b/sql/patch_94_95_a.sql
index 94a08b2ce..8b57afea9 100644
--- a/sql/patch_94_95_a.sql
+++ b/sql/patch_94_95_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_94_95_b.sql b/sql/patch_94_95_b.sql
index a431932ea..11f5c2a0b 100644
--- a/sql/patch_94_95_b.sql
+++ b/sql/patch_94_95_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_95_96_a.sql b/sql/patch_95_96_a.sql
index a5ace02f1..d23918cc9 100644
--- a/sql/patch_95_96_a.sql
+++ b/sql/patch_95_96_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_a.sql b/sql/patch_96_97_a.sql
index a6b87fbc6..3aa2641e6 100644
--- a/sql/patch_96_97_a.sql
+++ b/sql/patch_96_97_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_b.sql b/sql/patch_96_97_b.sql
index 71c633956..34367a992 100644
--- a/sql/patch_96_97_b.sql
+++ b/sql/patch_96_97_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_c.sql b/sql/patch_96_97_c.sql
index 085470cce..da78c3285 100644
--- a/sql/patch_96_97_c.sql
+++ b/sql/patch_96_97_c.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_d.sql b/sql/patch_96_97_d.sql
index 5449accfc..fb9bce3dc 100644
--- a/sql/patch_96_97_d.sql
+++ b/sql/patch_96_97_d.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_e.sql b/sql/patch_96_97_e.sql
index 5c6158bb4..7749cf793 100644
--- a/sql/patch_96_97_e.sql
+++ b/sql/patch_96_97_e.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_96_97_f.sql b/sql/patch_96_97_f.sql
index 526f82962..f862d40ec 100644
--- a/sql/patch_96_97_f.sql
+++ b/sql/patch_96_97_f.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_97_98_a.sql b/sql/patch_97_98_a.sql
index 9bfce4019..fb5055676 100644
--- a/sql/patch_97_98_a.sql
+++ b/sql/patch_97_98_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_98_99_a.sql b/sql/patch_98_99_a.sql
index 54619e467..8877f4de3 100644
--- a/sql/patch_98_99_a.sql
+++ b/sql/patch_98_99_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_98_99_b.sql b/sql/patch_98_99_b.sql
index cc3820ff6..1aa6dd37f 100644
--- a/sql/patch_98_99_b.sql
+++ b/sql/patch_98_99_b.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/patch_99_100_a.sql b/sql/patch_99_100_a.sql
index 6fe8fa689..532a2b298 100644
--- a/sql/patch_99_100_a.sql
+++ b/sql/patch_99_100_a.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/sql/table.sql b/sql/table.sql
index 4cbe5a09d..a72e11ee5 100644
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -1,5 +1,5 @@
 -- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
--- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
 --
 -- Licensed under the Apache License, Version 2.0 (the "License");
 -- you may not use this file except in compliance with the License.
diff --git a/src/python/scripts/dcparse.py b/src/python/scripts/dcparse.py
index e2c50ee5b..b14896ae1 100755
--- a/src/python/scripts/dcparse.py
+++ b/src/python/scripts/dcparse.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
diff --git a/src/python/scripts/dcstat.py b/src/python/scripts/dcstat.py
index 76c3f9eb9..dce7ca061 100755
--- a/src/python/scripts/dcstat.py
+++ b/src/python/scripts/dcstat.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 # Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-# Copyright [2016-2023] EMBL-European Bioinformatics Institute
+# Copyright [2016-2024] EMBL-European Bioinformatics Institute
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
diff --git a/src/python/scripts/genome_info.py b/src/python/scripts/genome_info.py
index 228186abb..48ade41b2 100755
--- a/src/python/scripts/genome_info.py
+++ b/src/python/scripts/genome_info.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.
diff --git a/src/python/scripts/meta_hive_species.py b/src/python/scripts/meta_hive_species.py
index f6e0733bd..cd61cd425 100755
--- a/src/python/scripts/meta_hive_species.py
+++ b/src/python/scripts/meta_hive_species.py
@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 """
 Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2023] EMBL-European Bioinformatics Institute
+Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
 Licensed under the Apache License, Version 2.0 (the "License");
 you may not use this file except in compliance with the License.

From c8606fa36dcb0a3050711d81250c7cb17591ee61 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-login-04.ebi.ac.uk>
Date: Tue, 30 Jan 2024 10:37:08 +0000
Subject: [PATCH 037/128] Add check for unvalid readdir output

---
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 011dc5fa2..2228f94e3 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -131,6 +131,7 @@ sub run {
       closedir($dir_handle);
       if ($preparse) { @list_files = $preparse; }
       foreach my $file (@list_files) {
+        next if ($file =~ /^\./);
         $file =~ s/\n//;
         $file = $file_name . "/" . $file;
         if (defined $release_file and $file eq $release_file) { next; }

From 6a8c1c4eec147fa258277688eb387658768e64f4 Mon Sep 17 00:00:00 2001
From: Arne Becker <arne@ebi.ac.uk>
Date: Thu, 1 Feb 2024 13:23:27 +0000
Subject: [PATCH 038/128] Rework alphafold pipeline cleanup logic

- Pieline ran cleanup too early, after the first datacheck finished. Fixed.
- Removed a few newlines that we were storing but don't need
---
 .../Pipeline/AlphaFold/CreateAlphaDB.pm       |  2 +-
 .../Pipeline/AlphaFold/CreateUniparcDB.pm     |  5 ++-
 .../AlphaFold/InsertProteinFeatures.pm        |  1 +
 .../Pipeline/PipeConfig/AlphaDBImport_conf.pm | 31 ++++++++++---------
 4 files changed, 20 insertions(+), 19 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
index a896a09ef..021a1d4ff 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateAlphaDB.pm
@@ -98,13 +98,13 @@ sub run {
     open($map, '<', $map_file) or die "Opening map file $map_file failed: $!";
 
     while (my $line = <$map>) {
+        chomp $line;
         # A line from accession_ids.csv looks like this:
         # Uniprot accession, hit start, hit end, Alphafold accession, Alphafold version
         # A0A2I1PIX0,1,200,AF-A0A2I1PIX0-F1,4
         # Currently, all entries in this file have a unique uniprot accession and
         # have a hit starting at 1
         unless ($line =~ /^\w+,\d+,\d+,[\w_-]+,\d+$/) {
-            chomp $line;
             die "Data error. Line is not what we expect: '$line'";
         }
         my @x = split(",", $line, 2);
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
index b983ca689..825d9d7ca 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/CreateUniparcDB.pm
@@ -90,7 +90,7 @@ sub run {
     # hash collision handling. These are tuned for write speed and for approx. 300M entries.
     # Uniparc has 251M entries at the moment.
     # As with a regular Perl hash, a duplicate entry will overwrite the previous
-    # # value.
+    # value.
     $db->open("$idx_dir/uniparc-to-uniprot.kch#bnum=600000000#msiz=$mapsize_gb#opts=l",
         $db->OWRITER | $db->OCREATE | $db->OTRUNCATE
     ) or die "Error opening DB: " . $db->error();
@@ -105,13 +105,12 @@ sub run {
     my $line;
 
     while ($line = <$map>) {
+        chomp $line;
         unless ($line =~ /^\w+\t[[:print:]\t]+$/) {
-            chomp $line;
             die "Data error: Uniparc accession is not what we expect: '$line'";
         }
         my @x = split("\t", $line, 12);
         unless ($x[10] and $x[10] =~ /^UPI\w+$/) {
-            chomp $line;
             die "Data error: Uniparc accession is not what we expect: '$line'";
         }
         # This is the DB write operation.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 5721e3ed4..5bdef59f1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -138,6 +138,7 @@ sub run {
     # traverse records by iterator
     while (my ($key, $value) = each(%db)) {
         $alpha_version = (split ',', $value)[-1];
+        chomp($alpha_version);
         last;
     }
     untie %db;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
index 263bb7cef..7d8cca5be 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
@@ -1,7 +1,7 @@
 =head1 LICENSE
 
  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
- Copyright [2016-2023] EMBL-European Bioinformatics Institute
+ Copyright [2016-2024] EMBL-European Bioinformatics Institute
 
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
@@ -102,11 +102,14 @@ sub pipeline_analyses {
             -input_ids       => [{}],
             -meadow_type     => 'LOCAL',
             -flow_into  => {
-                '1' => [
+                '1->A' => [
                     'copy_alphafold',
                     'copy_uniparc',
                     'species_factory'
                 ],
+                'A->1' => [
+                    'cleanup'
+                ],
             },
         },
         {
@@ -156,7 +159,6 @@ sub pipeline_analyses {
                 antispecies => $self->o('antispecies'),
             },
             -flow_into  => {
-                '1' => [ 'cleanup' ],
                 '2' => [ 'insert_features' ],
             },
             -rc_name    => '500M',
@@ -184,28 +186,27 @@ sub pipeline_analyses {
             -parameters => {
                 datacheck_names => [ 'CheckAlphafoldEntries' ],
             },
-            -flow_into  => 'report',
             -rc_name    => '200M',
         },
         {
-            -logic_name        => 'report',
-            -module            => 'Bio::EnsEMBL::DataCheck::Pipeline::EmailReport',
+            -logic_name        => 'cleanup',
+            -module            => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
             -max_retry_count   => 1,
-            -analysis_capacity => 10,
+            -flow_into  => {
+                '1' => [ 'report' ]
+            },
             -parameters        => {
-                dbname        => $self->o('pipeline_db')->{'-dbname'},
-                email         => $self->o('email'),
+                cmd => 'rm -rf ' . $self->o('scratch_large_dir'),
             },
         },
         {
-            -logic_name        => 'cleanup',
-            -module            => 'Bio::EnsEMBL::Hive::RunnableDB::SystemCmd',
+            -logic_name        => 'report',
+            -module            => 'Bio::EnsEMBL::DataCheck::Pipeline::EmailReport',
             -max_retry_count   => 1,
-            -wait_for => [
-                'datacheck'
-            ],
+            -analysis_capacity => 10,
             -parameters        => {
-                cmd => 'rm -rf ' . $self->o('scratch_large_dir'),
+                dbname        => $self->o('pipeline_db')->{'-dbname'},
+                email         => $self->o('email'),
             },
         },
     );

From 19a9c3154808f2f8b39be9443f0e95f82c7e9c7d Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-login-06.ebi.ac.uk>
Date: Tue, 6 Feb 2024 15:40:37 +0000
Subject: [PATCH 039/128] Fix uniprot gene name + cleanup bugs

---
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm | 2 +-
 .../Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
index 522a74080..df744e250 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/CleanupUniprot.pm
@@ -116,7 +116,7 @@ sub run {
         $_ =~ s/\nCC\s{3}.*//g; # Remove comments
         $_ =~ s/\nCT(\s{3}.*)CAUTION: The sequence shown here is derived from an Ensembl(.*)/\nCC$1CAUTION: The sequence shown here is derived from an Ensembl$2/g; # Set temp line back to comment
 	$_ =~ s/\nFT\s{3}.*//g; # Remove feature coordinates
-        $_ =~ s/\nDR\s{3}($sources_to_remove);.*\n//g; # Remove sources skipped at processing
+        $_ =~ s/\nDR\s{3}($sources_to_remove);.*//g; # Remove sources skipped at processing
 
         # Added lines that we do need into output
         print $out_fh $_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
index e47bcc2de..e8db14138 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Parser/UniProtDatabaseParser.pm
@@ -242,7 +242,7 @@ sub run {
         # Make sure these are still lines with Name or Synonyms
         if (($gn !~ /^GN/ || $gn !~ /Name=/) && $gn !~ /Synonyms=/) { last; }
 
-        if ($gn =~ / Name=([A-Za-z0-9_\-\.\s]+)/s) { #/s for multi-line entries ; is the delimiter
+        if ($gn =~ / Name=([A-Za-z0-9_\-\.\s:]+)/s) { #/s for multi-line entries ; is the delimiter
           # Example line 
           # GN   Name=ctrc {ECO:0000313|Xenbase:XB-GENE-5790348};
           my $name = $1;

From 79b1f2e2c617558dcb34a85bc782e4907458b302 Mon Sep 17 00:00:00 2001
From: Thomas Walsh <twalsh@ebi.ac.uk>
Date: Thu, 15 Feb 2024 12:58:17 +0000
Subject: [PATCH 040/128] Flag outdated taxon_ids in TaxonomyInfoCore pipeline

---
 .../Pipeline/TaxonomyUpdate/QueryMetadata.pm  | 47 ++++++++++++++++++-
 1 file changed, 46 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
index 3438dd571..025cc3a65 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/TaxonomyUpdate/QueryMetadata.pm
@@ -82,7 +82,24 @@ sub _meta {
   $self->warning('Querying Taxonomy');
   #my $tdba =  Bio::EnsEMBL::Registry->get_DBAdaptor( "multi", "taxonomy" );
   my $taxonomy  = $self->_taxonomy( $tdba, $metadata->{'species.taxonomy_id'});
-  $metadata->{'species.classification'} = $taxonomy; 	
+
+  if (scalar(@{$taxonomy}) == 0) {
+    my $dbname = $self->param('dbname');
+    my $species = $self->param('species');
+    my $taxon_id = $metadata->{'species.taxonomy_id'};
+    my $msg = "Cannot retrieve taxonomy classification for species $species with taxonomy_id $taxon_id in database $dbname;";
+
+    my $primary_taxon_id = $self->_fetch_primary_taxon_id($tdba, $taxon_id);
+    if (defined $primary_taxon_id) {
+      $msg = $msg
+             ." taxon_id $taxon_id has been merged into primary taxon_id $primary_taxon_id."
+             ." Would you kindly set the 'species.taxonomy_id' meta entry for this species to the"
+             ." primary taxon_id and ensure the change is propagated to other relevant databases ?";
+    }
+    throw $msg;
+  }
+
+  $metadata->{'species.classification'} = $taxonomy;
   $self->warning('Updating meta');
   foreach my $key ( keys %{$metadata} ) {
     my $array = wrap_array( $metadata->{$key} );
@@ -150,6 +167,34 @@ SQL
 }
 
 
+sub _fetch_primary_taxon_id {
+  my ( $self, $tdba, $taxon_id ) = @_;
+  $self->warning('Querying taxonomy to fetch primary taxon_id');
+  my $sql            = <<'SQL';
+select taxon_id
+from ncbi_taxa_name
+where name = ?
+and name_class = 'merged_taxon_id'
+SQL
+  my $dbc = $tdba->dbc();
+  my $res = $dbc->sql_helper()->execute_simple(
+    -SQL    => $sql,
+    -PARAMS => [ $taxon_id ]
+  );
+  $self->debug( 'Result is [%s]', join( q{, }, @{$res} ) );
+  my $result_count = scalar(@{$res});
+
+  my $primary_taxon_id;
+  if ($result_count == 1) {
+    $primary_taxon_id = $res->[0];
+  } elsif ($result_count > 1) {
+    throw "Expected at most 1 primary taxon_id for $taxon_id but got $result_count";
+  }
+
+  return $primary_taxon_id;
+}
+
+
 sub _remove_deprecated {
   my ($self, $meta_container) = @_;
 

From 610d7a9975ff47c5b06fc9ee67c4db3ef1a8c212 Mon Sep 17 00:00:00 2001
From: Thomas Walsh <twalsh@ebi.ac.uk>
Date: Mon, 26 Feb 2024 08:25:02 +0000
Subject: [PATCH 041/128] Load InterPro Family data only for canonicals

---
 .../Pipeline/LoadFamily/AddFamilyMembers.pm   | 71 ++++++++++++-------
 .../Pipeline/LoadFamily/CreateFamilies.pm     | 53 ++++++++------
 2 files changed, 77 insertions(+), 47 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
index 37da4aabe..043c98ebc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/AddFamilyMembers.pm
@@ -78,11 +78,13 @@ sub run {
   # create a hash first though, which can then be processed
   # gene_id as key, then sets of protein-family pairs
   my $gene_families = {};
+  # retrieve family data for canonical translations
   my $sql = qq/select t.gene_id, t.transcript_id, pf.hit_name
 		from coord_system c
 		join seq_region s using (coord_system_id)
-		join transcript t using (seq_region_id)
-		join translation tl using (transcript_id)
+        join gene g using(seq_region_id)
+        join transcript t on t.transcript_id = g.canonical_transcript_id
+        join translation tl on tl.translation_id = t.canonical_translation_id
 		join protein_feature pf using (translation_id)
 		join analysis pfa ON (pf.analysis_id=pfa.analysis_id)
 		where pfa.logic_name in ($logic_names)
@@ -104,37 +106,52 @@ sub run {
   my $family_members     = {};
   while ( my ( $gene_id, $hits ) = each %$gene_families ) {
     my $gene = $gene_adaptor->fetch_by_dbID($gene_id);
-    # create and store gene member
-    my $gene_member =
-      Bio::EnsEMBL::Compara::GeneMember->new_from_Gene(
-        -GENE          => $gene,
-        -GENOME_DB     => $genome_db,
-        -BIOTYPE_GROUP => $gene->get_Biotype->biotype_group()
-      );
-    # If there are duplicate stable IDs, trap fatal error from compara
-    # method, so we can skip it and carry on with others.
-    eval {
-      $gene_member_dba->store($gene_member);
-    };
-    if ($@) {
-      my ($msg) = $@ =~ /MSG:\s+([^\n]+)/m;
-      $self->warning('Duplicate stable ID: '.$msg);
+
+    # retrieve or create-and-store gene_member from the current genome_db
+    my $gene_member = $gene_member_dba->fetch_by_stable_id_GenomeDB($gene->stable_id,
+                                                                    $genome_db);
+    my $existing_canonical;
+    if (defined $gene_member) {
+      $existing_canonical = $seq_member_dba->fetch_by_dbID( $gene_member->canonical_member_id );
     } else {
-      for my $hit (@$hits) {
-        my $transcript =
-          $transcript_adaptor->fetch_by_dbID( $hit->[0] );
-          my $seq_member =
-            Bio::EnsEMBL::Compara::SeqMember->new_from_Transcript(
-              -TRANSCRIPT => $transcript,
-              -TRANSLATE  => 'yes',
-              -GENOME_DB  => $genome_db
-            );
+      $gene_member =
+        Bio::EnsEMBL::Compara::GeneMember->new_from_Gene(
+          -GENE          => $gene,
+          -GENOME_DB     => $genome_db,
+          -BIOTYPE_GROUP => $gene->get_Biotype->biotype_group()
+        );
+      $gene_member_dba->store($gene_member);
+    }
+
+    for my $hit (@$hits) {
+      my $transcript =
+        $transcript_adaptor->fetch_by_dbID( $hit->[0] );
+      my $translation_stable_id = $transcript->translation->stable_id;
+
+      if (defined $existing_canonical && $translation_stable_id ne $existing_canonical->stable_id) {
+        $self->warning(sprintf('skipping translation %s because stable ID does not match canonical member %s',
+                               $translation_stable_id, $existing_canonical->stable_id));
+        next;
+      }
+
+      # retrieve or create-and-store seq_member from the current genome_db
+      my $seq_member =
+        $seq_member_dba->fetch_by_stable_id_GenomeDB($translation_stable_id,
+                                                     $genome_db);
+      if (!defined $seq_member) {
+        $seq_member =
+          Bio::EnsEMBL::Compara::SeqMember->new_from_Transcript(
+            -TRANSCRIPT => $transcript,
+            -TRANSLATE  => 'yes',
+            -GENOME_DB  => $genome_db
+          );
         # TODO store CDS too?
         $seq_member->gene_member_id( $gene_member->dbID );
         $seq_member_dba->store($seq_member);
         $seq_member_dba->_set_member_as_canonical($seq_member);
-        push @{ $family_members->{ $hit->[1] } }, $seq_member->dbID();
       }
+
+      push @{ $family_members->{ $hit->[1] } }, $seq_member->dbID();
     }
   } ## end while ( my ( $gene_id, $hits...))
   print "Saving familes for ".$dba->species()."\n";
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
index e5cd4784c..f505d87fd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/LoadFamily/CreateFamilies.pm
@@ -66,7 +66,9 @@ sub run {
   my $compara_dba = $compara_dbas[0];
   $self->param('compara_url', $compara_dba->url);
   my $schema_version = $compara_dba->get_MetaContainer->get_schema_version();
-  $compara_dba->dbc()->sql_helper()->execute_update(-SQL=>'delete family.*,family_member.* from family left join family_member using (family_id)');
+  my $compara_sql_helper = $compara_dba->dbc()->sql_helper();
+  $compara_sql_helper->execute_update(-SQL=>'delete family.*,family_member.* from family left join family_member using (family_id)');
+
   # get compara
   my $genome_dba = $compara_dba->get_GenomeDBAdaptor();
 
@@ -143,25 +145,36 @@ sub run {
   print "Found ".scalar(keys(%{$families}))." familes\n";
 
   # create and store MLSS
-  my $sso = Bio::EnsEMBL::Compara::SpeciesSet->new(
-    -GENOME_DBS => $genome_dbs,
-    -NAME => "collection-all_division",
-  );
-  $sso->first_release($schema_version);
-  $compara_dba->get_SpeciesSetAdaptor()->store($sso);
-
-  my $mlss =
-    Bio::EnsEMBL::Compara::MethodLinkSpeciesSet->new(
-      -method =>
-        Bio::EnsEMBL::Compara::Method->new(
-          -type  => 'FAMILY',
-          -class => 'Family.family',
-          -display_name => 'families'
-        ),
-      -species_set => $sso );
-  $mlss->first_release($schema_version);
-
-  $compara_dba->get_MethodLinkSpeciesSetAdaptor()->store($mlss);
+  my $sql = q/
+      insert ignore into method_link (method_link_id, type, class, display_name)
+      values (301, 'FAMILY', 'Family.family', 'families')/;
+  $compara_sql_helper->execute_update( -SQL => $sql );
+  my $method_dba = $compara_dba->get_MethodAdaptor();
+  my $method = $method_dba->fetch_by_type('FAMILY');
+
+  my $species_set_dba = $compara_dba->get_SpeciesSetAdaptor();
+  my $sso = $species_set_dba->fetch_by_GenomeDBs($genome_dbs);
+  if (!defined $sso) {
+    $sso = Bio::EnsEMBL::Compara::SpeciesSet->new(
+      -GENOME_DBS => $genome_dbs,
+      -NAME => "collection-all_division",
+    );
+    $sso->first_release($schema_version);
+    $species_set_dba->store($sso);
+  }
+
+  my $mlss_dba = $compara_dba->get_MethodLinkSpeciesSetAdaptor();
+  my $mlss = $mlss_dba->fetch_by_method_link_type_GenomeDBs($method->type, $genome_dbs);
+  if (!defined $mlss) {
+    $mlss =
+      Bio::EnsEMBL::Compara::MethodLinkSpeciesSet->new(
+        -method => $method,
+        -name => 'all_division families',
+        -species_set => $sso );
+    $mlss->first_release($schema_version);
+    $mlss_dba->store($mlss);
+  }
+
   my $family_dba = $compara_dba->get_FamilyAdaptor();
   while ( my ( $id, $name ) = each %$families ) {
     print "Storing family $id $name\n";

From a2596d4121206e6f218d97dda7e0c715922de46c Mon Sep 17 00:00:00 2001
From: Daniel Poppleton <111403332+dpopleton@users.noreply.github.com>
Date: Fri, 15 Mar 2024 12:01:46 +0000
Subject: [PATCH 042/128] Update ProteinFeatures_conf.pm

Just added a single comment to explain seq
---
 .../Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index 5ee1a1297..ec402777e 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -227,12 +227,12 @@ sub default_options {
         ipscan_xml      => 'TMHMM',
         ipscan_lookup   => 0,
       },
+      #seg replaces low complexity regions in protein sequences with X characters(https://rothlab.ucdavis.edu/genhelp/seg.html)
       {
         logic_name      => 'seg',
         db              => 'Seg',
       },
     ],
-
     xref_analyses =>
     [
       {

From d376dea45b84251e41e25e63fabb287c8756cdcf Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Sat, 16 Mar 2024 23:19:07 +0000
Subject: [PATCH 043/128] Reduced field lengths and optimised index on
 stable_id_lookup

---
 .../Production/Pipeline/StableID/sql/index.sql  |  3 +--
 .../Production/Pipeline/StableID/sql/table.sql  | 17 +++++++----------
 2 files changed, 8 insertions(+), 12 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
index a807f370a..d05766336 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/index.sql
@@ -13,5 +13,4 @@
 -- See the License for the specific language governing permissions and
 -- limitations under the License.
 
-CREATE INDEX stable_id_db_type ON stable_id_lookup(stable_id, db_type, object_type);
-CREATE INDEX stable_id_object_type ON stable_id_lookup(stable_id, object_type);
+CREATE INDEX stable_id_db_type ON stable_id_lookup(stable_id, object_type, db_type);
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
index 4ae7ac6ec..6319894a5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/StableID/sql/table.sql
@@ -14,15 +14,12 @@
 -- limitations under the License.
 
 CREATE TABLE archive_id_lookup (
-  archive_id  VARCHAR(128) NOT NULL,
+  archive_id  VARCHAR(100) NOT NULL,
   species_id  INTEGER UNSIGNED NOT NULL,
-  db_type     VARCHAR(255) NOT NULL,
-  object_type VARCHAR(255) NOT NULL,
-
-  UNIQUE INDEX archive_id_lookup_idx (archive_id, species_id, db_type, object_type),
-  KEY archive_id_db_type (archive_id, db_type, object_type),
-  KEY archive_id_object_type (archive_id, object_type)
+  db_type     VARCHAR(20) NOT NULL,
+  object_type VARCHAR(20) NOT NULL,
 
+  UNIQUE INDEX archive_id_lookup_idx (archive_id, object_type, db_type, species_id)
 ) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
 
 CREATE TABLE meta (
@@ -48,9 +45,9 @@ CREATE TABLE species (
 ) COLLATE=latin1_swedish_ci ENGINE=MyISAM;
 
 CREATE TABLE stable_id_lookup (
-  stable_id   VARCHAR(128) NOT NULL,	      
+  stable_id   VARCHAR(100) NOT NULL,	      
   species_id  INTEGER UNSIGNED NOT NULL,
-  db_type     VARCHAR(255) NOT NULL,
-  object_type VARCHAR(255) NOT NULL
+  db_type     VARCHAR(20) NOT NULL,
+  object_type VARCHAR(20) NOT NULL
 
 ) COLLATE=latin1_swedish_ci ENGINE=MyISAM;

From 009cb6d5ce6e7eb7f296bf3518437a3e1bab89bc Mon Sep 17 00:00:00 2001
From: Marc Chakiachvili <mchakiachvili@ebi.ac.uk>
Date: Mon, 18 Mar 2024 09:55:52 +0000
Subject: [PATCH 044/128] Fixed dependencies conflict in requirements.in

---
 requirements.in  |   5 +-
 requirements.txt | 123 +++++++++++++++++++++++++++++++++--------------
 2 files changed, 87 insertions(+), 41 deletions(-)

diff --git a/requirements.in b/requirements.in
index a5a3b2fac..603b015f3 100644
--- a/requirements.in
+++ b/requirements.in
@@ -1,6 +1,3 @@
 requests>=2.25.0,<3
-mysqlclient~=2.0.1
-sqlalchemy~=1.4.0
 pydantic~=1.10.5
-git+https://github.com/Ensembl/ensembl-py.git#egg=ensembl-py
-git+https://github.com/Ensembl/ensembl-metadata-api.git#egg=ensembl-metadata-api
+git+https://github.com/Ensembl/ensembl-metadata-api.git@2.0.1a2#egg=ensembl-metadata-api
diff --git a/requirements.txt b/requirements.txt
index 17639dec7..71c0445d4 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,63 +1,112 @@
 #
-# This file is autogenerated by pip-compile with python 3.8
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.8
+# by the following command:
 #
-#    pip-compile --output-file=requirements.txt requirements.in
+#    pip-compile requirements.in
 #
-certifi==2023.5.7
-    # via requests
-charset-normalizer==3.1.0
-    # via requests
+certifi==2024.2.2
+    # via
+    #   ensembl-metadata-api
+    #   requests
+charset-normalizer==3.3.2
+    # via
+    #   ensembl-metadata-api
+    #   requests
 ensembl-hive @ git+https://github.com/Ensembl/ensembl-hive.git
-    # via ensembl-py
-ensembl-metadata-api @ git+https://github.com/Ensembl/ensembl-metadata-api.git
+    # via
+    #   ensembl-metadata-api
+    #   ensembl-py
+ensembl-metadata-api @ git+https://github.com/Ensembl/ensembl-metadata-api.git@2.0.1a2
     # via -r requirements.in
-ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git
+ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git@1.2.2
+    # via ensembl-metadata-api
+exceptiongroup==1.2.0
+    # via
+    #   ensembl-metadata-api
+    #   pytest
+greenlet==3.0.3
+    # via
+    #   ensembl-metadata-api
+    #   sqlalchemy
+grpcio==1.62.0
+    # via
+    #   ensembl-metadata-api
+    #   grpcio-reflection
+    #   grpcio-tools
+grpcio-reflection==1.62.0
+    # via ensembl-metadata-api
+grpcio-tools==1.62.0
+    # via ensembl-metadata-api
+idna==3.6
     # via
-    #   -r requirements.in
     #   ensembl-metadata-api
-exceptiongroup==1.0.4
-    # via pytest
-greenlet==2.0.2
-    # via sqlalchemy
-idna==3.4
-    # via requests
+    #   requests
 iniconfig==2.0.0
-    # via pytest
-mysqlclient==2.0.3
     # via
-    #   -r requirements.in
+    #   ensembl-metadata-api
+    #   pytest
+mysqlclient==2.1.1
+    # via
+    #   ensembl-metadata-api
     #   ensembl-py
-packaging==23.1
-    # via pytest
-pluggy==1.0.0
-    # via pytest
-pydantic==1.10.9
+packaging==23.2
+    # via
+    #   ensembl-metadata-api
+    #   pytest
+pluggy==1.4.0
+    # via
+    #   ensembl-metadata-api
+    #   pytest
+protobuf==4.25.3
+    # via
+    #   ensembl-metadata-api
+    #   grpcio-reflection
+    #   grpcio-tools
+pydantic==1.10.14
     # via -r requirements.in
-pytest==7.3.1
+pytest==8.0.2
     # via
+    #   ensembl-metadata-api
     #   ensembl-py
     #   pytest-dependency
 pytest-dependency==0.5.1
-    # via ensembl-py
+    # via
+    #   ensembl-metadata-api
+    #   ensembl-py
 python-dotenv==0.19.2
-    # via ensembl-py
-pyyaml==6.0
-    # via ensembl-py
+    # via
+    #   ensembl-metadata-api
+    #   ensembl-py
+pyyaml==6.0.1
+    # via
+    #   ensembl-metadata-api
+    #   ensembl-py
 requests==2.31.0
     # via
     #   -r requirements.in
+    #   ensembl-metadata-api
     #   ensembl-py
-sqlalchemy==1.4.48
+sqlalchemy==1.4.52
     # via
-    #   -r requirements.in
+    #   ensembl-metadata-api
     #   ensembl-py
     #   sqlalchemy-utils
 sqlalchemy-utils==0.38.3
-    # via ensembl-py
+    # via
+    #   ensembl-metadata-api
+    #   ensembl-py
 tomli==2.0.1
-    # via pytest
-typing-extensions==4.6.3
+    # via
+    #   ensembl-metadata-api
+    #   pytest
+types-pymysql==1.1.0.1
+    # via ensembl-metadata-api
+typing-extensions==4.10.0
     # via pydantic
-urllib3==2.0.3
-    # via requests
+urllib3==1.26.18
+    # via
+    #   ensembl-metadata-api
+    #   requests
+
+# The following packages are considered to be unsafe in a requirements file:
+# setuptools

From c617b54d5174a8d314306710553c2ba7193f6ce0 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Thu, 28 Mar 2024 15:26:01 +0000
Subject: [PATCH 045/128] New xref download pipeline using python and nextflow

---
 .../Pipeline/Xrefs/ScheduleSource.pm          |    8 +
 nextflow/config/xref.config                   |   44 +
 nextflow/workflows/xrefDownload.nf            |  233 +++
 scripts/xrefs/cleanup_and_split_source.pl     |  275 +++
 scripts/xrefs/cleanup_source.pl               |  235 +++
 src/python/ensembl/common/Params.py           |  233 +++
 src/python/ensembl/databases/core_db_model.py |  997 ++++++++++
 .../ensembl/databases/xref_source_db_model.py |   39 +
 .../ensembl/databases/xref_update_db_model.py |  266 +++
 src/python/ensembl/xrefs/Base.py              |  863 +++++++++
 src/python/ensembl/xrefs/Checksum.py          |   46 +
 src/python/ensembl/xrefs/DownloadSource.py    |   63 +
 src/python/ensembl/xrefs/EmailNotification.py |  139 ++
 src/python/ensembl/xrefs/ScheduleCleanup.py   |   57 +
 src/python/ensembl/xrefs/ScheduleDownload.py  |   73 +
 .../xrefs/config/xref_all_sources.json        |  248 +++
 .../ensembl/xrefs/config/xref_config.ini      | 1680 +++++++++++++++++
 src/python/scripts/run_module.py              |   34 +
 18 files changed, 5533 insertions(+)
 create mode 100644 nextflow/config/xref.config
 create mode 100644 nextflow/workflows/xrefDownload.nf
 create mode 100644 scripts/xrefs/cleanup_and_split_source.pl
 create mode 100644 scripts/xrefs/cleanup_source.pl
 create mode 100644 src/python/ensembl/common/Params.py
 create mode 100644 src/python/ensembl/databases/core_db_model.py
 create mode 100644 src/python/ensembl/databases/xref_source_db_model.py
 create mode 100644 src/python/ensembl/databases/xref_update_db_model.py
 create mode 100644 src/python/ensembl/xrefs/Base.py
 create mode 100644 src/python/ensembl/xrefs/Checksum.py
 create mode 100644 src/python/ensembl/xrefs/DownloadSource.py
 create mode 100644 src/python/ensembl/xrefs/EmailNotification.py
 create mode 100644 src/python/ensembl/xrefs/ScheduleCleanup.py
 create mode 100644 src/python/ensembl/xrefs/ScheduleDownload.py
 create mode 100644 src/python/ensembl/xrefs/config/xref_all_sources.json
 create mode 100644 src/python/ensembl/xrefs/config/xref_config.ini
 create mode 100644 src/python/scripts/run_module.py

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 48f20cbc3..e1b32ec39 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -128,6 +128,14 @@ sub run {
       # Create list of files
       my @list_files = `ls $file_name`;
       if ($preparse) { @list_files = $preparse; }
+
+      # For Uniprot and Refseq, files might have been split by species
+      if (!$preparse && ($name =~ /^Uniprot/ || $name =~ /^RefSeq_peptide/ || $name =~ /^RefSeq_dna/)) {
+        my $file_prefix = ($name =~ /SPTREMBL/ ? 'uniprot_trembl' : ($name =~ /SWISSPROT/ ? 'uniprot_sprot' : ($name =~ /_dna/ ? 'refseq_rna' : 'refseq_protein')));
+        @list_files = glob($file_name . "/**/" . $file_prefix . "-" . $species_id);
+        $_ = basename(dirname($_)) . "/" . basename($_) foreach (@list_files);
+      }
+
       foreach my $file (@list_files) {
         $file =~ s/\n//;
         $file = $file_name . "/" . $file;
diff --git a/nextflow/config/xref.config b/nextflow/config/xref.config
new file mode 100644
index 000000000..bc36b8617
--- /dev/null
+++ b/nextflow/config/xref.config
@@ -0,0 +1,44 @@
+includeConfig './base.config'
+
+params.pipeline_dir = "$PWD"
+params.user = "$USER"
+params.email = "${params.user}@ebi.ac.uk"
+params.email_server = "hh-smtp.ebi.ac.uk:25"
+
+params.work_dir = "$BASE_DIR"
+params.scripts_dir = "${params.work_dir}/ensembl-production/src/python/scripts/"
+params.perl_scripts_dir = "${params.work_dir}/ensembl-production/scripts/xrefs/"
+
+params.config_file = "${params.work_dir}/ensembl-production/src/python/ensembl/xrefs/config/xref_all_sources.json"
+params.sources_config_file = "${params.work_dir}/ensembl-production/src/python/ensembl/xrefs/config/xref_config.ini"
+params.source_db_url = ''
+params.skip_download = 0
+params.reuse_db = 0
+params.skip_preparse = 1
+params.split_files_by_species = 1
+params.tax_ids_file = ''
+
+params.base_path = ''
+params.clean_files = 1
+params.clean_dir = "${params.base_path}/clean_files"
+
+executor {
+  name = 'slurm'
+  queue = 'production'
+  queueSize = 100
+}
+
+process {
+  errorStrategy = { task.attempt <= process.maxRetries  ? 'retry' : 'finish' }
+  maxRetries = 3
+  time = '1d'
+
+  withLabel:small_process {
+    memory = 200.MB
+    executor.perTaskReserve = 200.MB
+  }
+
+  withLabel:mem4GB {
+    time = '3d'
+  }
+}
diff --git a/nextflow/workflows/xrefDownload.nf b/nextflow/workflows/xrefDownload.nf
new file mode 100644
index 000000000..7552fc08a
--- /dev/null
+++ b/nextflow/workflows/xrefDownload.nf
@@ -0,0 +1,233 @@
+#!/usr/bin/env nextflow
+
+// Parameter default values
+params.pipeline_name = 'Xref Download Pipeline'
+params.help = false
+
+println """\
+        XREF DOWNLOAD PIPELINE
+        ======================
+        source_db_url             : ${params.source_db_url}
+        base_path                 : ${params.base_path}
+        reuse_db                  : ${params.reuse_db}
+        skip_download             : ${params.skip_download}
+        skip_preparse             : ${params.skip_preparse}
+        clean_files               : ${params.clean_files}
+        split_files_by_species    : ${params.split_files_by_species}
+        config_file               : ${params.config_file}
+        sources_config_file       : ${params.sources_config_file}
+        clean_dir                 : ${params.clean_dir}
+        tax_ids_file              : ${params.tax_ids_file}
+        """
+        .stripIndent()
+
+def helpMessage() {
+  log.info"""
+  Usage:
+  nextflow run ensembl-production/xrefDownload.nf <ARGUMENTS>
+    --source_db_url             (mandatory)     Database URL to store information about xref sources.
+                                                Syntax: 'mysql://user:password@host:port/dbname'
+
+    --base_path                 (mandatory)     Path where log and source files will be stored,
+                                                a scratch space with sufficient storage is recommended.
+
+    --reuse_db                  (optional)      If set to 1, an existing source database (specified in --source_db_url) will be reused.
+                                                Default: 0
+
+    --skip_download             (optional)      If set to 1, source files will only be downloaded if they don't already exist in --base_path.
+                                                Default: 0
+
+    --skip_preparse             (optional)      If set to 1, the pre-parse step will be skipped (no central DB).
+                                                Default: 1
+
+    --clean_files               (optional)      If set to 1, the Cleanup analysis will be run for RefSeq and UniProt files.
+                                                Default: 1
+
+    --split_files_by_species    (optional)      If set to 1, UniProt and RefSeq file will be split according to taxonomy ID.
+                                                Default: 1
+
+    --config_file               (optional)      Path to the json file containing information about xref sources to download.
+                                                Default: $BASE_DIR/ensembl_nf/src/python/ensembl/xrefs/config/xref_all_sources.json
+
+    --sources_config_file       (optional)      Path to the ini file containing information about all xref sources and species/divisions.
+                                                Default: $BASE_DIR/ensembl_nf/src/python/ensembl/xrefs/config/xref_config.ini
+
+    --clean_dir                 (optional)      Path where to save the cleaned up files.
+                                                Default: [--base_path]/clean_files
+
+    --tax_ids_file              (optional)      Path to the file containing the taxonomy IDs of the species to extract data for.
+                                                Used to update the data for the provided species.
+  """.stripIndent()
+}
+
+workflow {
+  if (params.help || !params.source_db_url || !params.base_path) {
+    helpMessage()
+
+    if (!params.source_db_url) {
+      println """
+      Missing required param source_db_url
+      """.stripIndent()
+    }
+    if (!params.base_path) {
+      println """
+      Missing required param base_path
+      """.stripIndent()
+    }
+
+    exit 1
+  }
+
+  ScheduleDownload()
+  timestamp = ScheduleDownload.out[0]
+
+  DownloadSource(ScheduleDownload.out[1].splitText(), timestamp)
+
+  CleanupTmpFiles(DownloadSource.out.collect())
+  ScheduleCleanup(CleanupTmpFiles.out, timestamp)
+
+  Checksum(ScheduleCleanup.out[0], timestamp)
+  if (params.split_files_by_species) {
+    CleanupSplitSource(ScheduleCleanup.out[1].ifEmpty([]).splitText(), timestamp)
+    NotifyByEmail(Checksum.out.concat(CleanupSplitSource.out.collect()).collect(), timestamp)
+  } else {
+    CleanupSource(ScheduleCleanup.out[1].ifEmpty([]).splitText(), timestamp)
+    NotifyByEmail(Checksum.out.concat(CleanupSource.out.collect()).collect(), timestamp)
+  }
+}
+
+process ScheduleDownload {
+  label 'small_process'
+
+  output:
+  val timestamp
+  path 'dataflow_sources.json'
+
+  script:
+  timestamp = new java.util.Date().format("yyyyMMdd_HHmmss")
+
+  """
+  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.ScheduleDownload --config_file ${params.config_file} --source_db_url ${params.source_db_url} --reuse_db ${params.reuse_db} --skip_preparse ${params.skip_preparse} --base_path ${params.base_path} --log_timestamp $timestamp
+  """
+}
+
+process DownloadSource {
+  label 'dm'
+
+  input:
+  val x
+  val timestamp
+
+  output:
+  val 'DownloadSourceDone'
+
+  """
+  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.DownloadSource --dataflow '$x' --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --skip_download ${params.skip_download}
+  """
+}
+
+process CleanupTmpFiles {
+  label 'small_process'
+
+  input:
+  val x
+
+  output:
+  val 'TmpCleanupDone'
+
+  """
+  find ${params.base_path} -type f -name "*.tmp" -delete
+  """
+}
+
+process ScheduleCleanup {
+  label 'small_process'
+
+  input:
+  val x
+  val timestamp
+
+  output:
+  val 'ScheduleCleanupDone'
+  path 'dataflow_cleanup_sources.json'
+
+  """
+  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.ScheduleCleanup --base_path ${params.base_path} --source_db_url ${params.source_db_url} --clean_files ${params.clean_files} --clean_dir ${params.clean_dir} --split_files_by_species ${params.split_files_by_species} --log_timestamp $timestamp
+  """
+}
+
+process Checksum {
+  label 'default_process'
+
+  input:
+  val x
+  val timestamp
+
+  output:
+  val 'ChecksumDone'
+
+  """
+  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.Checksum --base_path ${params.base_path} --source_db_url ${params.source_db_url} --skip_download ${params.skip_download} --log_timestamp $timestamp
+  """
+}
+
+process CleanupSplitSource {
+  label 'mem4GB'
+
+  input:
+  each x
+  val timestamp
+
+  output:
+  val 'CleanupDone'
+
+  shell:
+  cmd_params = ""
+  src_name = (x =~ /"name":\s*"([A-Za-z0-9_.-\/]+)"/)[0][1]
+  if (x =~ /"version_file":/) {
+    version_file = (x =~ /"version_file":\s*"(.*?)"/)[0][1]
+    cmd_params = "${cmd_params} --version_file '${version_file}'"
+  }
+  if (params.tax_ids_file) {
+    cmd_params = "${cmd_params} --tax_ids_file ${params.tax_ids_file}"
+  }
+
+  """
+  perl ${params.perl_scripts_dir}/cleanup_and_split_source.pl --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --name $src_name --clean_dir ${params.clean_dir} --skip_download ${params.skip_download} --clean_files ${params.clean_files} $cmd_params
+  """
+}
+
+process CleanupSource {
+  label 'mem4GB'
+
+  input:
+  val x
+  val timestamp
+
+  output:
+  val 'CleanupDone'
+
+  shell:
+  cmd_params = ""
+  src_name = (x =~ /"name":\s*"([A-Za-z0-9_.-\/]+)"/)[0][1]
+  if (x =~ /"version_file":/) {
+    version_file = (x =~ /"version_file":\s*"(.*?)"/)[0][1]
+    cmd_params = "${cmd_params} --version_file '${version_file}'"
+  }
+
+  """
+  perl ${params.perl_scripts_dir}/cleanup_source.pl --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --name $src_name --clean_dir ${params.clean_dir} --skip_download ${params.skip_download} --clean_files ${params.clean_files} $cmd_params
+  """
+}
+
+process NotifyByEmail {
+  label 'small_process'
+
+  input:
+  val x
+  val timestamp
+
+  """
+  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.EmailNotification --pipeline_name '${params.pipeline_name}' --base_path ${params.base_path} --email ${params.email} --email_server ${params.email_server} --log_timestamp $timestamp
+  """
+}
diff --git a/scripts/xrefs/cleanup_and_split_source.pl b/scripts/xrefs/cleanup_and_split_source.pl
new file mode 100644
index 000000000..e538503c2
--- /dev/null
+++ b/scripts/xrefs/cleanup_and_split_source.pl
@@ -0,0 +1,275 @@
+#!/usr/bin/env perl
+#  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+#  Copyright [2016-2024] EMBL-European Bioinformatics Institute
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+use strict;
+use warnings;
+use Data::Dumper;
+use Getopt::Long;
+use Carp;
+use DBI;
+use File::Path qw/make_path/;
+use File::Spec::Functions;
+use HTTP::Tiny;
+use JSON;
+use File::Basename;
+use POSIX qw(strftime);
+
+use Nextflow::Utils;
+
+my ($base_path, $source_db_url, $source_name, $clean_dir, $clean_files, $version_file, $tax_ids_file, $log_timestamp);
+GetOptions(
+  'base_path=s'     => \$base_path,
+  'source_db_url=s' => \$source_db_url,
+  'name=s'          => \$source_name,
+  'clean_dir=s'     => \$clean_dir,
+  'clean_files=i'   => \$clean_files,
+  'version_file:s'  => \$version_file,
+  'tax_ids_file:s'  => \$tax_ids_file,
+  'log_timestamp:s' => \$log_timestamp
+);
+
+# Check that all mandatory parameters are passed
+if (!defined($base_path) || !defined($source_db_url) || !defined($source_name) || !defined($clean_dir) || !defined($clean_files)) {
+  croak "Usage: cleanup_source.pl --base_path <base_path> --source_db_url <source_db_url> --name <name> --clean_dir <clean_dir> --clean_files <clean_files> [--version_file <version_file>] [--tax_ids_file <tax_ids_file>] [--log_timestamp <log_timestamp>]";
+}
+
+my $log_file;
+if (defined($log_timestamp)) {
+  my $log_path = catdir($base_path, 'logs', $log_timestamp);
+  make_path($log_path);
+  $log_file = catfile($log_path, "tmp_logfile_CleanupSplitSource_".int(rand(500)));
+
+  add_to_log_file($log_file, "CleanupSplitSource starting for source $source_name");
+  add_to_log_file($log_file, "Param: tax_ids_file = $tax_ids_file");
+}
+
+# Do nothing if not a uniprot or refseq source
+if ($source_name !~ /^Uniprot/ && $source_name !~ /^RefSeq_/) {
+  add_to_log_file($log_file, "Provided source name is invalid. Can only clean up and split Uniprot or RefSeq files.");
+  exit;
+}
+
+# Remove last '/' character if it exists
+if ($base_path =~ /\/$/) {chop($base_path);}
+
+# Remove / char from source name to access directory
+my $clean_name = $source_name;
+$clean_name =~ s/\///g;
+
+my $output_path = $clean_dir."/".$clean_name;
+
+# Create needed directories
+make_path($output_path);
+
+my $sources_to_remove;
+my ($is_uniprot, $is_refseq_dna, $is_refseq_peptide) = (0, 0, 0);
+
+# Decide which files are being processed
+my $output_file_name = '';
+if ($source_name =~ /^Uniprot/) {
+  $is_uniprot = 1;
+  $output_file_name = ($source_name =~ /SPTREMBL/ ? 'uniprot_trembl' : 'uniprot_sprot');
+
+  # Set sources to skip in parsing step
+  my @source_names = (
+    'GO', 'UniGene', 'RGD', 'CCDS', 'IPI', 'UCSC', 'SGD', 'HGNC', 'MGI', 'VGNC', 'Orphanet',
+    'ArrayExpress', 'GenomeRNAi', 'EPD', 'Xenbase', 'Reactome', 'MIM_GENE', 'MIM_MORBID', 'MIM',
+    'Interpro'
+  );
+  $sources_to_remove = join("|", @source_names);
+} elsif ($source_name =~ /^RefSeq_dna/) {
+  $is_refseq_dna = 1;
+  $output_file_name = 'refseq_rna';
+} elsif ($source_name =~ /^RefSeq_peptide/) {
+  $is_refseq_peptide = 1;
+  $output_file_name = 'refseq_protein';
+} else {
+  croak "Unknown file type $source_name";
+}
+
+# Extract taxonomy IDs
+my %tax_ids;
+my $skipped_species = 0;
+if ($tax_ids_file) {
+  open my $fh, '<', $tax_ids_file;
+  chomp(my @lines = <$fh>);
+  close $fh;
+  my %tax_ids = map { $_ => 1 } @lines;
+
+  # Check if any taxonomy IDs already have files
+  foreach my $tax_id (keys(%tax_ids)) {
+    my @tax_files = glob($output_path . "/**/" . $output_file_name . "-" . $tax_id);
+    if (scalar(@tax_files) > 0) {
+      $tax_ids{$tax_id} = 0;
+      $skipped_species++;
+    }
+  }
+
+  # Do nothing if all taxonomy IDs already have files
+  if ($skipped_species == scalar(keys(%tax_ids))) {
+    add_to_log_file($log_file, "All provided tax IDs already have files. Doing nothing.");
+    exit;
+  }
+}
+
+# Get all files for source
+my $files_path = $base_path."/".$clean_name;
+my @files = glob($files_path."/*");
+my $out_fh;
+my $current_species_id;
+
+# Process each file
+foreach my $input_file_name (@files) {
+  local $/ = "//\n";
+
+  add_to_log_file($log_file, "Splitting up file $input_file_name");
+
+  $input_file_name = basename($input_file_name);
+  my $input_file = $files_path."/".$input_file_name;
+  my $in_fh;
+
+  # Skip the release file
+  if (defined($version_file) && $input_file eq $version_file) {next;}
+
+  # Open file normally or with zcat for zipped filed
+  if ($input_file_name =~ /\.(gz|Z)$/x) {
+    open($in_fh, "zcat $input_file |") or die "Couldn't call 'zcat' to open input file '$input_file' $!";
+    $output_file_name =~ s/\.[^.]+$//;
+  } else {
+    open($in_fh, '<', $input_file) or die "Couldn't open file input '$input_file' $!";
+  }
+
+  # Only start processing if could get filehandle
+  if (defined($in_fh)) {
+    my ($write_path, $write_file);
+
+    # Read full records
+    while (my $record = $in_fh->getline()) {
+      # Extract the species id from record
+      my $species_id;
+      if ($is_uniprot) {
+        ($species_id) = $record =~ /OX\s+[a-zA-Z_]+=([0-9 ,]+).*;/;
+        $species_id =~ s/\s//;
+      } else {
+        ($species_id) = $record =~ /db_xref=.taxon:(\d+)/;
+      }
+
+      # Only continue with wanted species
+      next if ($tax_ids_file && (!defined($tax_ids{$species_id}) || !$tax_ids{$species_id}));
+
+      # Clean up data
+      if ($clean_files) {
+        if ($is_uniprot) {
+          $record =~ s/\nR(N|P|X|A|T|R|L|C|G)\s{3}.*//g; # Remove references lines
+          $record =~ s/\nCC(\s{3}.*)CAUTION: The sequence shown here is derived from an Ensembl(.*)/\nCT$1CAUTION: The sequence shown here is derived from an Ensembl$2/g; # Set specific caution comment to temporary
+          $record =~ s/\nCC\s{3}.*//g; # Remove comments
+          $record =~ s/\nCT(\s{3}.*)CAUTION: The sequence shown here is derived from an Ensembl(.*)/\nCC$1CAUTION: The sequence shown here is derived from an Ensembl$2/g; # Set temp line back to comment
+          $record =~ s/\nFT\s{3}.*//g; # Remove feature coordinates
+          $record =~ s/\nDR\s{3}($sources_to_remove);.*//g; # Remove sources skipped at processing
+        } else {
+          my $skip_data = 0;
+          my @lines = split("\n", $record);
+          my @new_record;
+
+          for my $line (@lines) {
+            if ($is_refseq_dna) {
+              if ($line =~ /^REFERENCE/ || $line =~ /^COMMENT/ || $line =~ /^\s{5}exon/ || $line =~ /^\s{5}misc_feature/ || $line =~ /^\s{5}variation/) {
+                $skip_data = 1;
+              } elsif ($line =~ /^\s{5}source/ || $line =~ /^ORIGIN/) {
+                $skip_data = 0;
+              }
+            } elsif ($is_refseq_peptide) {
+              if ($line =~ /^REFERENCE/ || $line =~ /^COMMENT/ || $line =~ /^\s{5}Protein/) {
+                $skip_data = 1;
+              } elsif ($line =~ /^\s{5}source/ || $line =~ /^\s{5}CDS/ || $line =~ /^ORIGIN/) {
+                $skip_data = 0;
+              }
+            }
+
+            if (!$skip_data) {
+              push(@new_record, $line);
+            }
+
+            $record = join("\n", @new_record);
+          }
+        }
+      }
+
+      # Write the record in the appropriate file
+      if (!defined($current_species_id) || (defined($current_species_id) && $species_id ne $current_species_id)) {
+        close($out_fh) if (defined($current_species_id));
+
+        my @digits = split('', $species_id);
+        $write_path = catdir($output_path, $digits[0], (scalar(@digits)>1 ? $digits[1] : ""), (scalar(@digits)>2 ? $digits[2] : ""), (scalar(@digits)>3 ? $digits[3] : ""));
+        make_path($write_path);
+
+        $write_file = $write_path."/".$output_file_name."-".$species_id;
+        open($out_fh, '>>', $write_file) or die "Couldn't open output file '$write_file' $!";
+
+        $current_species_id = $species_id;
+      }
+
+      print $out_fh $record.($is_uniprot ? "" : "\n");
+    }
+
+    close($in_fh);
+    close($out_fh);
+  }
+}
+
+add_to_log_file($log_file, "Source $source_name cleaned up");
+add_to_log_file($log_file, "$source_name skipped species = $skipped_species");
+
+# Save the clean files directory in source db
+my ($user, $pass, $host, $port, $source_db) = parse_url($source_db_url);
+my $dbi = get_dbi($host, $port, $user, $pass, $source_db);
+my $update_version_sth = $dbi->prepare("UPDATE IGNORE version set clean_uri=? where source_id=(SELECT source_id FROM source WHERE name=?)");
+$update_version_sth->execute($output_path, $source_name);
+$update_version_sth->finish();
+
+sub get_dbi {
+  my ($host, $port, $user, $pass, $dbname) = @_;
+  my $dbconn;
+  if (defined $dbname) {
+    $dbconn = sprintf("dbi:mysql:host=%s;port=%s;database=%s", $host, $port, $dbname);
+  } else {
+    $dbconn = sprintf("dbi:mysql:host=%s;port=%s", $host, $port);
+  }
+  my $dbi = DBI->connect( $dbconn, $user, $pass, { 'RaiseError' => 1 } ) or croak( "Can't connect to database: " . $DBI::errstr );
+  return $dbi;
+}
+
+sub parse_url {
+  my ($url) = @_;
+  my $parsed_url = Nextflow::Utils::parse($url);
+  my $user = $parsed_url->{'user'};
+  my $pass = $parsed_url->{'pass'};
+  my $host = $parsed_url->{'host'};
+  my $port = $parsed_url->{'port'};
+  my $db   = $parsed_url->{'dbname'};
+  return ($user, $pass, $host, $port, $db);
+}
+
+sub add_to_log_file {
+  my ($log_file, $message) = @_;
+
+  if (defined($log_file)) {
+    my $current_timestamp = strftime "%d-%b-%Y %H:%M:%S", localtime;
+
+    open(my $fh, '>>', $log_file);
+    print $fh "$current_timestamp | INFO | $message\n";
+    close($fh);
+  }
+}
diff --git a/scripts/xrefs/cleanup_source.pl b/scripts/xrefs/cleanup_source.pl
new file mode 100644
index 000000000..5ce29a0f5
--- /dev/null
+++ b/scripts/xrefs/cleanup_source.pl
@@ -0,0 +1,235 @@
+#!/usr/bin/env perl
+#  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+#  Copyright [2016-2024] EMBL-European Bioinformatics Institute
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+use strict;
+use warnings;
+use Data::Dumper;
+use Getopt::Long;
+use Carp;
+use DBI;
+use File::Path qw/make_path/;
+use File::Spec::Functions;
+
+use Nextflow::Utils;
+
+my ($base_path, $source_db_url, $source_name, $clean_dir, $skip_download, $clean_files, $version_file, $log_timestamp);
+GetOptions(
+  'base_path=s'     => \$base_path,
+  'source_db_url=s' => \$source_db_url,
+  'name=s'          => \$source_name,
+  'clean_dir=s'     => \$clean_dir,
+  'skip_download=i' => \$skip_download,
+  'clean_files=i'   => \$clean_files,
+  'version_file:s'  => \$version_file,
+  'log_timestamp:s' => \$log_timestamp
+);
+
+# Check that all mandatory parameters are passed
+if (!defined($base_path) || !defined($source_db_url) || !defined($source_name) || !defined($clean_dir) || !defined($skip_download) || !defined($clean_files)) {
+  croak "Usage: cleanup_source.pl --base_path <base_path> --source_db_url <source_db_url> --name <name> --clean_dir <clean_dir> --skip_download <skip_download> --clean_files <clean_files> [--version_file <version_file>] [--log_timestamp <log_timestamp>]";
+}
+
+my $log_file;
+if (defined($log_timestamp)) {
+  my $log_path = catdir($base_path, 'logs', $log_timestamp);
+  make_path($log_path);
+  $log_file = catfile($log_path, "tmp_logfile_CleanupSource_".int(rand(500)));
+
+  add_to_log_file($log_file, "CleanupSource starting for source $source_name");
+}
+
+# Do nothing if not cleaning files, not a uniprot or refseq source, or no new download
+if ($clean_files && ($source_name =~ /^Uniprot/ || $source_name =~ /^RefSeq_/)) {
+  # Remove last '/' character if it exists
+  if ($base_path =~ /\/$/) {chop($base_path);}
+
+  # Remove / char from source name to access directory
+  my $clean_name = $source_name;
+  $clean_name =~ s/\///g;
+
+  my $output_path = $clean_dir."/".$clean_name;
+  my $update_clean_uri = 0;
+
+  # If not a new download, check if clean files exist
+  if ($skip_download) {
+    if (-d $output_path) {
+      $update_clean_uri = 1
+    }
+  } else {
+    # Create needed directories
+    make_path($output_path);
+
+    $update_clean_uri = 1;
+
+    my $sources_to_remove;
+    my ($is_uniprot, $is_refseq_dna, $is_refseq_peptide) = (0, 0, 0);
+    my $file_size = 0;
+
+    # Set sources to skip in parsing step (uniprot only)
+    if ($source_name =~ /^Uniprot/) {
+      $is_uniprot = 1;
+      my @source_names = (
+        'GO', 'UniGene', 'RGD', 'CCDS', 'IPI', 'UCSC', 'SGD', 'HGNC', 'MGI', 'VGNC', 'Orphanet',
+        'ArrayExpress', 'GenomeRNAi', 'EPD', 'Xenbase', 'Reactome', 'MIM_GENE', 'MIM_MORBID', 'MIM',
+        'Interpro'
+      );
+      $sources_to_remove = join("|", @source_names);
+      $file_size = 200000;
+    } elsif ($source_name =~ /^RefSeq_dna/) {
+      $is_refseq_dna = 1;
+    } elsif ($source_name =~ /^RefSeq_peptide/) {
+      $is_refseq_peptide = 1;
+    } else {
+      croak "Unknown file type $source_name";
+    }
+
+    # Get all files for source
+    my $files_path = $base_path."/".$clean_name;
+    my @files = `ls $files_path`;
+    foreach my $file_name (@files) {
+      $file_name =~ s/\n//;
+      my $file = $files_path."/".$file_name;
+
+      # Skip the release file
+      if (defined($version_file) && $file eq $version_file) {next;}
+
+      my ($in_fh, $out_fh);
+      my $output_file = $file_name;
+
+      # Open file normally or with zcat for zipped filed
+      if ($file_name =~ /\.(gz|Z)$/x) {
+        open($in_fh, "zcat $file |")
+          or die "Couldn't call 'zcat' to open input file '$file' $!";
+
+        $output_file =~ s/\.[^.]+$//;
+      } else {
+        open($in_fh, '<', $file)
+          or die "Couldn't open file input '$file' $!";
+      }
+
+      # Only start cleaning up if could get filehandle
+      my $count = 0;
+      my $file_count = 1;
+      if (defined($in_fh)) {
+        if ($is_uniprot) {
+          local $/ = "//\n";
+
+          my $write_file = $output_path."/".$output_file . "-$file_count";
+          open($out_fh, '>', $write_file) or die "Couldn't open output file '$write_file' $!";
+
+          # Read full records
+          while ($_ = $in_fh->getline()) {
+            # Remove unused data
+            $_ =~ s/\nR(N|P|X|A|T|R|L|C|G)\s{3}.*//g; # Remove references lines
+            $_ =~ s/\nCC(\s{3}.*)CAUTION: The sequence shown here is derived from an Ensembl(.*)/\nCT$1CAUTION: The sequence shown here is derived from an Ensembl$2/g; # Set specific caution comment to temporary
+            $_ =~ s/\nCC\s{3}.*//g; # Remove comments
+            $_ =~ s/\nCT(\s{3}.*)CAUTION: The sequence shown here is derived from an Ensembl(.*)/\nCC$1CAUTION: The sequence shown here is derived from an Ensembl$2/g; # Set temp line back to comment
+            $_ =~ s/\nFT\s{3}.*//g; # Remove feature coordinates
+            $_ =~ s/\nDR\s{3}($sources_to_remove);.*//g; # Remove sources skipped at processing
+
+            # Added lines that we do need into output
+            print $out_fh $_;
+
+            # Check how many lines have been processed and write to new file if size exceeded
+            $count++;
+            if ($count > $file_size) {
+              close($out_fh);
+              $file_count++;
+              $write_file = $output_path."/".$output_file . "-$file_count";
+              open($out_fh, '>', $write_file)
+                or die "Couldn't open output file '$write_file' $!";
+              $count = 0;
+            }
+          }
+
+          close($in_fh);
+          close($out_fh);
+        } else {
+          $output_file = $output_path."/".$output_file;
+          open($out_fh, '>', $output_file) or die "Couldn't open output file '$output_file' $!";
+
+          # Remove unuused data
+          my $skip_data = 0;
+          while (<$in_fh>) {
+            if ($is_refseq_dna) {
+              if ($_ =~ /^REFERENCE/ || $_ =~ /^COMMENT/ || $_ =~ /^\s{5}exon/ || $_ =~ /^\s{5}misc_feature/ || $_ =~ /^\s{5}variation/) {
+                $skip_data = 1;
+              } elsif ($_ =~ /^\s{5}source/ || $_ =~ /^ORIGIN/) {
+                $skip_data = 0;
+              }
+            } elsif ($is_refseq_peptide) {
+              if ($_ =~ /^REFERENCE/ || $_ =~ /^COMMENT/ || $_ =~ /^\s{5}Protein/) {
+                $skip_data = 1;
+              } elsif ($_ =~ /^\s{5}source/ || $_ =~ /^\s{5}CDS/ || $_ =~ /^ORIGIN/) {
+                $skip_data = 0;
+              }
+            }
+
+            if (!$skip_data) {print $out_fh $_;}
+          }
+
+          close($in_fh);
+          close($out_fh);
+        }
+      }
+    }
+
+    add_to_log_file($log_file, "Source $source_name cleaned up");
+  }
+
+  # Save the clean files directory in source db
+  if ($update_clean_uri) {
+    my ($user, $pass, $host, $port, $source_db) = parse_url($source_db_url);
+    my $dbi = get_dbi($host, $port, $user, $pass, $source_db);
+    my $update_version_sth = $dbi->prepare("UPDATE IGNORE version set clean_uri=? where source_id=(SELECT source_id FROM source WHERE name=?)");
+    $update_version_sth->execute($output_path, $source_name);
+    $update_version_sth->finish();
+  }
+}
+
+sub get_dbi {
+  my ($host, $port, $user, $pass, $dbname) = @_;
+  my $dbconn;
+  if (defined $dbname) {
+    $dbconn = sprintf("dbi:mysql:host=%s;port=%s;database=%s", $host, $port, $dbname);
+  } else {
+    $dbconn = sprintf("dbi:mysql:host=%s;port=%s", $host, $port);
+  }
+  my $dbi = DBI->connect( $dbconn, $user, $pass, { 'RaiseError' => 1 } ) or croak( "Can't connect to database: " . $DBI::errstr );
+  return $dbi;
+}
+
+sub parse_url {
+  my ($url) = @_;
+  my $parsed_url = Nextflow::Utils::parse($url);
+  my $user = $parsed_url->{'user'};
+  my $pass = $parsed_url->{'pass'};
+  my $host = $parsed_url->{'host'};
+  my $port = $parsed_url->{'port'};
+  my $db   = $parsed_url->{'dbname'};
+  return ($user, $pass, $host, $port, $db);
+}
+
+sub add_to_log_file {
+  my ($log_file, $message) = @_;
+
+  if (defined($log_file)) {
+    my $current_timestamp = strftime "%d-%b-%Y %H:%M:%S", localtime;
+
+    open(my $fh, '>>', $log_file);
+    print $fh "$current_timestamp | INFO | $message\n";
+    close($fh);
+  }
+}
diff --git a/src/python/ensembl/common/Params.py b/src/python/ensembl/common/Params.py
new file mode 100644
index 000000000..ef9371f99
--- /dev/null
+++ b/src/python/ensembl/common/Params.py
@@ -0,0 +1,233 @@
+#  See the NOTICE file distributed with this work for additional information
+#  regarding copyright ownership.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Params module to handle parameter manipulation between pipeline processes."""
+
+import sys
+import re
+import json
+import argparse
+
+sys.tracebacklimit = 0
+
+class Params:
+  def __init__(self, params: dict=None, parse_dataflow_json: bool=True) -> None:
+    """
+    Parameters
+    ----------
+    params: dict, optional
+        The parameters to start the object with. If defined, command-line parameters won't be parsed (default is None)
+    parse_dataflow_json: bool, optional
+        Specifies whether to parse an option called 'dataflow' in the provided options (default is True)
+    """
+    if params:
+      self._params = params
+    else:
+      self._params = {}
+      self.parse_argv_params(parse_dataflow_json)
+
+  def parse_argv_params(self, parse_dataflow_json: bool=True):
+    """Parses command-line arguments and extracts them into the Params object.
+    Command-line arguments need to be passed in the format "--name value".
+
+    Parameters
+    ----------
+    parse_dataflow_json: bool, optional
+        Specifies whether to parse an option called 'dataflow' in the provided options (default is True)
+    """
+    args = sys.argv[1:]
+
+    # Extract param names from command line
+    r = re.compile(r"^--")
+    param_names = list(filter(r.match, args))
+
+    parser = argparse.ArgumentParser()
+    for name in param_names:
+      parser.add_argument(name)
+
+    params = parser.parse_args()
+    for param_name in vars(params):
+      if param_name == 'dataflow' and parse_dataflow_json:
+        dataflow_params = json.loads(getattr(params, param_name))
+        for name,value in dataflow_params.items():
+          self.param(name, value)
+      else:
+        self.param(param_name, getattr(params, param_name))
+
+  def param(self, name: str, new_value=None, options: dict={}):
+    """ Gets or sets a parameter value.
+
+    Parameters
+    ----------
+    name: str
+        The name of the paramater
+    new_value: any, optional
+        The value to set the parameter to (default is None)
+    options: dict, optional
+        Extra options, including:
+        - default: The default value to use if parameter has no value (sets the parameter value to this)
+        - type: The type of the parameter value, used to check if value is valid
+
+    Returns
+    -------
+    The value of the parameter with provided name.
+
+    Raises
+    ------
+    AttributeError
+        If no parameter name was passed.
+    """
+    if not name:
+      raise AttributeError('You must supply a parameter name')
+
+    value = None
+
+    if new_value is not None:
+      self._params[name] = new_value
+      value = new_value
+    else:
+      value = self._params.get(name)
+      if value is None and options.get('default') is not None:
+        default = options['default']
+        self._params[name] = default
+        value = default
+
+    if options.get('type'):
+      return self.check_type(name, value, options['type'])
+
+    return value
+
+  def param_required(self, name: str, options: dict={}):
+    """ Gets a parameter value, raising an error if no value is found.
+    
+    Parameters
+    ----------
+    name: str
+        The name of th parameter
+    options: dict, optional
+        Extra options, including:
+        - default: The default value to use if parameter has no value (sets the parameter value to this)
+        - type: The type of the parameter value, used to check if value is valid
+
+    Returns
+    -------
+    The value of the parameter with provided name.
+
+    Raises
+    ------
+    AttributeError
+        If no value is found for the required paramater.
+    """
+    value = self.param(name, None, options)
+
+    if value is None:
+      raise AttributeError(f'Parameter \'{name}\' is required but has no value')
+
+    return value
+
+  def check_type(self, name: str, value, value_type: str):
+    """ Checks if the parameter value provided is valid.
+    For specific types, this function can change the parameter value.
+
+    Parameters
+    ----------
+    name: str
+        The name of the parameter
+    value: any
+        The value of the parameter
+    value_type: str
+        The type of the parameter value. Accepted types:
+        - hash, dict, or dictionary
+        - array or list
+        - int or integer
+        - bool or boolean
+        - str or string
+
+    Returns
+    -------
+    None if no value is found, or the new value of the parameter with provided name.
+
+    Raises
+    ------
+    AttributeError
+        If no parameter name is provided.
+        If parameter value is not valid.
+    """
+    if not name:
+      raise AttributeError('You must supply a parameter name')
+    if value is None:
+      return
+
+    value_type = value_type.lower()
+    error = 0
+    new_value = None
+
+    if value_type in ['hash', 'dict', 'dictionary'] and not isinstance(value, dict):
+      error = 1
+    elif value_type in ['array', 'list'] and not isinstance(value, list):
+      # Try to split by commas
+      if re.search(",", value):
+        new_value = value.split(",")
+      else:
+        new_value = [value]
+    elif value_type in ['integer', 'int'] and not isinstance(value, int):
+      # Try to make it an integer
+      try:
+        new_value = int(value)
+      except ValueError:
+        error = 1
+    elif value_type in ['bool', 'boolean'] and not isinstance(value, bool):
+      # Try to make it a boolean
+      if isinstance(value, int):
+        new_value = bool(value)
+      elif value in ['0', '1']:
+        new_value = bool(int(value))
+      else:
+        error = 1
+    elif value_type in ['str', 'string'] and not isinstance(value, str):
+      new_value = str(value)
+
+    if error:
+      raise AttributeError(f'Parameter \'{name}\' has an invalid value \'{value}\'. Must be of type {value_type}')
+
+    self.param(name, new_value)
+    return new_value
+
+  def write_output(self, suffix: str, params: dict):
+    """ Appends data to the dataflow json file (passed into next pipeline process).
+
+    Parameters
+    ----------
+    suffix: str
+        The file suffix to add to the output file name (dataflow_[suffix].json)
+    params: dict
+        The data to append into the file
+    """
+    # Remove null params
+    params = {k: v for k, v in params.items() if v is not None}
+
+    with open(f'dataflow_{suffix}.json', 'a') as fh:
+      json.dump(params, fh)
+      fh.write("\n")
+
+  def write_all_output(self, suffix: str):
+    """ Appends all of the parameters in the object into the dataflow json file.
+    This calls the write_output function.
+
+    Parameters
+    ----------
+    suffix: str
+        The file suffix to add to the output file name (dataflow_[suffix].json)
+    """
+    self.write_output(suffix, self._params)
diff --git a/src/python/ensembl/databases/core_db_model.py b/src/python/ensembl/databases/core_db_model.py
new file mode 100644
index 000000000..2ca2c3213
--- /dev/null
+++ b/src/python/ensembl/databases/core_db_model.py
@@ -0,0 +1,997 @@
+from sqlalchemy import (Column, Index, Enum, ForeignKey, DateTime, Float, DECIMAL, text)
+from sqlalchemy.dialects.mysql import (INTEGER, VARCHAR, TINYINT, SET, SMALLINT, TEXT, LONGTEXT, BIGINT, DOUBLE, MEDIUMTEXT, TINYTEXT)
+from sqlalchemy.ext.declarative import declarative_base
+
+Base = declarative_base()
+
+class Assembly(Base):
+  __tablename__ = "assembly"
+  __table_args__ = (
+    Index("asm_seq_region_idx", "asm_seq_region_id", "asm_start"),
+  )
+
+  asm_seq_region_id = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True)
+  cmp_seq_region_id = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True)
+  asm_start         = Column(INTEGER(10), primary_key=True)
+  asm_end           = Column(INTEGER(10), primary_key=True)
+  cmp_start         = Column(INTEGER(10), primary_key=True)
+  cmp_end           = Column(INTEGER(10), primary_key=True)
+  ori               = Column(TINYINT(4), primary_key=True)
+
+class AssemblyException(Base):
+  __tablename__ = "assembly_exception"
+  __table_args__ = (
+    Index("sr_idx", "seq_region_id", "seq_region_start"),
+    Index("ex_idx", "exc_seq_region_id", "exc_seq_region_start")
+  )
+
+  assembly_exception_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id         = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start      = Column(INTEGER(10), nullable=False)
+  seq_region_end        = Column(INTEGER(10), nullable=False)
+  exc_type              = Column(Enum('HAP', 'PAR', 'PATCH_FIX', 'PATCH_NOVEL'), nullable=False)
+  exc_seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  exc_seq_region_start  = Column(INTEGER(10), nullable=False)
+  exc_seq_region_end    = Column(INTEGER(10), nullable=False)
+  ori                   = Column(INTEGER(11), nullable=False)
+
+class CoordSystem(Base):
+  __tablename__ = "coord_system"
+  __table_args__ = (
+    Index("rank_idx", "rank", "species_id", unique=True),
+    Index("name_idx", "name", "version", "species_id", unique=True)
+  )
+
+  coord_system_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  species_id      = Column(INTEGER(10), nullable=False, server_default=text("1"), index=True)
+  name            = Column(VARCHAR(40), nullable=False)
+  version         = Column(VARCHAR(255))
+  rank            = Column(INTEGER(11), nullable=False)
+  attrib          = Column(SET('default_version', 'sequence_level'))
+
+class DataFile(Base):
+  __tablename__ = "data_file"
+  __table_args__ = (
+    Index("df_unq_idx", "coord_system_id", "analysis_id", "name", "file_type", unique=True),
+  )
+
+  data_file_id    = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  coord_system_id = Column(INTEGER(10), ForeignKey("coord_system.coord_system_id"), nullable=False)
+  analysis_id     = Column(SMALLINT(5), nullable=False, index=True)
+  name            = Column(VARCHAR(100), nullable=False, index=True)
+  version_lock    = Column(TINYINT(1), nullable=False, server_default=text("0"))
+  absolute        = Column(TINYINT(1), nullable=False, server_default=text("0"))
+  url             = Column(TEXT)
+  file_type       = Column(Enum('BAM', 'BAMCOV', 'BIGBED', 'BIGWIG', 'VCF'))
+
+class Dna(Base):
+  __tablename__ = "dna"
+
+  seq_region_id = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True)
+  sequence      = Column(LONGTEXT, nullable=False)
+
+class GenomeStatistics(Base):
+  __tablename__ = "genome_statistics"
+  __table_args__ = (
+    Index("stats_uniq", "statistic", "attrib_type_id", "species_id", unique=True),
+  )
+
+  genome_statistics_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  statistic            = Column(VARCHAR(128), nullable=False)
+  value                = Column(BIGINT(11), nullable=False, server_default=text("0"))
+  species_id           = Column(INTEGER(10), server_default=text("1"))
+  attrib_type_id       = Column(INTEGER(10), nullable=False)
+  timestamp            = Column(DateTime)
+
+class Karyotype(Base):
+  __tablename__ = "karyotype"
+  __table_args__ = (
+    Index("region_band_idx", "seq_region_id", "band"),
+  )
+
+  karyotype_id     = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id    = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start = Column(INTEGER(10), nullable=False)
+  seq_region_end   = Column(INTEGER(10), nullable=False)
+  band             = Column(VARCHAR(40))
+  stain            = Column(VARCHAR(40))
+
+class Meta(Base):
+  __tablename__ = "meta"
+  __table_args__ = (
+    Index("species_value_idx", "species_id", "meta_value"),
+    Index("species_key_value_idx", "species_id", "meta_key", "meta_value", unique=True)
+  )
+
+  meta_id    = Column(INTEGER(11), primary_key=True, autoincrement=True)
+  species_id = Column(INTEGER(10), server_default=text("1"))
+  meta_key   = Column(VARCHAR(40), nullable=False)
+  meta_value = Column(VARCHAR(255), nullable=False)
+
+class MetaCoord(Base):
+  __tablename__ = "meta_coord"
+
+  table_name      = Column(VARCHAR(40), primary_key=True)
+  coord_system_id = Column(INTEGER(10), ForeignKey("coord_system.coord_system_id"), primary_key=True)
+  max_length      = Column(INTEGER(11))
+
+class SeqRegion(Base):
+  __tablename__ = "seq_region"
+  __table_args__ = (
+    Index("name_cs_idx", "name", "coord_system_id", unique=True),
+  )
+
+  seq_region_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  name            = Column(VARCHAR(255), nullable=False)
+  coord_system_id = Column(INTEGER(10), ForeignKey("coord_system.coord_system_id"), nullable=False, index=True)
+  length          = Column(INTEGER(10), nullable=False)
+
+class SeqRegionSynonym(Base):
+  __tablename__ = "seq_region_synonym"
+  __table_args__ = (
+    Index("syn_idx", "synonym", "seq_region_id", unique=True),
+  )
+
+  seq_region_synonym_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id         = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, index=True)
+  synonym               = Column(VARCHAR(250), nullable=False)
+  external_db_id        = Column(INTEGER(10), ForeignKey("external_db.external_db_id"))
+
+class SeqRegionAttrib(Base):
+  __tablename__ = "seq_region_attrib"
+  __table_args__ = (
+    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
+    Index("val_only_idx", "value", mysql_length=40),
+    Index("region_attribx", "seq_region_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
+  )
+
+  seq_region_id  = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True, server_default=text("0"), index=True)
+  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
+      primary_key=True, server_default=text("0"))
+  value          = Column(TEXT, primary_key=True)
+
+class AltAllele(Base):
+  __tablename__ = "alt_allele"
+  __table_args__ = (
+    Index("gene_alt_group_idx", "gene_id", "alt_allele_group_id"),
+  )
+
+  alt_allele_id       = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  alt_allele_group_id = Column(INTEGER(10), ForeignKey("alt_allele_group.alt_allele_group_id"), nullable=False)
+  gene_id             = Column(INTEGER(10), ForeignKey("gene.gene_id"), nullable=False, index=True)
+
+class AltAlleleAttrib(Base):
+  __tablename__ = "alt_allele_attrib"
+
+  alt_allele_id = Column(INTEGER(10), primary_key=True)
+  attrib        = Column(Enum('IS_REPRESENTATIVE', 'IS_MOST_COMMON_ALLELE', 'IN_CORRECTED_ASSEMBLY', 'HAS_CODING_POTENTIAL', 'IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY', 'IN_SYNTENIC_REGION', 'HAS_SAME_UNDERLYING_DNA_SEQUENCE', 'IN_BROKEN_ASSEMBLY_REGION', 'IS_VALID_ALTERNATE', 'SAME_AS_REPRESENTATIVE', 'SAME_AS_ANOTHER_ALLELE', 'MANUALLY_ASSIGNED', 'AUTOMATICALLY_ASSIGNED', 'IS_PAR'), primary_key=True)
+
+class AltAlleleGroup(Base):
+  __tablename__ = "alt_allele_group"
+
+  alt_allele_group_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+
+class Analysis(Base):
+  __tablename__ = "analysis"
+
+  analysis_id     = Column(SMALLINT(5), primary_key=True, autoincrement=True)
+  created         = Column(DateTime)
+  logic_name      = Column(VARCHAR(128), nullable=False, index=True, unique=True)
+  db              = Column(VARCHAR(120))
+  db_version      = Column(VARCHAR(40))
+  db_file         = Column(VARCHAR(120))
+  program         = Column(VARCHAR(80))
+  program_version = Column(VARCHAR(40))
+  program_file    = Column(VARCHAR(80))
+  parameters      = Column(TEXT)
+  module          = Column(VARCHAR(80))
+  module_version  = Column(VARCHAR(40))
+  gff_source      = Column(VARCHAR(40))
+  gff_feature     = Column(VARCHAR(40))
+
+class AnalysisDescription(Base):
+  __tablename__ = "analysis_description"
+
+  analysis_id   = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), primary_key=True)
+  description   = Column(TEXT)
+  display_label = Column(VARCHAR(255), nullable=False)
+  displayable   = Column(TINYINT(1), nullable=False, server_default=text("1"))
+  web_data      = Column(TEXT)
+
+class AttribType(Base):
+  __tablename__ = "attrib_type"
+
+  attrib_type_id = Column(SMALLINT(5), primary_key=True, autoincrement=True)
+  code           = Column(VARCHAR(20), nullable=False, index=True, unique=True, server_default=text("''"))
+  name           = Column(VARCHAR(255), nullable=False, server_default=text("''"))
+  description    = Column(TEXT)
+
+class DnaAlignFeature(Base):
+  __tablename__ = "dna_align_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "analysis_id", "seq_region_start", "score"),
+    Index("seq_region_idx_2", "seq_region_id", "seq_region_start")
+  )
+
+  dna_align_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id        = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start     = Column(INTEGER(10), nullable=False)
+  seq_region_end       = Column(INTEGER(10), nullable=False)
+  seq_region_strand    = Column(TINYINT(1), nullable=False)
+  hit_start            = Column(INTEGER(11), nullable=False)
+  hit_end              = Column(INTEGER(11), nullable=False)
+  hit_strand           = Column(TINYINT(1), nullable=False)
+  hit_name             = Column(VARCHAR(40), nullable=False, index=True)
+  analysis_id          = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  score                = Column(DOUBLE)
+  evalue               = Column(DOUBLE)
+  perc_ident           = Column(Float)
+  cigar_line           = Column(TEXT)
+  external_db_id       = Column(INTEGER(10), ForeignKey("external_db.external_db_id"), index=True)
+  hcoverage            = Column(DOUBLE)
+  align_type           = Column(Enum('ensembl', 'cigar', 'vulgar', 'mdtag'), server_default=text("'ensembl'"))
+
+class DnaAlignFeatureAttrib(Base):
+  __tablename__ = "dna_align_feature_attrib"
+  __table_args__ = (
+    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
+    Index("val_only_idx", "value", mysql_length=40),
+    Index("dna_align_feature_attribx", "dna_align_feature_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
+  )
+
+  dna_align_feature_id = Column(INTEGER(10), ForeignKey("dna_align_feature.dna_align_feature_id"), primary_key=True, index=True)
+  attrib_type_id       = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"), primary_key=True)
+  value                = Column(TEXT, primary_key=True)
+
+class Exon(Base):
+  __tablename__ = "exon"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+    Index("stable_id_idx", "stable_id", "version")
+  )
+
+  exon_id           = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start  = Column(INTEGER(10), nullable=False)
+  seq_region_end    = Column(INTEGER(10), nullable=False)
+  seq_region_strand = Column(TINYINT(2), nullable=False)
+  phase             = Column(TINYINT(2), nullable=False)
+  end_phase         = Column(TINYINT(2), nullable=False)
+  is_current        = Column(TINYINT(1), nullable=False, server_default=text("1"))
+  is_constitutive   = Column(TINYINT(1), nullable=False, server_default=text("0"))
+  stable_id         = Column(VARCHAR(128))
+  version           = Column(SMALLINT(5))
+  created_date      = Column(DateTime)
+  modified_date     = Column(DateTime)
+
+class ExonTranscript(Base):
+  __tablename__ = "exon_transcript"
+
+  exon_id       = Column(INTEGER(10), ForeignKey("exon.exon_id"), primary_key=True, index=True)
+  transcript_id = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, index=True)
+  rank          = Column(INTEGER(10), primary_key=True)
+
+class Gene(Base):
+  __tablename__ = "gene"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+    Index("stable_id_idx", "stable_id", "version")
+  )
+
+  gene_id                 = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  biotype                 = Column(VARCHAR(40), nullable=False)
+  analysis_id             = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  seq_region_id           = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start        = Column(INTEGER(10), nullable=False)
+  seq_region_end          = Column(INTEGER(10), nullable=False)
+  seq_region_strand       = Column(TINYINT(2), nullable=False)
+  display_xref_id         = Column(INTEGER(10), ForeignKey("xref.xref_id"), index=True)
+  source                  = Column(VARCHAR(40), nullable=False)
+  description             = Column(TEXT)
+  is_current              = Column(TINYINT(1), nullable=False, server_default=text("1"))
+  canonical_transcript_id = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), nullable=False, index=True)
+  stable_id               = Column(VARCHAR(128))
+  version                 = Column(SMALLINT(5))
+  created_date            = Column(DateTime)
+  modified_date           = Column(DateTime)
+
+class GeneAttrib(Base):
+  __tablename__ = "gene_attrib"
+  __table_args__ = (
+    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
+    Index("val_only_idx", "value", mysql_length=40),
+    Index("gene_attribx", "gene_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
+  )
+
+  gene_id        = Column(INTEGER(10), ForeignKey("gene.gene_id"), primary_key=True, server_default=text("0"), index=True)
+  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
+      primary_key=True, server_default=text("0"))
+  value          = Column(TEXT, primary_key=True)
+
+class ProteinAlignFeature(Base):
+  __tablename__ = "protein_align_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "analysis_id", "seq_region_start", "score"),
+    Index("seq_region_idx_2", "seq_region_id", "seq_region_start")
+  )
+
+  protein_align_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start         = Column(INTEGER(10), nullable=False)
+  seq_region_end           = Column(INTEGER(10), nullable=False)
+  seq_region_strand        = Column(TINYINT(1), nullable=False, server_default=text("1"))
+  hit_start                = Column(INTEGER(10), nullable=False)
+  hit_end                  = Column(INTEGER(10), nullable=False)
+  hit_name                 = Column(VARCHAR(40), nullable=False, index=True)
+  analysis_id              = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  score                    = Column(DOUBLE)
+  evalue                   = Column(DOUBLE)
+  perc_ident               = Column(Float)
+  cigar_line               = Column(TEXT)
+  external_db_id           = Column(INTEGER(10), ForeignKey("external_db.external_db_id"), index=True)
+  hcoverage                = Column(DOUBLE)
+  align_type               = Column(Enum('ensembl', 'cigar', 'vulgar', 'mdtag'), server_default=text("'ensembl'"))
+
+class ProteinFeature(Base):
+  __tablename__ = "protein_feature"
+  __table_args__ = (
+    Index("aln_idx", "translation_id", "hit_name", "seq_start", "seq_end", "hit_start", "hit_end", "analysis_id", unique=True),
+  )
+
+  protein_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  translation_id     = Column(INTEGER(10), ForeignKey("translation.translation_id"), nullable=False, index=True)
+  seq_start          = Column(INTEGER(10), nullable=False)
+  seq_end            = Column(INTEGER(10), nullable=False)
+  hit_start          = Column(INTEGER(10), nullable=False)
+  hit_end            = Column(INTEGER(10), nullable=False)
+  hit_name           = Column(VARCHAR(40), nullable=False, index=True)
+  analysis_id        = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  score              = Column(DOUBLE)
+  evalue             = Column(DOUBLE)
+  perc_ident         = Column(Float)
+  external_data      = Column(TEXT)
+  hit_description    = Column(TEXT)
+  cigar_line         = Column(TEXT)
+  align_type         = Column(Enum('ensembl', 'cigar', 'cigarplus', 'vulgar', 'mdtag'))
+
+class SupportingFeature(Base):
+  __tablename__ = "supporting_feature"
+  __table_args__ = (
+    Index("all_idx", "exon_id", "feature_type", "feature_id", unique=True),
+    Index("feature_idx", "feature_type", "feature_id")
+  )
+
+  exon_id      = Column(INTEGER(10), ForeignKey("exon.exon_id"), primary_key=True, server_default=text("0"))
+  feature_type = Column(Enum('dna_align_feature', 'protein_align_feature'), primary_key=True)
+  feature_id   = Column(INTEGER(10), primary_key=True, server_default=text("0"))
+
+class Transcript(Base):
+  __tablename__ = "transcript"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+    Index("stable_id_idx", "stable_id", "version")
+  )
+
+  transcript_id            = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  gene_id                  = Column(INTEGER(10), ForeignKey("gene.gene_id"), index=True)
+  analysis_id              = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start         = Column(INTEGER(10), nullable=False)
+  seq_region_end           = Column(INTEGER(10), nullable=False)
+  seq_region_strand        = Column(TINYINT(2), nullable=False)
+  display_xref_id          = Column(INTEGER(10), ForeignKey("xref.xref_id"), index=True)
+  source                   = Column(VARCHAR(40), nullable=False, server_default=text("'ensembl'"))
+  biotype                  = Column(VARCHAR(40), nullable=False)
+  description              = Column(TEXT)
+  is_current               = Column(TINYINT(1), nullable=False, server_default=text("1"))
+  canonical_translation_id = Column(INTEGER(10), ForeignKey("translation.translation_id"), index=True, unique=True)
+  stable_id                = Column(VARCHAR(128))
+  version                  = Column(SMALLINT(5))
+  created_date             = Column(DateTime)
+  modified_date            = Column(DateTime)
+
+class TranscriptAttrib(Base):
+  __tablename__ = "transcript_attrib"
+  __table_args__ = (
+    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
+    Index("val_only_idx", "value", mysql_length=40),
+    Index("transcript_attribx", "transcript_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
+  )
+
+  transcript_id  = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, server_default=text("0"), index=True)
+  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
+      primary_key=True, server_default=text("0"))
+  value          = Column(TEXT, primary_key=True)
+
+class TranscriptSupportingFeature(Base):
+  __tablename__ = "transcript_supporting_feature"
+  __table_args__ = (
+    Index("feature_idx", "feature_type", "feature_id"),
+    Index("all_idx", "transcript_id", "feature_type", "feature_id", unique=True)
+  )
+
+  transcript_id = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, server_default=text("0"))
+  feature_type  = Column(Enum('dna_align_feature', 'protein_align_feature'), primary_key=True)
+  feature_id    = Column(INTEGER(10), primary_key=True, server_default=text("0"))
+
+class Translation(Base):
+  __tablename__ = "translation"
+  __table_args__ = (
+    Index("stable_id_idx", "stable_id", "version"),
+  )
+
+  translation_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  transcript_id  = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), nullable=False, index=True)
+  seq_start      = Column(INTEGER(10), nullable=False)
+  start_exon_id  = Column(INTEGER(10), ForeignKey("exon.exon_id"), nullable=False)
+  seq_end        = Column(INTEGER(10), nullable=False)
+  end_exon_id    = Column(INTEGER(10), ForeignKey("exon.exon_id"), nullable=False)
+  stable_id      = Column(VARCHAR(128))
+  version        = Column(SMALLINT(5))
+  created_date   = Column(DateTime)
+  modified_date  = Column(DateTime)
+
+class TranslationAttrib(Base):
+  __tablename__ = "translation_attrib"
+  __table_args__ = (
+    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
+    Index("val_only_idx", "value", mysql_length=40),
+    Index("translation_attribx", "translation_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
+  )
+
+  translation_id = Column(INTEGER(10), ForeignKey("translation.translation_id"), primary_key=True, server_default=text("0"), index=True)
+  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
+      primary_key=True, server_default=text("0"))
+  value          = Column(TEXT, primary_key=True)
+
+class DensityFeature(Base):
+  __tablename__ = "density_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "density_type_id", "seq_region_id", "seq_region_start"),
+  )
+
+  density_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  density_type_id    = Column(INTEGER(10), ForeignKey("density_type.density_type_id"), nullable=False)
+  seq_region_id      = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, index=True)
+  seq_region_start   = Column(INTEGER(10), nullable=False)
+  seq_region_end     = Column(INTEGER(10), nullable=False)
+  density_value      = Column(Float, nullable=False)
+
+class DensityType(Base):
+  __tablename__ = "density_type"
+  __table_args__ = (
+    Index("analysis_idx", "analysis_id", "block_size", "region_features", unique=True),
+  )
+
+  density_type_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  analysis_id     = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
+  block_size      = Column(INTEGER(11), nullable=False)
+  region_features = Column(INTEGER(11), nullable=False)
+  value_type      = Column(Enum('sum', 'ratio'), nullable=False)
+
+class Ditag(Base):
+  __tablename__ = "ditag"
+
+  ditag_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  name      = Column(VARCHAR(30), nullable=False)
+  tag_type  = Column("type", VARCHAR(30), nullable=False)
+  tag_count = Column(SMALLINT(6), nullable=False, server_default=text("1"))
+  sequence  = Column(TINYTEXT, nullable=False)
+
+class DitagFeature(Base):
+  __tablename__ = "ditag_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start", "seq_region_end"),
+  )
+
+  ditag_feature_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  ditag_id          = Column(INTEGER(10), ForeignKey("ditag.ditag_id"), nullable=False, index=True, server_default=text("0"))
+  ditag_pair_id     = Column(INTEGER(10), nullable=False, index=True, server_default=text("0"))
+  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, server_default=text("0"))
+  seq_region_start  = Column(INTEGER(10), nullable=False, server_default=text("0"))
+  seq_region_end    = Column(INTEGER(10), nullable=False, server_default=text("0"))
+  seq_region_strand = Column(TINYINT(1), nullable=False, server_default=text("0"))
+  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, server_default=text("0"))
+  hit_start         = Column(INTEGER(10), nullable=False, server_default=text("0"))
+  hit_end           = Column(INTEGER(10), nullable=False, server_default=text("0"))
+  hit_strand        = Column(TINYINT(1), nullable=False, server_default=text("0"))
+  cigar_line        = Column(TINYTEXT, nullable=False)
+  ditag_side        = Column(Enum('F', 'L', 'R'), nullable=False)
+
+class IntronSupportingEvidence(Base):
+  __tablename__ = "intron_supporting_evidence"
+  __table_args__ = (
+    Index("intron_all_idx", "analysis_id", "analysis_id", "seq_region_id", "seq_region_start", "seq_region_end", "seq_region_strand", "hit_name", unique=True),
+    Index("seq_region_idx", "seq_region_id", "seq_region_start")
+  )
+
+  intron_supporting_evidence_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  analysis_id                   = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
+  seq_region_id                 = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start              = Column(INTEGER(10), nullable=False)
+  seq_region_end                = Column(INTEGER(10), nullable=False)
+  seq_region_strand             = Column(TINYINT(2), nullable=False)
+  hit_name                      = Column(VARCHAR(100), nullable=False)
+  score                         = Column(DECIMAL(10, 3))
+  score_type                    = Column(Enum('NONE', 'DEPTH'), server_default=text("'NONE'"))
+  is_splice_canonical           = Column(TINYINT(1), nullable=False, server_default=text("0"))
+
+class Map(Base):
+  __tablename__ = "map"
+
+  map_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  map_name = Column(VARCHAR(30), nullable=False)
+
+class Marker(Base):
+  __tablename__ = "marker"
+  __table_args__ = (
+    Index("marker_idx", "marker_id", "priority"),
+  )
+
+  marker_id                 = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  display_marker_synonym_id = Column(INTEGER(10), ForeignKey("marker_synonym.marker_synonym_id"), index=True)
+  left_primer               = Column(VARCHAR(100), nullable=False)
+  right_primer              = Column(VARCHAR(100), nullable=False)
+  min_primer_dist           = Column(INTEGER(10), nullable=False)
+  max_primer_dist           = Column(INTEGER(10), nullable=False)
+  priority                  = Column(INTEGER(11))
+  marker_type               = Column("type", Enum('est', 'microsatellite'))
+
+class MarkerFeature(Base):
+  __tablename__ = "marker_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+  )
+
+  marker_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  marker_id         = Column(INTEGER(10), ForeignKey("marker.marker_id"), nullable=False)
+  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start  = Column(INTEGER(10), nullable=False)
+  seq_region_end    = Column(INTEGER(10), nullable=False)
+  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  map_weight        = Column(INTEGER(10))
+
+class MarkerMapLocation(Base):
+  __tablename__ = "marker_map_location"
+  __table_args__ = (
+    Index("map_idx", "map_id", "chromosome_name", "position"),
+  )
+
+  marker_id         = Column(INTEGER(10), ForeignKey("marker.marker_id"), primary_key=True)
+  map_id            = Column(INTEGER(10), ForeignKey("map.map_id"), primary_key=True)
+  chromosome_name   = Column(VARCHAR(15), nullable=False)
+  marker_synonym_id = Column(INTEGER(10), ForeignKey("marker_synonym.marker_synonym_id"), nullable=False)
+  position          = Column(VARCHAR(15), nullable=False)
+  lod_score         = Column(DOUBLE)
+
+class MarkerSynonym(Base):
+  __tablename__ = "marker_synonym"
+  __table_args__ = (
+    Index("marker_synonym_idx", "marker_synonym_id", "name"),
+  )
+
+  marker_synonym_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  marker_id         = Column(INTEGER(10), ForeignKey("marker.marker_id"), nullable=False, index=True)
+  source            = Column(VARCHAR(20))
+  name              = Column(VARCHAR(50))
+
+class MiscAttrib(Base):
+  __tablename__ = "misc_attrib"
+  __table_args__ = (
+    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
+    Index("val_only_idx", "value", mysql_length=40),
+    Index("misc_attribx", "misc_feature_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
+  )
+
+  misc_feature_id = Column(INTEGER(10), ForeignKey("misc_feature.misc_feature_id"), primary_key=True, index=True, server_default=text("0"))
+  attrib_type_id  = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"), primary_key=True, server_default=text("0"))
+  value           = Column(TEXT, primary_key=True, index=True)
+
+class MiscFeature(Base):
+  __tablename__ = "misc_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+  )
+
+  misc_feature_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, server_default=text("0"))
+  seq_region_start  = Column(INTEGER(10), nullable=False, server_default=text("0"))
+  seq_region_end    = Column(INTEGER(10), nullable=False, server_default=text("0"))
+  seq_region_strand = Column(TINYINT(4), nullable=False, server_default=text("0"))
+
+class MiscFeatureMiscSet(Base):
+  __tablename__ = "misc_feature_misc_set"
+  __table_args__ = (
+    Index("reverse_idx", "misc_set_id", "misc_feature_id"),
+  )
+
+  misc_feature_id = Column(INTEGER(10), ForeignKey("misc_feature.misc_feature_id"), primary_key=True, server_default=text("0"))
+  misc_set_id     = Column(SMALLINT(5), ForeignKey("misc_set.misc_set_id"), primary_key=True, server_default=text("0"))
+
+class MiscSet(Base):
+  __tablename__ = "misc_set"
+
+  misc_set_id = Column(SMALLINT(5), primary_key=True, autoincrement=True)
+  code        = Column(VARCHAR(25), nullable=False, index=True, unique=True, server_default=text("''"))
+  name        = Column(VARCHAR(255), nullable=False, server_default=text("''"))
+  description = Column(TEXT, nullable=False)
+  max_length  = Column(INTEGER(10), nullable=False)
+
+class PredictionExon(Base):
+  __tablename__ = "prediction_exon"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+  )
+
+  prediction_exon_id       = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  prediction_transcript_id = Column(INTEGER(10), ForeignKey("prediction_transcript.prediction_transcript_id"), nullable=False, index=True)
+  exon_rank                = Column(SMALLINT(5), nullable=False)
+  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start         = Column(INTEGER(10), nullable=False)
+  seq_region_end           = Column(INTEGER(10), nullable=False)
+  seq_region_strand        = Column(TINYINT(4), nullable=False)
+  start_phase              = Column(TINYINT(4), nullable=False)
+  score                    = Column(DOUBLE)
+  p_value                  = Column(DOUBLE)
+
+class PredictionTranscript(Base):
+  __tablename__ = "prediction_transcript"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+  )
+
+  prediction_transcript_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start         = Column(INTEGER(10), nullable=False)
+  seq_region_end           = Column(INTEGER(10), nullable=False)
+  seq_region_strand        = Column(TINYINT(4), nullable=False)
+  analysis_id              = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  display_label            = Column(VARCHAR(255))
+
+class RepeatConsensus(Base):
+  __tablename__ = "repeat_consensus"
+  __table_args__ = (
+    Index("consensus", "repeat_consensus", mysql_length=10),
+  )
+
+  repeat_consensus_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  repeat_name         = Column(VARCHAR(255), nullable=False, index=True)
+  repeat_class        = Column(VARCHAR(100), nullable=False, index=True)
+  repeat_type         = Column(VARCHAR(40), nullable=False, index=True)
+  repeat_consensus    = Column(TEXT)
+
+class RepeatFeature(Base):
+  __tablename__ = "repeat_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+  )
+
+  repeat_feature_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id       = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start    = Column(INTEGER(10), nullable=False)
+  seq_region_end      = Column(INTEGER(10), nullable=False)
+  seq_region_strand   = Column(TINYINT(1), nullable=False, server_default=text("1"))
+  repeat_start        = Column(INTEGER(10), nullable=False)
+  repeat_end          = Column(INTEGER(10), nullable=False)
+  repeat_consensus_id = Column(INTEGER(10), ForeignKey("repeat_consensus.repeat_consensus_id"), nullable=False, index=True)
+  analysis_id         = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  score               = Column(DOUBLE)
+
+class SimpleFeature(Base):
+  __tablename__ = "simple_feature"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+  )
+
+  simple_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start  = Column(INTEGER(10), nullable=False)
+  seq_region_end    = Column(INTEGER(10), nullable=False)
+  seq_region_strand = Column(TINYINT(1), nullable=False)
+  display_label     = Column(VARCHAR(255), nullable=False, index=True)
+  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
+  score             = Column(DOUBLE)
+
+class TranscriptIntronSupportingEvidence(Base):
+  __tablename__ = "transcript_intron_supporting_evidence"
+
+  transcript_id                 = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, index=True)
+  intron_supporting_evidence_id = Column(INTEGER(10), primary_key=True)
+  previous_exon_id              = Column(INTEGER(10), nullable=False)
+  next_exon_id                  = Column(INTEGER(10), nullable=False)
+
+# class GeneArchive(Base):
+#   __tablename__ = "gene_archive"
+
+#   gene_stable_id        = Column(VARCHAR(128), nullable=False)
+#   gene_version          = Column(SMALLINT(6), nullable=False, server_default=text("1"))
+#   transcript_stable_id  = Column(VARCHAR(128), nullable=False)
+#   transcript_version    = Column(SMALLINT(6), nullable=False, server_default=text("1"))
+#   translation_stable_id = Column(VARCHAR(128))
+#   translation_version   = Column(SMALLINT(6), nullable=False, server_default=text("1"))
+#   peptide_archive_id    = Column(INTEGER(10), index=True)
+#   mapping_session_id    = Column(INTEGER(10), ForeignKey("mapping_session.mapping_session_id"), nullable=False)
+
+#   Index("gene_idx", "gene_stable_id", "gene_version")
+#   Index("transcript_idx", "transcript_stable_id", "transcript_version")
+#   Index("translation_idx", "translation_stable_id", "translation_version")
+
+class MappingSession(Base):
+  __tablename__ = "mapping_session"
+
+  mapping_session_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  old_db_name        = Column(VARCHAR(80), nullable=False, server_default=text("''"))
+  new_db_name        = Column(VARCHAR(80), nullable=False, server_default=text("''"))
+  old_release        = Column(VARCHAR(5), nullable=False, server_default=text("''"))
+  new_release        = Column(VARCHAR(5), nullable=False, server_default=text("''"))
+  old_assembly       = Column(VARCHAR(80), nullable=False, server_default=text("''"))
+  new_assembly       = Column(VARCHAR(80), nullable=False, server_default=text("''"))
+  created            = Column(DateTime, nullable=False)
+
+class PeptideArchive(Base):
+  __tablename__ = "peptide_archive"
+
+  peptide_archive_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  md5_checksum       = Column(VARCHAR(32), index=True)
+  peptide_seq        = Column(MEDIUMTEXT, nullable=False)
+
+class MappingSet(Base):
+  __tablename__ = "mapping_set"
+  __table_args__ = (
+    Index("mapping_idx", "internal_schema_build", "external_schema_build", unique=True),
+  )
+
+  mapping_set_id        = Column(INTEGER(10), primary_key=True)
+  internal_schema_build = Column(VARCHAR(20), nullable=False)
+  external_schema_build = Column(VARCHAR(20), nullable=False)
+
+class StableIdEvent(Base):
+  __tablename__ = "stable_id_event"
+
+  old_stable_id      = Column(VARCHAR(128), primary_key=True, index=True)
+  old_version        = Column(SMALLINT(6))
+  new_stable_id      = Column(VARCHAR(128), primary_key=True, index=True)
+  new_version        = Column(SMALLINT(6))
+  mapping_session_id = Column(INTEGER(10), ForeignKey("mapping_session.mapping_session_id"), primary_key=True, server_default=text("0"))
+  id_type            = Column("type", Enum('gene', 'transcript', 'translation', 'rnaproduct'), primary_key=True)
+  score              = Column(Float, nullable=False, server_default=text("0"))
+
+class SeqRegionMapping(Base):
+  __tablename__ = "seq_region_mapping"
+
+  external_seq_region_id = Column(INTEGER(10), primary_key=True)
+  internal_seq_region_id = Column(INTEGER(10), primary_key=True)
+  mapping_set_id         = Column(INTEGER(10), primary_key=True, index=True)
+
+class AssociatedGroup(Base):
+  __tablename__ = "associated_group"
+
+  associated_group_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  description         = Column(VARCHAR(128))
+
+class AssociatedXref(Base):
+  __tablename__ = "associated_xref"
+  __table_args__ = (
+    Index("object_associated_source_type_idx", "object_xref_id", "xref_id", "source_xref_id", "condition_type", "associated_group_id", unique=True),
+  )
+
+  associated_xref_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  object_xref_id      = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), nullable=False, index=True, server_default=text("0"))
+  xref_id             = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False, index=True, server_default=text("0"))
+  source_xref_id      = Column(INTEGER(10), index=True)
+  condition_type      = Column(VARCHAR(128))
+  associated_group_id = Column(INTEGER(10), ForeignKey("associated_group.associated_group_id"), index=True)
+  rank                = Column(INTEGER(10), server_default=text("0"))
+
+class DependentXref(Base):
+  __tablename__ = "dependent_xref"
+
+  object_xref_id    = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), primary_key=True)
+  master_xref_id    = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False, index=True)
+  dependent_xref_id = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False, index=True)
+
+class ExternalDb(Base):
+  __tablename__ = "external_db"
+  __table_args__ = (
+    Index("db_name_db_release_idx", "db_name", "db_release", unique=True),
+  )
+
+  external_db_id     = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  db_name            = Column(VARCHAR(100), nullable=False)
+  db_release         = Column(VARCHAR(255))
+  status             = Column(Enum('KNOWNXREF', 'KNOWN', 'XREF', 'PRED', 'ORTH', 'PSEUDO'), nullable=False)
+  priority           = Column(INTEGER(11), nullable=False)
+  db_display_name    = Column(VARCHAR(255))
+  db_type            = Column("type", Enum('ARRAY', 'ALT_TRANS', 'ALT_GENE', 'MISC', 'LIT', 'PRIMARY_DB_SYNONYM', 'ENSEMBL'), nullable=False)
+  secondary_db_name  = Column(VARCHAR(255))
+  secondary_db_table = Column(VARCHAR(255))
+  description        = Column(TEXT)
+
+class Biotype(Base):
+  __tablename__ = "biotype"
+  __table_args__ = (
+    Index("name_type_idx", "name", "object_type", unique=True),
+  )
+
+  biotype_id     = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  name           = Column(VARCHAR(64), nullable=False)
+  object_type    = Column(Enum('gene', 'transcript'), nullable=False, server_default=text("'gene'"))
+  db_type        = Column(SET('cdna', 'core', 'coreexpressionatlas', 'coreexpressionest', 'coreexpressiongnf', 'funcgen', 'otherfeatures', 'rnaseq', 'variation', 'vega', 'presite', 'sangervega'), nullable=False, server_default=text("'core'"))
+  attrib_type_id = Column(INTEGER(11))
+  description    = Column(TEXT)
+  biotype_group  = Column(Enum('coding', 'pseudogene', 'snoncoding', 'lnoncoding', 'mnoncoding', 'LRG', 'undefined', 'no_group'))
+  so_acc         = Column(VARCHAR(64))
+  so_term        = Column(VARCHAR(1023))
+
+class ExternalSynonym(Base):
+  __tablename__ = "external_synonym"
+
+  xref_id = Column(INTEGER(10), ForeignKey("xref.xref_id"), primary_key=True)
+  synonym = Column(VARCHAR(100), primary_key=True, index=True)
+
+class IdentityXref(Base):
+  __tablename__ = "identity_xref"
+
+  object_xref_id   = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), primary_key=True)
+  xref_identity    = Column(INTEGER(5))
+  ensembl_identity = Column(INTEGER(5))
+  xref_start       = Column(INTEGER(11))
+  xref_end         = Column(INTEGER(11))
+  ensembl_start    = Column(INTEGER(11))
+  ensembl_end      = Column(INTEGER(11))
+  cigar_line       = Column(TEXT)
+  score            = Column(DOUBLE)
+  evalue           = Column(DOUBLE)
+
+class Interpro(Base):
+  __tablename__ = "interpro"
+
+  interpro_ac = Column(VARCHAR(40), primary_key=True)
+  interpro_id = Column("id", VARCHAR(40), primary_key=True, index=True)
+
+class ObjectXref(Base):
+  __tablename__ = "object_xref"
+  __table_args__ = (
+    Index("ensembl_idx", "ensembl_object_type", "ensembl_id"),
+    Index("xref_idx", "xref_id", "ensembl_object_type", "ensembl_id", "analysis_id", unique=True)
+  )
+
+  object_xref_id      = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  ensembl_id          = Column(INTEGER(10), nullable=False)
+  ensembl_object_type = Column(Enum('RawContig', 'Transcript', 'Gene', 'Translation', 'Operon', 'OperonTranscript', 'Marker', 'RNAProduct'), nullable=False)
+  xref_id             = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False)
+  linkage_annotation  = Column(VARCHAR(255))
+  analysis_id         = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), index=True)
+
+class OntologyXref(Base):
+  __tablename__ = "ontology_xref"
+
+  object_xref_id = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), primary_key=True, index=True, server_default=text("0"))
+  source_xref_id = Column(INTEGER(10), ForeignKey("xref.xref_id"), primary_key=True, index=True)
+  linkage_type   = Column(VARCHAR(3), primary_key=True)
+
+class UnmappedObject(Base):
+  __tablename__ = "unmapped_object"
+  __table_args__ = (
+    Index("unique_unmapped_obj_idx", "ensembl_id", "ensembl_object_type", "identifier", "unmapped_reason_id", "parent", "external_db_id", unique=True),
+    Index("id_idx", "identifier", mysql_length=50),
+    Index("anal_exdb_idx", "analysis_id", "external_db_id"),
+    Index("ext_db_identifier_idx", "external_db_id", "identifier")
+  )
+
+  unmapped_object_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  unmapped_object_type = Column("type", Enum('xref', 'cDNA', 'Marker'), nullable=False)
+  analysis_id          = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
+  external_db_id       = Column(INTEGER(10), ForeignKey("external_db.external_db_id"))
+  identifier           = Column(VARCHAR(255), nullable=False)
+  unmapped_reason_id   = Column(INTEGER(10), ForeignKey("unmapped_reason.unmapped_reason_id"), nullable=False)
+  query_score          = Column(DOUBLE)
+  target_score         = Column(DOUBLE)
+  ensembl_id           = Column(INTEGER(10), server_default=text("0"))
+  ensembl_object_type  = Column(Enum('RawContig', 'Transcript', 'Gene', 'Translation'), server_default=text("'RawContig'"))
+  parent               = Column(VARCHAR(255))
+
+class UnmappedReason(Base):
+  __tablename__ = "unmapped_reason"
+
+  unmapped_reason_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  summary_description = Column(VARCHAR(255))
+  full_description    = Column(VARCHAR(255))
+
+class Xref(Base):
+  __tablename__ = "xref"
+  __table_args__ = (
+    Index("id_index", "dbprimary_acc", "external_db_id", "info_type", "info_text", "version", unique=True),
+  )
+
+  xref_id        = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  external_db_id = Column(INTEGER(10), ForeignKey("external_db.external_db_id"), nullable=False)
+  dbprimary_acc  = Column(VARCHAR(512), nullable=False)
+  display_label  = Column(VARCHAR(512), nullable=False, index=True)
+  version        = Column(VARCHAR(10))
+  description    = Column(TEXT)
+  info_type      = Column(Enum('NONE', 'PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM'), nullable=False, index=True, server_default=text("'NONE'"))
+  info_text      = Column(VARCHAR(255), nullable=False, server_default=text("''"))
+
+class Operon(Base):
+  __tablename__ = "operon"
+  __table_args__ = (
+    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
+    Index("stable_id_idx", "stable_id", "version")
+  )
+
+  operon_id         = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start  = Column(INTEGER(10), nullable=False)
+  seq_region_end    = Column(INTEGER(10), nullable=False)
+  seq_region_strand = Column(TINYINT(2), nullable=False)
+  display_label     = Column(VARCHAR(255), index=True)
+  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
+  stable_id         = Column(VARCHAR(128))
+  version           = Column(SMALLINT(5))
+  created_date      = Column(DateTime)
+  modified_date     = Column(DateTime)
+
+class OperonTranscript(Base):
+  __tablename__ = "operon_transcript"
+  __table_args__ = (
+    Index("stable_id_idx", "stable_id", "version"),
+    Index("seq_region_idx", "seq_region_id", "seq_region_start")
+  )
+
+  operon_transcript_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  seq_region_id        = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
+  seq_region_start     = Column(INTEGER(10), nullable=False)
+  seq_region_end       = Column(INTEGER(10), nullable=False)
+  seq_region_strand    = Column(TINYINT(2), nullable=False)
+  operon_id            = Column(INTEGER(10), ForeignKey("operon.operon_id"), nullable=False, index=True)
+  display_label        = Column(VARCHAR(255))
+  analysis_id          = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
+  stable_id            = Column(VARCHAR(128))
+  version              = Column(SMALLINT(5))
+  created_date         = Column(DateTime)
+  modified_date        = Column(DateTime)
+
+class OperonTranscriptGene(Base):
+  __tablename__ = "operon_transcript_gene"
+
+  operon_transcript_id = Column(INTEGER(10), ForeignKey("operon_transcript.operon_transcript_id"), primary_key=True)
+  gene_id              = Column(INTEGER(10), ForeignKey("gene.gene_id"), primary_key=True)
+
+class Rnaproduct(Base):
+  __tablename__ = "rnaproduct"
+  __table_args__ = (
+    Index("stable_id_idx", "stable_id", "version"),
+  )
+
+  rnaproduct_id      = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  rnaproduct_type_id = Column(SMALLINT(5), ForeignKey("rnaproduct_type.rnaproduct_type_id"), nullable=False)
+  transcript_id      = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), nullable=False, index=True)
+  seq_start          = Column(INTEGER(10), nullable=False)
+  start_exon_id      = Column(INTEGER(10), ForeignKey("exon.exon_id"))
+  seq_end            = Column(INTEGER(10), nullable=False)
+  end_exon_id        = Column(INTEGER(10), ForeignKey("exon.exon_id"))
+  stable_id          = Column(VARCHAR(128))
+  version            = Column(SMALLINT(5))
+  created_date       = Column(DateTime)
+  modified_date      = Column(DateTime)
+
+class RnaproductAttrib(Base):
+  __tablename__ = "rnaproduct_attrib"
+  __table_args__ = (
+    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
+    Index("val_only_idx", "value", mysql_length=40),
+    Index("rnaproduct_attribx", "rnaproduct_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
+  )
+
+  rnaproduct_id  = Column(INTEGER(10), ForeignKey("rnaproduct.rnaproduct_id"), primary_key=True, index=True)
+  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"), primary_key=True)
+  value          = Column(TEXT, primary_key=True)
+
+class RnaproductType(Base):
+  __tablename__ = "rnaproduct_type"
+
+  rnaproduct_type_id = Column(SMALLINT(5), primary_key=True, autoincrement=True)
+  code               = Column(VARCHAR(20), nullable=False, index=True, unique=True, server_default=text("''"))
+  name               = Column(VARCHAR(255), nullable=False, server_default=text("''"))
+  description        = Column(TEXT)
diff --git a/src/python/ensembl/databases/xref_source_db_model.py b/src/python/ensembl/databases/xref_source_db_model.py
new file mode 100644
index 000000000..90f874e9a
--- /dev/null
+++ b/src/python/ensembl/databases/xref_source_db_model.py
@@ -0,0 +1,39 @@
+from sqlalchemy import (Column, Index, ForeignKey, text)
+from sqlalchemy.dialects.mysql import (INTEGER, VARCHAR, BOOLEAN)
+from sqlalchemy.ext.declarative import declarative_base
+
+Base = declarative_base()
+
+class ChecksumXref(Base):
+  __tablename__ = "checksum_xref"
+  __table_args__ = (
+    Index("checksum_idx", "checksum", mysql_length=10),
+  )
+
+  checksum_xref_id = Column(INTEGER, primary_key=True, autoincrement=True)
+  source_id        = Column(INTEGER, nullable=False)
+  accession        = Column(VARCHAR(14), nullable=False)
+  checksum         = Column(VARCHAR(32), nullable=False)
+
+class Source(Base):
+  __tablename__ = "source"
+
+  source_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  name      = Column(VARCHAR(128), index=True, unique=True)
+  active    = Column(BOOLEAN, nullable=False, server_default=text("1"))
+  parser    = Column(VARCHAR(128))
+
+class Version(Base):
+  __tablename__ = "version"
+  __table_args__ = (
+    Index("version_idx", "source_id", "revision")
+  )
+
+  version_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  source_id  = Column(INTEGER(10), ForeignKey("source.source_id"))
+  revision   = Column(VARCHAR(255))
+  count_seen = Column(INTEGER(10), nullable=False)
+  uri        = Column(VARCHAR(255))
+  index_uri  = Column(VARCHAR(255))
+  clean_uri  = Column(VARCHAR(255))
+  preparse   = Column(BOOLEAN, nullable=False, server_default=text("0"))
diff --git a/src/python/ensembl/databases/xref_update_db_model.py b/src/python/ensembl/databases/xref_update_db_model.py
new file mode 100644
index 000000000..f68249230
--- /dev/null
+++ b/src/python/ensembl/databases/xref_update_db_model.py
@@ -0,0 +1,266 @@
+from sqlalchemy import (Column, Index, Enum, DateTime, text)
+from sqlalchemy.dialects.mysql import (INTEGER, VARCHAR, BOOLEAN, TEXT, MEDIUMTEXT, TINYINT, CHAR, SMALLINT, DOUBLE)
+from sqlalchemy.ext.declarative import declarative_base
+
+Base = declarative_base()
+
+class Xref(Base):
+  __tablename__ = "xref"
+  __table_args__ = (
+    Index("acession_idx", "accession", "source_id", "species_id", "label", unique=True, mysql_length={'accession': 100, 'label': 100}),
+    Index("species_source_idx", "species_id", "source_id")
+  )
+
+  xref_id     = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  accession   = Column(VARCHAR(255), nullable=False)
+  version     = Column(INTEGER(10, unsigned=True))
+  label       = Column(VARCHAR(255))
+  description = Column(TEXT)
+  source_id   = Column(INTEGER(10, unsigned=True), nullable=False)
+  species_id  = Column(INTEGER(10, unsigned=True), nullable=False, primary_key=True)
+  info_type   = Column(Enum('NONE', 'PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM'), nullable=False, server_default=text("'NONE'"))
+  info_text   = Column(VARCHAR(255), nullable=False, server_default=text("''"))
+  dumped      = Column(Enum('MAPPED', 'NO_DUMP_ANOTHER_PRIORITY', 'UNMAPPED_NO_MAPPING', 'UNMAPPED_NO_MASTER', 'UNMAPPED_MASTER_FAILED', 'UNMAPPED_NO_STABLE_ID', 'UNMAPPED_INTERPRO'))
+
+class PrimaryXref(Base):
+  __tablename__ = "primary_xref"
+
+  xref_id       = Column(INTEGER(10, unsigned=True), primary_key=True)
+  sequence      = Column(MEDIUMTEXT)
+  sequence_type = Column(Enum('dna', 'peptide'))
+  status        = Column(Enum('experimental', 'predicted'))
+
+class DependentXref(Base):
+  __tablename__ = "dependent_xref"
+
+  object_xref_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
+  master_xref_id     = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
+  dependent_xref_id  = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
+  linkage_annotation = Column(VARCHAR(255))
+  linkage_source_id  = Column(INTEGER(10, unsigned=True), nullable=False, primary_key=True)
+
+class Synonym(Base):
+  __tablename__ = "synonym"
+
+  xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
+  synonym = Column(VARCHAR(255), index=True, primary_key=True)
+
+class Source(Base):
+  __tablename__ = "source"
+
+  source_id            = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  name                 = Column(VARCHAR(255), nullable=False, index=True)
+  status               = Column(Enum('KNOWN', 'XREF', 'PRED', 'ORTH', 'PSEUDO', 'LOWEVIDENCE', 'NOIDEA'), nullable=False, server_default=text("'NOIDEA'"))
+  source_release       = Column(VARCHAR(255))
+  ordered              = Column(INTEGER(10, unsigned=True), nullable=False)
+  priority             = Column(INTEGER(5, unsigned=True), server_default=text("1"))
+  priority_description = Column(VARCHAR(40), server_default=text("''"))
+
+class SourceURL(Base):
+  __tablename__ = "source_url"
+
+  source_url_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  source_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
+  species_id    = Column(INTEGER(10, unsigned=True), nullable=False)
+  parser        = Column(VARCHAR(255))
+
+class SourceMappingMethod(Base):
+  __tablename__ = "source_mapping_method"
+
+  source_id = Column(INTEGER(10, unsigned=True), primary_key=True)
+  method    = Column(VARCHAR(255), primary_key=True)
+
+class GeneDirectXref(Base):
+  __tablename__ = "gene_direct_xref"
+
+  general_xref_id   = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
+  ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True)
+  linkage_xref      = Column(VARCHAR(255))
+
+class TranscriptDirectXref(Base):
+  __tablename__ = "transcript_direct_xref"
+
+  general_xref_id   = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
+  ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True)
+  linkage_xref      = Column(VARCHAR(255))
+
+class TranslationDirectXref(Base):
+  __tablename__ = "translation_direct_xref"
+
+  general_xref_id   = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
+  ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True)
+  linkage_xref      = Column(VARCHAR(255))
+
+class Species(Base):
+  __tablename__ = "species"
+
+  species_id  = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True)
+  taxonomy_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True)
+  name        = Column(VARCHAR(255), nullable=False, index=True)
+  aliases     = Column(VARCHAR(255))
+
+class Pairs(Base):
+  __tablename__ = "pairs"
+
+  pair_id    = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  source_id  = Column(INTEGER(10, unsigned=True), nullable=False)
+  accession1 = Column(VARCHAR(255), nullable=False, index=True)
+  accession2 = Column(VARCHAR(255), nullable=False, index=True)
+
+class CoordinateXref(Base):
+  __tablename__ = "coordinate_xref"
+  __table_args__ = (
+    Index("start_pos_idx", "species_id", "chromosome", "strand", "txStart"),
+    Index("end_pos_idx", "species_id", "chromosome", "strand", "txEnd")
+  )
+
+  coord_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  source_id     = Column(INTEGER(10, unsigned=True), nullable=False)
+  species_id    = Column(INTEGER(10, unsigned=True), nullable=False)
+  accession     = Column(VARCHAR(255), nullable=False)
+  chromosome    = Column(VARCHAR(255), nullable=False)
+  strand        = Column(TINYINT(2), nullable=False)
+  txStart       = Column(INTEGER(10), nullable=False)
+  txEnd         = Column(INTEGER(10), nullable=False)
+  cdsStart      = Column(INTEGER(10))
+  cdsEnd        = Column(INTEGER(10))
+  exonStarts    = Column(TEXT, nullable=False)
+  exonEnds      = Column(TEXT, nullable=False)
+
+class ChecksumXref(Base):
+  __tablename__ = "checksum_xref"
+  __table_args__ = (
+    Index("checksum_idx", "checksum", mysql_length=10),
+  )
+
+  checksum_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  source_id        = Column(INTEGER(10, unsigned=True), nullable=False)
+  accession        = Column(CHAR(14), nullable=False)
+  checksum         = Column(CHAR(32), nullable=False)
+
+class Mapping(Base):
+  __tablename__ = "mapping"
+
+  job_id                = Column(INTEGER(10, unsigned=True), primary_key=True)
+  type                  = Column(Enum('dna', 'peptide', 'UCSC'))
+  command_line          = Column(TEXT)
+  percent_query_cutoff  = Column(INTEGER(10, unsigned=True))
+  percent_target_cutoff = Column(INTEGER(10, unsigned=True))
+  method                = Column(VARCHAR(255))
+  array_size            = Column(INTEGER(10, unsigned=True))
+
+class MappingJobs(Base):
+  __tablename__ = "mapping_jobs"
+
+  mapping_job_id    = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  root_dir          = Column(TEXT)
+  map_file          = Column(VARCHAR(255))
+  status            = Column(Enum('SUBMITTED', 'FAILED', 'SUCCESS'))
+  out_file          = Column(VARCHAR(255))
+  err_file          = Column(VARCHAR(255))
+  array_number      = Column(INTEGER(10, unsigned=True))
+  job_id            = Column(INTEGER(10, unsigned=True))
+  failed_reason     = Column(VARCHAR(255))
+  object_xref_start = Column(INTEGER(10, unsigned=True))
+  object_xref_end   = Column(INTEGER(10, unsigned=True))
+
+class GeneTranscriptTranslation(Base):
+  __tablename__ = "gene_transcript_translation"
+
+  gene_id        = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
+  transcript_id  = Column(INTEGER(10, unsigned=True), primary_key=True)
+  translation_id = Column(INTEGER(10, unsigned=True), index=True)
+
+class ProcessStatus(Base):
+  __tablename__ = "process_status"
+
+  id     = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  status = Column(Enum('xref_created', 'parsing_started', 'parsing_finished', 'alt_alleles_added', 'xref_fasta_dumped', 'core_fasta_dumped', 'core_data_loaded', 'mapping_submitted', 'mapping_finished', 'mapping_processed', 'direct_xrefs_parsed', 'prioritys_flagged', 'processed_pairs', 'biomart_test_finished', 'source_level_move_finished', 'alt_alleles_processed', 'official_naming_done', 'checksum_xrefs_started', 'checksum_xrefs_finished', 'coordinate_xrefs_started', 'coordinate_xref_finished', 'tests_started', 'tests_failed', 'tests_finished', 'core_loaded', 'display_xref_done', 'gene_description_done'))
+  date   = Column(DateTime, nullable=False)
+
+class DisplayXrefPriority(Base):
+  __tablename__ = "display_xref_priority"
+
+  ensembl_object_type = Column(VARCHAR(100), primary_key=True)
+  source_id           = Column(INTEGER(10, unsigned=True), primary_key=True)
+  priority            = Column(SMALLINT(unsigned=True), nullable=False)
+
+class GeneDescPriority(Base):
+  __tablename__ = "gene_desc_priority"
+
+  source_id = Column(INTEGER(10, unsigned=True), primary_key=True)
+  priority  = Column(SMALLINT(unsigned=True), nullable=False)
+
+class AltAllele(Base):
+  __tablename__ = "alt_allele"
+
+  alt_allele_id = Column(INTEGER(10, unsigned=True), autoincrement=True, primary_key=True)
+  gene_id       = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
+  is_reference  = Column(INTEGER(2, unsigned=True), server_default=text("0"))
+
+class GeneStableId(Base):
+  __tablename__ = "gene_stable_id"
+
+  internal_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
+  stable_id       = Column(VARCHAR(128), primary_key=True)
+  display_xref_id = Column(INTEGER(10, unsigned=True))
+  desc_set        = Column(INTEGER(10, unsigned=True), server_default=text("0"))
+
+class TranscriptStableId(Base):
+  __tablename__ = "transcript_stable_id"
+
+  internal_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
+  stable_id       = Column(VARCHAR(128), primary_key=True)
+  display_xref_id = Column(INTEGER(10, unsigned=True))
+  biotype         = Column(VARCHAR(40), nullable=False)
+
+class TranslationStableId(Base):
+  __tablename__ = "translation_stable_id"
+
+  internal_id = Column(INTEGER(10, unsigned=True), primary_key=True)
+  stable_id   = Column(VARCHAR(128), nullable=False, index=True)
+
+class ObjectXref(Base):
+  __tablename__ = "object_xref"
+  __table_args__ = (
+    Index("unique_idx", "ensembl_object_type", "ensembl_id", "xref_id", "ox_status", "master_xref_id", unique=True),
+    Index("oxref_idx", "object_xref_id", "xref_id", "ensembl_object_type", "ensembl_id"),
+    Index("xref_idx", "xref_id", "ensembl_object_type")
+  )
+
+  object_xref_id      = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
+  ensembl_id          = Column(INTEGER(10, unsigned=True), nullable=False)
+  ensembl_object_type = Column(Enum('RawContig', 'Transcript', 'Gene', 'Translation'), nullable=False)
+  xref_id             = Column(INTEGER(10, unsigned=True), nullable=False)
+  linkage_annotation  = Column(VARCHAR(255))
+  linkage_type        = Column(Enum('PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM'))
+  ox_status           = Column(Enum('DUMP_OUT', 'FAILED_PRIORITY', 'FAILED_CUTOFF', 'NO_DISPLAY', 'MULTI_DELETE'), nullable=False, server_default=text("'DUMP_OUT'"))
+  unused_priority     = Column(INTEGER(10, unsigned=True))
+  master_xref_id      = Column(INTEGER(10, unsigned=True))
+
+class IdentityXref(Base):
+  __tablename__ = "identity_xref"
+
+  object_xref_id    = Column(INTEGER(10, unsigned=True), primary_key=True)
+  query_identity    = Column(INTEGER(5))
+  target_identity   = Column(INTEGER(5))
+  hit_start         = Column(INTEGER(10))
+  hit_end           = Column(INTEGER(10))
+  translation_start = Column(INTEGER(10))
+  translation_end   = Column(INTEGER(10))
+  cigar_line        = Column(TEXT)
+  score             = Column(DOUBLE)
+  evalue            = Column(DOUBLE)
+
+class Meta(Base):
+  __tablename__ = "meta"
+  __table_args__ = (
+    Index("species_key_value_idx", "meta_id", "species_id", "meta_key", "meta_value", unique=True),
+    Index("species_value_idx", "species_id", "meta_value")
+  )
+
+  meta_id    = Column(INTEGER(10), primary_key=True, autoincrement=True)
+  species_id = Column(INTEGER(10, unsigned=True), server_default=text("1"))
+  meta_key   = Column(VARCHAR(40), nullable=False)
+  meta_value = Column(VARCHAR(255, binary=True), nullable=False)
+  date       = Column(DateTime, nullable=False)
diff --git a/src/python/ensembl/xrefs/Base.py b/src/python/ensembl/xrefs/Base.py
new file mode 100644
index 000000000..2122fc94c
--- /dev/null
+++ b/src/python/ensembl/xrefs/Base.py
@@ -0,0 +1,863 @@
+#  See the NOTICE file distributed with this work for additional information
+#  regarding copyright ownership.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Base xref module to include all common functions used by xref modules."""
+
+import re
+import os
+import shutil
+import requests
+import fnmatch
+import gzip
+import importlib
+import wget
+import threading
+import json
+import logging
+import time
+import random
+import csv
+import subprocess
+
+from sqlalchemy import create_engine, select, insert, update, text, func, and_
+from sqlalchemy.engine.url import make_url, URL
+from sqlalchemy.engine import Connection
+from sqlalchemy.orm import aliased
+from sqlalchemy_utils import database_exists, create_database, drop_database
+from urllib.parse import urlparse
+from ftplib import FTP
+from itertools import groupby
+from configparser import ConfigParser
+from datetime import datetime
+
+from ensembl.databases.xref_source_db_model import Base as XrefSourceDB, Source as SourceSORM, Version as VersionORM, ChecksumXref as ChecksumXrefSORM
+
+from ensembl.databases.xref_update_db_model import Base as XrefUpdateDB, Source as SourceUORM, SourceURL as SourceURLORM, Xref as XrefUORM, \
+  PrimaryXref as PrimaryXrefORM, DependentXref as DependentXrefUORM, GeneDirectXref as GeneDirectXrefORM, TranscriptDirectXref as TranscriptDirectXrefORM, \
+  TranslationDirectXref as TranslationDirectXrefORM, Synonym as SynonymORM, Pairs as PairsORM, Species as SpeciesORM, \
+  SourceMappingMethod as SourceMappingMethodORM, MappingJobs as MappingJobsORM, Mapping as MappingORM
+
+from ensembl.databases.core_db_model import Meta as MetaCORM, Gene as GeneORM, Transcript as TranscriptORM, Analysis as AnalysisORM, \
+  ExonTranscript as ExonTranscriptORM, SupportingFeature as SupportingFeatureORM, DnaAlignFeature as DnaAlignFeatureORM, \
+  TranscriptAttrib as TranscriptAttribORM, AttribType as AttribTypeORM, AnalysisDescription as AnalysisDescriptionORM, \
+  SeqRegion as SeqRegionORM, SeqRegionAttrib as SeqRegionAttribORM, CoordSystem as CoordSystemORM, Translation as TranslationORM, \
+  Exon as ExonORM, Xref as XrefCORM, DependentXref as DependentXrefCORM, ExternalDb as ExternalDbORM, Dna as DnaORM, ObjectXref as ObjectXrefCORM
+
+from ensembl.common.Params import Params
+
+class Base(Params):
+  """ Class to represent the base of xref modules. Inherits the Params class.
+  """
+  def __init__(self, params: dict=None, parse_dataflow_json: bool=True) -> None:
+    """ Calls the parent __init__ then sets some specific parameters.
+
+    Parameters
+    ----------
+    params: dict, optional
+        The parameters to start the object with. If defined, command-line parameters won't be parsed (default is None)
+    parse_dataflow_json: bool, optional
+        Specifies whether to parse an option called 'dataflow' in the provided options (default is True)
+    """
+    super().__init__(params, parse_dataflow_json)
+
+    self.param('metasearch_url', "http://registry-grpc.ebi.ac.uk:8080/registry/metaSearch")
+
+    # Initialize the logfile for this run
+    if self.param('log_timestamp'):
+      current_timestamp = self.param('log_timestamp')
+    else:
+      current_timestamp = datetime.now().strftime('%Y%m%d_%H%M%S')
+
+    log_path = os.path.join(self.param_required('base_path'), 'logs', current_timestamp)
+    if not os.path.exists(log_path): os.makedirs(log_path, exist_ok = True)
+
+    log_file = os.path.join(log_path, 'tmp_logfile_'+self.__class__.__name__+'_'+str(random.randint(0, 5000)))
+    self._log_file = log_file
+
+    console_handler = logging.StreamHandler()
+    file_handler = logging.FileHandler(log_file, mode='a')
+    console_handler.setLevel(logging.WARNING)
+    file_handler.setLevel(logging.DEBUG)
+
+    logging.basicConfig(
+      level=logging.DEBUG,
+      format='%(asctime)s | %(levelname)s | %(message)s',
+      datefmt='%d-%b-%Y %H:%M:%S',
+      handlers=[console_handler, file_handler]
+    )
+
+  def create_source_db(self, source_url: str, reuse_db_if_present: bool):
+    """ Creates the xref source database from model.
+
+    Parameters
+    ----------
+    source_url: str
+        The source database URL with format: [driver]://[user]:[password]@[host]:[port]/[dbname]
+    reuse_db_if_present: bool
+        If set to False, the database defined by provided URL will be dropped before creating a new one
+    """
+    url = make_url(source_url)
+    engine = create_engine(url, isolation_level="AUTOCOMMIT")
+
+    if url.database and reuse_db_if_present:
+      return
+
+    if database_exists(engine.url):
+      drop_database(engine.url)
+    create_database(engine.url)
+    XrefSourceDB.metadata.create_all(engine)
+
+  def download_file(self, file: str, base_path: str, source_name: str, extra_args: dict):
+    """ Downloads an xref file and saves into provided space.
+
+    Parameters
+    ----------
+    file: str
+        The URL of the file to download. Acceptable URL schemes: ftp, http, and https
+    base_path: str
+        The path to save the downloaded file into
+    source_name: str
+        The xref source name
+    extra_args: dict
+        Extra options, including:
+        - skip_download_if_file_present: If set to True, file is only downloaded if does not exist
+        - db: The type of external db for the xref source (only relevent here if equal to 'checksum')
+        - release: If set to 'version', then this is a version file download
+        - rel_number: The URL used to retrieve the release number (only for RefSeq)
+        - catalog: The URL used to retrieve the release catalog (only for RefSeq)
+
+    Returns
+    -------
+    The path of the downloaded file.
+
+    Raises
+    ------
+    LookupError
+        If rel_number is provided but no release number was found in URL.
+    AttributeError
+        If file URL scheme is invalid.
+    """
+    # Create uri object and get scheme
+    uri = urlparse(file)
+    if not uri.scheme:
+      return file
+
+    # Get extra parameters
+    skip_download_if_file_present = extra_args.get('skip_download_if_file_present') or False
+    db = extra_args.get('db')
+    release = extra_args.get('release')
+    rel_number = extra_args.get('rel_number')
+    catalog = extra_args.get('catalog')
+
+    # Create file download path
+    orig_source_name = source_name
+    source_name = re.sub(r"\/", "", source_name)
+    dest_dir = os.path.join(base_path, source_name)
+    if db and db == 'checksum':
+      dest_dir = os.path.join(base_path, 'Checksum')
+    if not os.path.exists(dest_dir): os.makedirs(dest_dir, exist_ok = True)
+
+    file_path = ""
+
+    # If file is in local ftp, copy from there
+    if re.search("ftp.ebi.ac.uk", file):
+      # Construct local path
+      local_file = file
+      local_file = re.sub("https://ftp.ebi.ac.uk/pub/", "/nfs/ftp/public/", local_file)
+
+      # Check if local file exists
+      if os.path.exists(local_file):
+        file_path = os.path.join(dest_dir, os.path.basename(uri.path))
+        if db and db == 'checksum':
+          file_path = os.path.join(dest_dir, f'{source_name}-{os.path.basename(uri.path)}')
+
+        logging.info(f'I am here inside local ftp with {orig_source_name}')
+
+        if not (skip_download_if_file_present and os.path.exists(file_path)):
+          shutil.copy(local_file, file_path)
+
+          # Check if copy was successful
+          if os.path.exists(file_path):
+            logging.info(f'{orig_source_name} file copied from local FTP: {file_path}')
+            if release:
+              return file_path
+            return os.path.dirname(file_path)
+        else:
+          logging.info(f'{orig_source_name} file already exists, skipping download ({file_path})')
+
+    # Handle Refseq files
+    if re.search("RefSeq", source_name) and rel_number and catalog and not release:
+      # Get current release number
+      release_number = requests.get(rel_number).json()
+      if not release_number:
+        raise LookupError(f'No release number in {rel_number}')
+
+      # Get list of files in release catalog
+      catalog = re.sub(r"\*", str(release_number), catalog)
+      files_list = requests.get(catalog).text
+      refseq_files = files_list.split("\n")
+      files_to_download = []
+
+      # Download each refseq file
+      for refseq_file in refseq_files:
+        if not refseq_file: continue
+        checksum, filename = refseq_file.split("\t")
+
+        # Only interested in files matching pattern
+        if not fnmatch.fnmatch(filename, os.path.basename(uri.path)): continue
+        if re.search("nonredundant_protein", filename) or re.search("wp_protein", filename): continue
+
+        file_path = os.path.join(dest_dir, os.path.basename(filename))
+        if os.path.exists(file_path):
+          if skip_download_if_file_present:
+            logging.info(f'{orig_source_name} file already exists, skipping download ({file_path})')
+            continue
+          os.remove(file_path)
+
+        file_url = os.path.join(os.path.dirname(file), filename)
+        files_to_download.append({'url': file_url, 'path': file_path})
+        logging.info(f'{orig_source_name} file downloaded via HTTP: {file_path}')
+
+      self.refseq_multithreading(files_to_download)
+    elif uri.scheme == 'ftp':
+      ftp = FTP(uri.netloc)
+      ftp.login('anonymous', '-anonymous@')
+      ftp.cwd(os.path.dirname(uri.path))
+      remote_files = ftp.nlst()
+
+      # Download files in ftp server
+      for remote_file in remote_files:
+        # Only interested in files matching pattern
+        if not fnmatch.fnmatch(remote_file, os.path.basename(uri.path)): continue
+
+        remote_file = re.sub(r"\n", "", remote_file)
+        file_path = os.path.join(dest_dir, os.path.basename(remote_file))
+        if db and db == 'checksum':
+          file_path = os.path.join(dest_dir, f'{source_name}-{os.path.basename(remote_file)}')
+
+        if not (skip_download_if_file_present and os.path.exists(file_path)):
+          ftp.retrbinary("RETR " + remote_file , open(file_path, 'wb').write)
+          logging.info(f'{orig_source_name} file downloaded via FTP: {file_path}')
+        else:
+          logging.info(f'{orig_source_name} file already exists, skipping download ({file_path})')
+        ftp.close()
+    elif uri.scheme == 'http' or uri.scheme == 'https':
+      # This is the case for the release file
+      if re.search("RefSeq", source_name) and rel_number and release:
+        # Get current release number
+        release_number = requests.get(rel_number).json()
+        if not release_number:
+          raise LookupError(f'No release number in {rel_number}')
+
+        file = re.sub(r"\*", str(release_number), file)
+        uri = urlparse(file)
+
+      file_path = os.path.join(dest_dir, os.path.basename(uri.path))
+      if db and db == 'checksum':
+        file_path = os.path.join(dest_dir, f'{source_name}-{os.path.basename(uri.path)}')
+
+      if not os.path.exists(file_path) or not skip_download_if_file_present:
+        if not skip_download_if_file_present and os.path.exists(file_path):
+          os.remove(file_path)
+        wget.download(file, file_path)
+        logging.info(f'{orig_source_name} file downloaded via HTTP: {file_path}')
+      else:
+        logging.info(f'{orig_source_name} file already exists, skipping download ({file_path})')
+    else:
+      raise AttributeError(f'Invalid URL scheme {uri.scheme}')
+
+    if release:
+      return file_path
+    return os.path.dirname(file_path)
+
+  def refseq_multithreading(self, files):
+    """ Creates multiple threads to download RefSeq files in parallel.
+
+    Parameters
+    ----------
+    files: list
+        The list of file URLs and paths to download.
+    """
+    number_of_threads = 20
+    chunk_size = int(len(files) / number_of_threads)
+    threads = []
+
+    for thread_index in range(number_of_threads):
+      array_start = thread_index * chunk_size
+      array_end = len(files) if thread_index+1 == number_of_threads else (thread_index+1) * chunk_size
+
+      thread = threading.Thread(target=self.download_refseq_files, args=(files, array_start, array_end))
+      threads.append(thread)
+      threads[thread_index].start()
+
+    for thread in threads:
+      thread.join()
+
+  def download_refseq_files(self, files, start: int, end: int):
+    """ Downloads RefSeq files from a subset of files.
+
+    Parameters
+    ----------
+    files: list
+        The list of file URLs and paths to download.
+    start: int
+        The start index of the files list.
+    end: int
+        The end index of the files list.
+
+    Raises
+    ------
+    Exception
+        If file download fails all attempts.
+    """
+    for index in range(start, end):
+      failed = 0
+      file_url = files[index]['url']
+      local_path = files[index]['path']
+
+      for retry in range(0,3):
+        try:
+          wget.download(file_url, local_path)
+        except:
+          failed += 1
+          continue
+        break
+
+      if failed > 0:
+        raise Exception(f'Failed to download file {file_url}')
+
+  def get_dbi(self, url: str):
+    """ Returns a DB connection for a provided URL.
+
+    Parameters
+    ----------
+    url: str
+        The database URL to connect to
+
+    Returns
+    -------
+    An sqlalchemy engine connection.
+    """
+    connect_url = make_url(url)
+    engine = create_engine(connect_url, isolation_level="AUTOCOMMIT")
+
+    return engine.connect()
+
+  def get_db_engine(self, url: str):
+    """ Returns a DB engine for a provided URL.
+
+    Parameters
+    ----------
+    url: str
+        The database URL to create an engine for
+
+    Returns
+    -------
+    An sqlalchemy engine.
+    """
+    connect_url = make_url(url)
+    engine = create_engine(connect_url, isolation_level="AUTOCOMMIT")
+
+    return engine
+
+  def load_checksum(self, path: str, url: str):
+    """ Loads the xref checksum files into a provided database.
+    This first combines the checksum data from different xref sources into 1 file called checksum.txt before loading into the DB.
+
+    Parameters
+    ----------
+    path: str
+        The path where the checksum files can be found
+    url: str
+        The database URL to load the checksum data into
+    """
+    checksum_dir = os.path.join(path, 'Checksum')
+    if not os.path.exists(checksum_dir): os.makedirs(checksum_dir, exist_ok = True)
+
+    # Connect to db
+    url = url + "?local_infile=1"
+    db_engine = self.get_db_engine(url)
+    with db_engine.connect() as dbi:
+      counter = 1
+      source_id = 1
+
+      # Open the checksum output file
+      files = os.listdir(checksum_dir)
+      checksum_file = os.path.join(checksum_dir, 'checksum.txt')
+      with open(checksum_file, 'w') as output_fh:
+        # Go through all available checksum files
+        for file in files:
+          if re.search("checksum", file): continue
+
+          input_file = os.path.join(checksum_dir, file)
+          match = re.search(r"\/([A-Za-z]*)-.*$", input_file)
+          source_name = match.group(1)
+          source_id = self.get_source_id_from_name(dbi, source_name)
+
+          input_fh = self.get_filehandle(input_file)
+          for line in input_fh:
+            line = line.rstrip()
+            (id, checksum) = re.split(r"\s+", line)
+
+            counter += 1
+            output = [str(counter), str(source_id), id, checksum]
+            output_str = "\t".join(output)
+            output_fh.write(f'{output_str}\n')
+
+          input_fh.close()
+
+      query = f'load data local infile \'{checksum_file}\' into table checksum_xref'
+      dbi.execute(text(query))
+
+  def get_filehandle(self, filename: str):
+    """ Opens an appropriate read filehandle for a file based on its type.
+
+    Parameters
+    ----------
+    filename: str
+        The name and path of the file to read
+
+    Returns
+    -------
+    A read filehandle.
+
+    Raises
+    ------
+    FileNotFoundError
+        If no file name was provided.
+        If provided file could not be found.
+    """
+    if not filename or filename == '':
+      raise FileNotFoundError('No file name')
+
+    alt_filename = filename
+    alt_filename = re.sub(r"\.(gz|Z)$", "", alt_filename)
+    if alt_filename == filename:
+      alt_filename = alt_filename + ".gz"
+
+    if not os.path.exists(filename):
+      if not os.path.exists(alt_filename):
+        raise FileNotFoundError(f'Could not find either {filename} or {alt_filename}')
+      filename = alt_filename
+
+    if re.search(r"\.(gz|Z)$", filename):
+      fh = gzip.open(filename, 'rt')
+    else:
+      fh = open(filename, 'r')
+
+    return fh
+
+  def get_source_id_from_name(self, dbi, source_name: str):
+    """ Retrieves a source ID from its name from a database.
+
+    Parameters
+    ----------
+    dbi: db connection
+        The database connection to query in
+    source_name: str
+        The name of the source
+
+    Returns
+    -------
+    The source ID.
+    """
+    query = select(SourceSORM.source_id).where(SourceSORM.name==source_name)
+    source_id = dbi.execute(query).scalar()
+
+    return source_id
+
+  def get_file_sections(self, file: str, delimiter: str):
+    """ Reads a provided file by sections, separated by a provided delimiter.
+    This function uses 'yield' to provide the file sections one by one.
+
+    Parameters
+    ----------
+    file: str
+        The name and path of the file to read
+    delimiter: str
+        The character or string separating the file sections
+
+    Returns
+    -------
+    A yield of file sections.
+    """
+    if re.search(r"\.(gz|Z)$", file):
+      with gzip.open(file, 'rt') as fh:
+        groups = groupby(fh, key=lambda x: x.lstrip().startswith(delimiter))
+        for key,group in groups:
+          yield list(group)
+    else:
+      with open(file, 'r') as fh:
+        groups = groupby(fh, key=lambda x: x.lstrip().startswith(delimiter))
+        for key,group in groups:
+          yield list(group)
+
+  def create_xref_db(self, url: str, config_file: str, preparse:bool):
+    """ Creates the xref database from model.
+    This function always drops the database defined by the provided URL (if it exists) before creating a new one.
+
+    Parameters
+    ----------
+    url: str
+        The database URL with format: [driver]://[user]:[password]@[host]:[port]/[dbname]
+    config_file: str
+        The name and path of the .ini file that has information about xref sources and species
+    preparse: bool
+        Specifies whether source preparsing will be done or not
+    """
+    engine = create_engine(url, isolation_level="AUTOCOMMIT")
+
+    # Drop database and create again
+    if database_exists(engine.url):
+      drop_database(engine.url)
+    create_database(engine.url)
+    XrefUpdateDB.metadata.create_all(engine)
+
+    xref_dbi = engine.connect()
+    self.populate_xref_db(xref_dbi, config_file, preparse)
+
+  def populate_xref_db(self, dbi, config_file:str, preparse:bool):
+    """ Populates the xref database with configuration data.
+
+    Parameters
+    ----------
+    dbi: db connection
+        The xref database connection
+    config_file: str
+        The name and path of the .ini file that has information about xref sources and species to populate the database with
+    preparse: bool
+        Specifies whether source preparsing will be done or not (needed to decide if to use old parsers)
+
+    Raises
+    ------
+    KeyError
+        If a source exists in a species section in the configuration file, but has no source section of its own.
+    """
+    source_ids = {}
+    source_parsers = {}
+    species_sources = {}
+
+    config = ConfigParser()
+    config.read(config_file)
+
+    species_sections, sources_sections = {}, {}
+
+    for section_name in config.sections():
+      section = config[section_name]
+      (keyword, name) = re.split(r"\s+", section_name)
+
+      if keyword == 'source':
+        sources_sections[name] = section
+      elif keyword == 'species':
+        species_sections[name] = section
+
+    # Parse species sections
+    for species_name, section in species_sections.items():
+      taxonomy_ids = section.get('taxonomy_id').split(",")
+      sources = section.get('sources')
+      aliases = section.get('aliases', species_name)
+
+      species_id = taxonomy_ids[0]
+
+      for tax_id in taxonomy_ids:
+        # Add new species
+        query = insert(SpeciesORM).values(species_id=species_id, taxonomy_id=tax_id, name=species_name, aliases=aliases)
+        dbi.execute(query)
+
+      species_sources[species_id] = sources
+
+    source_id = 0
+    # Parse source sections
+    for source_name, section in sorted(sources_sections.items()):
+      source_id += 1
+      source_name = section.get('name')
+      order = section.get('order')
+      priority = section.get('priority')
+      priority_description = section.get('prio_descr', '')
+      status = section.get('status', 'NOIDEA')
+
+      old_parser = section.get('old_parser')
+      if old_parser and not preparse:
+        parser = old_parser
+      else:
+        parser = section.get('parser')
+
+      # Add new source
+      query = insert(SourceUORM).values(name=source_name, source_release='1', ordered=order, priority=priority, priority_description=priority_description, status=status)
+      dbi.execute(query)
+
+      source_ids[source_name] = source_id
+      source_parsers[source_id] = parser
+
+    # Add source url rows
+    for species_id, sources in species_sources.items():
+      source_names = sources.split(",")
+
+      for source_name in source_names:
+        if not source_ids.get(source_name):
+          raise KeyError(f'No source section found for {source_name} in config file')
+
+        source_id = source_ids[source_name]
+        parser = source_parsers[source_id]
+        query = insert(SourceURLORM).values(source_id=source_id, species_id=species_id, parser=parser)
+        dbi.execute(query)
+
+  def get_source_id(self, dbi, parser: str, species_id: int, name: str, division_id: int):
+    """ Retrieves a source ID from its parser, species ID, name or division ID.
+
+    Parameters
+    ----------
+    dbi: db connection
+        The database connection to query in
+    parser: str
+        The source parser
+    species_id: int
+        The ID of the species related to the source
+    name: str
+        The source name
+    division_id: int
+        The ID of the division related to the source
+
+    Returns
+    -------
+    The source ID.
+    """
+    name = "%"+name+"%"
+    source_id = None
+
+    query = select(SourceURLORM.source_id).where(SourceUORM.source_id==SourceURLORM.source_id, SourceURLORM.parser==parser, SourceURLORM.species_id==species_id)
+    result = dbi.execute(query)
+    if result.rowcount == 1:
+      source_id = result.scalar()
+
+    query = select(SourceURLORM.source_id).where(SourceUORM.source_id==SourceURLORM.source_id, SourceURLORM.parser==parser, SourceURLORM.species_id==species_id).filter(SourceUORM.name.like(name))
+    result = dbi.execute(query)
+    if result.rowcount == 1:
+      source_id = result.scalar()
+
+    if not source_id:
+      query = select(SourceURLORM.source_id).where(SourceUORM.source_id==SourceURLORM.source_id, SourceURLORM.parser==parser, SourceURLORM.species_id==division_id).filter(SourceUORM.name.like(name))
+      result = dbi.execute(query).first()
+      if result:
+        source_id = result[0]
+
+    return source_id
+
+  def get_taxon_id(self, dbi):
+    """ Retrieves the species.taxonomy_id value of the meta table in a database.
+
+    Parameters
+    ----------
+    dbi: db connection
+        The database connection to query in
+
+    Returns
+    -------
+    The taxonomy ID in the database or 1 if not found.
+    """
+    query = select(MetaCORM.meta_value).where(MetaCORM.meta_key=='species.taxonomy_id')
+    result = dbi.execute(query)
+    if result.rowcount > 0:
+      return result.scalar()
+
+    return 1
+
+  def get_division_id(self, dbi):
+    """ Retrives the division ID from a database based on the species.division value of the meta table.
+
+    Parameters
+    ----------
+    dbi: db connection
+        The database connection to query in
+
+    Returns
+    -------
+    The division ID in the database or 1 if not found
+    """
+    query = select(MetaCORM.meta_value).where(MetaCORM.meta_key=='species.division')
+    result = dbi.execute(query)
+
+    if result.rowcount > 0:
+      division = result.scalar()
+
+      division_taxon = {
+        'Ensembl'            : 7742,
+        'EnsemblVertebrates' : 7742,
+        'Vertebrates'        : 7742,
+        'EnsemblMetazoa'     : 33208,
+        'Metazoa'            : 33208,
+        'Plants'             : 33090,
+        'EnsemblPlants'      : 33090,
+      }
+
+      division_id = division_taxon.get(division)
+      if division_id:
+        return division_id
+
+    return 1
+
+  def get_path(self, base_path: str, species: str, release: int, category: str, file_name: str=None):
+    """ Creates directories based on provided data.
+
+    Parameters
+    ----------
+    base_path: str
+        The base file path
+    species: str
+        The species name
+    release: int
+        The ensEMBL release number
+    category: str
+        The file category
+    file_name: str, optional
+        The file name
+
+    Returns
+    -------
+    A file path.
+    """
+    full_path = os.path.join(base_path, species, release, category)
+    if not os.path.exists(full_path):
+      os.makedirs(full_path, exist_ok = True)
+
+    if file_name:
+      return os.path.join(full_path, file_name)
+    else:
+      return full_path
+
+  def get_db_from_registry(self, species: str, group: str, release: int, registry: str):
+    """ Looks up a db in the registry and returns an sqlaclehmy angine for it.
+
+    Parameters
+    ----------
+    species: str
+        The species name
+    group: str
+        The db group (core, ccds, otherfeatures, etc...)
+    release: int
+        The ensEMBL release number
+    registry: str
+        The registry url
+
+    Returns
+    -------
+    A db engine or 0 if no db is found.
+    """
+    # Fix registry url, if needed
+    match = re.search(r"^(.*)://(.*)", registry)
+    if match: registry = match.group(2)
+    match = re.search(r"(.*)/(.*)", registry)
+    if match: registry = match.group(1)
+
+    metasearch_url  = self.param_required('metasearch_url')
+    metasearch_body = {
+      "name_pattern":f'{species}_{group}%',
+      "filters":[
+        {
+          "meta_key":"schema_version",
+          "meta_value":release
+        },
+      ],
+      "servers":[registry]
+    }
+
+    dbs = requests.post(metasearch_url, json=metasearch_body).json()
+    dbs = dbs[registry]
+
+    if len(dbs) > 0:
+      db_url = 'mysql://' + dbs[0]
+      return db_url
+    else:
+      return 0
+
+  # def get_spark_session(self, data_type):
+  #   if data_type == 'mysql':
+  #     spark = SparkSession.builder.appName('SparkByExamples.com').config("spark.jars", "mysql-connector-java-8.0.13.jar").getOrCreate()
+  #     return spark
+  #   else:
+  #     raise Exception(f'Spark data type {data_type} not supported yet')
+
+  # def get_spark_reader(self, spark_session, data_type, data_url):
+  #   if data_type == 'mysql':
+  #     reader = spark_session.read.format("jdbc").option("driver", "com.mysql.cj.jdbc.Driver").option("url", f'jdbc:{data_url}')
+  #     return reader
+  #   else:
+  #     raise Exception(f'Spark data type {data_type} not supported yet')
+
+  def get_xref_mapper(self, xref_url: str, species: str, base_path: str, release: int, core_url: str=None, registry: str=None):
+    """ Retrives a mapper object based on species.
+
+    Parameters
+    ----------
+    xref_url: str
+        The xref db connection url
+    species: str
+        The species name
+    base_path: str
+        The base file path
+    release: int
+        The ensEMBL release number
+    core_db: str, optional
+        The species core db connection url
+    registry: str, optional
+        The registry url
+
+    Returns
+    -------
+    A mapper object
+    """
+    # Need either core_db or registry
+    if not core_url and not registry:
+      raise AttributeError(f'Method get_xref_mapper: need to provide either a core DB URL or a registry URL')
+
+    # Create needed db connections
+    if not core_url:
+      core_url = self.get_db_from_registry(species, 'core', release, registry)
+
+    core_db = self.get_db_engine(core_url)
+    xref_db = self.get_db_engine(xref_url)
+
+    # Extract host and dbname from xref url
+    xref_url_obj = make_url(xref_url)
+    host = xref_url_obj.host
+    dbname = xref_url_obj.database
+
+    # Locate the fasta files
+    cdna_path = self.get_path(base_path, species, release, 'ensembl', 'transcripts.fa');
+    pep_path = self.get_path(base_path, species, release, 'ensembl', 'peptides.fa');
+
+    # Try to find a species-specific mapper first
+    module_name = f'ensembl.xrefs.mapper.{species}'
+    class_name = species
+    found = importlib.find_loader(module_name)
+    if not found:
+      module_name = 'ensembl.xrefs.mapper.BasicMapper'
+      class_name = 'BasicMapper'
+
+    # Create a mapper object
+    module = importlib.import_module(module_name)
+    module_class = getattr(module, class_name)
+    mapper = module_class()
+
+    mapper.xref(xref_db)
+    mapper.add_meta_pair('xref', f'{host}:{dbname}')
+    mapper.core(core_db)
+    mapper.add_meta_pair('species', f'{host}:{dbname}')
+    mapper.dna_file(cdna_path)
+    mapper.protein_file(pep_path)
+    mapper.log_file(self._log_file)
+
+    return mapper
+
+
diff --git a/src/python/ensembl/xrefs/Checksum.py b/src/python/ensembl/xrefs/Checksum.py
new file mode 100644
index 000000000..dc59d5c3f
--- /dev/null
+++ b/src/python/ensembl/xrefs/Checksum.py
@@ -0,0 +1,46 @@
+#  See the NOTICE file distributed with this work for additional information
+#  regarding copyright ownership.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Checksum module for the Xref Download pipeline."""
+
+from ensembl.xrefs.Base import *
+
+class Checksum(Base):
+  def run(self):
+    base_path     = self.param_required('base_path')
+    source_db_url = self.param_required('source_db_url')
+    skip_download = self.param_required('skip_download', {'type': 'bool'})
+
+    logging.info('Checksum starting with parameters:')
+    logging.info(f'Param: base_path = {base_path}')
+    logging.info(f'Param: source_db_url = {source_db_url}')
+    logging.info(f'Param: skip_download = {skip_download}')
+
+    # Connect to source db
+    db_engine = self.get_db_engine(source_db_url)
+
+    # Check if checksums already exist
+    table_nonempty = 0
+    if skip_download:
+      with db_engine.connect() as dbi:
+        query = select(func.count(ChecksumXrefSORM.checksum_xref_id))
+        table_nonempty = dbi.execute(query).scalar()
+
+    # Load checksums from files into db
+    if not table_nonempty:
+      self.load_checksum(base_path, source_db_url)
+      logging.info('Checksum data loaded')
+    else:
+      logging.info('Checksum data already exists, skipping loading')
+
diff --git a/src/python/ensembl/xrefs/DownloadSource.py b/src/python/ensembl/xrefs/DownloadSource.py
new file mode 100644
index 000000000..b88088960
--- /dev/null
+++ b/src/python/ensembl/xrefs/DownloadSource.py
@@ -0,0 +1,63 @@
+#  See the NOTICE file distributed with this work for additional information
+#  regarding copyright ownership.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Download module to download xref and version files."""
+
+from ensembl.xrefs.Base import *
+
+class DownloadSource(Base):
+  def run(self):
+    base_path     = self.param_required('base_path')
+    parser        = self.param_required('parser')
+    name          = self.param_required('name')
+    priority      = self.param_required('priority')
+    source_db_url = self.param_required('source_db_url')
+    file          = self.param_required('file')
+    skip_download = self.param_required('skip_download', {'type': 'bool'})
+    db            = self.param('db')
+    version_file  = self.param('version_file')
+    preparse      = self.param('preparse', None, {'type': 'bool'})
+    rel_number    = self.param('rel_number')
+    catalog       = self.param('catalog')
+
+    logging.info(f'DownloadSource starting for source {name}')
+
+    # Download the main xref file
+    extra_args = {}
+    extra_args['skip_download_if_file_present'] = skip_download
+    extra_args['db'] = db
+    if rel_number and catalog:
+      extra_args['rel_number'] = rel_number
+      extra_args['catalog'] = catalog
+    file_name = self.download_file(file, base_path, name, extra_args)
+
+    # Download the version file
+    version = ""
+    if version_file:
+      extra_args['release'] = 'version'
+      version = self.download_file(version_file, base_path, name, extra_args)
+
+    # Update source db
+    db_engine = self.get_db_engine(source_db_url)
+    with db_engine.connect() as dbi:
+      query = insert(SourceSORM).values(name=name, parser=parser).prefix_with('IGNORE')
+      dbi.execute(query)
+
+      query = select(SourceSORM.source_id).where(SourceSORM.name==name)
+      source_id = dbi.execute(query).scalar()
+
+      if preparse is None: preparse = False
+      query = insert(VersionORM).values(source_id=source_id, uri=file_name, index_uri=db, count_seen=priority, revision=version, preparse=preparse).prefix_with('IGNORE')
+      dbi.execute(query)
+
diff --git a/src/python/ensembl/xrefs/EmailNotification.py b/src/python/ensembl/xrefs/EmailNotification.py
new file mode 100644
index 000000000..dae71e738
--- /dev/null
+++ b/src/python/ensembl/xrefs/EmailNotification.py
@@ -0,0 +1,139 @@
+#  See the NOTICE file distributed with this work for additional information
+#  regarding copyright ownership.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Email module to send user emails notifying of xref pipelines end, with important information and statistics."""
+
+from ensembl.xrefs.Base import *
+
+from smtplib import SMTP
+from email.message import EmailMessage
+
+class EmailNotification(Base):
+  def run(self):
+    pipeline_name = self.param_required('pipeline_name')
+    base_path     = self.param_required('base_path')
+    email_address = self.param_required('email')
+    email_server  = self.param_required('email_server')
+    log_timestamp = self.param('log_timestamp')
+
+    email_message = f'The <b>{pipeline_name}</b> has completed its run.<br>'
+
+    if log_timestamp:
+      # Get the path of the log files
+      log_path = os.path.join(base_path, 'logs', log_timestamp)
+
+      # Read the log file
+      if os.path.exists(log_path):
+        log_files = os.listdir(log_path)
+
+        parameters = {}
+        sources = {}
+        added_species = {}
+        skipped_species = {}
+
+        main_log_file = os.path.join(base_path, 'logs', log_timestamp, 'logfile_'+log_timestamp)
+
+        # Copy different log files into a main one
+        with open(main_log_file, 'a') as out_fh:
+          for log_file in log_files:
+            if not re.search(r"^tmp_", log_file): continue
+            log_file = os.path.join(log_path, log_file)
+            with open(log_file) as in_fh:
+              log_data = in_fh.read()
+              out_fh.write(log_data)
+            os.remove(log_file)
+
+        # Read the full logs
+        with open(main_log_file) as fh:
+          data = fh.read()
+
+        # Extract parameter data
+        parameters_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| Param: (\w+) = (.*)", data)
+        parameters = {param[0]: param[1] for param in parameters_list}
+
+        email_message += '<br>The pipeline was run with the following parameters:<br>'
+        for param_name,param_value in parameters.items():
+          email_message += f'<b>{param_name}</b> = {param_value}<br>'
+
+        if re.search('Download', pipeline_name):
+          #Extract data from logs
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| Source to download: ([\w\/]+)", data)
+          sources = {source : {'to_download' : 1} for source in sources_list}
+
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| Source to cleanup: ([\w\/]+)", data)
+          for source in sources_list: sources[source].update({'to_cleanup' : 1})
+
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| Source to preparse: ([\w\/]+)", data)
+          for source in sources_list: sources[source].update({'to_preparse' : 1})
+
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| Source ([\w\/]+) cleaned up", data)
+          for source in sources_list: sources[source].update({'cleaned_up' : 1})
+
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| Source ([\w\/]+) preparsed", data)
+          for source in sources_list: sources[source].update({'preparsed' : 1})
+
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| ([\w\/]+) file already exists, skipping download \((.*)\)", data)
+          for source in sources_list: sources[source[0]].update({'skipped' : os.path.dirname(source[1])})
+
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| ([\w\/]+) file downloaded via (HTTP|FTP): (.*)", data)
+          for source in sources_list: sources[source[0]].update({'downloaded' : source[1]+"|"+os.path.dirname(source[2])})
+
+          sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| ([\w\/]+) file copied from local FTP: (.*)", data)
+          for source in sources_list: sources[source[0]].update({'copied' : os.path.dirname(source[1])})
+
+          # skipped_species_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| (\w+) skipped species = (\d+)", data)
+          # skipped_species = {source[0]: source[1] for source in skipped_species_list}
+
+          # added_species_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| (\w+) taxonomy IDs added to filter = (\d+)", data)
+          # added_species = {division[0]: division[1] for division in added_species_list}
+
+          # Include source statistics
+          email_message += '<br>--Source Statistics--<br>'
+          for source_name,source_values in sources.items():
+            email_message += f'<b>{source_name}:</b><br>'
+            if source_values.get('to_download'): email_message += '&nbsp;&nbsp;&nbsp;Scheduled for download &#10004;<br>'
+
+            if source_values.get('downloaded'):
+              (download_type, file_path) = source_values['downloaded'].split("|")
+              email_message += f' File downloaded via {download_type} into {file_path}<br>'
+            elif source_values.get('copied'): email_message += '&nbsp;&nbsp;&nbsp;File(s) copied from local FTP into %s<br>' % (source_values['copied'])
+            elif source_values.get('skipped'): email_message += '&nbsp;&nbsp;&nbsp;File(s) download skipped, already exists in %s<br>' % (source_values['skipped'])
+
+            if source_values.get('to_cleanup'): email_message += '&nbsp;&nbsp;&nbsp;Scheduled for cleanup &#10004;<br>'
+            if source_values.get('cleaned_up'): email_message += '&nbsp;&nbsp;&nbsp;Cleaned up &#10004;<br>'
+
+            if source_values.get('to_preparse'): email_message += '&nbsp;&nbsp;&nbsp;Scheduled for pre-parse &#10004;<br>'
+            if source_values.get('preparsed'): email_message += '&nbsp;&nbsp;&nbsp;Pre-parsed &#10004;<br>'
+
+          # Include species statistics
+          # email_message += '<br>--Species Statistics--<br>'
+          # for division,count in added_species.items():
+          #   if division == 'Total': continue
+          #   email_message += f'{species_type} taxonomy IDs = {count}<br>'
+          # email_message += 'Skipped Species per source file:<br>'
+          # for source_name,count in skipped_species.items():
+          #   email_message += f'&nbsp;&nbsp;&nbsp;{source_name}: {count}<br>'
+
+          email_message += '<br>To run the Xref Process Pipeline based on the data from this pipeline, use the same <b>--base_path</b>, <b>--source_db_url</b>, and <b>--central_db_url</b> (if preparse was run) values provided to this pipeline.'
+
+    # Send email
+    message = EmailMessage()
+    message['Subject'] = f'{pipeline_name} Finished'
+    message['From'] = email_address
+    message['To'] = email_address
+    message.set_content(email_message, 'html')
+
+    smtp = SMTP(email_server)
+    smtp.send_message(message)
+
diff --git a/src/python/ensembl/xrefs/ScheduleCleanup.py b/src/python/ensembl/xrefs/ScheduleCleanup.py
new file mode 100644
index 000000000..515150e9d
--- /dev/null
+++ b/src/python/ensembl/xrefs/ScheduleCleanup.py
@@ -0,0 +1,57 @@
+#  See the NOTICE file distributed with this work for additional information
+#  regarding copyright ownership.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Scheduling module to create cleanup jobs for specific xref sources."""
+
+from ensembl.xrefs.Base import *
+
+class ScheduleCleanup(Base):
+  def run(self):
+    base_path              = self.param_required('base_path')
+    source_db_url          = self.param_required('source_db_url')
+    clean_files            = self.param('clean_files')
+    clean_dir              = self.param('clean_dir')
+    split_files_by_species = self.param('split_files_by_species')
+
+    logging.info('ScheduleCleanup starting with parameters:')
+    logging.info(f'Param: base_path = {base_path}')
+    logging.info(f'Param: source_db_url = {source_db_url}')
+    logging.info(f'Param: clean_files = {clean_files}')
+    logging.info(f'Param: clean_dir = {clean_dir}')
+    logging.info(f'Param: split_files_by_species = {split_files_by_species}')
+
+    # Connect to source db
+    db_engine = self.get_db_engine(source_db_url)
+    with db_engine.connect() as dbi:
+      # Get name and version file for each source
+      query = select(SourceSORM.name, VersionORM.revision).where(SourceSORM.source_id==VersionORM.source_id).distinct()
+      sources = dbi.execute(query).mappings().all()
+
+    for source in sources:
+      # Only cleaning RefSeq and UniProt for now
+      if not (re.search(r"^RefSeq_(dna|peptide)", source.name) or re.search(r"^Uniprot", source.name)): continue
+
+      # Remove / char from source name to access directory
+      clean_name = source.name
+      clean_name = re.sub(r"\/", "", clean_name)
+
+      # Send parameters into cleanup jobs for each source
+      if os.path.exists(os.path.join(base_path, clean_name)):
+        logging.info(f'Source to cleanup: {source.name}')
+
+        self.write_output('cleanup_sources', {
+          'name'         : source.name,
+          'version_file' : source.revision
+        })
+
diff --git a/src/python/ensembl/xrefs/ScheduleDownload.py b/src/python/ensembl/xrefs/ScheduleDownload.py
new file mode 100644
index 000000000..b2e48aa86
--- /dev/null
+++ b/src/python/ensembl/xrefs/ScheduleDownload.py
@@ -0,0 +1,73 @@
+#  See the NOTICE file distributed with this work for additional information
+#  regarding copyright ownership.
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+"""Scheduling module to create download jobs for all xref sources in config file."""
+
+from ensembl.xrefs.Base import *
+
+class ScheduleDownload(Base):
+  def run(self):
+    config_file     = self.param_required('config_file')
+    source_db_url   = self.param_required('source_db_url')
+    reuse_db        = self.param_required('reuse_db', {'type': 'bool'})
+    skip_preparse   = self.param('skip_preparse', None, {'type': 'bool', 'default' : False})
+
+    logging.info('ScheduleDownload starting with parameters:')
+    logging.info(f'Param: config_file = {config_file}')
+    logging.info(f'Param: source_db_url = {source_db_url}')
+    logging.info(f'Param: reuse_db = {reuse_db}')
+    logging.info(f'Param: skip_preparse = {skip_preparse}')
+
+    # Create the source db from url
+    self.create_source_db(source_db_url, reuse_db)
+
+    # Extract sources to download from config file
+    sources = []
+    with open(config_file) as conf_file:
+      sources = json.load(conf_file)
+
+    if len(sources) < 1:
+      raise IOError(f'No sources found in config file {config_file}. Need sources to run pipeline')
+
+    for source_data in sources:
+      name         = source_data['name']
+      parser       = source_data['parser']
+      priority     = source_data['priority']
+      file         = source_data['file']
+      db           = source_data.get('db')
+      version_file = source_data.get('release')
+      preparse     = source_data.get('preparse')
+      rel_number   = source_data.get('release_number')
+      catalog      = source_data.get('catalog')
+
+      logging.info(f'Source to download: {name}')
+
+      # Revert to the old parser if not pre-parsing
+      if preparse and skip_preparse:
+        parser = source_data['old_parser']
+        preparse = 0
+
+      # Pass the source parameters into download jobs
+      self.write_output('sources', {
+        'parser'       : parser,
+        'name'         : name,
+        'priority'     : priority,
+        'db'           : db,
+        'version_file' : version_file,
+        'preparse'     : preparse,
+        'file'         : file,
+        'rel_number'   : rel_number,
+        'catalog'      : catalog
+      })
+
diff --git a/src/python/ensembl/xrefs/config/xref_all_sources.json b/src/python/ensembl/xrefs/config/xref_all_sources.json
new file mode 100644
index 000000000..1edc6e1da
--- /dev/null
+++ b/src/python/ensembl/xrefs/config/xref_all_sources.json
@@ -0,0 +1,248 @@
+[
+    {
+      "name" : "ArrayExpress",
+      "parser" : "ArrayExpressParser",
+      "file" : "Database",
+      "db" : "core",
+      "priority" : 1
+    },
+    {
+      "name" : "CCDS",
+      "parser" : "CCDSParser",
+      "file" : "Database",
+      "db" : "ccds",
+      "priority" : 1
+    },
+    {
+      "name" : "UniParc",
+      "parser" : "ChecksumParser",
+      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis",
+      "db" : "checksum",
+      "priority" : 1
+    },
+    {
+      "name" : "RNACentral",
+      "parser" : "ChecksumParser",
+      "file" : "https://ftp.ebi.ac.uk/pub/databases/RNAcentral/current_release/md5/md5.tsv.gz",
+      "db" : "checksum",
+      "priority" : 1
+    },
+    {
+      "name" : "DBASS3",
+      "parser" : "DBASSParser",
+      "file" : "https://www.dbass.soton.ac.uk/Dbass3/DownloadCsv",
+      "priority" : 1
+    },
+    {
+      "name" : "DBASS5",
+      "parser" : "DBASSParser",
+      "file" : "https://www.dbass.soton.ac.uk/Dbass5/DownloadCsv",
+      "priority" : 1
+    },
+    {
+      "name" : "EntrezGene",
+      "parser" : "EntrezGeneParser",
+      "file" : "https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz",
+      "priority" : 1
+    },
+    {
+      "name" : "HPA",
+      "parser" : "HPAParser",
+      "file" : "https://www.proteinatlas.org/download/xref.php",
+      "priority" : 1
+    },
+    {
+      "name" : "MGI",
+      "parser" : "MGIParser",
+      "file" : "https://www.informatics.jax.org/downloads/reports/MRK_ENSEMBL.rpt",
+      "priority" : 2
+    },
+    {
+      "name" : "MGI_desc",
+      "parser" : "MGI_Desc_Parser",
+      "file" : "https://www.informatics.jax.org/downloads/reports/MRK_List2.rpt",
+      "priority" : 1
+    },
+    {
+      "name" : "MGI_ccds",
+      "parser" : "MGI_CCDS_Parser",
+      "file" : "https://ftp.ncbi.nlm.nih.gov/pub/CCDS/current_mouse/CCDS.current.txt",
+      "priority" : 2
+    },
+    {
+      "name" : "MIM2GENE",
+      "parser" : "Mim2GeneParser",
+      "file" : "https://ftp.ncbi.nlm.nih.gov/gene/DATA/mim2gene_medgen",
+      "priority" : 3
+    },
+    {
+      "name" : "MIM",
+      "parser" : "MIMParser",
+      "file" : "https://data.omim.org/downloads/ZpPlmgwjuTBK9T5vf2sFjA/omim.txt.gz",
+      "priority" : 2
+    },
+    {
+      "name" : "RFAM",
+      "parser" : "RFAMParser",
+      "file" : "https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.seed.gz",
+      "db" : "core",
+      "priority" : 1
+    },
+    {
+      "name" : "RGD",
+      "parser" : "RGDParser",
+      "file" : "https://download.rgd.mcw.edu/pub/data_release/GENES.RAT.txt",
+      "priority" : 2
+    },
+    {
+      "name" : "Reactome",
+      "parser" : "ReactomeParser",
+      "file" : "https://www.reactome.org/download/current/Ensembl2Reactome_All_Levels.txt",
+      "release" : "https://www.reactome.org/ReactomeRESTfulAPI/RESTfulWS/version",
+      "priority" : 1
+    },
+    {
+      "name" : "Reactome",
+      "parser" : "ReactomeParser",
+      "file" : "https://www.reactome.org/download/current/UniProt2Reactome_All_Levels.txt",
+      "release" : "https://www.reactome.org/ReactomeRESTfulAPI/RESTfulWS/version",
+      "priority" : 2
+    },
+    {
+      "name" : "RefSeq_dna",
+      "parser" : "RefSeqDatabaseParser",
+      "old_parser" : "RefSeqGPFFParser",
+      "file" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/complete/complete.*rna.gbff.gz",
+      "method" : "--bestn 5",
+      "query_cutoff" : 90,
+      "target_cutoff" : 90,
+      "release" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release*.txt",
+      "preparse" : 1,
+      "priority" : 2,
+      "release_number" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER",
+      "catalog" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release*.files.installed"
+    },
+    {
+      "name" : "RefSeq_peptide",
+      "parser" : "RefSeqDatabaseParser",
+      "old_parser" : "RefSeqGPFFParser",
+      "file" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/complete/complete.*.protein.gpff.gz",
+      "method" : "--bestn 1",
+      "query_cutoff" : 100,
+      "target_cutoff" : 100,
+      "release" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/release-notes/RefSeq-release*.txt",
+      "preparse" : 1,
+      "priority" : 3,
+      "release_number" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER",
+      "catalog" : "https://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/release*.files.installed"
+    },
+    {
+      "name" : "Refseq_import",
+      "parser" : "RefSeqCoordinateParser",
+      "file" : "Database",
+      "db" : "otherfeatures",
+      "priority" : 2
+    },
+    {
+      "name" : "UCSC_hg38",
+      "parser" : "UCSCParser",
+      "file" : "https://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/knownGene.txt.gz",
+      "release" : "https://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/README.txt",
+      "priority" : 1
+    },
+    {
+      "name" : "UCSC_mm10",
+      "parser" : "UCSCParser",
+      "file" : "https://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz",
+      "release" : "https://hgdownload.cse.ucsc.edu/goldenPath/mm10/database/README.txt",
+      "priority" : 1
+    },
+    {
+      "name" : "Uniprot/SWISSPROT",
+      "parser" : "UniProtDatabaseParser",
+      "old_parser" : "UniProtParser",
+      "file" : "https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.dat.gz",
+      "method" : "--bestn 1",
+      "query_cutoff" : 100,
+      "target_cutoff" : 100,
+      "preparse" : 1,
+      "release" : "https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt",
+      "priority" : 1
+    },
+    {
+      "name" : "Uniprot/SPTREMBL",
+      "parser" : "UniProtDatabaseParser",
+      "old_parser" : "UniProtParser",
+      "file" : "https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_trembl.dat.gz",
+      "method" : "--bestn 1",
+      "query_cutoff" : 100,
+      "target_cutoff" : 100,
+      "preparse" : 1,
+      "release" : "https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/reldate.txt",
+      "priority" : 1
+    },
+    {
+      "name" : "VGNC",
+      "parser" : "VGNCParser",
+      "file" : "https://ftp.ebi.ac.uk/pub/databases/genenames/vgnc/tsv/vgnc_gene_set_All.txt.gz",
+      "priority" : 1
+    },
+    {
+      "name" : "ZFIN_ID",
+      "parser" : "ZFINParser",
+      "file" : "https://zfin.org/data_transfer/Downloads/refseq.txt",
+      "priority" : 3
+    },
+    {
+      "name" : "ZFIN_ID",
+      "parser" : "ZFINParser",
+      "file" : "https://zfin.org/data_transfer/Downloads/uniprot.txt",
+      "priority" : 2
+    },
+    {
+      "name" : "ZFIN_ID",
+      "parser" : "ZFINParser",
+      "file" : "https://zfin.org/data_transfer/Downloads/aliases.txt",
+      "priority" : 2
+    },
+    {
+      "name" : "ZFIN_ID",
+      "parser" : "ZFINParser",
+      "file" : "https://zfin.org/data_transfer/Downloads/gene_seq.txt",
+      "priority" : 1
+    },
+    {
+      "name" : "ZFIN_desc",
+      "parser" : "ZFINDescParser",
+      "file" : "ftp://zfin.org/pub/transfer/MEOW/zfin_genes.txt",
+      "priority" : 1
+    },
+    {
+      "name" : "cint_jgi_v1",
+      "parser" : "JGI_ProteinParser",
+      "file" : "https://ftp.ensembl.org/pub/misc/cint_jgi/v1/ciona.prot.fasta.gz",
+      "priority" : 1
+    },
+    {
+      "name" : "Xenbase",
+      "parser" : "XenopusJamboreeParser",
+      "file" : "http://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt",
+      "priority" : 1
+    },
+    {
+      "name" : "miRBase",
+      "parser" : "miRBaseParser",
+      "file" : "https://mirbase.org/download/miRNA.dat",
+      "method" : "--bestn 1",
+      "query_cutoff" : 90,
+      "target_cutoff" : 90,
+      "priority" : 1
+    },
+    {
+      "name" : "HGNC",
+      "parser" : "HGNCParser",
+      "file" : "https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit",
+      "db" : "ccds",
+      "priority" : 3
+    }
+]
diff --git a/src/python/ensembl/xrefs/config/xref_config.ini b/src/python/ensembl/xrefs/config/xref_config.ini
new file mode 100644
index 000000000..5a4830d52
--- /dev/null
+++ b/src/python/ensembl/xrefs/config/xref_config.ini
@@ -0,0 +1,1680 @@
+##########################################################################
+# SOURCES                                                                #
+#                                                                        #
+# Keys:                                                                  #
+#   name          - name of this source (required)                       #
+#   order         - parsing order for this source (required)             #
+#   priority      - priority of these data files when more files belong  #
+#                   to the same source 'name' (required)                 #
+#   prio_descr    - label for the 'priority' (optional)                  #
+#   parser        - the parser to be used (required)                     #
+#   dependent_on  - Comma separated list of sources which must be loaded #
+#                   first (optional)                                     #
+#                   Note that if species does not have xrefs from a      #
+#                   master source specified in this list than the        #
+#                   dependency is ignored                                #
+#                                                                        #
+##########################################################################
+
+[source EC_NUMBER::saccharomyces_cerevisiae]
+# Used by S.cerevisiae
+name            = EC_NUMBER
+order           = 50
+priority        = 70
+parser          = UniProtParser
+
+[source BioGRID::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = BioGRID
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source EPD::drosophila_melanogaster]
+# Used by the 12 drosophila genomes
+name            = EPD
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source FlyExpress::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyExpress
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source FlyReactome::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyReactome
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source GenomeRNAi::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = GenomeRNAi
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source InteractiveFly::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = InteractiveFly
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source miRBase::drosophila_melanogaster]
+# Used by the 12 drosophila genomes
+name            = miRBase
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source MitoDrome::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = MitoDrome
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source TransFac::drosophila_melanogaster]
+# Used by the 12 drosophila genomes
+name            = TransFac
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source TransFac::drosophila_pseudoobscura]
+# Used by the 12 drosophila genomes
+name            = TransFac
+order           = 50
+priority        = 1
+parser          = FlybaseParser
+
+[source flybase_annotation_id::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = flybase_annotation_id
+order           = 50
+priority        = 1
+prio_descr      = Annotation ID assigned by FlyBase
+parser          = FlybaseParser
+
+[source flybase_gene_id::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = flybase_gene_id
+order           = 75
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_pseudoobscura]
+# Used by drosophila_pseudoobscura
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_grimshawi]
+# Used by drosophila_grimshawi
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_willistoni]
+# Used by drosophila_willistoni
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_ananassae]
+# Used by drosophila_ananassae
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_yakuba]
+# Used by drosophila_yakuba
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_simulans]
+# Used by drosophila_simulans
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_sechellia]
+# Used by drosophila_sechellia
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_erecta]
+# Used by drosophila_erecta
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_persimilis]
+# Used by drosophila_persimilis
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_mojavensis]
+# Used by drosophila_mojavensis
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_gene_id::drosophila_virilis]
+# Used by drosophila_virilis
+name            = flybase_gene_id
+order           = 100
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+dependent_on    = Uniprot/SPTREMBL,Uniprot/SWISSPROT
+
+[source flybase_transcript_id::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = flybase_transcript_id
+order           = 50
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+
+[source flybase_translation_id::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = flybase_translation_id
+order           = 50
+priority        = 1
+prio_descr      = ID assigned by FlyBase
+parser          = FlybaseParser
+
+[source FlyBaseCGID_gene::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyBaseCGID_gene
+order           = 50
+priority        = 1
+prio_descr      = FlyBase_Annotation_IDs
+parser          = FlybaseParser
+
+[source FlyBaseCGID_transcript::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyBaseCGID_transcript
+order           = 50
+priority        = 1
+prio_descr      = FlyBase_Annotation_IDs
+parser          = FlybaseParser
+
+[source FlyBaseCGID_translation::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyBaseCGID_translation
+order           = 50
+priority        = 1
+prio_descr      = FlyBase_Annotation_IDs
+parser          = FlybaseParser
+
+[source FlyBaseName_gene::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyBaseName_gene
+order           = 50
+priority        = 1
+prio_descr      = Name assigned to gene in FlyBase gff
+parser          = FlybaseParser
+
+[source FlyBaseName_transcript::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyBaseName_transcript
+order           = 50
+priority        = 1
+prio_descr      = Transcript name in FlyBase gff
+parser          = FlybaseParser
+
+[source FlyBaseName_translations::drosophila_melanogaster]
+# Used by drosophila_melanogaster
+name            = FlyBaseName_translation
+order           = 50
+priority        = 1
+prio_descr      = Translation name in FlyBase gff
+parser          = FlybaseParser
+
+[source PHIbase::MULTI]
+name            = PHIbase
+order           = 50
+priority        = 1
+parser          = PHIbaseParser
+dependent_on    = Uniprot/SWISSPROT,Uniprot/SPTREMBL
+
+[source ArrayExpress::MULTI]
+# Used by all ensembl species
+name            = ArrayExpress
+order           = 50
+priority        = 1
+parser          = ArrayExpressParser
+
+[source ArrayExpress::EG]
+name            = ArrayExpress
+order           = 50
+priority        = 1
+parser          = ArrayExpressParser
+
+[source CCDS::homo_sapiens]
+# Used by homo_sapiens
+name            = CCDS
+order           = 10
+priority        = 1
+parser          = CCDSParser
+
+[source CCDS::mus_musculus]
+# Used by mus_musculus
+name            = CCDS
+order           = 10
+priority        = 1
+parser          = CCDSParser
+
+[source DBASS5::homo_sapiens]
+# Used by homo_sapiens
+name            = DBASS5
+order           = 50
+priority        = 1
+prio_descr      = Database of aberrant 5\' splice sites.
+parser          = DBASSParser
+
+[source DBASS3::homo_sapiens]
+# Used by homo_sapiens
+name            = DBASS3
+order           = 50
+priority        = 1
+prio_descr      = Database of aberrant 3\' splice sites.
+parser          = DBASSParser
+
+[source EntrezGene::MULTI]
+# Used by aedes_aegypti, anolis_carolinensis, anopheles_gambiae, acyrthosiphon_pisum, apis_mellifera, bos_taurus, caenorhabditis_elegans, canis_familiaris, cavia_porcellus, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_melanogaster, drosophila_pseudoobscura, echinops_telfairi, erinaceus_europaeus, equus_caballus, felis_catus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, gorilla_gorilla, homo_sapiens, ixodes_scappularis, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, ochotona_princeps, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes, pongo_abelii,  rattus_norvegicus, saccharomyces_cerevisiae, ictidomys_tridecemlineatus, sus_scrofa, taeniopygia_guttata, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis,phaeodactylum_tricornutum,thalassiosira_pseudonana, lepisosteus_oculatus
+name            = EntrezGene
+order           = 10
+priority        = 1
+parser          = EntrezGeneParser
+
+[source EntrezGene_trans_name]
+# Used by homo_sapiens,mus_musculus,danio_rerio,sus_scrofa
+name            = EntrezGene_trans_name
+order           = 70
+priority        = 1
+parser          = comes via official naming
+
+[source WikiGene::MULTI]
+# used via the EntrezGeneParser, for all species
+name            = WikiGene
+order           = 100
+priority        = 1
+parser          = EntrezGeneParser
+
+[source HPA::homo_sapiens]
+# Used by homo_sapiens
+name            = HPA
+order           = 50
+priority        = 1
+prio_descr      = Human Protein Atlas (HPA) database
+parser          = HPAParser
+
+[source LRG_HGNC_notransfer]
+name            = LRG_HGNC_notransfer
+order           = 30
+priority        = 5
+parser          = HGNCParser
+
+[source VGNC::vertebrate]
+name            = VGNC
+order           = 29
+priority        = 1
+parser          = VGNCParser
+
+[source HGNC::homo_sapiens#07]
+# used by #02
+name            = HGNC
+order           = 30
+priority        = 1
+prio_descr      = ensembl_manual
+parser          = HGNCParser
+
+[source HGNC::homo_sapiens#01]
+# Used by homo_sapiens
+name            = HGNC
+order           = 30
+priority        = 2
+prio_descr      = ccds
+parser          = HGNCParser
+
+
+[source HGNC::homo_sapiens#02]
+# Used by homo_sapiens
+name            = HGNC
+order           = 29
+priority        = 4
+prio_descr      = entrezgene_manual
+parser          = HGNCParser
+dependent_on    = EntrezGene,Uniprot/SWISSPROT,RefSeq_dna,RefSeq_peptide
+
+
+[source HGNC::homo_sapiens#03]
+# Used by #02
+name            = HGNC
+order           = 30
+priority        = 5
+prio_descr      = refseq_manual
+parser          = HGNCParser
+
+[source HGNC::homo_sapiens#08]
+# used by #02
+name            = HGNC
+order           = 30
+priority        = 100
+prio_descr      = desc_only
+parser          = HGNCParser
+
+[source MIM_GENE::homo_sapiens]
+# MIM parse loads data as MIM_GENE or MIM_MORBID not as MIM
+name            = MIM_GENE
+order           = 40
+priority        = 1
+parser          = MIMParser
+
+[source MIM_MORBID::homo_sapiens]
+# MIM parse loads data as MIM_GENE or MIM_MORBID not as MIM
+name            = MIM_MORBID
+order           = 40
+priority        = 1
+parser          = MIMParser
+
+[source MIM::homo_sapiens]
+# Used by homo_sapiens
+name            = MIM
+order           = 10
+priority        = 1
+parser          = MIMParser
+
+[source MIM2GENE::homo_sapiens]
+# Used by homo_sapiens
+name            = MIM2GENE
+order           = 60
+priority        = 1
+parser          = Mim2GeneParser
+dependent_on    = MIM,EntrezGene
+
+[source GeneCards::homo_sapiens]
+# used via the HGNCParser, for homo_sapiens
+name            = GeneCards
+order           = 100
+priority        = 1
+parser          = HGNCParser
+
+[source MGI::mus_musculus#01]
+# Used by mus_musculus
+name            = MGI
+order           = 30
+priority        = 1
+prio_descr      = official
+parser          = MGIParser
+
+[source MGI::mus_musculus#05]
+# Used by mus_musculus
+name            = MGI
+order           = 1
+priority        = 10
+prio_descr      = descriptions
+parser          = MGI_Desc_Parser
+
+[source Reactome::MULTI]
+# Used by all species
+name            = Reactome
+order           = 80
+priority        = 1
+prio_descr      = direct
+parser          = ReactomeParser
+
+[source Reactome_transcript::MULTI]
+# Species source used in ReactomeParser. No species uses this source
+name            = Reactome_transcript
+order           = 20
+priority        = 1
+prio_descr      = transcript
+parser          = ReactomeParser
+
+[source Reactome_gene::MULTI]
+# Species source used in ReactomeParser. No species uses this source
+name            = Reactome_gene
+order           = 20
+priority        = 1
+prio_descr      = gene
+parser          = ReactomeParser
+
+[source Reactome::MULTI-Uniprot]
+# Special source used in ReactomeParser.  No species uses this source.
+name            = Reactome
+order           = 20
+priority        = 1
+prio_descr      = uniprot
+parser          = ReactomeParser
+
+[source RGD::rattus_norvegicus]
+# Used by rattus_norvegicus
+name            = RGD
+order           = 30
+priority        = 2
+parser          = RGDParser
+dependent_on    = RefSeq_dna,RefSeq_peptide
+
+[source RGD::rattus_norvegicus#02]
+# Used by rattus_norvegicus
+name            = RGD
+order           = 30
+priority        = 1
+prio_descr      = direct_xref
+parser          = done_in_RGDParser
+
+[source RGD_trans_name]
+name            = RGD_trans_name
+order           = 49
+priority        = 1
+parser          = done_in_official_naming
+
+[source RefSeq_dna::MULTI-vertebrate]
+# Used by vertebrates
+name            = RefSeq_dna
+order           = 15
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqDatabaseParser
+old_parser      = RefSeqGPFFParser
+
+[source RefSeq_dna::gencode]
+# Used by human and mouse
+name            = RefSeq_dna
+order           = 15
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqGPFFParser
+
+[source RefSeq_dna::MULTI-fungi]
+# Used by saccharomyces_cerevisiae
+name            = RefSeq_dna
+order           = 15
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_dna::MULTI-Plants]
+name            = RefSeq_dna
+order           = 15
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqDatabaseParser
+old_parser      = RefSeqGPFFParser
+
+[source RefSeq_dna::MULTI-complete]
+# Used by phaeodactylum_tricornutum
+name            = RefSeq_dna
+order           = 15
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_dna::MULTI-protozoa]
+# Used by dictyostelium_discoideum
+name            = RefSeq_dna
+order           = 15
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_dna::MULTI-invertebrate]
+# Used by drosophila_melanogaster
+name            = RefSeq_dna
+order           = 15
+priority        = 1
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_dna::MULTI-predicted]
+# Special source used in RefSeqParser.  No species uses this source.
+name            = RefSeq_dna_predicted
+order           = 20
+priority        = 1
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_mRNA::MULTI]
+# Special source used in RefSeqParser.  No species uses this source.
+# dependent source is used to provide a link between RefSeq_dna source in SubmitMapper
+name            = RefSeq_mRNA
+order           = 15
+priority        = 3
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_mRNA::otherfeatures]
+# Special source used in RefSeqCoordinateParser.  No species uses this source.
+name            = RefSeq_mRNA
+order           = 15
+priority        = 1
+prio_descr      = otherfeatures
+parser          = RefSeqCoordinateParser
+
+[source RefSeq_peptide::otherfeatures]
+# Special source used in RefSeqCoordinateParser.  No species uses this source.
+name            = RefSeq_peptide
+order           = 15
+priority        = 1
+prio_descr      = otherfeatures
+parser          = RefSeqCoordinateParser
+
+[source RefSeq_mRNA_predicted::otherfeatures]
+# Special source used in RefSeqCoordinateParser.  No species uses this source.
+name            = RefSeq_mRNA_predicted
+order           = 20
+priority        = 1
+prio_descr      = otherfeatures
+parser          = RefSeqCoordinateParser
+
+[source RefSeq_peptide_predicted::otherfeatures]
+# Special source used in RefSeqCoordinateParser.  No species uses this source.
+name            = RefSeq_peptide_predicted
+order           = 20
+priority        = 1
+prio_descr      = otherfeatures
+parser          = RefSeqCoordinateParser
+
+[source RefSeq_import::otherfeatures]
+# Import RefSeq models from otherfeatures database
+# Used for human and mouse
+name            = RefSeq_import
+order           = 20
+priority        = 1
+prio_descr      = otherfeatures
+parser          = RefSeqCoordinateParser
+
+[source RefSeq_ncRNA::MULTI]
+# Special source used in RefSeqParser.  No species uses this source.
+name            = RefSeq_ncRNA
+order           = 15
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_ncRNA::otherfeatures]
+# Special source used in RefSeqCoordinateParser.  No species uses this source.
+name            = RefSeq_ncRNA
+order           = 15
+priority        = 1
+prio_descr      = otherfeatures
+parser          = RefSeqCoordinateParser
+
+[source RefSeq_ncRNA_predicted::otherfeatures]
+# Special source used in RefSeqCoordinateParser.  No species uses this source.
+name            = RefSeq_ncRNA_predicted
+order           = 20
+priority        = 1
+prio_descr      = otherfeatures
+parser          = RefSeqCoordinateParser
+
+[source RefSeq_mRNA_predicted::MULTI]
+# Special source used in RefSeqParser.  No species uses this source.
+name            = RefSeq_mRNA_predicted
+order           = 20
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_ncRNA_predicted::MULTI]
+# Special source used in RefSeqParser.  No species uses this source.
+name            = RefSeq_ncRNA_predicted
+order           = 20
+priority        = 1
+prio_descr      = refseq
+parser          = RefSeqParser
+
+[source RefSeq_peptide::MULTI]
+name            = RefSeq_peptide
+order           = 30
+priority        = 2
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide::gencode]
+name            = RefSeq_peptide
+order           = 30
+priority        = 2
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide::MULTI-fungi]
+# Used by saccharomyces_cerevisiae
+name            = RefSeq_peptide
+order           = 25
+priority        = 2
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide::MULTI-Plants]
+name            = RefSeq_peptide
+order           = 25
+priority        = 2
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide::MULTI-complete]
+# Used by phaeodactylum_tricornutum
+name            = RefSeq_peptide
+order           = 25
+priority        = 2
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide::MULTI-protozoa]
+# Used by dictyostelium_discoideum
+name            = RefSeq_peptide
+order           = 25
+priority        = 2
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide::MULTI-invertebrate]
+# Used by caenorhabditis_elegans, ciona_savignyi, drosophila_melanogaster
+name            = RefSeq_peptide
+order           = 25
+priority        = 2
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide_predicted::MULTI]
+# Special source used in RefSeqGPFFParser.  No species uses this source.
+name            = RefSeq_peptide_predicted
+order           = 30
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqGPFFParser
+
+[source RefSeq_peptide::MULTI-vertebrate]
+# Used by vertebrates
+name            = RefSeq_peptide
+order           = 25
+priority        = 2
+prio_descr      = refseq
+parser          = RefSeqDatabaseParser
+old_parser      = RefSeqGPFFParser
+
+[source SGD_GENE::saccharomyces_cerevisiae]
+# Used by saccharomyces_cerevisiae
+name            = SGD_GENE
+order           = 10
+priority        = 1
+parser          = SGDParser
+
+[source SGD_TRANSLATION::saccharomyces_cerevisiae]
+# Used by saccharomyces_cerevisiae
+name            = SGD_TRANSLATION
+order           = 10
+priority        = 1
+parser          = SGDParser
+
+[source SGD::saccharomyces_cerevisiae]
+# Used by saccharomyces_cerevisiae
+name            = SGD
+order           = 10
+priority        = 1
+parser          = SGDParser
+
+[source PomBase_GENE::schizosaccharomyces_pombe]
+# Used by schizosaccharomyces_pombe
+name            = PomBase_GENE
+order           = 10
+priority        = 1
+parser          = PomBaseParser
+
+[source PomBase_TRANSCRIPT::schizosaccharomyces_pombe]
+# Used by schizosaccharomyces_pombe
+name            = PomBase_TRANSCRIPT
+order           = 10
+priority        = 1
+parser          = PomBaseParser
+
+[source PomBase::schizosaccharomyces_pombe]
+# Used by schizosaccharomyces_pombe
+name            = PomBase
+order           = 10
+priority        = 1
+parser          = PomBaseParser
+
+[source PGSC_GENE::solanum_tuberosum]
+# Used by solanum_tuberosum
+name            = PGSC_GENE
+order           = 10
+priority        = 1
+parser          = PGSCParser
+
+[source PHYTOZOME_GMAX_GENE::glycine_max]
+# Used by glycine_max
+name            = PHYTOZOME_GMAX_GENE
+order           = 10
+priority        = 1
+parser          = PhytozomeGmaxParser
+
+[source UCSC::MULTI]
+# Special source used in UCSCParser.  No species uses this source.
+name            = UCSC
+order           = 70
+priority        = 1
+prio_descr      =
+parser          = UCSCParser
+
+[source UCSC::homo_sapiens]
+# Used by homo_sapiens
+name            = UCSC_hg38
+order           = 70
+priority        = 1
+parser          = UCSC_human_parser
+
+[source UCSC::mus_musculus]
+# Used by mus_musculus
+name            = UCSC_mm10
+order           = 70
+priority        = 1
+parser          = UCSC_mouse_parser
+
+[source Uniprot/SPTREMBL::MULTI-invertebrate]
+name            = Uniprot/SPTREMBL
+order           = 20
+priority        = 3
+parser          = UniProtParser
+dependent_on    = MIM
+
+[source Uniprot/SPTREMBL::MULTI]
+# Used by vertebrates
+name            = Uniprot/SPTREMBL
+order           = 20
+priority        = 3
+prio_descr      = sequence_mapped
+parser          = UniProtDatabaseParser
+old_parser      = UniProtParser
+dependent_on    = MIM
+
+[source Uniprot/SPTREMBL::gencode]
+# Used by human and mouse
+name            = Uniprot/SPTREMBL
+order           = 20
+priority        = 3
+prio_descr      = sequence_mapped
+parser          = UniProtParser
+dependent_on    = MIM
+
+[source Uniprot/SPTREMBL::MULTI-evidence_gt_2]
+# Additional source for entires with evidence at protein level > 2 (numerically) for Uniprot/SPTREMBL::MULTI
+# These are not taken into account when deriving display xrefs or assigning gene status
+name            = Uniprot/SPTREMBL
+order           = 20
+priority        = 10
+prio_descr      = protein_evidence_gt_2
+parser          = UniProtParser
+status          = LOWEVIDENCE
+
+[source Uniprot/SWISSPROT::MULTI]
+# Used by vertebrates
+name            = Uniprot/SWISSPROT
+order           = 20
+priority        = 3
+prio_descr      = sequence_mapped
+parser          = UniProtDatabaseParser
+old_parser      = UniProtParser
+dependent_on    = MIM
+
+[source Uniprot/SWISSPROT::gencode]
+# Used by human and mouse
+name            = Uniprot/SWISSPROT
+order           = 20
+priority        = 3
+prio_descr      = sequence_mapped
+parser          = UniProtParser
+dependent_on    = MIM
+
+[source Uniprot/SWISSPROT::MULTI-invertebrate]
+name            = Uniprot/SWISSPROT
+order           = 20
+priority        = 3
+prio_descr      = sequence_mapped
+parser          = UniProtParser
+dependent_on    = MIM
+
+[source Uniprot/SWISSPROT::DIRECT]
+# Special source used in UniProtParser for direct mappings from Uniprot
+name            = Uniprot/SWISSPROT
+order           = 22
+priority        = 1
+prio_descr      = direct
+parser          = UniProtParser
+
+[source Uniprot/SPTREMBL::DIRECT]
+# Special source used in UniProtParser for direct mappings from Uniprot
+name            = Uniprot/SPTREMBL
+order           = 22
+priority        = 1
+prio_descr      = direct
+parser          = UniProtParser
+
+[source Uniprot_gn]
+# Special source used in UniProtParser foir gene names..
+name            = Uniprot_gn
+order           = 20
+priority        = 1
+parser          = UniProtParser
+
+[source Uniprot_isoform]
+# Special source used in UniProtParser for protein isoforms
+name            = Uniprot_isoform
+order           = 30
+priority        = 1
+parser          = UniProtParser
+
+[source UniProt::protein_id]
+# Special source used in UniProtParser.  No species uses this source.
+name            = protein_id
+order           = 20
+priority        = 1
+parser          = UniProtParser
+
+[source UniProt::PDB]
+# Special source used in UniProtParser.  No species uses this source.
+name            = PDB
+order           = 20
+priority        = 1
+parser          = UniProtParser
+
+[source UniProt::MEROPS]
+# Special source used in UniProtParser.  No species uses this source.
+name            = MEROPS
+order           = 20
+priority        = 1
+parser          = UniProtParser
+
+[source UniProt::EMBL]
+# Special source used in UniProtParser.  No species uses this source.
+name            = EMBL
+order           = 20
+priority        = 1
+parser          = UniProtParser
+
+[source UniProt::ChEMBL]
+# Special source used in UniProtParser.  No species uses this source.
+name            = ChEMBL
+order           = 20
+priority        = 1
+parser          = UniProtParser
+
+[source UniParc::MULTI]
+name        = UniParc
+order       = 20
+priority    = 1
+parser      = ChecksumParser
+
+[source RNACentral::MULTI]
+name        = RNAcentral
+order       = 1
+priority    = 1
+parser      = ChecksumParser
+
+[source PIGGY_trans_name]
+name            = PIGGY_trans_name
+order           = 49
+priority        = 1
+parser          = done_in_official_naming
+
+[source HGNC_trans_name]
+name            = HGNC_trans_name
+order           = 49
+priority        = 1
+parser          = done_in_official_naming
+
+[source VGNC_trans_name]
+name            = VGNC_trans_name
+order           = 49
+priority        = 1
+parser          = done_in_official_naming
+
+[source MGI_automatic_transcript::mus_musculus]
+name            = MGI_automatic_transcript_notransfer
+order           = 49
+priority        = 1
+parser          = done_in_official_naming
+
+[source MGI_trans_name]
+# Used homo_sapiens,mus_musculus
+name            = MGI_trans_name
+order           = 70
+priority        = 1
+parser          = comes via official naming
+
+[source Clone_based_ensembl_transcript::homo_sapiens]
+name            = Clone_based_ensembl_transcript
+order           = 50
+priority        = 1
+parser          = done_in_official_naming
+
+[source Clone_based_ensembl_gene::homo_sapiens]
+name            = Clone_based_ensembl_gene
+order           = 50
+priority        = 1
+parser          = done_in_official_naming
+
+[source Xenopus_Jamboree::xenopus_tropicalis]
+# Used by xenopus_tropicalis
+name            = Xenbase
+order           = 20
+priority        = 1
+parser          = XenopusJamboreeParser
+
+[source ZFIN_ID::danio_rerio#01]
+# Used by danio_rerio
+name            = ZFIN_ID
+order           = 31
+priority        = 1
+prio_descr      = uniprot/refseq
+parser          = ZFINParser
+
+[source ZFIN_ID::danio_rerio#03]
+# Used by danio_rerio
+name            = ZFIN_ID
+order           = 1
+priority        = 10
+prio_descr      = description_only
+parser          = ZFINDescParser
+
+[source ZFIN_ID_trans_name]
+name            = ZFIN_ID_trans_name
+order           = 49
+priority        = 1
+parser          = done_in_official_naming
+
+[source cint_jgi_v1::ciona_intestinalis]
+# Used by ciona_intestinalis
+name            = cint_jgi_v1
+order           = 50
+priority        = 1
+parser          = JGI_ProteinParser
+
+[source RFAM::MULTI]
+# Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, drosophila_pseudoobscura, erinaceus_europaeus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, ictidomys_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus
+name            = RFAM
+order           = 70
+priority        = 1
+parser          = RFAMParser
+
+[source RFAM::EG]
+name            = RFAM
+order           = 70
+priority        = 1
+parser          = CoreXrefParser
+
+
+[source miRBase::MULTI]
+# Used by bos_taurus, canis_familiaris, ciona_intestinalis, ciona_savignyi, danio_rerio, dasypus_novemcinctus, erinaceus_europaeus, ficedula_albicollis, gallus_gallus, gasterosteus_aculeatus, homo_sapiens, loxodonta_africana, macaca_mulatta, monodelphis_domestica, mus_musculus, myotis_lucifugus, oryctolagus_cuniculus, oryzias_latipes, pan_troglodytes,pongo_abelii, rattus_norvegicus, ictidomys_tridecemlineatus, takifugu_rubripes, tupaia_belangeri, xenopus_tropicalis, ornithorhynchus_anatinus
+name            = miRBase
+order           = 70
+priority        = 1
+parser          = miRBaseParser
+
+[source miRBase_trans_name]
+# Used homo_sapiens,mus_musculus
+name            = miRBase_trans_name
+order           = 70
+priority        = 1
+parser          = comes via official naming
+
+[source RFAM_trans_name]
+# Used homo_sapiens,mus_musculus
+name            = RFAM_trans_name
+order           = 70
+priority        = 1
+parser          = comes via official naming
+
+[source Uniprot_gn_trans_name]
+# Used by merged species: homo_sapiens,mus_musculus, danio_rerio and sus_scrofa
+name            = Uniprot_gn_trans_name
+order           = 70
+priority        = 1
+parser          = comes via official naming
+
+[source RNAMMER::MULTI]
+# Used by EnsemblGenomes, e.g. aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
+name            = RNAMMER
+order           = 70
+priority        = 1
+parser          = CoreXrefParser
+
+[source TRNASCAN_SE::MULTI]
+# Used by EnsemblGenomes, e.g. aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
+name            = TRNASCAN_SE
+order           = 70
+priority        = 1
+parser          = CoreXrefParser
+
+[source ncRNA_EG::EG]
+# Used by EnsemblGenomes, e.g. aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
+# replaces TRNASCAN; RNAMMER and RFAM::EG
+name            = ncRNA_EG
+order           = 70
+priority        = 1
+parser          = CoreXrefParser
+
+[source misc_EG::EG]
+# Used by EnsemblGenomes to maintain sources of xrefs which don't have a proper parser yet.
+name            = misc_EG
+order           = 70
+priority        = 1
+parser          = EG_DBParser
+
+[source ENA_GENE::MULTI]
+# Used by aspergillus_niger
+name            = ENA_GENE
+order           = 70
+priority        = 1
+
+[source CADRE::MULTI]
+# Used by aspergillus_clavatus, aspergillus_flavus, aspergillus_fumigatus, aspergillus_nidulans, aspergillus_niger, aspergillus_oryzae, aspergillus_terreus, neosartorya_fischeri
+name            = CADRE
+order           = 70
+priority        = 1
+
+[source CADRE_AFum_A1163::MULTI]
+# Used by aspergillus_fumigatusa1163
+name            = CADRE_Afum_A1163
+order           = 70
+priority        = 1
+
+[source AspGD::MULTI]
+# Used by aspergillus_nidulans
+name            = AspGD
+order           = 70
+priority        = 1
+
+[source GeneDB::MULTI]
+# Used by plasmodium_falciparum, trypanosoma_brucei, leishmania_major, schistosoma_mansoni
+name            = GeneDB
+order           = 70
+priority        = 1
+
+[source phatr_jgi_v2::MULTI]
+# Used by Pt
+name            = phatr_jgi_v2
+order           = 70
+priority        = 1
+
+[source phatr_jgi_v2_bd::MULTI]
+# Used by Pt
+name            = phatr_jgi_v2_bd
+order           = 70
+priority        = 1
+
+[source thaps_jgi_v2::MULTI]
+# Used by Tp
+name            = thaps_jgi_v2
+order           = 70
+priority        = 1
+
+[source physo1_jgi_v1.1_gene::MULTI]
+# Used by Pt
+name            = physo1_jgi_v1.1_gene
+order           = 70
+priority        = 1
+
+[source PGD_GENE::MULTI]
+# Used by Tp
+name            = PGD_GENE
+order           = 70
+priority        = 1
+
+[source physo1_jgi_v1.1::MULTI]
+# Used by Pt
+name            = physo1_jgi_v1.1
+order           = 70
+priority        = 1
+
+[source phyra_jgi_v1.1::MULTI]
+# Used by Pt
+name            = phyra_jgi_v1.1
+order           = 70
+priority        = 1
+
+[source BROAD_P_infestans::MULTI]
+# Used by phytophthora_infestans
+name            = BROAD_P_infestans
+order           = 70
+priority        = 1
+
+[source thaps_jgi_v2_bd::MULTI]
+# Used by Tp
+name            = thaps_jgi_v2_bd
+order           = 70
+priority        = 1
+
+
+[source BROAD_U_maydis::MULTI]
+# Used by ustilago_maydis
+name            = BROAD_U_maydis
+order           = 70
+priority        = 1
+
+[source BROAD_F_oxysporum::MULTI]
+# Used by fusarium_oxysporum
+name            = BROAD_F_oxysporum
+order           = 70
+priority        = 1
+
+[source BROAD_g_zeae::MULTI]
+# Used by gibberella_zeae
+name            = BROAD_G_zeae
+order           = 70
+priority        = 1
+
+[source BROAD_G_moniliformis::MULTI]
+# Used by gibberella_moniliformis
+name            = BROAD_G_moniliformis
+order           = 70
+priority        = 1
+
+[source SCHISTODB::MULTI]
+# Used by schistosoma_mansoni
+name            = SCHISTODB
+order           = 70
+priority        = 1
+
+[source triad_jgi_v1.0::MULTI]
+# Used by trichoplax_adhaerens
+name            = triad_jgi_v1.0
+order           = 70
+priority        = 1
+
+[source wormbase::celegans]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::cbriggsae]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::cbrenneri]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::cremanei]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::cjaponica]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::ppacificus]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::sratti]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+
+[source wormbase::bmalayi]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::ovolvulus]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormbase::tmuris]
+name            = wormbase_all
+order           = 50
+priority        = 1
+parser          = WormbaseDirectParser
+
+[source wormpep_id::wormbase]
+# Used by wormbase core species
+name            = wormpep_id
+order           = 50
+priority        = 1
+parser          = comes from WormbaseDirectParser
+
+[source wormbase_gene::wormbase]
+# Used by wormbase core species
+name            = wormbase_gene
+order           = 50
+priority        = 1
+parser          = comes from WormbaseDirectParser
+
+[source wormbase_locus::wormbase]
+# Used by wormbase core species
+name            = wormbase_locus
+order           = 50
+priority        = 1
+parser          = comes from WormbaseDirectParser
+
+[source wormbase_gseqname::wormbase]
+# Used by wormbase core species
+name            = wormbase_gseqname
+order           = 50
+priority        = 1
+parser          = comes from WormbaseDirectParser
+
+[source wormbase_transcript::wormbase]
+# Used by wormbase core species
+name            = wormbase_transcript
+order           = 50
+priority        = 1
+parser          = comes from WormbaseDirectParser
+
+[source wormbase_cds::wormbase]
+# Used by wormbase core species
+name            = wormbase_cds
+order           = 50
+priority        = 1
+parser          = comes from WormbaseDirectParser
+
+[source Gramene_Pathway::arabidopsis_thaliana]
+# Used by Arabidopsis thaliana, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+[source Gramene_Pathway::brachypodium_distachyon]
+# Used by Brachypodium distachyon, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+[source Gramene_Pathway::solanum_lycopersicum]
+# Used by Tomato, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+[source Gramene_Pathway::zea_mays]
+# Used by Zea mays, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+[source Gramene_Pathway::populus_trichocarpa]
+# Used by Poplar, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+[source Gramene_Pathway::solanum_tuberosum]
+# Used by Solanum tuberosum, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+[source Gramene_Pathway::oryza_sativa]
+# Used by Oryza sativa, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+[source Gramene_Pathway::sorghum_bicolor]
+# Used by Sorghum bicolor, Gramene-specific
+name            = Gramene_Pathway
+order           = 50
+priority        = 1
+parser          = GramenePathwayParser
+
+
+[source PO_GROW::arabidopsis_thaliana]
+# Used by Arabidopsis thaliana, Gramene-specific
+name            = PO
+order           = 85
+priority        = 1
+prio_descr      = main
+dependent_on    = TAIR_TRANSLATION
+parser          = TAIROntologyParser
+
+[source PO_STRU::arabidopsis_thaliana]
+# Used by Arabidopsis thaliana, Gramene-specific
+name            = PO
+order           = 85
+priority        = 1
+prio_descr      = main
+dependent_on    = TAIR_TRANSLATION
+parser          = TAIROntologyParser
+
+[source TAIR_LOCUS::arabidopsis_thaliana]
+# Used by arabidopsis_thaliana
+name            = TAIR_LOCUS
+order           = 1
+priority        = 1
+parser          = TAIRIDParser
+
+[source TAIR_LOCUS_MODEL::arabidopsis_thaliana]
+# Used by arabidopsis_thaliana
+name            = TAIR_LOCUS_MODEL
+order           = 1
+priority        = 1
+parser          = TAIRIDParser
+
+[source TAIR_SYMBOL::arabidopsis_thaliana]
+# Used by arabidopsis_thaliana
+name            = TAIR_SYMBOL
+order           = 1
+priority        = 1
+parser          = TAIRIDParser
+
+[source TAIR_TRANSLATION::arabidopsis_thaliana]
+# Used by arabidopsis_thaliana
+name            = TAIR_TRANSLATION
+order           = 1
+priority        = 1
+
+[source NASC_GENE_ID::arabidopsis_thaliana]
+# Used by arabidopsis_thaliana
+name            = NASC_GENE_ID
+order           = 1
+priority        = 1
+parser          = TAIRIDParser
+
+[source CommunityGO::arabidopsis_thaliana]
+# Used by Arabidopsis thaliana, Gramene-specific
+name            = GO
+order           = 85
+priority        = 1
+prio_descr      = main
+dependent_on    = TAIR_TRANSLATION
+parser          = TAIROntologyParser
+
+
+
+
+########################################################################
+# SPECIES                                                              #
+#                                                                      #
+# Keys:                                                                #
+#   taxonomy_id - taxonomy ID of species/strain                        #
+#                 (multiple comma separated, required)                 #
+#   sources     - sources used for this species/strain                 #
+#                 (multiple comma separated, required)                 #
+#                                                                      #
+########################################################################
+
+########################################################################
+# VERTEBRATES                                                          #
+#                                                                      #
+# Default sources for vertebrates                                      #
+# Additional configuration for species-specific sources                #
+#                                                                      #
+########################################################################
+
+
+[species sars_cov_2]
+taxonomy_id     = 2697049
+sources         = RefSeq_peptide::MULTI,EntrezGene::MULTI,Uniprot/SWISSPROT::MULTI
+
+[species vertebrates]
+taxonomy_id     = 7742
+sources         = EntrezGene::MULTI,Reactome::MULTI,RNACentral::MULTI,RefSeq_dna::MULTI-vertebrate,RefSeq_peptide::MULTI-vertebrate,RefSeq_import::otherfeatures,Uniprot/SPTREMBL::MULTI,Uniprot/SWISSPROT::MULTI,UniParc::MULTI,RFAM::MULTI,miRBase::MULTI,ArrayExpress::MULTI,VGNC::vertebrate
+
+[species homo_sapiens]
+taxonomy_id     = 9606
+sources         = CCDS::homo_sapiens,DBASS3::homo_sapiens,DBASS5::homo_sapiens,HPA::homo_sapiens,HGNC::homo_sapiens#02,MIM::homo_sapiens,MIM2GENE::homo_sapiens,UCSC::homo_sapiens,RefSeq_dna::gencode,RefSeq_peptide::gencode,Uniprot/SPTREMBL::gencode,Uniprot/SWISSPROT::gencode
+
+[species mus_musculus]
+taxonomy_id     = 10090
+sources         = CCDS::mus_musculus,EntrezGene::MULTI,MGI::mus_musculus#01,MGI::mus_musculus#05,UCSC::mus_musculus,RefSeq_dna::gencode,RefSeq_peptide::gencode,Uniprot/SPTREMBL::gencode,Uniprot/SWISSPROT::gencode
+
+[species danio_rerio]
+taxonomy_id     = 7955
+sources         = ZFIN_ID::danio_rerio#01,ZFIN_ID::danio_rerio#03
+
+[species rattus_norvegicus]
+taxonomy_id     = 10116
+sources         = RGD::rattus_norvegicus,RGD::rattus_norvegicus#02
+
+
+
+[species ciona_intestinalis]
+taxonomy_id     = 7719
+sources         = cint_jgi_v1::ciona_intestinalis
+
+[species xenopus_tropicalis]
+taxonomy_id     = 8364
+sources         = Xenopus_Jamboree::xenopus_tropicalis
+
+########################################################################
+# METAZOA                                                              #
+#                                                                      #
+# Default sources for metazoa                                          #
+# Additional configuration for species-specific sources                #
+#                                                                      #
+########################################################################
+
+[species metazoa]
+taxonomy_id     = 33208
+sources         = EntrezGene::MULTI,RefSeq_dna::MULTI-invertebrate,RefSeq_peptide::MULTI-invertebrate,Uniprot/SPTREMBL::MULTI-invertebrate,Uniprot/SWISSPROT::MULTI-invertebrate,UniParc::MULTI,ArrayExpress::EG,ncRNA_EG::EG,RNAMMER::MULTI,miRBase::MULTI,RFAM::EG,TRNASCAN_SE::MULTI,misc_EG::EG
+
+[species drosophila_melanogaster]
+taxonomy_id     = 7227
+sources         = flybase_gene_id::drosophila_melanogaster
+
+[species drosophila_pseudoobscura]
+taxonomy_id     = 46245
+sources         = flybase_gene_id::drosophila_pseudoobscura
+
+[species drosophila_ananassae]
+taxonomy_id     = 7217
+sources         = flybase_gene_id::drosophila_ananassae
+
+[species drosophila_erecta]
+taxonomy_id     = 7220
+sources         = flybase_gene_id::drosophila_erecta
+
+[species drosophila_grimshawi]
+taxonomy_id     = 7222
+sources         = flybase_gene_id::drosophila_grimshawi
+
+[species drosophila_mojavensis]
+taxonomy_id     = 7230
+sources         = flybase_gene_id::drosophila_mojavensis
+
+[species drosophila_persimilis]
+taxonomy_id     = 7234
+sources         = flybase_gene_id::drosophila_persimilis
+
+[species drosophila_sechellia]
+taxonomy_id     = 7238
+sources         = flybase_gene_id::drosophila_sechellia
+
+[species drosophila_simulans]
+taxonomy_id     = 7240
+sources         = flybase_gene_id::drosophila_simulans
+
+[species drosophila_virilis]
+taxonomy_id     = 7244
+sources         = flybase_gene_id::drosophila_virilis
+
+[species drosophila_willistoni]
+taxonomy_id     = 7260
+sources         = flybase_gene_id::drosophila_willistoni
+
+[species drosophila_yakuba]
+taxonomy_id     = 7245
+sources         = flybase_gene_id::drosophila_yakuba
+
+########################################################################
+# FUNGI                                                                #
+#                                                                      #
+# Default sources for fungi                                            #
+# Additional configuration for species-specific sources                #
+#                                                                      #
+########################################################################
+
+[species fungi]
+taxonomy_id     = 4751
+sources         = EntrezGene::MULTI,RefSeq_dna::MULTI-fungi,RefSeq_peptide::MULTI-fungi,Uniprot/SPTREMBL::MULTI,Uniprot/SWISSPROT::MULTI,PHIbase::MULTI,ArrayExpress::EG,RFAM::EG,miRBase::MULTI,RNAMMER::MULTI,TRNASCAN_SE::MULTI,misc_EG::EG
+
+[species saccharomyces_cerevisiae]
+taxonomy_id     = 4932,559292
+sources         = SGD::saccharomyces_cerevisiae
+
+[species schizosaccharomyces_pombe]
+taxonomy_id     = 4896,284812
+sources         = PomBase::schizosaccharomyces_pombe
+
+########################################################################
+# PLANTS                                                               #
+#                                                                      #
+# Default sources for plants                                           #
+# Additional configuration for species-specific sources                #
+#                                                                      #
+########################################################################
+
+[species plants]
+taxonomy_id = 33090
+sources     = EntrezGene::MULTI,Reactome::MULTI,RNACentral::MULTI,RefSeq_dna::MULTI-Plants,RefSeq_import::otherfeatures,Uniprot/SPTREMBL::MULTI,Uniprot/SWISSPROT::MULTI,UniParc::MULTI,RFAM::MULTI,miRBase::MULTI,ArrayExpress::MULTI,ncRNA_EG::EG,misc_EG::EG
+
+[species glycine_max]
+taxonomy_id     = 3847
+sources         = PHYTOZOME_GMAX_GENE::glycine_max
+
+[species solanum_lycopersicum]
+taxonomy_id     = 4081
+sources         = Gramene_Pathway::solanum_lycopersicum
+
+[species solanum_tuberosum]
+taxonomy_id     = 4113
+sources         = PGSC_GENE::solanum_tuberosum,Gramene_Pathway::solanum_tuberosum
+
+[species arabidopsis_thaliana]
+taxonomy_id = 3702
+sources     = Gramene_Pathway::arabidopsis_thaliana,TAIR_LOCUS::arabidopsis_thaliana,CommunityGO::arabidopsis_thaliana,PO_GROW::arabidopsis_thaliana,PO_STRU::arabidopsis_thaliana
+
+[species brachypodium_distachyon]
+taxonomy_id = 15368
+sources     = Gramene_Pathway::brachypodium_distachyon
+
+[species oryza_sativa]
+taxonomy_id = 39947
+sources     = Gramene_Pathway::oryza_sativa
+
+[species populus_trichocarpa]
+taxonomy_id = 3694
+sources     = Gramene_Pathway::populus_trichocarpa
+
+[species sorghum_bicolor]
+taxonomy_id = 4558,91525,171959
+sources     = Gramene_Pathway::sorghum_bicolor
+
+[species zea_mays]
+taxonomy_id = 4577,112001,381124,334825,4579,76912
+sources     = Gramene_Pathway::zea_mays
+
+[species caenorhabditis_elegans]
+taxonomy_id     = 6239
+sources         = wormbase::celegans
+
+[species caenorhabditis_briggsae]
+taxonomy_id     = 6238
+sources         = wormbase::cbriggsae
+
+[species caenorhabditis_remanei]
+taxonomy_id     = 31234
+sources         = wormbase::cremanei
+
+[species caenorhabditis_brenneri]
+taxonomy_id     = 135651
+sources         = wormbase::cbrenneri
+
+[species caenorhabditis_japonica]
+taxonomy_id     = 281687
+sources         = wormbase::cjaponica
+
+[species brugia_malayi]
+taxonomy_id     = 6279
+sources         = wormbase::bmalayi
+
+[species onchocerca_volvulus]
+taxonomy_id     = 6282
+sources         = wormbase::ovolvulus
+
+[species pristionchus_pacificus]
+taxonomy_id     = 54126
+sources         = wormbase::ppacificus
+
+[species strongyloides_ratti]
+taxonomy_id     = 34506
+sources         = wormbase::sratti
+
+[species trichuris_muris]
+taxonomy_id     = 70415
+sources         = wormbase::tmuris
+
+########################################################################
+# PROTISTS                                                             #
+#                                                                      #
+# Default sources for protists                                         #
+# Additional configuration for species-specific sources                #
+#                                                                      #
+########################################################################
+
+[species protist]
+taxonomy_id     = 2759
+sources         = EntrezGene::MULTI,RefSeq_dna::MULTI-complete,RefSeq_peptide::MULTI-complete,Uniprot/SPTREMBL::MULTI,Uniprot/SWISSPROT::MULTI,TRNASCAN_SE::MULTI,RNAMMER::MULTI,ArrayExpress::EG,PHIbase::MULTI,miRBase::MULTI,misc_EG::EG,RFAM::EG
+
diff --git a/src/python/scripts/run_module.py b/src/python/scripts/run_module.py
new file mode 100644
index 000000000..874f02dd8
--- /dev/null
+++ b/src/python/scripts/run_module.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+
+#  Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+#  Copyright [2016-2024] EMBL-European Bioinformatics Institute
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+import importlib
+
+from ensembl.common.Params import Params
+
+def main():
+  params = Params()
+
+  module_name = params.param_required('module')
+  class_name = module_name.split(".")[-1]
+
+  module = importlib.import_module(module_name)
+  module_class = getattr(module, class_name)
+  module_instance = module_class()
+
+  module_instance.run()
+
+if __name__ == '__main__':
+  main()

From 93dfccd099894d55c1c12bb9955fb0c37bbcb915 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Thu, 28 Mar 2024 15:31:18 +0000
Subject: [PATCH 046/128] Add recent changes (112)

---
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index e1b32ec39..eeda0dc8c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -126,7 +126,9 @@ sub run {
       $self->dataflow_output_id($dataflow_params, 2);
     } else {
       # Create list of files
-      my @list_files = `ls $file_name`;
+      opendir(my $dir_handle, $file_name);
+      my @list_files = readdir($dir_handle);
+      closedir($dir_handle);
       if ($preparse) { @list_files = $preparse; }
 
       # For Uniprot and Refseq, files might have been split by species
@@ -137,6 +139,7 @@ sub run {
       }
 
       foreach my $file (@list_files) {
+        next if ($file =~ /^\./);
         $file =~ s/\n//;
         $file = $file_name . "/" . $file;
         if (defined $release_file and $file eq $release_file) { next; }

From d13bd11fcfc4fd92bbc4afdccef8b1a0962fb76b Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Wed, 3 Apr 2024 18:31:37 +0100
Subject: [PATCH 047/128] Added handling of new Transcript attribute
 'gencode_primary'

---
 modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm | 1 +
 modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm         | 1 +
 2 files changed, 2 insertions(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index 6a004324f..a68af0b01 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -264,6 +264,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
 
   my @tags;
   push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'GENCODE primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
   
   # A transcript can have different types of MANE-related attributes (MANE_Select, MANE_Plus_Clinical)
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index 6d88ab72a..f4b09445e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -280,6 +280,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
 
   my @tags;
   push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'GENCODE primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
 
   # A transcript can have different types of MANE-related attributes (MANE_Select, MANE_Plus_Clinical)

From 6765b859467fce2dc7e031c2fd008a54ad450dc0 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Mon, 22 Apr 2024 10:09:10 +0100
Subject: [PATCH 048/128] Using core model from ensembl-py

---
 src/python/ensembl/xrefs/Base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/python/ensembl/xrefs/Base.py b/src/python/ensembl/xrefs/Base.py
index 2122fc94c..9edd28cc4 100644
--- a/src/python/ensembl/xrefs/Base.py
+++ b/src/python/ensembl/xrefs/Base.py
@@ -48,7 +48,7 @@
   TranslationDirectXref as TranslationDirectXrefORM, Synonym as SynonymORM, Pairs as PairsORM, Species as SpeciesORM, \
   SourceMappingMethod as SourceMappingMethodORM, MappingJobs as MappingJobsORM, Mapping as MappingORM
 
-from ensembl.databases.core_db_model import Meta as MetaCORM, Gene as GeneORM, Transcript as TranscriptORM, Analysis as AnalysisORM, \
+from ensembl.core.models import Meta as MetaCORM, Gene as GeneORM, Transcript as TranscriptORM, Analysis as AnalysisORM, \
   ExonTranscript as ExonTranscriptORM, SupportingFeature as SupportingFeatureORM, DnaAlignFeature as DnaAlignFeatureORM, \
   TranscriptAttrib as TranscriptAttribORM, AttribType as AttribTypeORM, AnalysisDescription as AnalysisDescriptionORM, \
   SeqRegion as SeqRegionORM, SeqRegionAttrib as SeqRegionAttribORM, CoordSystem as CoordSystemORM, Translation as TranslationORM, \

From 68347b0ad3bfe66f2e2a97d1ada0e250f36145db Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Mon, 22 Apr 2024 16:13:22 +0000
Subject: [PATCH 049/128] Patched gencode_primary tag for harmonisation
 purposes

---
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm  | 4 +---
 modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm      | 4 +---
 2 files changed, 2 insertions(+), 6 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index f582702b0..269f2b8a4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -264,6 +264,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
 
   my @tags;
   push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
   
   # A transcript can have different types of MANE-related attributes (MANE_Select, MANE_Plus_Clinical)
@@ -274,9 +275,6 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
     push(@tags, $mane_type) if ($mane_type);
   }
 
-  my $gencode_primary = $self->get_all_Attributes('gencode_primary');
-  push(@tags, 'GENCODE Primary') if @{$gencode_primary};
-
   $summary{'tag'} = \@tags if @tags;
 
   # Check for seq-edits
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index b32ad3646..537675025 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -280,6 +280,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
 
   my @tags;
   push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
 
   # A transcript can have different types of MANE-related attributes (MANE_Select, MANE_Plus_Clinical)
@@ -290,9 +291,6 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
     push(@tags, $mane_type) if ($mane_type);
   }
 
-  my $gencode_primary = $self->get_all_Attributes('gencode_primary');
-  push(@tags, 'GENCODE Primary') if @{$gencode_primary};
-
   $summary{'tag'} = \@tags if @tags;
 
   # Add xrefs

From e1d6f8b8fc10177c1d0a806528db6b88941ecee3 Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Mon, 22 Apr 2024 16:22:05 +0000
Subject: [PATCH 050/128] Fixed gencode_primary string

---
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index a68af0b01..269f2b8a4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -264,7 +264,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
 
   my @tags;
   push(@tags, 'basic') if $self->gencode_basic();
-  push(@tags, 'GENCODE primary') if $self->gencode_primary();
+  push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
   
   # A transcript can have different types of MANE-related attributes (MANE_Select, MANE_Plus_Clinical)
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index f4b09445e..537675025 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -280,7 +280,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
 
   my @tags;
   push(@tags, 'basic') if $self->gencode_basic();
-  push(@tags, 'GENCODE primary') if $self->gencode_primary();
+  push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
 
   # A transcript can have different types of MANE-related attributes (MANE_Select, MANE_Plus_Clinical)

From bccac7367b3ef23e7ca1bac3f767d2d5cda11dbf Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-02.ebi.ac.uk>
Date: Tue, 23 Apr 2024 09:18:53 +0100
Subject: [PATCH 051/128] Moving all db models to ensembl-py

---
 src/python/ensembl/databases/core_db_model.py | 997 ------------------
 .../ensembl/databases/xref_source_db_model.py |  39 -
 .../ensembl/databases/xref_update_db_model.py | 266 -----
 src/python/ensembl/xrefs/Base.py              |   4 +-
 4 files changed, 2 insertions(+), 1304 deletions(-)
 delete mode 100644 src/python/ensembl/databases/core_db_model.py
 delete mode 100644 src/python/ensembl/databases/xref_source_db_model.py
 delete mode 100644 src/python/ensembl/databases/xref_update_db_model.py

diff --git a/src/python/ensembl/databases/core_db_model.py b/src/python/ensembl/databases/core_db_model.py
deleted file mode 100644
index 2ca2c3213..000000000
--- a/src/python/ensembl/databases/core_db_model.py
+++ /dev/null
@@ -1,997 +0,0 @@
-from sqlalchemy import (Column, Index, Enum, ForeignKey, DateTime, Float, DECIMAL, text)
-from sqlalchemy.dialects.mysql import (INTEGER, VARCHAR, TINYINT, SET, SMALLINT, TEXT, LONGTEXT, BIGINT, DOUBLE, MEDIUMTEXT, TINYTEXT)
-from sqlalchemy.ext.declarative import declarative_base
-
-Base = declarative_base()
-
-class Assembly(Base):
-  __tablename__ = "assembly"
-  __table_args__ = (
-    Index("asm_seq_region_idx", "asm_seq_region_id", "asm_start"),
-  )
-
-  asm_seq_region_id = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True)
-  cmp_seq_region_id = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True)
-  asm_start         = Column(INTEGER(10), primary_key=True)
-  asm_end           = Column(INTEGER(10), primary_key=True)
-  cmp_start         = Column(INTEGER(10), primary_key=True)
-  cmp_end           = Column(INTEGER(10), primary_key=True)
-  ori               = Column(TINYINT(4), primary_key=True)
-
-class AssemblyException(Base):
-  __tablename__ = "assembly_exception"
-  __table_args__ = (
-    Index("sr_idx", "seq_region_id", "seq_region_start"),
-    Index("ex_idx", "exc_seq_region_id", "exc_seq_region_start")
-  )
-
-  assembly_exception_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id         = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start      = Column(INTEGER(10), nullable=False)
-  seq_region_end        = Column(INTEGER(10), nullable=False)
-  exc_type              = Column(Enum('HAP', 'PAR', 'PATCH_FIX', 'PATCH_NOVEL'), nullable=False)
-  exc_seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  exc_seq_region_start  = Column(INTEGER(10), nullable=False)
-  exc_seq_region_end    = Column(INTEGER(10), nullable=False)
-  ori                   = Column(INTEGER(11), nullable=False)
-
-class CoordSystem(Base):
-  __tablename__ = "coord_system"
-  __table_args__ = (
-    Index("rank_idx", "rank", "species_id", unique=True),
-    Index("name_idx", "name", "version", "species_id", unique=True)
-  )
-
-  coord_system_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  species_id      = Column(INTEGER(10), nullable=False, server_default=text("1"), index=True)
-  name            = Column(VARCHAR(40), nullable=False)
-  version         = Column(VARCHAR(255))
-  rank            = Column(INTEGER(11), nullable=False)
-  attrib          = Column(SET('default_version', 'sequence_level'))
-
-class DataFile(Base):
-  __tablename__ = "data_file"
-  __table_args__ = (
-    Index("df_unq_idx", "coord_system_id", "analysis_id", "name", "file_type", unique=True),
-  )
-
-  data_file_id    = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  coord_system_id = Column(INTEGER(10), ForeignKey("coord_system.coord_system_id"), nullable=False)
-  analysis_id     = Column(SMALLINT(5), nullable=False, index=True)
-  name            = Column(VARCHAR(100), nullable=False, index=True)
-  version_lock    = Column(TINYINT(1), nullable=False, server_default=text("0"))
-  absolute        = Column(TINYINT(1), nullable=False, server_default=text("0"))
-  url             = Column(TEXT)
-  file_type       = Column(Enum('BAM', 'BAMCOV', 'BIGBED', 'BIGWIG', 'VCF'))
-
-class Dna(Base):
-  __tablename__ = "dna"
-
-  seq_region_id = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True)
-  sequence      = Column(LONGTEXT, nullable=False)
-
-class GenomeStatistics(Base):
-  __tablename__ = "genome_statistics"
-  __table_args__ = (
-    Index("stats_uniq", "statistic", "attrib_type_id", "species_id", unique=True),
-  )
-
-  genome_statistics_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  statistic            = Column(VARCHAR(128), nullable=False)
-  value                = Column(BIGINT(11), nullable=False, server_default=text("0"))
-  species_id           = Column(INTEGER(10), server_default=text("1"))
-  attrib_type_id       = Column(INTEGER(10), nullable=False)
-  timestamp            = Column(DateTime)
-
-class Karyotype(Base):
-  __tablename__ = "karyotype"
-  __table_args__ = (
-    Index("region_band_idx", "seq_region_id", "band"),
-  )
-
-  karyotype_id     = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id    = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start = Column(INTEGER(10), nullable=False)
-  seq_region_end   = Column(INTEGER(10), nullable=False)
-  band             = Column(VARCHAR(40))
-  stain            = Column(VARCHAR(40))
-
-class Meta(Base):
-  __tablename__ = "meta"
-  __table_args__ = (
-    Index("species_value_idx", "species_id", "meta_value"),
-    Index("species_key_value_idx", "species_id", "meta_key", "meta_value", unique=True)
-  )
-
-  meta_id    = Column(INTEGER(11), primary_key=True, autoincrement=True)
-  species_id = Column(INTEGER(10), server_default=text("1"))
-  meta_key   = Column(VARCHAR(40), nullable=False)
-  meta_value = Column(VARCHAR(255), nullable=False)
-
-class MetaCoord(Base):
-  __tablename__ = "meta_coord"
-
-  table_name      = Column(VARCHAR(40), primary_key=True)
-  coord_system_id = Column(INTEGER(10), ForeignKey("coord_system.coord_system_id"), primary_key=True)
-  max_length      = Column(INTEGER(11))
-
-class SeqRegion(Base):
-  __tablename__ = "seq_region"
-  __table_args__ = (
-    Index("name_cs_idx", "name", "coord_system_id", unique=True),
-  )
-
-  seq_region_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  name            = Column(VARCHAR(255), nullable=False)
-  coord_system_id = Column(INTEGER(10), ForeignKey("coord_system.coord_system_id"), nullable=False, index=True)
-  length          = Column(INTEGER(10), nullable=False)
-
-class SeqRegionSynonym(Base):
-  __tablename__ = "seq_region_synonym"
-  __table_args__ = (
-    Index("syn_idx", "synonym", "seq_region_id", unique=True),
-  )
-
-  seq_region_synonym_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id         = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, index=True)
-  synonym               = Column(VARCHAR(250), nullable=False)
-  external_db_id        = Column(INTEGER(10), ForeignKey("external_db.external_db_id"))
-
-class SeqRegionAttrib(Base):
-  __tablename__ = "seq_region_attrib"
-  __table_args__ = (
-    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
-    Index("val_only_idx", "value", mysql_length=40),
-    Index("region_attribx", "seq_region_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
-  )
-
-  seq_region_id  = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), primary_key=True, server_default=text("0"), index=True)
-  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
-      primary_key=True, server_default=text("0"))
-  value          = Column(TEXT, primary_key=True)
-
-class AltAllele(Base):
-  __tablename__ = "alt_allele"
-  __table_args__ = (
-    Index("gene_alt_group_idx", "gene_id", "alt_allele_group_id"),
-  )
-
-  alt_allele_id       = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  alt_allele_group_id = Column(INTEGER(10), ForeignKey("alt_allele_group.alt_allele_group_id"), nullable=False)
-  gene_id             = Column(INTEGER(10), ForeignKey("gene.gene_id"), nullable=False, index=True)
-
-class AltAlleleAttrib(Base):
-  __tablename__ = "alt_allele_attrib"
-
-  alt_allele_id = Column(INTEGER(10), primary_key=True)
-  attrib        = Column(Enum('IS_REPRESENTATIVE', 'IS_MOST_COMMON_ALLELE', 'IN_CORRECTED_ASSEMBLY', 'HAS_CODING_POTENTIAL', 'IN_ARTIFICIALLY_DUPLICATED_ASSEMBLY', 'IN_SYNTENIC_REGION', 'HAS_SAME_UNDERLYING_DNA_SEQUENCE', 'IN_BROKEN_ASSEMBLY_REGION', 'IS_VALID_ALTERNATE', 'SAME_AS_REPRESENTATIVE', 'SAME_AS_ANOTHER_ALLELE', 'MANUALLY_ASSIGNED', 'AUTOMATICALLY_ASSIGNED', 'IS_PAR'), primary_key=True)
-
-class AltAlleleGroup(Base):
-  __tablename__ = "alt_allele_group"
-
-  alt_allele_group_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-
-class Analysis(Base):
-  __tablename__ = "analysis"
-
-  analysis_id     = Column(SMALLINT(5), primary_key=True, autoincrement=True)
-  created         = Column(DateTime)
-  logic_name      = Column(VARCHAR(128), nullable=False, index=True, unique=True)
-  db              = Column(VARCHAR(120))
-  db_version      = Column(VARCHAR(40))
-  db_file         = Column(VARCHAR(120))
-  program         = Column(VARCHAR(80))
-  program_version = Column(VARCHAR(40))
-  program_file    = Column(VARCHAR(80))
-  parameters      = Column(TEXT)
-  module          = Column(VARCHAR(80))
-  module_version  = Column(VARCHAR(40))
-  gff_source      = Column(VARCHAR(40))
-  gff_feature     = Column(VARCHAR(40))
-
-class AnalysisDescription(Base):
-  __tablename__ = "analysis_description"
-
-  analysis_id   = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), primary_key=True)
-  description   = Column(TEXT)
-  display_label = Column(VARCHAR(255), nullable=False)
-  displayable   = Column(TINYINT(1), nullable=False, server_default=text("1"))
-  web_data      = Column(TEXT)
-
-class AttribType(Base):
-  __tablename__ = "attrib_type"
-
-  attrib_type_id = Column(SMALLINT(5), primary_key=True, autoincrement=True)
-  code           = Column(VARCHAR(20), nullable=False, index=True, unique=True, server_default=text("''"))
-  name           = Column(VARCHAR(255), nullable=False, server_default=text("''"))
-  description    = Column(TEXT)
-
-class DnaAlignFeature(Base):
-  __tablename__ = "dna_align_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "analysis_id", "seq_region_start", "score"),
-    Index("seq_region_idx_2", "seq_region_id", "seq_region_start")
-  )
-
-  dna_align_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id        = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start     = Column(INTEGER(10), nullable=False)
-  seq_region_end       = Column(INTEGER(10), nullable=False)
-  seq_region_strand    = Column(TINYINT(1), nullable=False)
-  hit_start            = Column(INTEGER(11), nullable=False)
-  hit_end              = Column(INTEGER(11), nullable=False)
-  hit_strand           = Column(TINYINT(1), nullable=False)
-  hit_name             = Column(VARCHAR(40), nullable=False, index=True)
-  analysis_id          = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  score                = Column(DOUBLE)
-  evalue               = Column(DOUBLE)
-  perc_ident           = Column(Float)
-  cigar_line           = Column(TEXT)
-  external_db_id       = Column(INTEGER(10), ForeignKey("external_db.external_db_id"), index=True)
-  hcoverage            = Column(DOUBLE)
-  align_type           = Column(Enum('ensembl', 'cigar', 'vulgar', 'mdtag'), server_default=text("'ensembl'"))
-
-class DnaAlignFeatureAttrib(Base):
-  __tablename__ = "dna_align_feature_attrib"
-  __table_args__ = (
-    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
-    Index("val_only_idx", "value", mysql_length=40),
-    Index("dna_align_feature_attribx", "dna_align_feature_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
-  )
-
-  dna_align_feature_id = Column(INTEGER(10), ForeignKey("dna_align_feature.dna_align_feature_id"), primary_key=True, index=True)
-  attrib_type_id       = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"), primary_key=True)
-  value                = Column(TEXT, primary_key=True)
-
-class Exon(Base):
-  __tablename__ = "exon"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-    Index("stable_id_idx", "stable_id", "version")
-  )
-
-  exon_id           = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start  = Column(INTEGER(10), nullable=False)
-  seq_region_end    = Column(INTEGER(10), nullable=False)
-  seq_region_strand = Column(TINYINT(2), nullable=False)
-  phase             = Column(TINYINT(2), nullable=False)
-  end_phase         = Column(TINYINT(2), nullable=False)
-  is_current        = Column(TINYINT(1), nullable=False, server_default=text("1"))
-  is_constitutive   = Column(TINYINT(1), nullable=False, server_default=text("0"))
-  stable_id         = Column(VARCHAR(128))
-  version           = Column(SMALLINT(5))
-  created_date      = Column(DateTime)
-  modified_date     = Column(DateTime)
-
-class ExonTranscript(Base):
-  __tablename__ = "exon_transcript"
-
-  exon_id       = Column(INTEGER(10), ForeignKey("exon.exon_id"), primary_key=True, index=True)
-  transcript_id = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, index=True)
-  rank          = Column(INTEGER(10), primary_key=True)
-
-class Gene(Base):
-  __tablename__ = "gene"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-    Index("stable_id_idx", "stable_id", "version")
-  )
-
-  gene_id                 = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  biotype                 = Column(VARCHAR(40), nullable=False)
-  analysis_id             = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  seq_region_id           = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start        = Column(INTEGER(10), nullable=False)
-  seq_region_end          = Column(INTEGER(10), nullable=False)
-  seq_region_strand       = Column(TINYINT(2), nullable=False)
-  display_xref_id         = Column(INTEGER(10), ForeignKey("xref.xref_id"), index=True)
-  source                  = Column(VARCHAR(40), nullable=False)
-  description             = Column(TEXT)
-  is_current              = Column(TINYINT(1), nullable=False, server_default=text("1"))
-  canonical_transcript_id = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), nullable=False, index=True)
-  stable_id               = Column(VARCHAR(128))
-  version                 = Column(SMALLINT(5))
-  created_date            = Column(DateTime)
-  modified_date           = Column(DateTime)
-
-class GeneAttrib(Base):
-  __tablename__ = "gene_attrib"
-  __table_args__ = (
-    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
-    Index("val_only_idx", "value", mysql_length=40),
-    Index("gene_attribx", "gene_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
-  )
-
-  gene_id        = Column(INTEGER(10), ForeignKey("gene.gene_id"), primary_key=True, server_default=text("0"), index=True)
-  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
-      primary_key=True, server_default=text("0"))
-  value          = Column(TEXT, primary_key=True)
-
-class ProteinAlignFeature(Base):
-  __tablename__ = "protein_align_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "analysis_id", "seq_region_start", "score"),
-    Index("seq_region_idx_2", "seq_region_id", "seq_region_start")
-  )
-
-  protein_align_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start         = Column(INTEGER(10), nullable=False)
-  seq_region_end           = Column(INTEGER(10), nullable=False)
-  seq_region_strand        = Column(TINYINT(1), nullable=False, server_default=text("1"))
-  hit_start                = Column(INTEGER(10), nullable=False)
-  hit_end                  = Column(INTEGER(10), nullable=False)
-  hit_name                 = Column(VARCHAR(40), nullable=False, index=True)
-  analysis_id              = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  score                    = Column(DOUBLE)
-  evalue                   = Column(DOUBLE)
-  perc_ident               = Column(Float)
-  cigar_line               = Column(TEXT)
-  external_db_id           = Column(INTEGER(10), ForeignKey("external_db.external_db_id"), index=True)
-  hcoverage                = Column(DOUBLE)
-  align_type               = Column(Enum('ensembl', 'cigar', 'vulgar', 'mdtag'), server_default=text("'ensembl'"))
-
-class ProteinFeature(Base):
-  __tablename__ = "protein_feature"
-  __table_args__ = (
-    Index("aln_idx", "translation_id", "hit_name", "seq_start", "seq_end", "hit_start", "hit_end", "analysis_id", unique=True),
-  )
-
-  protein_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  translation_id     = Column(INTEGER(10), ForeignKey("translation.translation_id"), nullable=False, index=True)
-  seq_start          = Column(INTEGER(10), nullable=False)
-  seq_end            = Column(INTEGER(10), nullable=False)
-  hit_start          = Column(INTEGER(10), nullable=False)
-  hit_end            = Column(INTEGER(10), nullable=False)
-  hit_name           = Column(VARCHAR(40), nullable=False, index=True)
-  analysis_id        = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  score              = Column(DOUBLE)
-  evalue             = Column(DOUBLE)
-  perc_ident         = Column(Float)
-  external_data      = Column(TEXT)
-  hit_description    = Column(TEXT)
-  cigar_line         = Column(TEXT)
-  align_type         = Column(Enum('ensembl', 'cigar', 'cigarplus', 'vulgar', 'mdtag'))
-
-class SupportingFeature(Base):
-  __tablename__ = "supporting_feature"
-  __table_args__ = (
-    Index("all_idx", "exon_id", "feature_type", "feature_id", unique=True),
-    Index("feature_idx", "feature_type", "feature_id")
-  )
-
-  exon_id      = Column(INTEGER(10), ForeignKey("exon.exon_id"), primary_key=True, server_default=text("0"))
-  feature_type = Column(Enum('dna_align_feature', 'protein_align_feature'), primary_key=True)
-  feature_id   = Column(INTEGER(10), primary_key=True, server_default=text("0"))
-
-class Transcript(Base):
-  __tablename__ = "transcript"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-    Index("stable_id_idx", "stable_id", "version")
-  )
-
-  transcript_id            = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  gene_id                  = Column(INTEGER(10), ForeignKey("gene.gene_id"), index=True)
-  analysis_id              = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start         = Column(INTEGER(10), nullable=False)
-  seq_region_end           = Column(INTEGER(10), nullable=False)
-  seq_region_strand        = Column(TINYINT(2), nullable=False)
-  display_xref_id          = Column(INTEGER(10), ForeignKey("xref.xref_id"), index=True)
-  source                   = Column(VARCHAR(40), nullable=False, server_default=text("'ensembl'"))
-  biotype                  = Column(VARCHAR(40), nullable=False)
-  description              = Column(TEXT)
-  is_current               = Column(TINYINT(1), nullable=False, server_default=text("1"))
-  canonical_translation_id = Column(INTEGER(10), ForeignKey("translation.translation_id"), index=True, unique=True)
-  stable_id                = Column(VARCHAR(128))
-  version                  = Column(SMALLINT(5))
-  created_date             = Column(DateTime)
-  modified_date            = Column(DateTime)
-
-class TranscriptAttrib(Base):
-  __tablename__ = "transcript_attrib"
-  __table_args__ = (
-    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
-    Index("val_only_idx", "value", mysql_length=40),
-    Index("transcript_attribx", "transcript_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
-  )
-
-  transcript_id  = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, server_default=text("0"), index=True)
-  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
-      primary_key=True, server_default=text("0"))
-  value          = Column(TEXT, primary_key=True)
-
-class TranscriptSupportingFeature(Base):
-  __tablename__ = "transcript_supporting_feature"
-  __table_args__ = (
-    Index("feature_idx", "feature_type", "feature_id"),
-    Index("all_idx", "transcript_id", "feature_type", "feature_id", unique=True)
-  )
-
-  transcript_id = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, server_default=text("0"))
-  feature_type  = Column(Enum('dna_align_feature', 'protein_align_feature'), primary_key=True)
-  feature_id    = Column(INTEGER(10), primary_key=True, server_default=text("0"))
-
-class Translation(Base):
-  __tablename__ = "translation"
-  __table_args__ = (
-    Index("stable_id_idx", "stable_id", "version"),
-  )
-
-  translation_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  transcript_id  = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), nullable=False, index=True)
-  seq_start      = Column(INTEGER(10), nullable=False)
-  start_exon_id  = Column(INTEGER(10), ForeignKey("exon.exon_id"), nullable=False)
-  seq_end        = Column(INTEGER(10), nullable=False)
-  end_exon_id    = Column(INTEGER(10), ForeignKey("exon.exon_id"), nullable=False)
-  stable_id      = Column(VARCHAR(128))
-  version        = Column(SMALLINT(5))
-  created_date   = Column(DateTime)
-  modified_date  = Column(DateTime)
-
-class TranslationAttrib(Base):
-  __tablename__ = "translation_attrib"
-  __table_args__ = (
-    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
-    Index("val_only_idx", "value", mysql_length=40),
-    Index("translation_attribx", "translation_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
-  )
-
-  translation_id = Column(INTEGER(10), ForeignKey("translation.translation_id"), primary_key=True, server_default=text("0"), index=True)
-  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"),
-      primary_key=True, server_default=text("0"))
-  value          = Column(TEXT, primary_key=True)
-
-class DensityFeature(Base):
-  __tablename__ = "density_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "density_type_id", "seq_region_id", "seq_region_start"),
-  )
-
-  density_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  density_type_id    = Column(INTEGER(10), ForeignKey("density_type.density_type_id"), nullable=False)
-  seq_region_id      = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, index=True)
-  seq_region_start   = Column(INTEGER(10), nullable=False)
-  seq_region_end     = Column(INTEGER(10), nullable=False)
-  density_value      = Column(Float, nullable=False)
-
-class DensityType(Base):
-  __tablename__ = "density_type"
-  __table_args__ = (
-    Index("analysis_idx", "analysis_id", "block_size", "region_features", unique=True),
-  )
-
-  density_type_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  analysis_id     = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
-  block_size      = Column(INTEGER(11), nullable=False)
-  region_features = Column(INTEGER(11), nullable=False)
-  value_type      = Column(Enum('sum', 'ratio'), nullable=False)
-
-class Ditag(Base):
-  __tablename__ = "ditag"
-
-  ditag_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  name      = Column(VARCHAR(30), nullable=False)
-  tag_type  = Column("type", VARCHAR(30), nullable=False)
-  tag_count = Column(SMALLINT(6), nullable=False, server_default=text("1"))
-  sequence  = Column(TINYTEXT, nullable=False)
-
-class DitagFeature(Base):
-  __tablename__ = "ditag_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start", "seq_region_end"),
-  )
-
-  ditag_feature_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  ditag_id          = Column(INTEGER(10), ForeignKey("ditag.ditag_id"), nullable=False, index=True, server_default=text("0"))
-  ditag_pair_id     = Column(INTEGER(10), nullable=False, index=True, server_default=text("0"))
-  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, server_default=text("0"))
-  seq_region_start  = Column(INTEGER(10), nullable=False, server_default=text("0"))
-  seq_region_end    = Column(INTEGER(10), nullable=False, server_default=text("0"))
-  seq_region_strand = Column(TINYINT(1), nullable=False, server_default=text("0"))
-  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, server_default=text("0"))
-  hit_start         = Column(INTEGER(10), nullable=False, server_default=text("0"))
-  hit_end           = Column(INTEGER(10), nullable=False, server_default=text("0"))
-  hit_strand        = Column(TINYINT(1), nullable=False, server_default=text("0"))
-  cigar_line        = Column(TINYTEXT, nullable=False)
-  ditag_side        = Column(Enum('F', 'L', 'R'), nullable=False)
-
-class IntronSupportingEvidence(Base):
-  __tablename__ = "intron_supporting_evidence"
-  __table_args__ = (
-    Index("intron_all_idx", "analysis_id", "analysis_id", "seq_region_id", "seq_region_start", "seq_region_end", "seq_region_strand", "hit_name", unique=True),
-    Index("seq_region_idx", "seq_region_id", "seq_region_start")
-  )
-
-  intron_supporting_evidence_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  analysis_id                   = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
-  seq_region_id                 = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start              = Column(INTEGER(10), nullable=False)
-  seq_region_end                = Column(INTEGER(10), nullable=False)
-  seq_region_strand             = Column(TINYINT(2), nullable=False)
-  hit_name                      = Column(VARCHAR(100), nullable=False)
-  score                         = Column(DECIMAL(10, 3))
-  score_type                    = Column(Enum('NONE', 'DEPTH'), server_default=text("'NONE'"))
-  is_splice_canonical           = Column(TINYINT(1), nullable=False, server_default=text("0"))
-
-class Map(Base):
-  __tablename__ = "map"
-
-  map_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  map_name = Column(VARCHAR(30), nullable=False)
-
-class Marker(Base):
-  __tablename__ = "marker"
-  __table_args__ = (
-    Index("marker_idx", "marker_id", "priority"),
-  )
-
-  marker_id                 = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  display_marker_synonym_id = Column(INTEGER(10), ForeignKey("marker_synonym.marker_synonym_id"), index=True)
-  left_primer               = Column(VARCHAR(100), nullable=False)
-  right_primer              = Column(VARCHAR(100), nullable=False)
-  min_primer_dist           = Column(INTEGER(10), nullable=False)
-  max_primer_dist           = Column(INTEGER(10), nullable=False)
-  priority                  = Column(INTEGER(11))
-  marker_type               = Column("type", Enum('est', 'microsatellite'))
-
-class MarkerFeature(Base):
-  __tablename__ = "marker_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-  )
-
-  marker_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  marker_id         = Column(INTEGER(10), ForeignKey("marker.marker_id"), nullable=False)
-  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start  = Column(INTEGER(10), nullable=False)
-  seq_region_end    = Column(INTEGER(10), nullable=False)
-  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  map_weight        = Column(INTEGER(10))
-
-class MarkerMapLocation(Base):
-  __tablename__ = "marker_map_location"
-  __table_args__ = (
-    Index("map_idx", "map_id", "chromosome_name", "position"),
-  )
-
-  marker_id         = Column(INTEGER(10), ForeignKey("marker.marker_id"), primary_key=True)
-  map_id            = Column(INTEGER(10), ForeignKey("map.map_id"), primary_key=True)
-  chromosome_name   = Column(VARCHAR(15), nullable=False)
-  marker_synonym_id = Column(INTEGER(10), ForeignKey("marker_synonym.marker_synonym_id"), nullable=False)
-  position          = Column(VARCHAR(15), nullable=False)
-  lod_score         = Column(DOUBLE)
-
-class MarkerSynonym(Base):
-  __tablename__ = "marker_synonym"
-  __table_args__ = (
-    Index("marker_synonym_idx", "marker_synonym_id", "name"),
-  )
-
-  marker_synonym_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  marker_id         = Column(INTEGER(10), ForeignKey("marker.marker_id"), nullable=False, index=True)
-  source            = Column(VARCHAR(20))
-  name              = Column(VARCHAR(50))
-
-class MiscAttrib(Base):
-  __tablename__ = "misc_attrib"
-  __table_args__ = (
-    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
-    Index("val_only_idx", "value", mysql_length=40),
-    Index("misc_attribx", "misc_feature_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
-  )
-
-  misc_feature_id = Column(INTEGER(10), ForeignKey("misc_feature.misc_feature_id"), primary_key=True, index=True, server_default=text("0"))
-  attrib_type_id  = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"), primary_key=True, server_default=text("0"))
-  value           = Column(TEXT, primary_key=True, index=True)
-
-class MiscFeature(Base):
-  __tablename__ = "misc_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-  )
-
-  misc_feature_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False, server_default=text("0"))
-  seq_region_start  = Column(INTEGER(10), nullable=False, server_default=text("0"))
-  seq_region_end    = Column(INTEGER(10), nullable=False, server_default=text("0"))
-  seq_region_strand = Column(TINYINT(4), nullable=False, server_default=text("0"))
-
-class MiscFeatureMiscSet(Base):
-  __tablename__ = "misc_feature_misc_set"
-  __table_args__ = (
-    Index("reverse_idx", "misc_set_id", "misc_feature_id"),
-  )
-
-  misc_feature_id = Column(INTEGER(10), ForeignKey("misc_feature.misc_feature_id"), primary_key=True, server_default=text("0"))
-  misc_set_id     = Column(SMALLINT(5), ForeignKey("misc_set.misc_set_id"), primary_key=True, server_default=text("0"))
-
-class MiscSet(Base):
-  __tablename__ = "misc_set"
-
-  misc_set_id = Column(SMALLINT(5), primary_key=True, autoincrement=True)
-  code        = Column(VARCHAR(25), nullable=False, index=True, unique=True, server_default=text("''"))
-  name        = Column(VARCHAR(255), nullable=False, server_default=text("''"))
-  description = Column(TEXT, nullable=False)
-  max_length  = Column(INTEGER(10), nullable=False)
-
-class PredictionExon(Base):
-  __tablename__ = "prediction_exon"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-  )
-
-  prediction_exon_id       = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  prediction_transcript_id = Column(INTEGER(10), ForeignKey("prediction_transcript.prediction_transcript_id"), nullable=False, index=True)
-  exon_rank                = Column(SMALLINT(5), nullable=False)
-  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start         = Column(INTEGER(10), nullable=False)
-  seq_region_end           = Column(INTEGER(10), nullable=False)
-  seq_region_strand        = Column(TINYINT(4), nullable=False)
-  start_phase              = Column(TINYINT(4), nullable=False)
-  score                    = Column(DOUBLE)
-  p_value                  = Column(DOUBLE)
-
-class PredictionTranscript(Base):
-  __tablename__ = "prediction_transcript"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-  )
-
-  prediction_transcript_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id            = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start         = Column(INTEGER(10), nullable=False)
-  seq_region_end           = Column(INTEGER(10), nullable=False)
-  seq_region_strand        = Column(TINYINT(4), nullable=False)
-  analysis_id              = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  display_label            = Column(VARCHAR(255))
-
-class RepeatConsensus(Base):
-  __tablename__ = "repeat_consensus"
-  __table_args__ = (
-    Index("consensus", "repeat_consensus", mysql_length=10),
-  )
-
-  repeat_consensus_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  repeat_name         = Column(VARCHAR(255), nullable=False, index=True)
-  repeat_class        = Column(VARCHAR(100), nullable=False, index=True)
-  repeat_type         = Column(VARCHAR(40), nullable=False, index=True)
-  repeat_consensus    = Column(TEXT)
-
-class RepeatFeature(Base):
-  __tablename__ = "repeat_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-  )
-
-  repeat_feature_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id       = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start    = Column(INTEGER(10), nullable=False)
-  seq_region_end      = Column(INTEGER(10), nullable=False)
-  seq_region_strand   = Column(TINYINT(1), nullable=False, server_default=text("1"))
-  repeat_start        = Column(INTEGER(10), nullable=False)
-  repeat_end          = Column(INTEGER(10), nullable=False)
-  repeat_consensus_id = Column(INTEGER(10), ForeignKey("repeat_consensus.repeat_consensus_id"), nullable=False, index=True)
-  analysis_id         = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  score               = Column(DOUBLE)
-
-class SimpleFeature(Base):
-  __tablename__ = "simple_feature"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-  )
-
-  simple_feature_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start  = Column(INTEGER(10), nullable=False)
-  seq_region_end    = Column(INTEGER(10), nullable=False)
-  seq_region_strand = Column(TINYINT(1), nullable=False)
-  display_label     = Column(VARCHAR(255), nullable=False, index=True)
-  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False, index=True)
-  score             = Column(DOUBLE)
-
-class TranscriptIntronSupportingEvidence(Base):
-  __tablename__ = "transcript_intron_supporting_evidence"
-
-  transcript_id                 = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), primary_key=True, index=True)
-  intron_supporting_evidence_id = Column(INTEGER(10), primary_key=True)
-  previous_exon_id              = Column(INTEGER(10), nullable=False)
-  next_exon_id                  = Column(INTEGER(10), nullable=False)
-
-# class GeneArchive(Base):
-#   __tablename__ = "gene_archive"
-
-#   gene_stable_id        = Column(VARCHAR(128), nullable=False)
-#   gene_version          = Column(SMALLINT(6), nullable=False, server_default=text("1"))
-#   transcript_stable_id  = Column(VARCHAR(128), nullable=False)
-#   transcript_version    = Column(SMALLINT(6), nullable=False, server_default=text("1"))
-#   translation_stable_id = Column(VARCHAR(128))
-#   translation_version   = Column(SMALLINT(6), nullable=False, server_default=text("1"))
-#   peptide_archive_id    = Column(INTEGER(10), index=True)
-#   mapping_session_id    = Column(INTEGER(10), ForeignKey("mapping_session.mapping_session_id"), nullable=False)
-
-#   Index("gene_idx", "gene_stable_id", "gene_version")
-#   Index("transcript_idx", "transcript_stable_id", "transcript_version")
-#   Index("translation_idx", "translation_stable_id", "translation_version")
-
-class MappingSession(Base):
-  __tablename__ = "mapping_session"
-
-  mapping_session_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  old_db_name        = Column(VARCHAR(80), nullable=False, server_default=text("''"))
-  new_db_name        = Column(VARCHAR(80), nullable=False, server_default=text("''"))
-  old_release        = Column(VARCHAR(5), nullable=False, server_default=text("''"))
-  new_release        = Column(VARCHAR(5), nullable=False, server_default=text("''"))
-  old_assembly       = Column(VARCHAR(80), nullable=False, server_default=text("''"))
-  new_assembly       = Column(VARCHAR(80), nullable=False, server_default=text("''"))
-  created            = Column(DateTime, nullable=False)
-
-class PeptideArchive(Base):
-  __tablename__ = "peptide_archive"
-
-  peptide_archive_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  md5_checksum       = Column(VARCHAR(32), index=True)
-  peptide_seq        = Column(MEDIUMTEXT, nullable=False)
-
-class MappingSet(Base):
-  __tablename__ = "mapping_set"
-  __table_args__ = (
-    Index("mapping_idx", "internal_schema_build", "external_schema_build", unique=True),
-  )
-
-  mapping_set_id        = Column(INTEGER(10), primary_key=True)
-  internal_schema_build = Column(VARCHAR(20), nullable=False)
-  external_schema_build = Column(VARCHAR(20), nullable=False)
-
-class StableIdEvent(Base):
-  __tablename__ = "stable_id_event"
-
-  old_stable_id      = Column(VARCHAR(128), primary_key=True, index=True)
-  old_version        = Column(SMALLINT(6))
-  new_stable_id      = Column(VARCHAR(128), primary_key=True, index=True)
-  new_version        = Column(SMALLINT(6))
-  mapping_session_id = Column(INTEGER(10), ForeignKey("mapping_session.mapping_session_id"), primary_key=True, server_default=text("0"))
-  id_type            = Column("type", Enum('gene', 'transcript', 'translation', 'rnaproduct'), primary_key=True)
-  score              = Column(Float, nullable=False, server_default=text("0"))
-
-class SeqRegionMapping(Base):
-  __tablename__ = "seq_region_mapping"
-
-  external_seq_region_id = Column(INTEGER(10), primary_key=True)
-  internal_seq_region_id = Column(INTEGER(10), primary_key=True)
-  mapping_set_id         = Column(INTEGER(10), primary_key=True, index=True)
-
-class AssociatedGroup(Base):
-  __tablename__ = "associated_group"
-
-  associated_group_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  description         = Column(VARCHAR(128))
-
-class AssociatedXref(Base):
-  __tablename__ = "associated_xref"
-  __table_args__ = (
-    Index("object_associated_source_type_idx", "object_xref_id", "xref_id", "source_xref_id", "condition_type", "associated_group_id", unique=True),
-  )
-
-  associated_xref_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  object_xref_id      = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), nullable=False, index=True, server_default=text("0"))
-  xref_id             = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False, index=True, server_default=text("0"))
-  source_xref_id      = Column(INTEGER(10), index=True)
-  condition_type      = Column(VARCHAR(128))
-  associated_group_id = Column(INTEGER(10), ForeignKey("associated_group.associated_group_id"), index=True)
-  rank                = Column(INTEGER(10), server_default=text("0"))
-
-class DependentXref(Base):
-  __tablename__ = "dependent_xref"
-
-  object_xref_id    = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), primary_key=True)
-  master_xref_id    = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False, index=True)
-  dependent_xref_id = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False, index=True)
-
-class ExternalDb(Base):
-  __tablename__ = "external_db"
-  __table_args__ = (
-    Index("db_name_db_release_idx", "db_name", "db_release", unique=True),
-  )
-
-  external_db_id     = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  db_name            = Column(VARCHAR(100), nullable=False)
-  db_release         = Column(VARCHAR(255))
-  status             = Column(Enum('KNOWNXREF', 'KNOWN', 'XREF', 'PRED', 'ORTH', 'PSEUDO'), nullable=False)
-  priority           = Column(INTEGER(11), nullable=False)
-  db_display_name    = Column(VARCHAR(255))
-  db_type            = Column("type", Enum('ARRAY', 'ALT_TRANS', 'ALT_GENE', 'MISC', 'LIT', 'PRIMARY_DB_SYNONYM', 'ENSEMBL'), nullable=False)
-  secondary_db_name  = Column(VARCHAR(255))
-  secondary_db_table = Column(VARCHAR(255))
-  description        = Column(TEXT)
-
-class Biotype(Base):
-  __tablename__ = "biotype"
-  __table_args__ = (
-    Index("name_type_idx", "name", "object_type", unique=True),
-  )
-
-  biotype_id     = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  name           = Column(VARCHAR(64), nullable=False)
-  object_type    = Column(Enum('gene', 'transcript'), nullable=False, server_default=text("'gene'"))
-  db_type        = Column(SET('cdna', 'core', 'coreexpressionatlas', 'coreexpressionest', 'coreexpressiongnf', 'funcgen', 'otherfeatures', 'rnaseq', 'variation', 'vega', 'presite', 'sangervega'), nullable=False, server_default=text("'core'"))
-  attrib_type_id = Column(INTEGER(11))
-  description    = Column(TEXT)
-  biotype_group  = Column(Enum('coding', 'pseudogene', 'snoncoding', 'lnoncoding', 'mnoncoding', 'LRG', 'undefined', 'no_group'))
-  so_acc         = Column(VARCHAR(64))
-  so_term        = Column(VARCHAR(1023))
-
-class ExternalSynonym(Base):
-  __tablename__ = "external_synonym"
-
-  xref_id = Column(INTEGER(10), ForeignKey("xref.xref_id"), primary_key=True)
-  synonym = Column(VARCHAR(100), primary_key=True, index=True)
-
-class IdentityXref(Base):
-  __tablename__ = "identity_xref"
-
-  object_xref_id   = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), primary_key=True)
-  xref_identity    = Column(INTEGER(5))
-  ensembl_identity = Column(INTEGER(5))
-  xref_start       = Column(INTEGER(11))
-  xref_end         = Column(INTEGER(11))
-  ensembl_start    = Column(INTEGER(11))
-  ensembl_end      = Column(INTEGER(11))
-  cigar_line       = Column(TEXT)
-  score            = Column(DOUBLE)
-  evalue           = Column(DOUBLE)
-
-class Interpro(Base):
-  __tablename__ = "interpro"
-
-  interpro_ac = Column(VARCHAR(40), primary_key=True)
-  interpro_id = Column("id", VARCHAR(40), primary_key=True, index=True)
-
-class ObjectXref(Base):
-  __tablename__ = "object_xref"
-  __table_args__ = (
-    Index("ensembl_idx", "ensembl_object_type", "ensembl_id"),
-    Index("xref_idx", "xref_id", "ensembl_object_type", "ensembl_id", "analysis_id", unique=True)
-  )
-
-  object_xref_id      = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  ensembl_id          = Column(INTEGER(10), nullable=False)
-  ensembl_object_type = Column(Enum('RawContig', 'Transcript', 'Gene', 'Translation', 'Operon', 'OperonTranscript', 'Marker', 'RNAProduct'), nullable=False)
-  xref_id             = Column(INTEGER(10), ForeignKey("xref.xref_id"), nullable=False)
-  linkage_annotation  = Column(VARCHAR(255))
-  analysis_id         = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), index=True)
-
-class OntologyXref(Base):
-  __tablename__ = "ontology_xref"
-
-  object_xref_id = Column(INTEGER(10), ForeignKey("object_xref.object_xref_id"), primary_key=True, index=True, server_default=text("0"))
-  source_xref_id = Column(INTEGER(10), ForeignKey("xref.xref_id"), primary_key=True, index=True)
-  linkage_type   = Column(VARCHAR(3), primary_key=True)
-
-class UnmappedObject(Base):
-  __tablename__ = "unmapped_object"
-  __table_args__ = (
-    Index("unique_unmapped_obj_idx", "ensembl_id", "ensembl_object_type", "identifier", "unmapped_reason_id", "parent", "external_db_id", unique=True),
-    Index("id_idx", "identifier", mysql_length=50),
-    Index("anal_exdb_idx", "analysis_id", "external_db_id"),
-    Index("ext_db_identifier_idx", "external_db_id", "identifier")
-  )
-
-  unmapped_object_id   = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  unmapped_object_type = Column("type", Enum('xref', 'cDNA', 'Marker'), nullable=False)
-  analysis_id          = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
-  external_db_id       = Column(INTEGER(10), ForeignKey("external_db.external_db_id"))
-  identifier           = Column(VARCHAR(255), nullable=False)
-  unmapped_reason_id   = Column(INTEGER(10), ForeignKey("unmapped_reason.unmapped_reason_id"), nullable=False)
-  query_score          = Column(DOUBLE)
-  target_score         = Column(DOUBLE)
-  ensembl_id           = Column(INTEGER(10), server_default=text("0"))
-  ensembl_object_type  = Column(Enum('RawContig', 'Transcript', 'Gene', 'Translation'), server_default=text("'RawContig'"))
-  parent               = Column(VARCHAR(255))
-
-class UnmappedReason(Base):
-  __tablename__ = "unmapped_reason"
-
-  unmapped_reason_id  = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  summary_description = Column(VARCHAR(255))
-  full_description    = Column(VARCHAR(255))
-
-class Xref(Base):
-  __tablename__ = "xref"
-  __table_args__ = (
-    Index("id_index", "dbprimary_acc", "external_db_id", "info_type", "info_text", "version", unique=True),
-  )
-
-  xref_id        = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  external_db_id = Column(INTEGER(10), ForeignKey("external_db.external_db_id"), nullable=False)
-  dbprimary_acc  = Column(VARCHAR(512), nullable=False)
-  display_label  = Column(VARCHAR(512), nullable=False, index=True)
-  version        = Column(VARCHAR(10))
-  description    = Column(TEXT)
-  info_type      = Column(Enum('NONE', 'PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM'), nullable=False, index=True, server_default=text("'NONE'"))
-  info_text      = Column(VARCHAR(255), nullable=False, server_default=text("''"))
-
-class Operon(Base):
-  __tablename__ = "operon"
-  __table_args__ = (
-    Index("seq_region_idx", "seq_region_id", "seq_region_start"),
-    Index("stable_id_idx", "stable_id", "version")
-  )
-
-  operon_id         = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id     = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start  = Column(INTEGER(10), nullable=False)
-  seq_region_end    = Column(INTEGER(10), nullable=False)
-  seq_region_strand = Column(TINYINT(2), nullable=False)
-  display_label     = Column(VARCHAR(255), index=True)
-  analysis_id       = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
-  stable_id         = Column(VARCHAR(128))
-  version           = Column(SMALLINT(5))
-  created_date      = Column(DateTime)
-  modified_date     = Column(DateTime)
-
-class OperonTranscript(Base):
-  __tablename__ = "operon_transcript"
-  __table_args__ = (
-    Index("stable_id_idx", "stable_id", "version"),
-    Index("seq_region_idx", "seq_region_id", "seq_region_start")
-  )
-
-  operon_transcript_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  seq_region_id        = Column(INTEGER(10), ForeignKey("seq_region.seq_region_id"), nullable=False)
-  seq_region_start     = Column(INTEGER(10), nullable=False)
-  seq_region_end       = Column(INTEGER(10), nullable=False)
-  seq_region_strand    = Column(TINYINT(2), nullable=False)
-  operon_id            = Column(INTEGER(10), ForeignKey("operon.operon_id"), nullable=False, index=True)
-  display_label        = Column(VARCHAR(255))
-  analysis_id          = Column(SMALLINT(5), ForeignKey("analysis.analysis_id"), nullable=False)
-  stable_id            = Column(VARCHAR(128))
-  version              = Column(SMALLINT(5))
-  created_date         = Column(DateTime)
-  modified_date        = Column(DateTime)
-
-class OperonTranscriptGene(Base):
-  __tablename__ = "operon_transcript_gene"
-
-  operon_transcript_id = Column(INTEGER(10), ForeignKey("operon_transcript.operon_transcript_id"), primary_key=True)
-  gene_id              = Column(INTEGER(10), ForeignKey("gene.gene_id"), primary_key=True)
-
-class Rnaproduct(Base):
-  __tablename__ = "rnaproduct"
-  __table_args__ = (
-    Index("stable_id_idx", "stable_id", "version"),
-  )
-
-  rnaproduct_id      = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  rnaproduct_type_id = Column(SMALLINT(5), ForeignKey("rnaproduct_type.rnaproduct_type_id"), nullable=False)
-  transcript_id      = Column(INTEGER(10), ForeignKey("transcript.transcript_id"), nullable=False, index=True)
-  seq_start          = Column(INTEGER(10), nullable=False)
-  start_exon_id      = Column(INTEGER(10), ForeignKey("exon.exon_id"))
-  seq_end            = Column(INTEGER(10), nullable=False)
-  end_exon_id        = Column(INTEGER(10), ForeignKey("exon.exon_id"))
-  stable_id          = Column(VARCHAR(128))
-  version            = Column(SMALLINT(5))
-  created_date       = Column(DateTime)
-  modified_date      = Column(DateTime)
-
-class RnaproductAttrib(Base):
-  __tablename__ = "rnaproduct_attrib"
-  __table_args__ = (
-    Index("type_val_idx", "attrib_type_id", "value", mysql_length={"value" : 40}),
-    Index("val_only_idx", "value", mysql_length=40),
-    Index("rnaproduct_attribx", "rnaproduct_id", "attrib_type_id", "value", unique=True, mysql_length={"value" : 500})
-  )
-
-  rnaproduct_id  = Column(INTEGER(10), ForeignKey("rnaproduct.rnaproduct_id"), primary_key=True, index=True)
-  attrib_type_id = Column(SMALLINT(5), ForeignKey("attrib_type.attrib_type_id"), primary_key=True)
-  value          = Column(TEXT, primary_key=True)
-
-class RnaproductType(Base):
-  __tablename__ = "rnaproduct_type"
-
-  rnaproduct_type_id = Column(SMALLINT(5), primary_key=True, autoincrement=True)
-  code               = Column(VARCHAR(20), nullable=False, index=True, unique=True, server_default=text("''"))
-  name               = Column(VARCHAR(255), nullable=False, server_default=text("''"))
-  description        = Column(TEXT)
diff --git a/src/python/ensembl/databases/xref_source_db_model.py b/src/python/ensembl/databases/xref_source_db_model.py
deleted file mode 100644
index 90f874e9a..000000000
--- a/src/python/ensembl/databases/xref_source_db_model.py
+++ /dev/null
@@ -1,39 +0,0 @@
-from sqlalchemy import (Column, Index, ForeignKey, text)
-from sqlalchemy.dialects.mysql import (INTEGER, VARCHAR, BOOLEAN)
-from sqlalchemy.ext.declarative import declarative_base
-
-Base = declarative_base()
-
-class ChecksumXref(Base):
-  __tablename__ = "checksum_xref"
-  __table_args__ = (
-    Index("checksum_idx", "checksum", mysql_length=10),
-  )
-
-  checksum_xref_id = Column(INTEGER, primary_key=True, autoincrement=True)
-  source_id        = Column(INTEGER, nullable=False)
-  accession        = Column(VARCHAR(14), nullable=False)
-  checksum         = Column(VARCHAR(32), nullable=False)
-
-class Source(Base):
-  __tablename__ = "source"
-
-  source_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  name      = Column(VARCHAR(128), index=True, unique=True)
-  active    = Column(BOOLEAN, nullable=False, server_default=text("1"))
-  parser    = Column(VARCHAR(128))
-
-class Version(Base):
-  __tablename__ = "version"
-  __table_args__ = (
-    Index("version_idx", "source_id", "revision")
-  )
-
-  version_id = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  source_id  = Column(INTEGER(10), ForeignKey("source.source_id"))
-  revision   = Column(VARCHAR(255))
-  count_seen = Column(INTEGER(10), nullable=False)
-  uri        = Column(VARCHAR(255))
-  index_uri  = Column(VARCHAR(255))
-  clean_uri  = Column(VARCHAR(255))
-  preparse   = Column(BOOLEAN, nullable=False, server_default=text("0"))
diff --git a/src/python/ensembl/databases/xref_update_db_model.py b/src/python/ensembl/databases/xref_update_db_model.py
deleted file mode 100644
index f68249230..000000000
--- a/src/python/ensembl/databases/xref_update_db_model.py
+++ /dev/null
@@ -1,266 +0,0 @@
-from sqlalchemy import (Column, Index, Enum, DateTime, text)
-from sqlalchemy.dialects.mysql import (INTEGER, VARCHAR, BOOLEAN, TEXT, MEDIUMTEXT, TINYINT, CHAR, SMALLINT, DOUBLE)
-from sqlalchemy.ext.declarative import declarative_base
-
-Base = declarative_base()
-
-class Xref(Base):
-  __tablename__ = "xref"
-  __table_args__ = (
-    Index("acession_idx", "accession", "source_id", "species_id", "label", unique=True, mysql_length={'accession': 100, 'label': 100}),
-    Index("species_source_idx", "species_id", "source_id")
-  )
-
-  xref_id     = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  accession   = Column(VARCHAR(255), nullable=False)
-  version     = Column(INTEGER(10, unsigned=True))
-  label       = Column(VARCHAR(255))
-  description = Column(TEXT)
-  source_id   = Column(INTEGER(10, unsigned=True), nullable=False)
-  species_id  = Column(INTEGER(10, unsigned=True), nullable=False, primary_key=True)
-  info_type   = Column(Enum('NONE', 'PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM'), nullable=False, server_default=text("'NONE'"))
-  info_text   = Column(VARCHAR(255), nullable=False, server_default=text("''"))
-  dumped      = Column(Enum('MAPPED', 'NO_DUMP_ANOTHER_PRIORITY', 'UNMAPPED_NO_MAPPING', 'UNMAPPED_NO_MASTER', 'UNMAPPED_MASTER_FAILED', 'UNMAPPED_NO_STABLE_ID', 'UNMAPPED_INTERPRO'))
-
-class PrimaryXref(Base):
-  __tablename__ = "primary_xref"
-
-  xref_id       = Column(INTEGER(10, unsigned=True), primary_key=True)
-  sequence      = Column(MEDIUMTEXT)
-  sequence_type = Column(Enum('dna', 'peptide'))
-  status        = Column(Enum('experimental', 'predicted'))
-
-class DependentXref(Base):
-  __tablename__ = "dependent_xref"
-
-  object_xref_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
-  master_xref_id     = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
-  dependent_xref_id  = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
-  linkage_annotation = Column(VARCHAR(255))
-  linkage_source_id  = Column(INTEGER(10, unsigned=True), nullable=False, primary_key=True)
-
-class Synonym(Base):
-  __tablename__ = "synonym"
-
-  xref_id = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
-  synonym = Column(VARCHAR(255), index=True, primary_key=True)
-
-class Source(Base):
-  __tablename__ = "source"
-
-  source_id            = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  name                 = Column(VARCHAR(255), nullable=False, index=True)
-  status               = Column(Enum('KNOWN', 'XREF', 'PRED', 'ORTH', 'PSEUDO', 'LOWEVIDENCE', 'NOIDEA'), nullable=False, server_default=text("'NOIDEA'"))
-  source_release       = Column(VARCHAR(255))
-  ordered              = Column(INTEGER(10, unsigned=True), nullable=False)
-  priority             = Column(INTEGER(5, unsigned=True), server_default=text("1"))
-  priority_description = Column(VARCHAR(40), server_default=text("''"))
-
-class SourceURL(Base):
-  __tablename__ = "source_url"
-
-  source_url_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  source_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
-  species_id    = Column(INTEGER(10, unsigned=True), nullable=False)
-  parser        = Column(VARCHAR(255))
-
-class SourceMappingMethod(Base):
-  __tablename__ = "source_mapping_method"
-
-  source_id = Column(INTEGER(10, unsigned=True), primary_key=True)
-  method    = Column(VARCHAR(255), primary_key=True)
-
-class GeneDirectXref(Base):
-  __tablename__ = "gene_direct_xref"
-
-  general_xref_id   = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
-  ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True)
-  linkage_xref      = Column(VARCHAR(255))
-
-class TranscriptDirectXref(Base):
-  __tablename__ = "transcript_direct_xref"
-
-  general_xref_id   = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
-  ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True)
-  linkage_xref      = Column(VARCHAR(255))
-
-class TranslationDirectXref(Base):
-  __tablename__ = "translation_direct_xref"
-
-  general_xref_id   = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
-  ensembl_stable_id = Column(VARCHAR(255), index=True, primary_key=True)
-  linkage_xref      = Column(VARCHAR(255))
-
-class Species(Base):
-  __tablename__ = "species"
-
-  species_id  = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True)
-  taxonomy_id = Column(INTEGER(10, unsigned=True), nullable=False, index=True, primary_key=True)
-  name        = Column(VARCHAR(255), nullable=False, index=True)
-  aliases     = Column(VARCHAR(255))
-
-class Pairs(Base):
-  __tablename__ = "pairs"
-
-  pair_id    = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  source_id  = Column(INTEGER(10, unsigned=True), nullable=False)
-  accession1 = Column(VARCHAR(255), nullable=False, index=True)
-  accession2 = Column(VARCHAR(255), nullable=False, index=True)
-
-class CoordinateXref(Base):
-  __tablename__ = "coordinate_xref"
-  __table_args__ = (
-    Index("start_pos_idx", "species_id", "chromosome", "strand", "txStart"),
-    Index("end_pos_idx", "species_id", "chromosome", "strand", "txEnd")
-  )
-
-  coord_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  source_id     = Column(INTEGER(10, unsigned=True), nullable=False)
-  species_id    = Column(INTEGER(10, unsigned=True), nullable=False)
-  accession     = Column(VARCHAR(255), nullable=False)
-  chromosome    = Column(VARCHAR(255), nullable=False)
-  strand        = Column(TINYINT(2), nullable=False)
-  txStart       = Column(INTEGER(10), nullable=False)
-  txEnd         = Column(INTEGER(10), nullable=False)
-  cdsStart      = Column(INTEGER(10))
-  cdsEnd        = Column(INTEGER(10))
-  exonStarts    = Column(TEXT, nullable=False)
-  exonEnds      = Column(TEXT, nullable=False)
-
-class ChecksumXref(Base):
-  __tablename__ = "checksum_xref"
-  __table_args__ = (
-    Index("checksum_idx", "checksum", mysql_length=10),
-  )
-
-  checksum_xref_id = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  source_id        = Column(INTEGER(10, unsigned=True), nullable=False)
-  accession        = Column(CHAR(14), nullable=False)
-  checksum         = Column(CHAR(32), nullable=False)
-
-class Mapping(Base):
-  __tablename__ = "mapping"
-
-  job_id                = Column(INTEGER(10, unsigned=True), primary_key=True)
-  type                  = Column(Enum('dna', 'peptide', 'UCSC'))
-  command_line          = Column(TEXT)
-  percent_query_cutoff  = Column(INTEGER(10, unsigned=True))
-  percent_target_cutoff = Column(INTEGER(10, unsigned=True))
-  method                = Column(VARCHAR(255))
-  array_size            = Column(INTEGER(10, unsigned=True))
-
-class MappingJobs(Base):
-  __tablename__ = "mapping_jobs"
-
-  mapping_job_id    = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  root_dir          = Column(TEXT)
-  map_file          = Column(VARCHAR(255))
-  status            = Column(Enum('SUBMITTED', 'FAILED', 'SUCCESS'))
-  out_file          = Column(VARCHAR(255))
-  err_file          = Column(VARCHAR(255))
-  array_number      = Column(INTEGER(10, unsigned=True))
-  job_id            = Column(INTEGER(10, unsigned=True))
-  failed_reason     = Column(VARCHAR(255))
-  object_xref_start = Column(INTEGER(10, unsigned=True))
-  object_xref_end   = Column(INTEGER(10, unsigned=True))
-
-class GeneTranscriptTranslation(Base):
-  __tablename__ = "gene_transcript_translation"
-
-  gene_id        = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
-  transcript_id  = Column(INTEGER(10, unsigned=True), primary_key=True)
-  translation_id = Column(INTEGER(10, unsigned=True), index=True)
-
-class ProcessStatus(Base):
-  __tablename__ = "process_status"
-
-  id     = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  status = Column(Enum('xref_created', 'parsing_started', 'parsing_finished', 'alt_alleles_added', 'xref_fasta_dumped', 'core_fasta_dumped', 'core_data_loaded', 'mapping_submitted', 'mapping_finished', 'mapping_processed', 'direct_xrefs_parsed', 'prioritys_flagged', 'processed_pairs', 'biomart_test_finished', 'source_level_move_finished', 'alt_alleles_processed', 'official_naming_done', 'checksum_xrefs_started', 'checksum_xrefs_finished', 'coordinate_xrefs_started', 'coordinate_xref_finished', 'tests_started', 'tests_failed', 'tests_finished', 'core_loaded', 'display_xref_done', 'gene_description_done'))
-  date   = Column(DateTime, nullable=False)
-
-class DisplayXrefPriority(Base):
-  __tablename__ = "display_xref_priority"
-
-  ensembl_object_type = Column(VARCHAR(100), primary_key=True)
-  source_id           = Column(INTEGER(10, unsigned=True), primary_key=True)
-  priority            = Column(SMALLINT(unsigned=True), nullable=False)
-
-class GeneDescPriority(Base):
-  __tablename__ = "gene_desc_priority"
-
-  source_id = Column(INTEGER(10, unsigned=True), primary_key=True)
-  priority  = Column(SMALLINT(unsigned=True), nullable=False)
-
-class AltAllele(Base):
-  __tablename__ = "alt_allele"
-
-  alt_allele_id = Column(INTEGER(10, unsigned=True), autoincrement=True, primary_key=True)
-  gene_id       = Column(INTEGER(10, unsigned=True), index=True, primary_key=True)
-  is_reference  = Column(INTEGER(2, unsigned=True), server_default=text("0"))
-
-class GeneStableId(Base):
-  __tablename__ = "gene_stable_id"
-
-  internal_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
-  stable_id       = Column(VARCHAR(128), primary_key=True)
-  display_xref_id = Column(INTEGER(10, unsigned=True))
-  desc_set        = Column(INTEGER(10, unsigned=True), server_default=text("0"))
-
-class TranscriptStableId(Base):
-  __tablename__ = "transcript_stable_id"
-
-  internal_id     = Column(INTEGER(10, unsigned=True), nullable=False, index=True)
-  stable_id       = Column(VARCHAR(128), primary_key=True)
-  display_xref_id = Column(INTEGER(10, unsigned=True))
-  biotype         = Column(VARCHAR(40), nullable=False)
-
-class TranslationStableId(Base):
-  __tablename__ = "translation_stable_id"
-
-  internal_id = Column(INTEGER(10, unsigned=True), primary_key=True)
-  stable_id   = Column(VARCHAR(128), nullable=False, index=True)
-
-class ObjectXref(Base):
-  __tablename__ = "object_xref"
-  __table_args__ = (
-    Index("unique_idx", "ensembl_object_type", "ensembl_id", "xref_id", "ox_status", "master_xref_id", unique=True),
-    Index("oxref_idx", "object_xref_id", "xref_id", "ensembl_object_type", "ensembl_id"),
-    Index("xref_idx", "xref_id", "ensembl_object_type")
-  )
-
-  object_xref_id      = Column(INTEGER(10, unsigned=True), primary_key=True, autoincrement=True)
-  ensembl_id          = Column(INTEGER(10, unsigned=True), nullable=False)
-  ensembl_object_type = Column(Enum('RawContig', 'Transcript', 'Gene', 'Translation'), nullable=False)
-  xref_id             = Column(INTEGER(10, unsigned=True), nullable=False)
-  linkage_annotation  = Column(VARCHAR(255))
-  linkage_type        = Column(Enum('PROJECTION', 'MISC', 'DEPENDENT', 'DIRECT', 'SEQUENCE_MATCH', 'INFERRED_PAIR', 'PROBE', 'UNMAPPED', 'COORDINATE_OVERLAP', 'CHECKSUM'))
-  ox_status           = Column(Enum('DUMP_OUT', 'FAILED_PRIORITY', 'FAILED_CUTOFF', 'NO_DISPLAY', 'MULTI_DELETE'), nullable=False, server_default=text("'DUMP_OUT'"))
-  unused_priority     = Column(INTEGER(10, unsigned=True))
-  master_xref_id      = Column(INTEGER(10, unsigned=True))
-
-class IdentityXref(Base):
-  __tablename__ = "identity_xref"
-
-  object_xref_id    = Column(INTEGER(10, unsigned=True), primary_key=True)
-  query_identity    = Column(INTEGER(5))
-  target_identity   = Column(INTEGER(5))
-  hit_start         = Column(INTEGER(10))
-  hit_end           = Column(INTEGER(10))
-  translation_start = Column(INTEGER(10))
-  translation_end   = Column(INTEGER(10))
-  cigar_line        = Column(TEXT)
-  score             = Column(DOUBLE)
-  evalue            = Column(DOUBLE)
-
-class Meta(Base):
-  __tablename__ = "meta"
-  __table_args__ = (
-    Index("species_key_value_idx", "meta_id", "species_id", "meta_key", "meta_value", unique=True),
-    Index("species_value_idx", "species_id", "meta_value")
-  )
-
-  meta_id    = Column(INTEGER(10), primary_key=True, autoincrement=True)
-  species_id = Column(INTEGER(10, unsigned=True), server_default=text("1"))
-  meta_key   = Column(VARCHAR(40), nullable=False)
-  meta_value = Column(VARCHAR(255, binary=True), nullable=False)
-  date       = Column(DateTime, nullable=False)
diff --git a/src/python/ensembl/xrefs/Base.py b/src/python/ensembl/xrefs/Base.py
index 9edd28cc4..32b801e93 100644
--- a/src/python/ensembl/xrefs/Base.py
+++ b/src/python/ensembl/xrefs/Base.py
@@ -41,9 +41,9 @@
 from configparser import ConfigParser
 from datetime import datetime
 
-from ensembl.databases.xref_source_db_model import Base as XrefSourceDB, Source as SourceSORM, Version as VersionORM, ChecksumXref as ChecksumXrefSORM
+from ensembl.xrefs.xref_source_db_model import Base as XrefSourceDB, Source as SourceSORM, Version as VersionORM, ChecksumXref as ChecksumXrefSORM
 
-from ensembl.databases.xref_update_db_model import Base as XrefUpdateDB, Source as SourceUORM, SourceURL as SourceURLORM, Xref as XrefUORM, \
+from ensembl.xrefs.xref_update_db_model import Base as XrefUpdateDB, Source as SourceUORM, SourceURL as SourceURLORM, Xref as XrefUORM, \
   PrimaryXref as PrimaryXrefORM, DependentXref as DependentXrefUORM, GeneDirectXref as GeneDirectXrefORM, TranscriptDirectXref as TranscriptDirectXrefORM, \
   TranslationDirectXref as TranslationDirectXrefORM, Synonym as SynonymORM, Pairs as PairsORM, Species as SpeciesORM, \
   SourceMappingMethod as SourceMappingMethodORM, MappingJobs as MappingJobsORM, Mapping as MappingORM

From 5fa2a0fb6c4b57f36dc56a6c177f8b8e095b6a61 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-02.ebi.ac.uk>
Date: Tue, 23 Apr 2024 09:30:24 +0100
Subject: [PATCH 052/128] Adding tags to download and cleanup jobs

---
 nextflow/workflows/xrefDownload.nf | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/nextflow/workflows/xrefDownload.nf b/nextflow/workflows/xrefDownload.nf
index 7552fc08a..5c808038e 100644
--- a/nextflow/workflows/xrefDownload.nf
+++ b/nextflow/workflows/xrefDownload.nf
@@ -113,6 +113,7 @@ process ScheduleDownload {
 
 process DownloadSource {
   label 'dm'
+  tag "$src_name"
 
   input:
   val x
@@ -121,6 +122,9 @@ process DownloadSource {
   output:
   val 'DownloadSourceDone'
 
+  shell:
+  src_name = (x =~ /"name":\s*"([A-Za-z0-9_.-\/]+)"/)[0][1]
+
   """
   python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.DownloadSource --dataflow '$x' --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --skip_download ${params.skip_download}
   """
@@ -173,6 +177,7 @@ process Checksum {
 
 process CleanupSplitSource {
   label 'mem4GB'
+  tag "$src_name"
 
   input:
   each x
@@ -199,6 +204,7 @@ process CleanupSplitSource {
 
 process CleanupSource {
   label 'mem4GB'
+  tag "$src_name"
 
   input:
   val x

From 792c5f36991f41673eb63e0966b7eca654c4629e Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Tue, 23 Apr 2024 10:40:33 +0100
Subject: [PATCH 053/128] Updated patches for preperation of 113

---
 sql/patch_109_110_a.sql |  2 +-
 sql/patch_110_111_a.sql |  2 +-
 sql/patch_112_113_a.sql | 27 +++++++++++++++++++++++++++
 sql/table.sql           |  4 ++--
 4 files changed, 31 insertions(+), 4 deletions(-)
 create mode 100644 sql/patch_112_113_a.sql

diff --git a/sql/patch_109_110_a.sql b/sql/patch_109_110_a.sql
index 427981eec..27bc2d892 100644
--- a/sql/patch_109_110_a.sql
+++ b/sql/patch_109_110_a.sql
@@ -13,7 +13,7 @@
 -- See the License for the specific language governing permissions and
 -- limitations under the License.
 
-# patch_108_109_a.sql
+# patch_109_110_a.sql
 #
 # Title: Update schema version.
 #
diff --git a/sql/patch_110_111_a.sql b/sql/patch_110_111_a.sql
index 91ba1c712..e8725ff82 100644
--- a/sql/patch_110_111_a.sql
+++ b/sql/patch_110_111_a.sql
@@ -13,7 +13,7 @@
 -- See the License for the specific language governing permissions and
 -- limitations under the License.
 
-# patch_108_109_a.sql
+# patch_110_111_a.sql
 #
 # Title: Update schema version.
 #
diff --git a/sql/patch_112_113_a.sql b/sql/patch_112_113_a.sql
new file mode 100644
index 000000000..f89e3f0b9
--- /dev/null
+++ b/sql/patch_112_113_a.sql
@@ -0,0 +1,27 @@
+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_112_113_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 112.
+
+UPDATE meta SET meta_value='113' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+VALUES (NULL, 'patch', 'patch_112_113_a.sql|schema_version');
diff --git a/sql/table.sql b/sql/table.sql
index a72e11ee5..c701ef1fe 100644
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -32,11 +32,11 @@ CREATE TABLE IF NOT EXISTS meta (
 # Add schema type and schema version to the meta table
 INSERT INTO meta (species_id, meta_key, meta_value) VALUES
   (NULL, 'schema_type', 'production'),
-  (NULL, 'schema_version', 111);
+  (NULL, 'schema_version', 113);
 
 # Patches included in this schema file
 INSERT INTO meta (species_id, meta_key, meta_value)
-  VALUES (NULL, 'patch', 'patch_110_111_a.sql|schema version');
+  VALUES (NULL, 'patch', 'patch_112_113_a.sql|schema version');
 
 -- The 'master_biotype' table.
 -- Contains all the valid biotypes used for genes and transcripts.

From 127ad09efe56c32cdf7df70d8675052cac17138b Mon Sep 17 00:00:00 2001
From: Daniel Poppleton <danielp@hl-codon-15-03.ebi.ac.uk>
Date: Tue, 23 Apr 2024 13:55:01 +0100
Subject: [PATCH 054/128] Updating test dbs to latest schema

---
 modules/t/test-genome-DBs/homo_sapiens/core/meta.txt   | 5 ++++-
 modules/t/test-genome-DBs/homo_sapiens/core/table.sql  | 6 +++---
 modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt  | 5 ++++-
 modules/t/test-genome-DBs/homo_sapiens/empty/table.sql | 6 +++---
 modules/t/test-genome-DBs/hp_dump/core/meta.txt        | 5 ++++-
 modules/t/test-genome-DBs/hp_dump/core/table.sql       | 6 +++---
 modules/t/test-genome-DBs/multi/compara/meta.txt       | 4 +++-
 modules/t/test-genome-DBs/multi/compara/table.sql      | 4 ++--
 8 files changed, 26 insertions(+), 15 deletions(-)

diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index b78dcfe5c..cb763cbb4 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	112
+2	\N	schema_version	113
 3	\N	patch	patch_98_99_a.sql|schema_version
 2124	1	xref.timestamp	2013-07-22 11:20:10
 4	\N	patch	patch_52_53_c.sql|identity_xref_rename
@@ -263,3 +263,6 @@
 2219	\N	patch	patch_110_111_a.sql|schema_version
 2220	\N	patch	patch_111_112_a.sql|schema_version
 2221	\N	patch	patch_111_112_b.sql|Allow meta_value to be null
+2222	\N	patch	patch_111_112_c.sql|Extend meta_key length to 64
+2223	\N	patch	patch_112_113_a.sql|schema_version
+2224	\N	patch	patch_112_113_b.sql|Ensure meta_value is not null
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index 676521f52..784f016fb 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -485,12 +485,12 @@ CREATE TABLE `marker_synonym` (
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
-  `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) DEFAULT NULL,
+  `meta_key` varchar(64) NOT NULL,
+  `meta_value` varchar(255) NOT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2222 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2225 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 1af089f4f..ca8dc5b53 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -1,4 +1,4 @@
-1	\N	schema_version	112
+1	\N	schema_version	113
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -128,3 +128,6 @@
 178	\N	patch	patch_110_111_a.sql|schema_version
 179	\N	patch	patch_111_112_a.sql|schema_version
 180	\N	patch	patch_111_112_b.sql|Allow meta_value to be null
+181	\N	patch	patch_111_112_c.sql|Extend meta_key length to 64
+182	\N	patch	patch_112_113_a.sql|schema_version
+183	\N	patch	patch_112_113_b.sql|Ensure meta_value is not null
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index 7e0ab54ab..fda351bb8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -490,12 +490,12 @@ CREATE TABLE `marker_synonym` (
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
-  `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) DEFAULT NULL,
+  `meta_key` varchar(64) NOT NULL,
+  `meta_value` varchar(255) NOT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=181 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=184 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/hp_dump/core/meta.txt b/modules/t/test-genome-DBs/hp_dump/core/meta.txt
index b5f68a552..0b97df26e 100644
--- a/modules/t/test-genome-DBs/hp_dump/core/meta.txt
+++ b/modules/t/test-genome-DBs/hp_dump/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	112
+2	\N	schema_version	113
 3	\N	patch	patch_98_99_a.sql|schema_version
 2124	1	xref.timestamp	2013-07-22 11:20:10
 4	\N	patch	patch_52_53_c.sql|identity_xref_rename
@@ -267,3 +267,6 @@
 2223	\N	patch	patch_110_111_a.sql|schema_version
 2224	\N	patch	patch_111_112_a.sql|schema_version
 2225	\N	patch	patch_111_112_b.sql|Allow meta_value to be null
+2226	\N	patch	patch_111_112_c.sql|Extend meta_key length to 64
+2227	\N	patch	patch_112_113_a.sql|schema_version
+2228	\N	patch	patch_112_113_b.sql|Ensure meta_value is not null
diff --git a/modules/t/test-genome-DBs/hp_dump/core/table.sql b/modules/t/test-genome-DBs/hp_dump/core/table.sql
index 56d37618f..6130c7aa3 100644
--- a/modules/t/test-genome-DBs/hp_dump/core/table.sql
+++ b/modules/t/test-genome-DBs/hp_dump/core/table.sql
@@ -485,12 +485,12 @@ CREATE TABLE `marker_synonym` (
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
-  `meta_key` varchar(40) NOT NULL,
-  `meta_value` varchar(255) DEFAULT NULL,
+  `meta_key` varchar(64) NOT NULL,
+  `meta_value` varchar(255) NOT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2226 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2229 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/multi/compara/meta.txt b/modules/t/test-genome-DBs/multi/compara/meta.txt
index 75508c863..6f62244a1 100644
--- a/modules/t/test-genome-DBs/multi/compara/meta.txt
+++ b/modules/t/test-genome-DBs/multi/compara/meta.txt
@@ -1,6 +1,6 @@
 2	\N	schema_type	compara
 3	\N	patch	patch_98_99_a.sql|schema_version
-167	\N	schema_version	112
+169	\N	schema_version	113
 4	\N	patch	patch_72_73_b.sql|homology_genetree_links
 6	\N	patch	patch_73_74_a.sql|schema_version
 7	\N	patch	patch_73_74_b.sql|hmm_profile
@@ -127,3 +127,5 @@
 164	\N	patch	patch_109_110_c.sql|ncbi_taxa_name_varchar500
 166	\N	patch	patch_110_111_a.sql|schema_version
 168	\N	patch	patch_111_112_a.sql|schema_version
+170	\N	patch	patch_112_113_a.sql|schema_version
+171	\N	patch	patch_112_113_b.sql|meta_key_64
diff --git a/modules/t/test-genome-DBs/multi/compara/table.sql b/modules/t/test-genome-DBs/multi/compara/table.sql
index 8482668f9..a0afea73c 100644
--- a/modules/t/test-genome-DBs/multi/compara/table.sql
+++ b/modules/t/test-genome-DBs/multi/compara/table.sql
@@ -436,12 +436,12 @@ CREATE TABLE `member_xref` (
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
   `species_id` int(10) unsigned DEFAULT '1',
-  `meta_key` varchar(40) NOT NULL,
+  `meta_key` varchar(64) NOT NULL,
   `meta_value` text NOT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=169 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=172 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,

From d924e506ba888c5d1ba680a92375a0066012c001 Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Fri, 26 Apr 2024 17:38:49 +0000
Subject: [PATCH 055/128] Changed GENCODE Basic tag to 'gencode_basic' as per
 ENSINT-1885

---
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index 269f2b8a4..1024dc13c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -263,7 +263,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
   $summary{'transcript_support_level'} = $self->tsl if $self->tsl;
 
   my @tags;
-  push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'gencode_basic') if $self->gencode_basic();
   push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
   
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index 537675025..9efa955a6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -279,7 +279,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
   $summary{'transcript_support_level'} = $self->tsl if $self->tsl;
 
   my @tags;
-  push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'gencode_basic') if $self->gencode_basic();
   push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
 

From f09b9b79f6bd5b1dedcd75db6909260c27727623 Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Fri, 26 Apr 2024 17:38:49 +0000
Subject: [PATCH 056/128] Changed GENCODE Basic tag to 'gencode_basic' as per
 ENSINT-1885

---
 .../Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm    | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm        | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
index 269f2b8a4..1024dc13c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/FileDump/Geneset_GFF3.pm
@@ -263,7 +263,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
   $summary{'transcript_support_level'} = $self->tsl if $self->tsl;
 
   my @tags;
-  push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'gencode_basic') if $self->gencode_basic();
   push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
   
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
index 537675025..9efa955a6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GFF3/DumpFile.pm
@@ -279,7 +279,7 @@ sub Bio::EnsEMBL::Transcript::summary_as_hash {
   $summary{'transcript_support_level'} = $self->tsl if $self->tsl;
 
   my @tags;
-  push(@tags, 'basic') if $self->gencode_basic();
+  push(@tags, 'gencode_basic') if $self->gencode_basic();
   push(@tags, 'gencode_primary') if $self->gencode_primary();
   push(@tags, 'Ensembl_canonical') if $self->is_canonical();
 

From a0b629a2a37dec03ae34f9e8f64b973901b21c98 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Mon, 29 Apr 2024 09:49:11 +0100
Subject: [PATCH 057/128] Minor fixes

---
 scripts/xrefs/cleanup_and_split_source.pl     | 11 +++++--
 src/python/ensembl/xrefs/Base.py              |  6 ++--
 src/python/ensembl/xrefs/EmailNotification.py | 29 +++++++++----------
 3 files changed, 24 insertions(+), 22 deletions(-)

diff --git a/scripts/xrefs/cleanup_and_split_source.pl b/scripts/xrefs/cleanup_and_split_source.pl
index e538503c2..e5ddf5560 100644
--- a/scripts/xrefs/cleanup_and_split_source.pl
+++ b/scripts/xrefs/cleanup_and_split_source.pl
@@ -101,12 +101,12 @@
 
 # Extract taxonomy IDs
 my %tax_ids;
-my $skipped_species = 0;
+my ($skipped_species, $added_species) = (0, 0);
 if ($tax_ids_file) {
   open my $fh, '<', $tax_ids_file;
   chomp(my @lines = <$fh>);
   close $fh;
-  my %tax_ids = map { $_ => 1 } @lines;
+  %tax_ids = map { $_ => 1 } @lines;
 
   # Check if any taxonomy IDs already have files
   foreach my $tax_id (keys(%tax_ids)) {
@@ -216,6 +216,12 @@
         make_path($write_path);
 
         $write_file = $write_path."/".$output_file_name."-".$species_id;
+
+        # Check if creating new file
+        if (!-e $write_file) {
+          $added_species++;
+        }
+
         open($out_fh, '>>', $write_file) or die "Couldn't open output file '$write_file' $!";
 
         $current_species_id = $species_id;
@@ -231,6 +237,7 @@
 
 add_to_log_file($log_file, "Source $source_name cleaned up");
 add_to_log_file($log_file, "$source_name skipped species = $skipped_species");
+add_to_log_file($log_file, "$source_name species files created = $added_species")
 
 # Save the clean files directory in source db
 my ($user, $pass, $host, $port, $source_db) = parse_url($source_db_url);
diff --git a/src/python/ensembl/xrefs/Base.py b/src/python/ensembl/xrefs/Base.py
index 32b801e93..d5022627f 100644
--- a/src/python/ensembl/xrefs/Base.py
+++ b/src/python/ensembl/xrefs/Base.py
@@ -182,8 +182,6 @@ def download_file(self, file: str, base_path: str, source_name: str, extra_args:
         if db and db == 'checksum':
           file_path = os.path.join(dest_dir, f'{source_name}-{os.path.basename(uri.path)}')
 
-        logging.info(f'I am here inside local ftp with {orig_source_name}')
-
         if not (skip_download_if_file_present and os.path.exists(file_path)):
           shutil.copy(local_file, file_path)
 
@@ -838,11 +836,11 @@ def get_xref_mapper(self, xref_url: str, species: str, base_path: str, release:
     pep_path = self.get_path(base_path, species, release, 'ensembl', 'peptides.fa');
 
     # Try to find a species-specific mapper first
-    module_name = f'ensembl.xrefs.mapper.{species}'
+    module_name = f'ensembl.xrefs.mappers.{species}'
     class_name = species
     found = importlib.find_loader(module_name)
     if not found:
-      module_name = 'ensembl.xrefs.mapper.BasicMapper'
+      module_name = 'ensembl.xrefs.mappers.BasicMapper'
       class_name = 'BasicMapper'
 
     # Create a mapper object
diff --git a/src/python/ensembl/xrefs/EmailNotification.py b/src/python/ensembl/xrefs/EmailNotification.py
index dae71e738..75a23012d 100644
--- a/src/python/ensembl/xrefs/EmailNotification.py
+++ b/src/python/ensembl/xrefs/EmailNotification.py
@@ -37,10 +37,7 @@ def run(self):
       if os.path.exists(log_path):
         log_files = os.listdir(log_path)
 
-        parameters = {}
-        sources = {}
-        added_species = {}
-        skipped_species = {}
+        parameters, sources, added_species, skipped_species = {}, {}, {}, {}
 
         main_log_file = os.path.join(base_path, 'logs', log_timestamp, 'logfile_'+log_timestamp)
 
@@ -92,11 +89,11 @@ def run(self):
           sources_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| ([\w\/]+) file copied from local FTP: (.*)", data)
           for source in sources_list: sources[source[0]].update({'copied' : os.path.dirname(source[1])})
 
-          # skipped_species_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| (\w+) skipped species = (\d+)", data)
-          # skipped_species = {source[0]: source[1] for source in skipped_species_list}
+          skipped_species_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| (\w+) skipped species = (\d+)", data)
+          skipped_species = {source[0]: source[1] for source in skipped_species_list}
 
-          # added_species_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| (\w+) taxonomy IDs added to filter = (\d+)", data)
-          # added_species = {division[0]: division[1] for division in added_species_list}
+          added_species_list = re.findall(r"^\d{2}-\w{3}-\d{4} \\| INFO \\| (\w+) species files created = (\d+)", data)
+          added_species = {source[0]: source[1] for source in added_species_list}
 
           # Include source statistics
           email_message += '<br>--Source Statistics--<br>'
@@ -106,7 +103,7 @@ def run(self):
 
             if source_values.get('downloaded'):
               (download_type, file_path) = source_values['downloaded'].split("|")
-              email_message += f' File downloaded via {download_type} into {file_path}<br>'
+              email_message += f'&nbsp;&nbsp;&nbsp;File downloaded via {download_type} into {file_path}<br>'
             elif source_values.get('copied'): email_message += '&nbsp;&nbsp;&nbsp;File(s) copied from local FTP into %s<br>' % (source_values['copied'])
             elif source_values.get('skipped'): email_message += '&nbsp;&nbsp;&nbsp;File(s) download skipped, already exists in %s<br>' % (source_values['skipped'])
 
@@ -117,13 +114,13 @@ def run(self):
             if source_values.get('preparsed'): email_message += '&nbsp;&nbsp;&nbsp;Pre-parsed &#10004;<br>'
 
           # Include species statistics
-          # email_message += '<br>--Species Statistics--<br>'
-          # for division,count in added_species.items():
-          #   if division == 'Total': continue
-          #   email_message += f'{species_type} taxonomy IDs = {count}<br>'
-          # email_message += 'Skipped Species per source file:<br>'
-          # for source_name,count in skipped_species.items():
-          #   email_message += f'&nbsp;&nbsp;&nbsp;{source_name}: {count}<br>'
+          email_message += '<br>--Species Statistics--<br>'
+          email_message += 'Skipped Species (files already exist):<br>'
+          for source_name, count in skipped_species.items():
+            email_message += f'&nbsp;&nbsp;&nbsp;{source_name}: {count}<br>'
+          email_message += 'Added Species (files created):<br>'
+          for source_name, count in added_species.items():
+            email_message += f'&nbsp;&nbsp;&nbsp;{source_name}: {count}<br>'
 
           email_message += '<br>To run the Xref Process Pipeline based on the data from this pipeline, use the same <b>--base_path</b>, <b>--source_db_url</b>, and <b>--central_db_url</b> (if preparse was run) values provided to this pipeline.'
 

From ec58c92e3f0d0278e6ff50540e7c775025e7a43f Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Mon, 29 Apr 2024 10:08:06 +0100
Subject: [PATCH 058/128] Missing semicolon

---
 scripts/xrefs/cleanup_and_split_source.pl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/scripts/xrefs/cleanup_and_split_source.pl b/scripts/xrefs/cleanup_and_split_source.pl
index e5ddf5560..c08617751 100644
--- a/scripts/xrefs/cleanup_and_split_source.pl
+++ b/scripts/xrefs/cleanup_and_split_source.pl
@@ -237,7 +237,7 @@
 
 add_to_log_file($log_file, "Source $source_name cleaned up");
 add_to_log_file($log_file, "$source_name skipped species = $skipped_species");
-add_to_log_file($log_file, "$source_name species files created = $added_species")
+add_to_log_file($log_file, "$source_name species files created = $added_species");
 
 # Save the clean files directory in source db
 my ($user, $pass, $host, $port, $source_db) = parse_url($source_db_url);

From 6b97c441a1de4e376ddb317700ae286473cae293 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Mon, 29 Apr 2024 11:11:24 +0100
Subject: [PATCH 059/128] Change glob parameters

---
 .../Production/Pipeline/Xrefs/ScheduleSource.pm     |  2 +-
 scripts/xrefs/cleanup_and_split_source.pl           | 13 +++++++++----
 2 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index eeda0dc8c..b80ebd421 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -134,7 +134,7 @@ sub run {
       # For Uniprot and Refseq, files might have been split by species
       if (!$preparse && ($name =~ /^Uniprot/ || $name =~ /^RefSeq_peptide/ || $name =~ /^RefSeq_dna/)) {
         my $file_prefix = ($name =~ /SPTREMBL/ ? 'uniprot_trembl' : ($name =~ /SWISSPROT/ ? 'uniprot_sprot' : ($name =~ /_dna/ ? 'refseq_rna' : 'refseq_protein')));
-        @list_files = glob($file_name . "/**/" . $file_prefix . "-" . $species_id);
+        @list_files = glob($file_name . "/**/**/**/**/" . $file_prefix . "-" . $species_id);
         $_ = basename(dirname($_)) . "/" . basename($_) foreach (@list_files);
       }
 
diff --git a/scripts/xrefs/cleanup_and_split_source.pl b/scripts/xrefs/cleanup_and_split_source.pl
index c08617751..5687a5109 100644
--- a/scripts/xrefs/cleanup_and_split_source.pl
+++ b/scripts/xrefs/cleanup_and_split_source.pl
@@ -110,12 +110,15 @@
 
   # Check if any taxonomy IDs already have files
   foreach my $tax_id (keys(%tax_ids)) {
-    my @tax_files = glob($output_path . "/**/" . $output_file_name . "-" . $tax_id);
+    print Dumper $tax_id;
+    my @tax_files = glob($output_path . "/**/**/**/**/" . $output_file_name . "-" . $tax_id);
+    print Dumper @tax_files;
     if (scalar(@tax_files) > 0) {
       $tax_ids{$tax_id} = 0;
       $skipped_species++;
     }
   }
+  die;
 
   # Do nothing if all taxonomy IDs already have files
   if ($skipped_species == scalar(keys(%tax_ids))) {
@@ -211,8 +214,10 @@
       if (!defined($current_species_id) || (defined($current_species_id) && $species_id ne $current_species_id)) {
         close($out_fh) if (defined($current_species_id));
 
-        my @digits = split('', $species_id);
-        $write_path = catdir($output_path, $digits[0], (scalar(@digits)>1 ? $digits[1] : ""), (scalar(@digits)>2 ? $digits[2] : ""), (scalar(@digits)>3 ? $digits[3] : ""));
+	my $species_id_str = sprintf("%04d", $species_id);
+	my @digits = split('', $species_id_str);
+
+	$write_path = catdir($output_path, $digits[0], $digits[1], $digits[2], $digits[3]);
         make_path($write_path);
 
         $write_file = $write_path."/".$output_file_name."-".$species_id;
@@ -231,7 +236,7 @@
     }
 
     close($in_fh);
-    close($out_fh);
+    close($out_fh) if $out_fh;
   }
 }
 

From 5d99a70491d18a9525313c3e642620f86263d8a3 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Mon, 29 Apr 2024 11:15:02 +0100
Subject: [PATCH 060/128] Remove debugging

---
 scripts/xrefs/cleanup_and_split_source.pl | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/scripts/xrefs/cleanup_and_split_source.pl b/scripts/xrefs/cleanup_and_split_source.pl
index 5687a5109..f1ea49f9a 100644
--- a/scripts/xrefs/cleanup_and_split_source.pl
+++ b/scripts/xrefs/cleanup_and_split_source.pl
@@ -110,15 +110,12 @@
 
   # Check if any taxonomy IDs already have files
   foreach my $tax_id (keys(%tax_ids)) {
-    print Dumper $tax_id;
     my @tax_files = glob($output_path . "/**/**/**/**/" . $output_file_name . "-" . $tax_id);
-    print Dumper @tax_files;
     if (scalar(@tax_files) > 0) {
       $tax_ids{$tax_id} = 0;
       $skipped_species++;
     }
   }
-  die;
 
   # Do nothing if all taxonomy IDs already have files
   if ($skipped_species == scalar(keys(%tax_ids))) {

From 577c6bafb40da0de50d5d83b40842745e52cd992 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-03.ebi.ac.uk>
Date: Mon, 29 Apr 2024 11:27:43 +0100
Subject: [PATCH 061/128] Fixes to prevent warnings

---
 scripts/xrefs/cleanup_and_split_source.pl | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/xrefs/cleanup_and_split_source.pl b/scripts/xrefs/cleanup_and_split_source.pl
index f1ea49f9a..6a09971ea 100644
--- a/scripts/xrefs/cleanup_and_split_source.pl
+++ b/scripts/xrefs/cleanup_and_split_source.pl
@@ -161,12 +161,13 @@
       my $species_id;
       if ($is_uniprot) {
         ($species_id) = $record =~ /OX\s+[a-zA-Z_]+=([0-9 ,]+).*;/;
-        $species_id =~ s/\s//;
+        $species_id =~ s/\s// if $species_id;
       } else {
         ($species_id) = $record =~ /db_xref=.taxon:(\d+)/;
       }
 
       # Only continue with wanted species
+      next if (!$species_id);
       next if ($tax_ids_file && (!defined($tax_ids{$species_id}) || !$tax_ids{$species_id}));
 
       # Clean up data

From a29d373cb43887427f1c040d5c41070e96db3e9e Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@hl-codon-45-01.ebi.ac.uk>
Date: Tue, 30 Apr 2024 09:55:24 +0100
Subject: [PATCH 062/128] Fix file paths

---
 .../Production/Pipeline/Xrefs/ScheduleSource.pm       | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index b80ebd421..34da3141e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -127,21 +127,24 @@ sub run {
     } else {
       # Create list of files
       opendir(my $dir_handle, $file_name);
-      my @list_files = readdir($dir_handle);
+      my @temp_list_files = readdir($dir_handle);
       closedir($dir_handle);
+
+      my @list_files;
+      foreach my $file (@temp_list_files) {
+        next if ($file =~ /^\./);
+        push(@list_files, $file_name . "/" . $file);
+      }
       if ($preparse) { @list_files = $preparse; }
 
       # For Uniprot and Refseq, files might have been split by species
       if (!$preparse && ($name =~ /^Uniprot/ || $name =~ /^RefSeq_peptide/ || $name =~ /^RefSeq_dna/)) {
         my $file_prefix = ($name =~ /SPTREMBL/ ? 'uniprot_trembl' : ($name =~ /SWISSPROT/ ? 'uniprot_sprot' : ($name =~ /_dna/ ? 'refseq_rna' : 'refseq_protein')));
         @list_files = glob($file_name . "/**/**/**/**/" . $file_prefix . "-" . $species_id);
-        $_ = basename(dirname($_)) . "/" . basename($_) foreach (@list_files);
       }
 
       foreach my $file (@list_files) {
-        next if ($file =~ /^\./);
         $file =~ s/\n//;
-        $file = $file_name . "/" . $file;
         if (defined $release_file and $file eq $release_file) { next; }
   
         $dataflow_params = {

From 7fb4c0488dcb8b5d921a18b8db0dd937dd083835 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-01.ebi.ac.uk>
Date: Thu, 2 May 2024 09:11:45 +0100
Subject: [PATCH 063/128] Keep original files if no species file

---
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm  | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 34da3141e..17a04a762 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -140,7 +140,10 @@ sub run {
       # For Uniprot and Refseq, files might have been split by species
       if (!$preparse && ($name =~ /^Uniprot/ || $name =~ /^RefSeq_peptide/ || $name =~ /^RefSeq_dna/)) {
         my $file_prefix = ($name =~ /SPTREMBL/ ? 'uniprot_trembl' : ($name =~ /SWISSPROT/ ? 'uniprot_sprot' : ($name =~ /_dna/ ? 'refseq_rna' : 'refseq_protein')));
-        @list_files = glob($file_name . "/**/**/**/**/" . $file_prefix . "-" . $species_id);
+        my @species_list_files = glob($file_name . "/**/**/**/**/" . $file_prefix . "-" . $species_id);
+        if (scalar(@species_list_files) > 0) {
+          @list_files = @species_list_files;
+        }
       }
 
       foreach my $file (@list_files) {

From 74296b6af9b528c5d7eeb549cb4ce950892b5202 Mon Sep 17 00:00:00 2001
From: jmgonzmart <jmgonzalez@ebi.ac.uk>
Date: Fri, 10 May 2024 16:31:16 +0100
Subject: [PATCH 064/128] Updated HGNC custom download URL

---
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
index aebb77102..b0910be58 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
@@ -203,7 +203,7 @@
     {
       "name" : "HGNC",
       "parser" : "HGNCParser",
-      "file" : "https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit",
+      "file" : "https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit",
       "db" : "ccds",
       "priority" : 3
     }
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
index 0f24ec9a8..7fa14c977 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
@@ -241,7 +241,7 @@
     {
       "name" : "HGNC",
       "parser" : "HGNCParser",
-      "file" : "https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit",
+      "file" : "https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit",
       "db" : "ccds",
       "priority" : 3
     }
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
index 9bcbf7936..161a41186 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
@@ -269,7 +269,7 @@
     {
       "name" : "HGNC",
       "parser" : "HGNCParser",
-      "file" : "https://www.genenames.org/cgi-bin/download?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit",
+      "file" : "https://www.genenames.org/cgi-bin/download/custom?col=gd_hgnc_id&col=gd_app_sym&col=gd_app_name&col=gd_prev_sym&col=gd_aliases&col=gd_pub_eg_id&col=gd_pub_ensembl_id&col=gd_pub_refseq_ids&col=gd_ccds_ids&col=gd_lsdb_links&status=Approved&status_opt=2&where=&order_by=gd_app_sym_sort&format=text&limit=&hgnc_dbtag=on&submit=submit",
       "db" : "ccds",
       "priority" : 3
     }

From ca259d0d61399c552aa69cc6bd9d242a49640269 Mon Sep 17 00:00:00 2001
From: Matthieu Barba <mbarba@ebi.ac.uk>
Date: Tue, 14 May 2024 15:31:31 +0100
Subject: [PATCH 065/128] remove partition from slurm command

Slurm determines the queue automatically from the requested resources.
Setting the partition might lead to problems when Slurm switch to a
different queue and Hive only checks the queue it requested.
---
 .../Production/Pipeline/PipeConfig/Base_conf.pm     | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index ac0fca871..ed6737f30 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -88,14 +88,13 @@ sub resource_classes {
 
     );
 
-    my $pq = ' --partition=standard';
     my $dq = ' --partition=datamover';
 
     my %output = (
         #Default is a duplicate of 100M
-        'default'   => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'default_D' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'default_W' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
+        'default'   => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
+        'default_D' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
+        'default_W' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
         #Data mover nodes
         'dm'        => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
         'dm_D'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
@@ -105,7 +104,7 @@ sub resource_classes {
     );
     #Create a dictionary of all possible time and memory combinations. Format would be:
     #2G={
-    #   'SLURM' => ' --partition=standard --time=1:00:00  --mem=2000m',
+    #   'SLURM' => ' --time=1:00:00  --mem=2000m',
     #   'LSF' => '-q $self->o(production_queue) -M 2000 -R "rusage[mem=2000]"'
     # };
 
@@ -113,11 +112,11 @@ sub resource_classes {
         while ((my $memory_key, my $memory_value) = each(%memory)) {
             if ($time_key eq 'H') {
                 $output{$memory_key} = { 'LSF' => '-q ' . $self->o('production_queue') . ' -M ' . $memory_value . ' -R "rusage[mem=' . $memory_value . ']"',
-                    'SLURM'                    => $pq . $time_value . '  --mem=' . $memory_value . 'm' }
+                    'SLURM'                    => $time_value . '  --mem=' . $memory_value . 'm' }
             }
             else {
                 $output{$memory_key . '_' . $time_key} = { 'LSF' => '-q ' . $self->o('production_queue') . ' -M ' . $memory_value . ' -R "rusage[mem=' . $memory_value . ']"',
-                    'SLURM'                                      => $pq . $time_value . '  --mem=' . $memory_value . 'm' }
+                    'SLURM'                                      => $time_value . '  --mem=' . $memory_value . 'm' }
             }
         }
     }

From 0c7c41fe7656659400e48200bc2cd47c7df0a5fc Mon Sep 17 00:00:00 2001
From: vinay-ebi <vinay@ebi.ac.uk>
Date: Wed, 15 May 2024 20:58:04 +0100
Subject: [PATCH 066/128] moved ensembl/xrefs to ensembl/production/xrefs

---
 nextflow/config/xref.config                   | 65 +++++++++++++++----
 nextflow/workflows/xrefDownload.nf            | 10 +--
 .../ensembl/{ => production}/xrefs/Base.py    |  0
 .../{ => production}/xrefs/Checksum.py        |  0
 .../{ => production}/xrefs/DownloadSource.py  |  0
 .../xrefs/EmailNotification.py                |  0
 .../{ => production}/xrefs/ScheduleCleanup.py |  0
 .../xrefs/ScheduleDownload.py                 |  0
 .../xrefs/config/xref_all_sources.json        |  0
 .../xrefs/config/xref_config.ini              |  0
 10 files changed, 57 insertions(+), 18 deletions(-)
 rename src/python/ensembl/{ => production}/xrefs/Base.py (100%)
 rename src/python/ensembl/{ => production}/xrefs/Checksum.py (100%)
 rename src/python/ensembl/{ => production}/xrefs/DownloadSource.py (100%)
 rename src/python/ensembl/{ => production}/xrefs/EmailNotification.py (100%)
 rename src/python/ensembl/{ => production}/xrefs/ScheduleCleanup.py (100%)
 rename src/python/ensembl/{ => production}/xrefs/ScheduleDownload.py (100%)
 rename src/python/ensembl/{ => production}/xrefs/config/xref_all_sources.json (100%)
 rename src/python/ensembl/{ => production}/xrefs/config/xref_config.ini (100%)

diff --git a/nextflow/config/xref.config b/nextflow/config/xref.config
index bc36b8617..66bebf05d 100644
--- a/nextflow/config/xref.config
+++ b/nextflow/config/xref.config
@@ -22,23 +22,62 @@ params.base_path = ''
 params.clean_files = 1
 params.clean_dir = "${params.base_path}/clean_files"
 
-executor {
-  name = 'slurm'
-  queue = 'production'
-  queueSize = 100
+trace {
+    enabled = true
+    file = "trace"
+    overwrite = true
 }
 
-process {
-  errorStrategy = { task.attempt <= process.maxRetries  ? 'retry' : 'finish' }
-  maxRetries = 3
-  time = '1d'
+report {
+    overwrite = true
+    file = "report.html"
+    enable = true
+}
+
+profiles {
 
-  withLabel:small_process {
-    memory = 200.MB
-    executor.perTaskReserve = 200.MB
+  lsf {
+   process {
+    errorStrategy = { task.attempt <= process.maxRetries  ? 'retry' : 'finish' }
+    executor = 'lsf'
+    queue = 'production'
+    queueSize = 100
+    maxRetries = 3
+     withLabel:small_process {
+        memory = 200.MB
+        //very specific to lsf
+        executor.perTaskReserve = 200.MB
+    }
+    withLabel: dm {
+        queue = 'datamover'
+        time = '2h'
+    }
   }
+ }
+
+  slurm {
+   process {
+    errorStrategy = { task.attempt <= process.maxRetries  ? 'retry' : 'finish' }
+    executor = 'slurm'
+    queue = 'production'
+    queueSize = 100
+    maxRetries = 3
+    time = '1d'
 
-  withLabel:mem4GB {
-    time = '3d'
+    withLabel:small_process {
+        memory = 200.MB
+    }
+
+    withLabel: dm {
+        queue = 'datamover'
+        time = '2h'
+        memory = 2.GB
+    }
+    withLabel:mem4GB {
+        time = '3d'
+    }
   }
+ }
 }
+
+
diff --git a/nextflow/workflows/xrefDownload.nf b/nextflow/workflows/xrefDownload.nf
index 5c808038e..51cc53552 100644
--- a/nextflow/workflows/xrefDownload.nf
+++ b/nextflow/workflows/xrefDownload.nf
@@ -107,7 +107,7 @@ process ScheduleDownload {
   timestamp = new java.util.Date().format("yyyyMMdd_HHmmss")
 
   """
-  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.ScheduleDownload --config_file ${params.config_file} --source_db_url ${params.source_db_url} --reuse_db ${params.reuse_db} --skip_preparse ${params.skip_preparse} --base_path ${params.base_path} --log_timestamp $timestamp
+  python ${params.scripts_dir}/run_module.py --module ensembl.production.xrefs.ScheduleDownload --config_file ${params.config_file} --source_db_url ${params.source_db_url} --reuse_db ${params.reuse_db} --skip_preparse ${params.skip_preparse} --base_path ${params.base_path} --log_timestamp $timestamp
   """
 }
 
@@ -126,7 +126,7 @@ process DownloadSource {
   src_name = (x =~ /"name":\s*"([A-Za-z0-9_.-\/]+)"/)[0][1]
 
   """
-  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.DownloadSource --dataflow '$x' --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --skip_download ${params.skip_download}
+  python ${params.scripts_dir}/run_module.py --module ensembl.production.xrefs.DownloadSource --dataflow '$x' --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --skip_download ${params.skip_download}
   """
 }
 
@@ -156,7 +156,7 @@ process ScheduleCleanup {
   path 'dataflow_cleanup_sources.json'
 
   """
-  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.ScheduleCleanup --base_path ${params.base_path} --source_db_url ${params.source_db_url} --clean_files ${params.clean_files} --clean_dir ${params.clean_dir} --split_files_by_species ${params.split_files_by_species} --log_timestamp $timestamp
+  python ${params.scripts_dir}/run_module.py --module ensembl.production.xrefs.ScheduleCleanup --base_path ${params.base_path} --source_db_url ${params.source_db_url} --clean_files ${params.clean_files} --clean_dir ${params.clean_dir} --split_files_by_species ${params.split_files_by_species} --log_timestamp $timestamp
   """
 }
 
@@ -171,7 +171,7 @@ process Checksum {
   val 'ChecksumDone'
 
   """
-  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.Checksum --base_path ${params.base_path} --source_db_url ${params.source_db_url} --skip_download ${params.skip_download} --log_timestamp $timestamp
+  python ${params.scripts_dir}/run_module.py --module ensembl.production.xrefs.Checksum --base_path ${params.base_path} --source_db_url ${params.source_db_url} --skip_download ${params.skip_download} --log_timestamp $timestamp
   """
 }
 
@@ -234,6 +234,6 @@ process NotifyByEmail {
   val timestamp
 
   """
-  python ${params.scripts_dir}/run_module.py --module ensembl.xrefs.EmailNotification --pipeline_name '${params.pipeline_name}' --base_path ${params.base_path} --email ${params.email} --email_server ${params.email_server} --log_timestamp $timestamp
+  python ${params.scripts_dir}/run_module.py --module ensembl.production.xrefs.EmailNotification --pipeline_name '${params.pipeline_name}' --base_path ${params.base_path} --email ${params.email} --email_server ${params.email_server} --log_timestamp $timestamp
   """
 }
diff --git a/src/python/ensembl/xrefs/Base.py b/src/python/ensembl/production/xrefs/Base.py
similarity index 100%
rename from src/python/ensembl/xrefs/Base.py
rename to src/python/ensembl/production/xrefs/Base.py
diff --git a/src/python/ensembl/xrefs/Checksum.py b/src/python/ensembl/production/xrefs/Checksum.py
similarity index 100%
rename from src/python/ensembl/xrefs/Checksum.py
rename to src/python/ensembl/production/xrefs/Checksum.py
diff --git a/src/python/ensembl/xrefs/DownloadSource.py b/src/python/ensembl/production/xrefs/DownloadSource.py
similarity index 100%
rename from src/python/ensembl/xrefs/DownloadSource.py
rename to src/python/ensembl/production/xrefs/DownloadSource.py
diff --git a/src/python/ensembl/xrefs/EmailNotification.py b/src/python/ensembl/production/xrefs/EmailNotification.py
similarity index 100%
rename from src/python/ensembl/xrefs/EmailNotification.py
rename to src/python/ensembl/production/xrefs/EmailNotification.py
diff --git a/src/python/ensembl/xrefs/ScheduleCleanup.py b/src/python/ensembl/production/xrefs/ScheduleCleanup.py
similarity index 100%
rename from src/python/ensembl/xrefs/ScheduleCleanup.py
rename to src/python/ensembl/production/xrefs/ScheduleCleanup.py
diff --git a/src/python/ensembl/xrefs/ScheduleDownload.py b/src/python/ensembl/production/xrefs/ScheduleDownload.py
similarity index 100%
rename from src/python/ensembl/xrefs/ScheduleDownload.py
rename to src/python/ensembl/production/xrefs/ScheduleDownload.py
diff --git a/src/python/ensembl/xrefs/config/xref_all_sources.json b/src/python/ensembl/production/xrefs/config/xref_all_sources.json
similarity index 100%
rename from src/python/ensembl/xrefs/config/xref_all_sources.json
rename to src/python/ensembl/production/xrefs/config/xref_all_sources.json
diff --git a/src/python/ensembl/xrefs/config/xref_config.ini b/src/python/ensembl/production/xrefs/config/xref_config.ini
similarity index 100%
rename from src/python/ensembl/xrefs/config/xref_config.ini
rename to src/python/ensembl/production/xrefs/config/xref_config.ini

From 039335714034a705b4708a6e7f9f42c66c299fa0 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Wed, 15 May 2024 21:38:07 +0100
Subject: [PATCH 067/128] Update xref.config

add memory 4gg to slurm profile
---
 nextflow/config/xref.config | 1 +
 1 file changed, 1 insertion(+)

diff --git a/nextflow/config/xref.config b/nextflow/config/xref.config
index 66bebf05d..3737c5aff 100644
--- a/nextflow/config/xref.config
+++ b/nextflow/config/xref.config
@@ -75,6 +75,7 @@ profiles {
     }
     withLabel:mem4GB {
         time = '3d'
+        memory = 4.GB
     }
   }
  }

From 4391762fb75228fed7626bd0c695037124450cfc Mon Sep 17 00:00:00 2001
From: vinay-ebi <vinay@ebi.ac.uk>
Date: Thu, 16 May 2024 10:00:31 +0100
Subject: [PATCH 068/128] base load changed to ensembl.production.xrefs

---
 src/python/ensembl/production/xrefs/Checksum.py          | 2 +-
 src/python/ensembl/production/xrefs/DownloadSource.py    | 2 +-
 src/python/ensembl/production/xrefs/EmailNotification.py | 2 +-
 src/python/ensembl/production/xrefs/ScheduleCleanup.py   | 2 +-
 src/python/ensembl/production/xrefs/ScheduleDownload.py  | 2 +-
 5 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/python/ensembl/production/xrefs/Checksum.py b/src/python/ensembl/production/xrefs/Checksum.py
index dc59d5c3f..7ccb401a7 100644
--- a/src/python/ensembl/production/xrefs/Checksum.py
+++ b/src/python/ensembl/production/xrefs/Checksum.py
@@ -14,7 +14,7 @@
 
 """Checksum module for the Xref Download pipeline."""
 
-from ensembl.xrefs.Base import *
+from ensembl.production.xrefs.Base import *
 
 class Checksum(Base):
   def run(self):
diff --git a/src/python/ensembl/production/xrefs/DownloadSource.py b/src/python/ensembl/production/xrefs/DownloadSource.py
index b88088960..060fcb116 100644
--- a/src/python/ensembl/production/xrefs/DownloadSource.py
+++ b/src/python/ensembl/production/xrefs/DownloadSource.py
@@ -14,7 +14,7 @@
 
 """Download module to download xref and version files."""
 
-from ensembl.xrefs.Base import *
+from ensembl.production.xrefs.Base import *
 
 class DownloadSource(Base):
   def run(self):
diff --git a/src/python/ensembl/production/xrefs/EmailNotification.py b/src/python/ensembl/production/xrefs/EmailNotification.py
index 75a23012d..22738d990 100644
--- a/src/python/ensembl/production/xrefs/EmailNotification.py
+++ b/src/python/ensembl/production/xrefs/EmailNotification.py
@@ -14,7 +14,7 @@
 
 """Email module to send user emails notifying of xref pipelines end, with important information and statistics."""
 
-from ensembl.xrefs.Base import *
+from ensembl.production.xrefs.Base import *
 
 from smtplib import SMTP
 from email.message import EmailMessage
diff --git a/src/python/ensembl/production/xrefs/ScheduleCleanup.py b/src/python/ensembl/production/xrefs/ScheduleCleanup.py
index 515150e9d..58396b33a 100644
--- a/src/python/ensembl/production/xrefs/ScheduleCleanup.py
+++ b/src/python/ensembl/production/xrefs/ScheduleCleanup.py
@@ -14,7 +14,7 @@
 
 """Scheduling module to create cleanup jobs for specific xref sources."""
 
-from ensembl.xrefs.Base import *
+from ensembl.production.xrefs.Base import *
 
 class ScheduleCleanup(Base):
   def run(self):
diff --git a/src/python/ensembl/production/xrefs/ScheduleDownload.py b/src/python/ensembl/production/xrefs/ScheduleDownload.py
index b2e48aa86..8001bccc8 100644
--- a/src/python/ensembl/production/xrefs/ScheduleDownload.py
+++ b/src/python/ensembl/production/xrefs/ScheduleDownload.py
@@ -14,7 +14,7 @@
 
 """Scheduling module to create download jobs for all xref sources in config file."""
 
-from ensembl.xrefs.Base import *
+from ensembl.production.xrefs.Base import *
 
 class ScheduleDownload(Base):
   def run(self):

From 6f63ae1947e8eace093818df1a99cbedcbf4ae4a Mon Sep 17 00:00:00 2001
From: "J. Alvarez-Jarreta" <jalvarez@ebi.ac.uk>
Date: Thu, 16 May 2024 10:53:51 +0100
Subject: [PATCH 069/128] Update requirements.txt

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 71c0445d4..529bccc7b 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -18,7 +18,7 @@ ensembl-hive @ git+https://github.com/Ensembl/ensembl-hive.git
     #   ensembl-py
 ensembl-metadata-api @ git+https://github.com/Ensembl/ensembl-metadata-api.git@2.0.1a2
     # via -r requirements.in
-ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git@1.2.2
+ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git
     # via ensembl-metadata-api
 exceptiongroup==1.2.0
     # via

From 15b4eade8a539cc93711e2b983d994abd8da77ec Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Mon, 20 May 2024 10:05:47 +0100
Subject: [PATCH 070/128] Updated default resources from 100mb to 1gb

---
 .../Production/Pipeline/PipeConfig/Base_conf.pm      | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index ac0fca871..a24322ef5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -93,13 +93,13 @@ sub resource_classes {
 
     my %output = (
         #Default is a duplicate of 100M
-        'default'   => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'default_D' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'default_W' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
+        'default'   => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'H'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'default_D' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'D'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'default_W' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $pq . $time{'W'} . ' --mem=' . $memory{'1GB'} . 'm' },
         #Data mover nodes
-        'dm'        => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'dm_D'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'dm_W'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
+        'dm'        => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'dm_D'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'dm_W'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'W'} . ' --mem=' . $memory{'1GB'} . 'm' },
         'dm32_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 32000 -R "rusage[mem=32000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'32GB'} . 'm' },
         'dmMAX_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 200000 -R "rusage[mem=200000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'200GB'} . 'm' },
     );

From 202130276fbf7ef45c9a993cd23c21964bff6110 Mon Sep 17 00:00:00 2001
From: danielp <danielp@ebi.ac.uk>
Date: Thu, 23 May 2024 23:26:15 +0100
Subject: [PATCH 071/128] Updated JSON remodeler to stop Experimental push on
 scalar is now forbidden with new perl version

---
 .../Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm   | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
index d8e8328da..a6738edc0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/JSON/JsonRemodeller.pm
@@ -292,7 +292,10 @@ sub merge_xrefs {
         $obj->{$dbname} = [];
       }
       for my $ann ( @{ $subobj->{$dbname} } ) {
-        push $obj->{$dbname}, $self->copy_hash($ann);
+        if (ref($obj->{$dbname}) ne 'ARRAY') {
+          $obj->{$dbname} = [];
+        }
+        push @{ $obj->{$dbname} }, $self->copy_hash($ann);
       }
     }
   }

From 3290f218d42f2e1e996d241c5b35426d735a2ffc Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Fri, 24 May 2024 12:16:18 +0100
Subject: [PATCH 072/128] Update xref_all_sources.json for RGD

---
 .../ensembl/production/xrefs/config/xref_all_sources.json       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/python/ensembl/production/xrefs/config/xref_all_sources.json b/src/python/ensembl/production/xrefs/config/xref_all_sources.json
index 1edc6e1da..e7b0065a4 100644
--- a/src/python/ensembl/production/xrefs/config/xref_all_sources.json
+++ b/src/python/ensembl/production/xrefs/config/xref_all_sources.json
@@ -91,7 +91,7 @@
     {
       "name" : "RGD",
       "parser" : "RGDParser",
-      "file" : "https://download.rgd.mcw.edu/pub/data_release/GENES.RAT.txt",
+      "file" : "https://download.rgd.mcw.edu/pub/data_release/GENES_RAT.txt",
       "priority" : 2
     },
     {

From 975fa4a81c940e90f05493fdedd70e37a9d77d3a Mon Sep 17 00:00:00 2001
From: nwillhoft <70575561+nwillhoft@users.noreply.github.com>
Date: Tue, 28 May 2024 11:04:12 +0100
Subject: [PATCH 073/128] Update tag names and info relating to gencode
 genesets

---
 modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
index 79358a04d..d95763721 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/GTF/DumpFile.pm
@@ -383,7 +383,8 @@ feature for the position of this on the genome
 - cds_start_NF: the coding region start could not be confirmed
 - mRNA_end_NF: the mRNA end could not be confirmed
 - mRNA_start_NF: the mRNA start could not be confirmed.
-- basic: the transcript is part of the gencode basic geneset
+- gencode_basic: the transcript is part of the gencode basic geneset
+- gencode_primary: the transcript is part of the gencode primary geneset
 
 Comments
 

From 95c13207e4ae13a8cdfc617095d395ac1d0cbc99 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-01.ebi.ac.uk>
Date: Wed, 29 May 2024 09:28:22 +0100
Subject: [PATCH 074/128] Bugfix for files not being overwritten

---
 nextflow/config/xref.config               |  5 +++--
 nextflow/workflows/xrefDownload.nf        |  6 +++++-
 scripts/xrefs/cleanup_and_split_source.pl | 20 +++++++++++++-------
 3 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/nextflow/config/xref.config b/nextflow/config/xref.config
index 3737c5aff..024f80e68 100644
--- a/nextflow/config/xref.config
+++ b/nextflow/config/xref.config
@@ -17,6 +17,7 @@ params.reuse_db = 0
 params.skip_preparse = 1
 params.split_files_by_species = 1
 params.tax_ids_file = ''
+params.update_mode = 0
 
 params.base_path = ''
 params.clean_files = 1
@@ -70,11 +71,11 @@ profiles {
 
     withLabel: dm {
         queue = 'datamover'
-        time = '2h'
+        time = '3h'
         memory = 2.GB
     }
     withLabel:mem4GB {
-        time = '3d'
+        time = '5d'
         memory = 4.GB
     }
   }
diff --git a/nextflow/workflows/xrefDownload.nf b/nextflow/workflows/xrefDownload.nf
index 51cc53552..65e255fda 100644
--- a/nextflow/workflows/xrefDownload.nf
+++ b/nextflow/workflows/xrefDownload.nf
@@ -18,6 +18,7 @@ println """\
         sources_config_file       : ${params.sources_config_file}
         clean_dir                 : ${params.clean_dir}
         tax_ids_file              : ${params.tax_ids_file}
+        update_mode               : ${params.update_mode}
         """
         .stripIndent()
 
@@ -57,6 +58,9 @@ def helpMessage() {
 
     --tax_ids_file              (optional)      Path to the file containing the taxonomy IDs of the species to extract data for.
                                                 Used to update the data for the provided species.
+
+    --update_mode               (optional)      If set to 1, pipeline is in update mode, refreshing/updating its data for new taxonomy IDs.
+                                                Only used if --tax_ids_file is set. Default: 0
   """.stripIndent()
 }
 
@@ -198,7 +202,7 @@ process CleanupSplitSource {
   }
 
   """
-  perl ${params.perl_scripts_dir}/cleanup_and_split_source.pl --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --name $src_name --clean_dir ${params.clean_dir} --skip_download ${params.skip_download} --clean_files ${params.clean_files} $cmd_params
+  perl ${params.perl_scripts_dir}/cleanup_and_split_source.pl --base_path ${params.base_path} --log_timestamp $timestamp --source_db_url ${params.source_db_url} --name $src_name --clean_dir ${params.clean_dir} --clean_files ${params.clean_files} --update_mode ${params.update_mode} $cmd_params
   """
 }
 
diff --git a/scripts/xrefs/cleanup_and_split_source.pl b/scripts/xrefs/cleanup_and_split_source.pl
index 6a09971ea..3beabbcd6 100644
--- a/scripts/xrefs/cleanup_and_split_source.pl
+++ b/scripts/xrefs/cleanup_and_split_source.pl
@@ -19,7 +19,7 @@
 use Getopt::Long;
 use Carp;
 use DBI;
-use File::Path qw/make_path/;
+use File::Path qw/make_path rmtree/;
 use File::Spec::Functions;
 use HTTP::Tiny;
 use JSON;
@@ -28,7 +28,7 @@
 
 use Nextflow::Utils;
 
-my ($base_path, $source_db_url, $source_name, $clean_dir, $clean_files, $version_file, $tax_ids_file, $log_timestamp);
+my ($base_path, $source_db_url, $source_name, $clean_dir, $clean_files, $version_file, $tax_ids_file, $update_mode, $log_timestamp);
 GetOptions(
   'base_path=s'     => \$base_path,
   'source_db_url=s' => \$source_db_url,
@@ -37,14 +37,17 @@
   'clean_files=i'   => \$clean_files,
   'version_file:s'  => \$version_file,
   'tax_ids_file:s'  => \$tax_ids_file,
+  'update_mode:i'   => \$update_mode,
   'log_timestamp:s' => \$log_timestamp
 );
 
 # Check that all mandatory parameters are passed
 if (!defined($base_path) || !defined($source_db_url) || !defined($source_name) || !defined($clean_dir) || !defined($clean_files)) {
-  croak "Usage: cleanup_source.pl --base_path <base_path> --source_db_url <source_db_url> --name <name> --clean_dir <clean_dir> --clean_files <clean_files> [--version_file <version_file>] [--tax_ids_file <tax_ids_file>] [--log_timestamp <log_timestamp>]";
+  croak "Usage: cleanup_source.pl --base_path <base_path> --source_db_url <source_db_url> --name <name> --clean_dir <clean_dir> --clean_files <clean_files> [--version_file <version_file>] [--tax_ids_file <tax_ids_file>] [--update_mode <update_mode>] [--log_timestamp <log_timestamp>]";
 }
 
+if (!defined($update_mode)) {$update_mode = 0;}
+
 my $log_file;
 if (defined($log_timestamp)) {
   my $log_path = catdir($base_path, 'logs', $log_timestamp);
@@ -71,6 +74,9 @@
 my $output_path = $clean_dir."/".$clean_name;
 
 # Create needed directories
+if (!$update_mode) {
+  rmtree($output_path);
+}
 make_path($output_path);
 
 my $sources_to_remove;
@@ -102,7 +108,7 @@
 # Extract taxonomy IDs
 my %tax_ids;
 my ($skipped_species, $added_species) = (0, 0);
-if ($tax_ids_file) {
+if ($tax_ids_file && $update_mode) {
   open my $fh, '<', $tax_ids_file;
   chomp(my @lines = <$fh>);
   close $fh;
@@ -212,10 +218,10 @@
       if (!defined($current_species_id) || (defined($current_species_id) && $species_id ne $current_species_id)) {
         close($out_fh) if (defined($current_species_id));
 
-	my $species_id_str = sprintf("%04d", $species_id);
-	my @digits = split('', $species_id_str);
+        my $species_id_str = sprintf("%04d", $species_id);
+        my @digits = split('', $species_id_str);
 
-	$write_path = catdir($output_path, $digits[0], $digits[1], $digits[2], $digits[3]);
+        $write_path = catdir($output_path, $digits[0], $digits[1], $digits[2], $digits[3]);
         make_path($write_path);
 
         $write_file = $write_path."/".$output_file_name."-".$species_id;

From 3ad6a021581c3a13d4279c26c76c4e038cddcf4e Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-01.ebi.ac.uk>
Date: Tue, 4 Jun 2024 08:59:16 +0100
Subject: [PATCH 075/128] Fix for when no species file is found

---
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 17a04a762..27d16dcca 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -148,6 +148,7 @@ sub run {
 
       foreach my $file (@list_files) {
         $file =~ s/\n//;
+        if (!-f $file) { next; }
         if (defined $release_file and $file eq $release_file) { next; }
   
         $dataflow_params = {

From 9586a89aee2ed9ab1db90a5daaa9eab023ceac50 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Tue, 4 Jun 2024 19:55:35 +0100
Subject: [PATCH 076/128] Update ProteinFeatures analysis

new member db Phobius (1.01) and SignalP_GRAM_POSITIVE (4.1)  added
---
 .../Pipeline/PipeConfig/ProteinFeatures_conf.pm  | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index ec402777e..2ffa87fdf 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -227,6 +227,22 @@ sub default_options {
         ipscan_xml      => 'TMHMM',
         ipscan_lookup   => 0,
       },
+      {
+        db               => 'Phobius',
+        ipscan_lookup    => 1,
+        ipscan_name      => 'Phobius',
+        ipscan_xml       => 'PHOBIUS',
+        logic_name       => 'Phobius',
+        program          => 'InterProScan',
+      },
+      {
+        db              => 'SignalP_GRAM_POSITIVE',
+        ipscan_lookup   => 1,
+        ipscan_name     => 'SignalP_GRAM_POSITIVE',
+        ipscan_xml      => 'SIGNALP_GRAM_POSITIVE',
+        logic_name      => 'SignalP_GRAM_POSITIVE',
+        program         => 'InterProScan',
+      },
       #seg replaces low complexity regions in protein sequences with X characters(https://rothlab.ucdavis.edu/genhelp/seg.html)
       {
         logic_name      => 'seg',

From f065884595904aa3e8d9c34b0444b376bc53f941 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Tue, 4 Jun 2024 20:25:59 +0100
Subject: [PATCH 077/128] Update ProteinFeatures_conf.pm

---
 .../Pipeline/PipeConfig/ProteinFeatures_conf.pm           | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index 2ffa87fdf..e449f7b51 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -243,6 +243,14 @@ sub default_options {
         logic_name      => 'SignalP_GRAM_POSITIVE',
         program         => 'InterProScan',
       },
+      {
+        db              => 'SignalP_GRAM_NEGATIVE',
+        ipscan_lookup   => 1,
+        ipscan_name     => 'SignalP_GRAM_NEGATIVE',
+        ipscan_xml      => 'SIGNALP_GRAM_NEGATIVE',
+        logic_name      => 'SignalP_GRAM_NEGATIVE',
+        program         => 'InterProScan',
+      },      
       #seg replaces low complexity regions in protein sequences with X characters(https://rothlab.ucdavis.edu/genhelp/seg.html)
       {
         logic_name      => 'seg',

From d283cf09fc2516876cb77df899d56903c604a2bb Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:07:03 +0100
Subject: [PATCH 078/128] Update xref_sources.json

update xref source Xenbase  mapping file GenePageEnsemblModelMapping_4.1.txt
---
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
index 161a41186..d12edb9cf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
@@ -254,7 +254,7 @@
     {
       "name" : "Xenbase",
       "parser" : "XenopusJamboreeParser",
-      "file" : "http://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt",
+      "file" : "http://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping_4.1.txt",
       "priority" : 1
     },
     {

From d74f87eb7e5bbc3b134366aa09b81b83136eab64 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Wed, 19 Jun 2024 15:08:57 +0100
Subject: [PATCH 079/128] Update xref_all_sources.json

update xenbase mapping file
---
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
index 7fa14c977..5b6361536 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
@@ -226,7 +226,7 @@
     {
       "name" : "Xenbase",
       "parser" : "XenopusJamboreeParser",
-      "file" : "http://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping.txt",
+      "file" : "http://ftp.xenbase.org/pub/GenePageReports/GenePageEnsemblModelMapping_4.1.txt",
       "priority" : 1
     },
     {

From b2da23c1840bb10dde5f29cfb9717ef93f913b4a Mon Sep 17 00:00:00 2001
From: Stefano Giorgetti <sgiorgetti@ebi.ac.uk>
Date: Thu, 20 Jun 2024 13:36:10 +0000
Subject: [PATCH 080/128] Fixed  as per ENSPROD-9493

---
 .../Production/Pipeline/AlphaFold/InsertProteinFeatures.pm      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
index 059ac4a3e..0178fc21e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/AlphaFold/InsertProteinFeatures.pm
@@ -164,7 +164,7 @@ sub run {
             -db            => 'alphafold',
             -db_version    => $alpha_version,
             -db_file       => $self->param('db_dir') . '/accession_ids.csv',
-            -display_label => 'AlphaFold DB import',
+            -display_label => 'AFDB-ENSP mapping',
             -displayable   => '1',
             -description   => 'Protein features based on AlphaFold predictions, mapped with GIFTS or UniParc'
     );

From 7e4aca521363e3550e1e3cb1deecc670a1339077 Mon Sep 17 00:00:00 2001
From: John Tate <jgt@ebi.ac.uk>
Date: Mon, 24 Jun 2024 17:26:01 +0100
Subject: [PATCH 081/128] Fix use of keys on a scalar

Change the use of an experimental, now removed, feature that allowed a hashref scalar to be used in place of a hash.
---
 .../Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
index 28aa1ba06..d5d8e3a8a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ga4ghChecksum/ChecksumGenerator.pm
@@ -218,7 +218,7 @@ sub all_hashes {
     } ## end foreach my $slice (@slices)
 
     for my $seq_type (keys %$batch) {
-        for my $attrib_table (keys $batch->{$seq_type}) {
+        for my $attrib_table (keys %{$batch->{$seq_type}}) {
             $attribute_adaptor->store_batch_on_Object($attrib_table, $batch->{$seq_type}->{$attrib_table}, 1000);
         }
     }

From a3ff2b44c29af7d4a6e819dfdf38f67178f32452 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-02.ebi.ac.uk>
Date: Wed, 26 Jun 2024 17:07:18 +0100
Subject: [PATCH 082/128] Fixes for 113 issues

---
 .../Pipeline/PipeConfig/XrefProcess_conf.pm        |  2 ++
 .../EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm | 14 +++++++++++---
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
index 2e11ce311..0903a1947 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
@@ -173,6 +173,7 @@ sub pipeline_analyses {
       base_path => $self->o('base_path'),
       release   => $self->o('release')
     },
+    -max_retry_count => 0,
     -flow_into  => {
       '2->A' => 'dump_xref',
       'A->1' => 'schedule_mapping'
@@ -187,6 +188,7 @@ sub pipeline_analyses {
       release     => $self->o('release'),
       config_file => $self->o('config_file')
     },
+    -max_retry_count => 0,
     -flow_into  => { 2 => 'align_factory' },
     -rc_name    => '1GB',
   },
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
index b3233ea9d..ef4868850 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/Alignment.pm
@@ -84,10 +84,18 @@ sub run {
   $exe =~ s/\n//g;
   my $command_string = sprintf ("%s --showalignment FALSE --showvulgar FALSE --ryo '%s' --gappedextension FALSE --model 'affine:local' %s --subopt no --query %s --target %s --querychunktotal %s --querychunkid %s", $exe, $ryo, $method, $source, $target, $max_chunks, $chunk);
   my $output = `$command_string`;
-  my @hits = grep {$_ =~ /^xref/} split "\n", $output; # not all lines in output are alignments
 
-  while (my $hit = shift @hits) {
-    print $fh $hit . "\n";
+  if ($? == 0) {
+    my @hits = grep {$_ =~ /^xref/} split "\n", $output; # not all lines in output are alignments
+
+    while (my $hit = shift @hits) {
+      print $fh $hit . "\n";
+    }
+  } else {
+    my $job = $self->input_job();
+    $job->adaptor()->db()->get_LogMessageAdaptor()->store_job_message($job->dbID(), $output, 'WORKER_ERROR');  
+
+    throw("Exonerate failed with exit_code: $?\n");
   }
 
   $fh->close();

From ee5da99d1786cf413d571478e1385b08bdef9961 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Fri, 5 Jul 2024 16:13:10 +0100
Subject: [PATCH 083/128] Update SourceFactory.pm

Fix for Experimental keys on a scalar is now forbidden
---
 .../Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm   | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
index 4599d8636..37cd8b09e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Ortholog/SourceFactory.pm
@@ -59,7 +59,7 @@ sub write_output {
     my $compara_param = $self->param('compara');
     my $cleanup_dir = $self->param('cleanup_dir');
 
-    foreach my $pair (keys $sp_config) {
+    foreach my $pair (keys %{$sp_config}) {
         my $compara = $sp_config->{$pair}->{'compara'};
         if (defined $compara_param && $compara ne $compara_param) {
             print STDERR "Skipping $compara\n";

From d1ce2933a759494c59e81d274029f9e8fd088618 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Fri, 19 Jul 2024 13:27:32 +0100
Subject: [PATCH 084/128] Updated Base class with slurm default resource 1GB

---
 .../Pipeline/PipeConfig/Base_conf.pm          | 44 +++++++------------
 1 file changed, 17 insertions(+), 27 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index 86d0ca7a9..a340f0602 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -66,14 +66,14 @@ sub beekeeper_extra_cmdline_options {
 sub resource_classes {
     my $self = shift;
 
+    ## String it together
+    my %time = (
+        H => ' --time=1:00:00',
+        D => ' --time=1-00:00:00',
+        W => ' --time=7-00:00:00'
+    );
 
-    ## Sting it together
-    my %time = (H => ' --time=1:00:00',
-        D         => ' --time=1-00:00:00',
-        W         => ' --time=7-00:00:00',);
-
-    my %memory = ('100M' => '100',
-        '200M'           => '200',
+    my %memory = (
         '500M'           => '500',
         '1GB'            => '1000',
         '2GB'            => '2000',
@@ -89,40 +89,30 @@ sub resource_classes {
     );
 
     my $dq = ' --partition=datamover';
-
     my %output = (
         #Default is a duplicate of 100M
-        'default'   => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $time{'H'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'default_D' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $time{'D'} . ' --mem=' . $memory{'100M'} . 'm' },
-        'default_W' => { 'LSF' => '-q ' . $self->o('production_queue'), 'SLURM' => $time{'W'} . ' --mem=' . $memory{'100M'} . 'm' },
+        'default'   => { 'SLURM' => $time{'H'} . ' --mem=' . $memory{'1G'} . 'm' },
+        'default_D' => { 'SLURM' => $time{'D'} . ' --mem=' . $memory{'1G'} . 'm' },
+        'default_W' => { 'SLURM' => $time{'W'} . ' --mem=' . $memory{'1G'} . 'm' },
         #Data mover nodes
-        'dm'        => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'1GB'} . 'm' },
-        'dm_D'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'1GB'} . 'm' },
-        'dm_W'      => { 'LSF' => '-q ' . $self->o('datamover_queue'), 'SLURM' => $dq . $time{'W'} . ' --mem=' . $memory{'1GB'} . 'm' },
-        'dm32_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 32000 -R "rusage[mem=32000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'32GB'} . 'm' },
-        'dmMAX_D'    => { 'LSF' => '-q ' . $self->o('datamover_queue') . ' -M 200000 -R "rusage[mem=200000]"', 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'200GB'} . 'm' },
+        'dm'       => { 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'dm_D'     => { 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'dm_W'     => { 'SLURM' => $dq . $time{'W'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'dm32_D'   => { 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'32GB'} . 'm' },
+        'dmMAX_D'  => { 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'200GB'} . 'm' },
     );
-    #Create a dictionary of all possible time and memory combinations. Format would be:
-    #2G={
-    #   'SLURM' => ' --time=1:00:00  --mem=2000m',
-    #   'LSF' => '-q $self->o(production_queue) -M 2000 -R "rusage[mem=2000]"'
-    # };
 
     while ((my $time_key, my $time_value) = each(%time)) {
         while ((my $memory_key, my $memory_value) = each(%memory)) {
             if ($time_key eq 'H') {
-                $output{$memory_key} = { 'LSF' => '-q ' . $self->o('production_queue') . ' -M ' . $memory_value . ' -R "rusage[mem=' . $memory_value . ']"',
-                    'SLURM'                    => $time_value . '  --mem=' . $memory_value . 'm' }
+                $output{$memory_key} = { 'SLURM' => $time_value . '  --mem=' . $memory_value . 'm' };
             }
             else {
-                $output{$memory_key . '_' . $time_key} = { 'LSF' => '-q ' . $self->o('production_queue') . ' -M ' . $memory_value . ' -R "rusage[mem=' . $memory_value . ']"',
-                    'SLURM'                                      => $time_value . '  --mem=' . $memory_value . 'm' }
+                $output{$memory_key . '_' . $time_key} = { 'SLURM' => $time_value . '  --mem=' . $memory_value . 'm' };
             }
         }
     }
-
     return \%output;
-
 }
 
 1;

From 772caf1c280ce8dc01706f741400674f1abe5367 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Fri, 19 Jul 2024 13:32:16 +0100
Subject: [PATCH 085/128] Update Typo GB

---
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index a340f0602..d57a14a70 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -91,9 +91,9 @@ sub resource_classes {
     my $dq = ' --partition=datamover';
     my %output = (
         #Default is a duplicate of 100M
-        'default'   => { 'SLURM' => $time{'H'} . ' --mem=' . $memory{'1G'} . 'm' },
-        'default_D' => { 'SLURM' => $time{'D'} . ' --mem=' . $memory{'1G'} . 'm' },
-        'default_W' => { 'SLURM' => $time{'W'} . ' --mem=' . $memory{'1G'} . 'm' },
+        'default'   => { 'SLURM' => $time{'H'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'default_D' => { 'SLURM' => $time{'D'} . ' --mem=' . $memory{'1GB'} . 'm' },
+        'default_W' => { 'SLURM' => $time{'W'} . ' --mem=' . $memory{'1GB'} . 'm' },
         #Data mover nodes
         'dm'       => { 'SLURM' => $dq . $time{'H'} . ' --mem=' . $memory{'1GB'} . 'm' },
         'dm_D'     => { 'SLURM' => $dq . $time{'D'} . ' --mem=' . $memory{'1GB'} . 'm' },

From 2b01517b2f6615cec5805a72435c14091e1d99ab Mon Sep 17 00:00:00 2001
From: vinay-ebi <vinay@ebi.ac.uk>
Date: Mon, 22 Jul 2024 16:25:21 +0100
Subject: [PATCH 086/128] decompress upidump.lis.gz file before load to hive db

---
 .../Pipeline/PipeConfig/ProteinFeatures_conf.pm     |  2 +-
 .../Pipeline/ProteinFeatures/LoadUniParc.pm         | 13 +++++++++++--
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index e449f7b51..dbc95951a 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -75,7 +75,7 @@ sub default_options {
 
     interpro_file    => 'names.dat',
     interpro2go_file => 'interpro2go',
-    uniparc_file     => 'upidump.lis',
+    uniparc_file     => 'upidump.lis.gz',
     mapping_file     => 'idmapping_selected.tab.gz',
 
     # Files are retrieved and stored locally with the same name.
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
index 40eddb1b4..4d97c8950 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
@@ -21,16 +21,25 @@ package Bio::EnsEMBL::Production::Pipeline::ProteinFeatures::LoadUniParc;
 
 use strict;
 use warnings;
-
+use IO::Uncompress::Gunzip qw(gunzip $GunzipError);
 use File::Basename;
-
 use base ('Bio::EnsEMBL::Production::Pipeline::Common::Base');
 
 sub run {
   my ($self) = @_;
   my $uniparc_file = $self->param_required('uniparc_file_local');
 
+
   if (-e $uniparc_file) {
+
+    #check if uniparc file is compressed
+    if ($uniparc_file =~ /\.gz$/){
+        my $uniparc_file_decompress = $uniparc_file;
+        $uniparc_file_decompress =~ s/\.gz$//;
+        gunzip $uniparc_file => $uniparc_file_decompress  or $self->throw("gunzip failed: $GunzipError");
+        $uniparc_file = $uniparc_file_decompress;
+    }
+
     my $dbh = $self->hive_dbh;
     my $sql = "LOAD DATA LOCAL INFILE '$uniparc_file' INTO TABLE uniparc FIELDS TERMINATED BY ' '";
     $dbh->do($sql) or self->throw($dbh->errstr);

From 434e865ab149ed266c76366d2f6820d2df424f64 Mon Sep 17 00:00:00 2001
From: vinay-ebi <vinay@ebi.ac.uk>
Date: Mon, 22 Jul 2024 16:55:38 +0100
Subject: [PATCH 087/128] delete the upidump file after loading into hive db

---
 .../Production/Pipeline/ProteinFeatures/LoadUniParc.pm     | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
index 4d97c8950..56eb488df 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
@@ -37,6 +37,8 @@ sub run {
         my $uniparc_file_decompress = $uniparc_file;
         $uniparc_file_decompress =~ s/\.gz$//;
         gunzip $uniparc_file => $uniparc_file_decompress  or $self->throw("gunzip failed: $GunzipError");
+        #delete compressed file .gz
+        unlink  $uniparc_file or $self->throw("unable to delete $uniparc_file");
         $uniparc_file = $uniparc_file_decompress;
     }
 
@@ -50,9 +52,14 @@ sub run {
     my $index_2 = 'ALTER TABLE uniparc ADD KEY md5sum_idx (md5sum) USING HASH';
     $dbh->do($index_2) or self->throw($dbh->errstr);
 
+    #delete upidump file from pipeline direcotry after loading into hive db
+    unlink  $uniparc_file or $self->throw("unable to delete $uniparc_file");
+
   } else {
     $self->throw("Checksum file '$uniparc_file' does not exist");
   }
+
+
 }
 
 1;

From 693c899042e1f1710f8875215daf9b92edaa55ab Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Mon, 22 Jul 2024 20:39:30 +0100
Subject: [PATCH 088/128] Update
 modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm

Co-authored-by: John Tate <jgt@ebi.ac.uk>
---
 .../EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
index 56eb488df..e54038880 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
@@ -38,7 +38,7 @@ sub run {
         $uniparc_file_decompress =~ s/\.gz$//;
         gunzip $uniparc_file => $uniparc_file_decompress  or $self->throw("gunzip failed: $GunzipError");
         #delete compressed file .gz
-        unlink  $uniparc_file or $self->throw("unable to delete $uniparc_file");
+        unlink  $uniparc_file or $self->throw("unable to delete $uniparc_file: $!");
         $uniparc_file = $uniparc_file_decompress;
     }
 

From 51cc0c35a49aa430ddc67092052b5fd6928053d4 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Mon, 22 Jul 2024 20:39:39 +0100
Subject: [PATCH 089/128] Update
 modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm

Co-authored-by: John Tate <jgt@ebi.ac.uk>
---
 .../EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
index e54038880..444b7a2bb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/ProteinFeatures/LoadUniParc.pm
@@ -53,7 +53,7 @@ sub run {
     $dbh->do($index_2) or self->throw($dbh->errstr);
 
     #delete upidump file from pipeline direcotry after loading into hive db
-    unlink  $uniparc_file or $self->throw("unable to delete $uniparc_file");
+    unlink  $uniparc_file or $self->throw("unable to delete $uniparc_file: $!");
 
   } else {
     $self->throw("Checksum file '$uniparc_file' does not exist");

From 0eae3f67f37be6f754347bb70d11ac411885df24 Mon Sep 17 00:00:00 2001
From: Paulo Lins <plins@ebi.ac.uk>
Date: Thu, 25 Jul 2024 09:45:23 +0100
Subject: [PATCH 090/128] Include human and mouse symlinks

---
 scripts/py/regulation_ftp_symlinks.py | 53 ++++++++++++++++++++-------
 1 file changed, 39 insertions(+), 14 deletions(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index a8a9c663b..ba66b919a 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -42,7 +42,7 @@
 from pathlib import Path
 
 # Human and Mouse follow a different dir structure
-SPECIES_TO_NOT_INCLUDE = ["homo_sapiens", "mus_musculus"]
+# SPECIES_TO_NOT_INCLUDE = ["homo_sapiens", "mus_musculus"]
 
 # GENE-SWITCH species
 GENE_SWITCH_SPECIES = [
@@ -54,8 +54,12 @@
 PUBLIC_PUB_PATH = "PUBLIC/pub"
 DATA_FILES_PATH = "data_files/"
 DATA_FILES_PATH_TEMPLATE = "{ftp_path}/data_files/{species}/{assembly}/funcgen"
-RELEASE_FOLDER_PATH_TEMPLATE = "{ftp_path}/release-{release}/regulation/{species}/{assembly}"
-MISC_GENE_SWITCH_PATH_TEMPLATE = "{ftp_path}/misc/gene-switch/regulation/{species}/{assembly}"
+RELEASE_FOLDER_PATH_TEMPLATE = (
+    "{ftp_path}/release-{release}/regulation/{species}/{assembly}"
+)
+MISC_GENE_SWITCH_PATH_TEMPLATE = (
+    "{ftp_path}/misc/gene-switch/regulation/{species}/{assembly}"
+)
 
 ANALYSIS_TYPE_PEAKS = "peaks"
 ANALYSIS_TYPE_SIGNAL = "signal"
@@ -135,7 +139,9 @@ def get_species_with_analysis_type_folder(analysis_type, ftp_path):
     def get_most_recent_release_data_file_path(data_file_path):
         validator.is_dir(Path(data_file_path))
         available_releases = listdir(data_file_path)
-        return Path(data_file_path) / str(max([int(release) for release in available_releases]))
+        return Path(data_file_path) / str(
+            max([int(release) for release in available_releases])
+        )
 
 
 utils = Utils()
@@ -156,10 +162,14 @@ def __init__(self, **path_specifics):
         )
         self.sources = {
             "release_folder": Path(
-                RELEASE_FOLDER_PATH_TEMPLATE.format(**self.aliased_paths(**path_specifics))
+                RELEASE_FOLDER_PATH_TEMPLATE.format(
+                    **self.aliased_paths(**path_specifics)
+                )
             ),
             "misc_folder": Path(
-                MISC_GENE_SWITCH_PATH_TEMPLATE.format(**self.aliased_paths(**path_specifics))
+                MISC_GENE_SWITCH_PATH_TEMPLATE.format(
+                    **self.aliased_paths(**path_specifics)
+                )
             ),
         }
 
@@ -172,7 +182,8 @@ def get(self, key):
 
     def symlink2rf(self, analysis_type, only_remove=False, relative=True):
         target = (
-            Path(path.relpath(self.target, self.sources["release_folder"])) / analysis_type
+            Path(path.relpath(self.target, self.sources["release_folder"]))
+            / analysis_type
             if relative
             else self.target / analysis_type
         )
@@ -188,7 +199,8 @@ def symlink2misc(self, analysis_type, only_remove=False, relative=True):
             makedirs(self.sources["misc_folder"])
 
         target = (
-            Path(path.relpath(self.target, self.sources["misc_folder"])) / analysis_type
+            Path(path.relpath(self.target, self.sources["misc_folder"]))
+            / analysis_type
             if relative
             else self.target / analysis_type
         )
@@ -203,17 +215,26 @@ def _symlink(self, source, target, only_remove):
         if not only_remove:
             source.symlink_to(target, target_is_directory=True)
             if validator.is_symlink(source, check=True):
-                logger.info(f"{source} -> {target} --- was successfully created")
+                logger.info(
+                    f"{source} -> {target} --- was successfully created"
+                )
         else:
             if not validator.is_symlink(source, check=True):
-                logger.info(f"{source} -> {target} -- was successfully removed")
+                logger.info(
+                    f"{source} -> {target} -- was successfully removed"
+                )
 
     def aliased_paths(self, **kwargs):
-        return {key: self.RELEASE_PATH_ALIASES.get(value, value) for key, value in kwargs.items()}
+        return {
+            key: self.RELEASE_PATH_ALIASES.get(value, value)
+            for key, value in kwargs.items()
+        }
 
     @staticmethod
     def search(analysis_type, ftp_path, release):
-        result = utils.get_species_with_analysis_type_folder(analysis_type, ftp_path)
+        result = utils.get_species_with_analysis_type_folder(
+            analysis_type, ftp_path
+        )
         return [
             RegulationSymlinkFTP(
                 analysis_type=analysis_type,
@@ -275,13 +296,17 @@ def parse_arguments():
     ftp_path = args.ftp_path / PUBLIC_PUB_PATH
 
     logger.info("Searching for peaks in data_files ...")
-    peaks = RegulationSymlinkFTP.search(ANALYSIS_TYPE_PEAKS, ftp_path, args.release_version)
+    peaks = RegulationSymlinkFTP.search(
+        ANALYSIS_TYPE_PEAKS, ftp_path, args.release_version
+    )
     for peak in peaks:
         peak.symlink2rf("peaks", only_remove=args.delete_symlinks)
         peak.symlink2misc("peaks", only_remove=args.delete_symlinks)
 
     logger.info("Searching for signals in data_files ...")
-    signals = RegulationSymlinkFTP.search(ANALYSIS_TYPE_SIGNAL, ftp_path, args.release_version)
+    signals = RegulationSymlinkFTP.search(
+        ANALYSIS_TYPE_SIGNAL, ftp_path, args.release_version
+    )
     for signal in signals:
         signal.symlink2rf("signal", only_remove=args.delete_symlinks)
         signal.symlink2misc("signal", only_remove=args.delete_symlinks)

From 3542ca1265fb905cba0675b3d52118ccac2e9391 Mon Sep 17 00:00:00 2001
From: Paulo Lins <plins@codon-slurm-login-02.ebi.ac.uk>
Date: Thu, 25 Jul 2024 10:36:20 +0100
Subject: [PATCH 091/128] include Mouse and Human symlinks

---
 scripts/py/regulation_ftp_symlinks.py | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index ba66b919a..938ae0f09 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -43,6 +43,7 @@
 
 # Human and Mouse follow a different dir structure
 # SPECIES_TO_NOT_INCLUDE = ["homo_sapiens", "mus_musculus"]
+SPECIES_TO_NOT_INCLUDE = []
 
 # GENE-SWITCH species
 GENE_SWITCH_SPECIES = [
@@ -139,8 +140,15 @@ def get_species_with_analysis_type_folder(analysis_type, ftp_path):
     def get_most_recent_release_data_file_path(data_file_path):
         validator.is_dir(Path(data_file_path))
         available_releases = listdir(data_file_path)
+        releases = []
+        for release in available_releases:
+            try:
+                releases.append(int(release))
+            except:
+                continue
+
         return Path(data_file_path) / str(
-            max([int(release) for release in available_releases])
+            max(releases)
         )
 
 
@@ -235,6 +243,7 @@ def search(analysis_type, ftp_path, release):
         result = utils.get_species_with_analysis_type_folder(
             analysis_type, ftp_path
         )
+        __import__("ipdb").set_trace()
         return [
             RegulationSymlinkFTP(
                 analysis_type=analysis_type,
@@ -244,7 +253,7 @@ def search(analysis_type, ftp_path, release):
                 release=release,
             )
             for species, assemblies in result.items()
-            for assembly in assemblies
+            for assembly in assemblies if assembly not in ["GRCh37", "GRCm38", "NCBIM37"]
         ]
 
 

From ac6c74187bd47a1717dca2bf0066fa783cc9875f Mon Sep 17 00:00:00 2001
From: Paulo Lins <plins@codon-slurm-login-02.ebi.ac.uk>
Date: Thu, 25 Jul 2024 10:43:11 +0100
Subject: [PATCH 092/128] include Mouse and Human symlinks

---
 scripts/py/regulation_ftp_symlinks.py | 2 --
 1 file changed, 2 deletions(-)

diff --git a/scripts/py/regulation_ftp_symlinks.py b/scripts/py/regulation_ftp_symlinks.py
index 938ae0f09..3ded73f0c 100644
--- a/scripts/py/regulation_ftp_symlinks.py
+++ b/scripts/py/regulation_ftp_symlinks.py
@@ -42,7 +42,6 @@
 from pathlib import Path
 
 # Human and Mouse follow a different dir structure
-# SPECIES_TO_NOT_INCLUDE = ["homo_sapiens", "mus_musculus"]
 SPECIES_TO_NOT_INCLUDE = []
 
 # GENE-SWITCH species
@@ -243,7 +242,6 @@ def search(analysis_type, ftp_path, release):
         result = utils.get_species_with_analysis_type_folder(
             analysis_type, ftp_path
         )
-        __import__("ipdb").set_trace()
         return [
             RegulationSymlinkFTP(
                 analysis_type=analysis_type,

From bbc136284d77f6acb7ba8d69026ccc6069401182 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Tue, 13 Aug 2024 12:15:13 +0100
Subject: [PATCH 093/128] Update ProteinFeatures_conf.pm

Update the Protein feature analysis logic name to lowercase
---
 .../Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm  | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index dbc95951a..41a743aa4 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -232,7 +232,7 @@ sub default_options {
         ipscan_lookup    => 1,
         ipscan_name      => 'Phobius',
         ipscan_xml       => 'PHOBIUS',
-        logic_name       => 'Phobius',
+        logic_name       => 'phobius',
         program          => 'InterProScan',
       },
       {
@@ -240,7 +240,7 @@ sub default_options {
         ipscan_lookup   => 1,
         ipscan_name     => 'SignalP_GRAM_POSITIVE',
         ipscan_xml      => 'SIGNALP_GRAM_POSITIVE',
-        logic_name      => 'SignalP_GRAM_POSITIVE',
+        logic_name      => 'signalp_gram_positive',
         program         => 'InterProScan',
       },
       {
@@ -248,7 +248,7 @@ sub default_options {
         ipscan_lookup   => 1,
         ipscan_name     => 'SignalP_GRAM_NEGATIVE',
         ipscan_xml      => 'SIGNALP_GRAM_NEGATIVE',
-        logic_name      => 'SignalP_GRAM_NEGATIVE',
+        logic_name      => 'signalp_gram_negative',
         program         => 'InterProScan',
       },      
       #seg replaces low complexity regions in protein sequences with X characters(https://rothlab.ucdavis.edu/genhelp/seg.html)

From 897ec8e659098d80e78ed09442982c832b99bd6d Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <ten@codon-slurm-login-04.ebi.ac.uk>
Date: Mon, 9 Sep 2024 09:40:17 +0100
Subject: [PATCH 094/128] Changes for xref for release 114

---
 .../Pipeline/PipeConfig/XrefProcess_conf.pm   | 14 +++-
 .../Production/Pipeline/Xrefs/DumpXref.pm     |  2 +-
 .../Production/Pipeline/Xrefs/ParseSource.pm  | 18 +++--
 .../Pipeline/Xrefs/ScheduleSource.pm          | 15 +++-
 .../Pipeline/Xrefs/xref_all_sources.json      | 15 +---
 src/python/ensembl/production/xrefs/Base.py   | 80 -------------------
 6 files changed, 43 insertions(+), 101 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
index 0903a1947..fcf875c2b 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
@@ -222,7 +222,7 @@ sub pipeline_analyses {
     },
     -flow_into  => {
       '2->A' => ['direct_xrefs', 'rnacentral_mapping'],
-      'A->1' => 'mapping'
+      'A->1' => 'object_xref_check'
     },
     -rc_name    => '1GB',
   },
@@ -281,6 +281,18 @@ sub pipeline_analyses {
     -rc_name    => '16GB',
     -analysis_capacity => 30
   },
+  {
+    -logic_name => 'object_xref_check',
+    -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck',
+    -parameters => {
+      db_conn       => '#xref_url#',
+      description   => 'Check that the object_xref table has rows'
+      query         => 'SELECT object_xref_id FROM object_xref',
+      expected_size => '> 0'
+    },
+    -flow_into  => { 1 => 'mapping' },
+    -rc_name    => 'default',
+  },
   {
     -logic_name => 'mapping',
     -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::Mapping',
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
index 3a184d14c..635e6fd8d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/DumpXref.pm
@@ -99,7 +99,7 @@ sub run {
         # Ambiguous peptides must be cleaned out to protect Exonerate from J,O and U codes
         $row[1] = uc($row[1]);
         $row[1] =~ s/(.{60})/$1\n/g;
-        if ($seq_type eq 'pep') { $row[1] =~ tr/JOU/X/ }
+        if ($seq_type eq 'peptide') { $row[1] =~ tr/JOU/X/ }
         print $DH ">".$row[0]."\n".$row[1]."\n";
       }
       $mapping_source_sth->execute($source_id, $seq_type);
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
index 068bf107f..e9d807beb 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ParseSource.pm
@@ -79,13 +79,17 @@ sub run {
                              file       => $file_name}) ;
     $self->cleanup_DBAdaptor($db);
   } else {
-    $failure += $xref_run->run( { source_id  => $source_id,
-                      species_id => $species_id,
-                      species    => $species,
-                      rel_file   => $release_file,
-                      dbi        => $dbi,
-		      xref_source => $source_dbi,
-                      files      => [@files] }) ;
+    my $run_params = {
+      source_id  => $source_id,
+      species_id => $species_id,
+      species    => $species,
+      rel_file   => $release_file,
+      dbi        => $dbi,
+      xref_source => $source_dbi,
+      files      => [@files]
+    };
+    $run_params->{hgnc_file} = $self->param('hgnc_file') if ($parser =~ /^UniProt/);
+    $failure += $xref_run->run( $run_params ) ;
   }
   if ($failure) { die; }
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
index 27d16dcca..fd56a7d5a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/ScheduleSource.pm
@@ -83,12 +83,16 @@ sub run {
   # Retrieve list of sources from versioning database
   my ($source_user, $source_pass, $source_host, $source_port, $source_db) = $self->parse_url($source_url);
   my $dbi = $self->get_dbi($source_host, $source_port, $source_user, $source_pass, $source_db);
-  my $select_source_sth = $dbi->prepare("SELECT distinct name, parser, uri, clean_uri, index_uri, count_seen, preparse, revision FROM source s, version v WHERE s.source_id = v.source_id");
+  my $select_source_sth = $dbi->prepare("SELECT distinct name, parser, uri, clean_uri, index_uri, count_seen, preparse, revision FROM source s, version v WHERE s.source_id = v.source_id order by name");
   my ($name, $parser, $file_name, $clean_file_name, $dataflow_params, $db, $priority, $release_file);
   $select_source_sth->execute();
   $select_source_sth->bind_columns(\$name, \$parser, \$file_name, \$clean_file_name, \$db, \$priority, \$preparse, \$release_file);
 
+  my $hgnc_path;
+
   while ($select_source_sth->fetch()) {
+    $hgnc_path = $file_name if ($name eq 'HGNC');
+
     if (defined $db && $db eq 'checksum') { next; }
     if ($priority != $order_priority) { next; }
     if (defined $clean_file_name) { $file_name = $clean_file_name; }
@@ -146,6 +150,11 @@ sub run {
         }
       }
 
+      # For ZFIN, we only need 1 job (parser handles all the files)
+      if ($name eq 'ZFIN_ID') {
+        @list_files = $list_files[0];
+      }
+
       foreach my $file (@list_files) {
         $file =~ s/\n//;
         if (!-f $file) { next; }
@@ -162,6 +171,10 @@ sub run {
           priority      => $priority,
           file_name     => $file
         };
+        if ($name =~ /^Uniprot/) {
+          my @hgnc_files = glob( $hgnc_path . '/*' );
+          $dataflow_params->{hgnc_file} = $hgnc_files[0];
+        }
         $self->dataflow_output_id($dataflow_params, 2);
       }
     }
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
index 5b6361536..777e735b1 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
@@ -6,13 +6,6 @@
       "db" : "core",
       "priority" : 1
     },
-    {
-      "name" : "CCDS",
-      "parser" : "CCDSParser",
-      "file" : "Database",
-      "db" : "ccds",
-      "priority" : 1
-    },
     {
       "name" : "UniParc",
       "parser" : "ChecksumParser",
@@ -197,19 +190,19 @@
       "name" : "ZFIN_ID",
       "parser" : "ZFINParser",
       "file" : "http://zfin.org/data_transfer/Downloads/uniprot.txt",
-      "priority" : 2
+      "priority" : 3
     },
     {
       "name" : "ZFIN_ID",
       "parser" : "ZFINParser",
       "file" : "http://zfin.org/data_transfer/Downloads/aliases.txt",
-      "priority" : 2
+      "priority" : 3
     },
     {
       "name" : "ZFIN_ID",
       "parser" : "ZFINParser",
-      "file" : "http://zfin.org/data_transfer/Downloads/gene_seq.txt",
-      "priority" : 1
+      "file" : "https://zfin.org/downloads/ensembl_1_to_1.txt",
+      "priority" : 3
     },
     {
       "name" : "ZFIN_desc",
diff --git a/src/python/ensembl/production/xrefs/Base.py b/src/python/ensembl/production/xrefs/Base.py
index d5022627f..fcf94dc42 100644
--- a/src/python/ensembl/production/xrefs/Base.py
+++ b/src/python/ensembl/production/xrefs/Base.py
@@ -779,83 +779,3 @@ def get_db_from_registry(self, species: str, group: str, release: int, registry:
     else:
       return 0
 
-  # def get_spark_session(self, data_type):
-  #   if data_type == 'mysql':
-  #     spark = SparkSession.builder.appName('SparkByExamples.com').config("spark.jars", "mysql-connector-java-8.0.13.jar").getOrCreate()
-  #     return spark
-  #   else:
-  #     raise Exception(f'Spark data type {data_type} not supported yet')
-
-  # def get_spark_reader(self, spark_session, data_type, data_url):
-  #   if data_type == 'mysql':
-  #     reader = spark_session.read.format("jdbc").option("driver", "com.mysql.cj.jdbc.Driver").option("url", f'jdbc:{data_url}')
-  #     return reader
-  #   else:
-  #     raise Exception(f'Spark data type {data_type} not supported yet')
-
-  def get_xref_mapper(self, xref_url: str, species: str, base_path: str, release: int, core_url: str=None, registry: str=None):
-    """ Retrives a mapper object based on species.
-
-    Parameters
-    ----------
-    xref_url: str
-        The xref db connection url
-    species: str
-        The species name
-    base_path: str
-        The base file path
-    release: int
-        The ensEMBL release number
-    core_db: str, optional
-        The species core db connection url
-    registry: str, optional
-        The registry url
-
-    Returns
-    -------
-    A mapper object
-    """
-    # Need either core_db or registry
-    if not core_url and not registry:
-      raise AttributeError(f'Method get_xref_mapper: need to provide either a core DB URL or a registry URL')
-
-    # Create needed db connections
-    if not core_url:
-      core_url = self.get_db_from_registry(species, 'core', release, registry)
-
-    core_db = self.get_db_engine(core_url)
-    xref_db = self.get_db_engine(xref_url)
-
-    # Extract host and dbname from xref url
-    xref_url_obj = make_url(xref_url)
-    host = xref_url_obj.host
-    dbname = xref_url_obj.database
-
-    # Locate the fasta files
-    cdna_path = self.get_path(base_path, species, release, 'ensembl', 'transcripts.fa');
-    pep_path = self.get_path(base_path, species, release, 'ensembl', 'peptides.fa');
-
-    # Try to find a species-specific mapper first
-    module_name = f'ensembl.xrefs.mappers.{species}'
-    class_name = species
-    found = importlib.find_loader(module_name)
-    if not found:
-      module_name = 'ensembl.xrefs.mappers.BasicMapper'
-      class_name = 'BasicMapper'
-
-    # Create a mapper object
-    module = importlib.import_module(module_name)
-    module_class = getattr(module, class_name)
-    mapper = module_class()
-
-    mapper.xref(xref_db)
-    mapper.add_meta_pair('xref', f'{host}:{dbname}')
-    mapper.core(core_db)
-    mapper.add_meta_pair('species', f'{host}:{dbname}')
-    mapper.dna_file(cdna_path)
-    mapper.protein_file(pep_path)
-    mapper.log_file(self._log_file)
-
-    return mapper
-
-

From be04bb1bfe3f89e8b6ad1d5467e4addbeeea59b9 Mon Sep 17 00:00:00 2001
From: Tamara El Naboulsi <48948777+TamaraNaboulsi@users.noreply.github.com>
Date: Tue, 10 Sep 2024 10:49:22 +0100
Subject: [PATCH 095/128] Update XrefProcess_conf.pm

Missing comma
---
 .../EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
index fcf875c2b..f490d8722 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
@@ -286,7 +286,7 @@ sub pipeline_analyses {
     -module     => 'Bio::EnsEMBL::Hive::RunnableDB::SqlHealthcheck',
     -parameters => {
       db_conn       => '#xref_url#',
-      description   => 'Check that the object_xref table has rows'
+      description   => 'Check that the object_xref table has rows',
       query         => 'SELECT object_xref_id FROM object_xref',
       expected_size => '> 0'
     },

From 5f1bd53f73ee13c99e1d8906f1b5677e9f53a927 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Tue, 10 Sep 2024 16:32:35 +0100
Subject: [PATCH 096/128] patch 114

---
 sql/patch_113_114_a.sql | 27 +++++++++++++++++++++++++++
 sql/table.sql           |  4 ++--
 2 files changed, 29 insertions(+), 2 deletions(-)
 create mode 100644 sql/patch_113_114_a.sql

diff --git a/sql/patch_113_114_a.sql b/sql/patch_113_114_a.sql
new file mode 100644
index 000000000..5637cb307
--- /dev/null
+++ b/sql/patch_113_114_a.sql
@@ -0,0 +1,27 @@
+-- Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+-- Copyright [2016-2024] EMBL-European Bioinformatics Institute
+--
+-- Licensed under the Apache License, Version 2.0 (the "License");
+-- you may not use this file except in compliance with the License.
+-- You may obtain a copy of the License at
+--
+--      http://www.apache.org/licenses/LICENSE-2.0
+--
+-- Unless required by applicable law or agreed to in writing, software
+-- distributed under the License is distributed on an "AS IS" BASIS,
+-- WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+-- See the License for the specific language governing permissions and
+-- limitations under the License.
+
+# patch_112_113_a.sql
+#
+# Title: Update schema version.
+#
+# Description:
+#   Update schema_version in meta table to 112.
+
+UPDATE meta SET meta_value='114' WHERE meta_key='schema_version';
+
+# Patch identifier
+INSERT INTO meta (species_id, meta_key, meta_value)
+VALUES (NULL, 'patch', 'patch_113_114_a.sql|schema_version');
diff --git a/sql/table.sql b/sql/table.sql
index c701ef1fe..19ce5692b 100644
--- a/sql/table.sql
+++ b/sql/table.sql
@@ -32,11 +32,11 @@ CREATE TABLE IF NOT EXISTS meta (
 # Add schema type and schema version to the meta table
 INSERT INTO meta (species_id, meta_key, meta_value) VALUES
   (NULL, 'schema_type', 'production'),
-  (NULL, 'schema_version', 113);
+  (NULL, 'schema_version', 114);
 
 # Patches included in this schema file
 INSERT INTO meta (species_id, meta_key, meta_value)
-  VALUES (NULL, 'patch', 'patch_112_113_a.sql|schema version');
+  VALUES (NULL, 'patch', 'patch_113_114_a.sql|schema version');
 
 -- The 'master_biotype' table.
 -- Contains all the valid biotypes used for genes and transcripts.

From e715bf65bd59b751c81612af2a6ab972e1535a45 Mon Sep 17 00:00:00 2001
From: Ensprod User <ensprod@ebi.ac.uk>
Date: Tue, 10 Sep 2024 17:18:50 +0100
Subject: [PATCH 097/128] Updating test dbs to latest schema

---
 modules/t/test-genome-DBs/homo_sapiens/core/meta.txt   | 3 ++-
 modules/t/test-genome-DBs/homo_sapiens/core/table.sql  | 2 +-
 modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt  | 3 ++-
 modules/t/test-genome-DBs/homo_sapiens/empty/table.sql | 2 +-
 modules/t/test-genome-DBs/hp_dump/core/meta.txt        | 3 ++-
 modules/t/test-genome-DBs/hp_dump/core/table.sql       | 2 +-
 modules/t/test-genome-DBs/multi/compara/meta.txt       | 3 ++-
 modules/t/test-genome-DBs/multi/compara/table.sql      | 2 +-
 8 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index cb763cbb4..1840fcdb1 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	113
+2	\N	schema_version	114
 3	\N	patch	patch_98_99_a.sql|schema_version
 2124	1	xref.timestamp	2013-07-22 11:20:10
 4	\N	patch	patch_52_53_c.sql|identity_xref_rename
@@ -266,3 +266,4 @@
 2222	\N	patch	patch_111_112_c.sql|Extend meta_key length to 64
 2223	\N	patch	patch_112_113_a.sql|schema_version
 2224	\N	patch	patch_112_113_b.sql|Ensure meta_value is not null
+2225	\N	patch	patch_113_114_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index 784f016fb..76867bd9b 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2225 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2226 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index ca8dc5b53..e3a5b80c8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -1,4 +1,4 @@
-1	\N	schema_version	113
+1	\N	schema_version	114
 2	1	assembly.default	NCBI34
 33	1	species.classification	Chordata
 32	1	species.classification	Vertebrata
@@ -131,3 +131,4 @@
 181	\N	patch	patch_111_112_c.sql|Extend meta_key length to 64
 182	\N	patch	patch_112_113_a.sql|schema_version
 183	\N	patch	patch_112_113_b.sql|Ensure meta_value is not null
+184	\N	patch	patch_113_114_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index fda351bb8..e5db71a2e 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -495,7 +495,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=184 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=185 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL DEFAULT '',
diff --git a/modules/t/test-genome-DBs/hp_dump/core/meta.txt b/modules/t/test-genome-DBs/hp_dump/core/meta.txt
index 0b97df26e..9a3a430a0 100644
--- a/modules/t/test-genome-DBs/hp_dump/core/meta.txt
+++ b/modules/t/test-genome-DBs/hp_dump/core/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	core
-2	\N	schema_version	113
+2	\N	schema_version	114
 3	\N	patch	patch_98_99_a.sql|schema_version
 2124	1	xref.timestamp	2013-07-22 11:20:10
 4	\N	patch	patch_52_53_c.sql|identity_xref_rename
@@ -270,3 +270,4 @@
 2226	\N	patch	patch_111_112_c.sql|Extend meta_key length to 64
 2227	\N	patch	patch_112_113_a.sql|schema_version
 2228	\N	patch	patch_112_113_b.sql|Ensure meta_value is not null
+2229	\N	patch	patch_113_114_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/hp_dump/core/table.sql b/modules/t/test-genome-DBs/hp_dump/core/table.sql
index 6130c7aa3..f6e687e50 100644
--- a/modules/t/test-genome-DBs/hp_dump/core/table.sql
+++ b/modules/t/test-genome-DBs/hp_dump/core/table.sql
@@ -490,7 +490,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=2229 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2230 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
diff --git a/modules/t/test-genome-DBs/multi/compara/meta.txt b/modules/t/test-genome-DBs/multi/compara/meta.txt
index 6f62244a1..69cf87d7d 100644
--- a/modules/t/test-genome-DBs/multi/compara/meta.txt
+++ b/modules/t/test-genome-DBs/multi/compara/meta.txt
@@ -1,6 +1,6 @@
 2	\N	schema_type	compara
 3	\N	patch	patch_98_99_a.sql|schema_version
-169	\N	schema_version	113
+172	\N	schema_version	114
 4	\N	patch	patch_72_73_b.sql|homology_genetree_links
 6	\N	patch	patch_73_74_a.sql|schema_version
 7	\N	patch	patch_73_74_b.sql|hmm_profile
@@ -129,3 +129,4 @@
 168	\N	patch	patch_111_112_a.sql|schema_version
 170	\N	patch	patch_112_113_a.sql|schema_version
 171	\N	patch	patch_112_113_b.sql|meta_key_64
+173	\N	patch	patch_113_114_a.sql|schema_version
diff --git a/modules/t/test-genome-DBs/multi/compara/table.sql b/modules/t/test-genome-DBs/multi/compara/table.sql
index a0afea73c..01d92fd28 100644
--- a/modules/t/test-genome-DBs/multi/compara/table.sql
+++ b/modules/t/test-genome-DBs/multi/compara/table.sql
@@ -441,7 +441,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM AUTO_INCREMENT=172 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=174 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `method_link` (
   `method_link_id` int(10) unsigned NOT NULL AUTO_INCREMENT,

From 9c5e81a00d01761258c2d87012150410972f4861 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Fri, 20 Sep 2024 18:30:24 +0100
Subject: [PATCH 098/128] Update python version to 3.10

---
 .travis.yml      |   2 +
 requirements.in  |   4 +-
 requirements.txt | 127 +++++++++++++----------------------------------
 3 files changed, 40 insertions(+), 93 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index dc162fd2e..0f7b7ca90 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,4 +1,5 @@
 language: perl
+dist: focal
 perl:
   - "5.14"
   - "5.26.2"
@@ -39,6 +40,7 @@ before_install:
   - cd htslib
   - make
   - export HTSLIB_DIR=$(pwd -P)
+  - mysql -e "SET GLOBAL local_infile=1;"
   - cd ..
 install:
   - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
diff --git a/requirements.in b/requirements.in
index 603b015f3..db7fc5acc 100644
--- a/requirements.in
+++ b/requirements.in
@@ -1,3 +1,5 @@
 requests>=2.25.0,<3
 pydantic~=1.10.5
-git+https://github.com/Ensembl/ensembl-metadata-api.git@2.0.1a2#egg=ensembl-metadata-api
+ensembl-py>=2.1.0
+ensembl-utils>=0.4.4
+git+https://github.com/Ensembl/ensembl-metadata-api.git@3.0.1#egg=ensembl-metadata-api
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 529bccc7b..137c03abc 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,112 +1,55 @@
 #
-# This file is autogenerated by pip-compile with Python 3.8
+# This file is autogenerated by pip-compile with Python 3.10
 # by the following command:
 #
-#    pip-compile requirements.in
+#    pip-compile --output-file=requirements.txt requirements.in
 #
 certifi==2024.2.2
-    # via
-    #   ensembl-metadata-api
-    #   requests
+    # via requests
 charset-normalizer==3.3.2
-    # via
-    #   ensembl-metadata-api
-    #   requests
-ensembl-hive @ git+https://github.com/Ensembl/ensembl-hive.git
-    # via
-    #   ensembl-metadata-api
-    #   ensembl-py
-ensembl-metadata-api @ git+https://github.com/Ensembl/ensembl-metadata-api.git@2.0.1a2
+    # via requests
+ensembl-metadata-api @ git+https://github.com/Ensembl/ensembl-metadata-api.git@3.0.1
     # via -r requirements.in
-ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git
-    # via ensembl-metadata-api
-exceptiongroup==1.2.0
-    # via
-    #   ensembl-metadata-api
-    #   pytest
-greenlet==3.0.3
-    # via
-    #   ensembl-metadata-api
-    #   sqlalchemy
-grpcio==1.62.0
-    # via
-    #   ensembl-metadata-api
-    #   grpcio-reflection
-    #   grpcio-tools
-grpcio-reflection==1.62.0
-    # via ensembl-metadata-api
-grpcio-tools==1.62.0
-    # via ensembl-metadata-api
+ensembl-py==2.1.3
+    # via -r requirements.in
+ensembl-utils==0.5.0
+    # via -r requirements.in
+exceptiongroup==1.2.2
+    # via pytest
+greenlet==3.1.1
+    # via sqlalchemy
 idna==3.6
-    # via
-    #   ensembl-metadata-api
-    #   requests
+    # via requests
 iniconfig==2.0.0
-    # via
-    #   ensembl-metadata-api
-    #   pytest
-mysqlclient==2.1.1
-    # via
-    #   ensembl-metadata-api
-    #   ensembl-py
-packaging==23.2
-    # via
-    #   ensembl-metadata-api
-    #   pytest
-pluggy==1.4.0
-    # via
-    #   ensembl-metadata-api
-    #   pytest
-protobuf==4.25.3
-    # via
-    #   ensembl-metadata-api
-    #   grpcio-reflection
-    #   grpcio-tools
+    # via pytest
+packaging==24.1
+    # via pytest
+pluggy==1.5.0
+    # via pytest
 pydantic==1.10.14
     # via -r requirements.in
-pytest==8.0.2
-    # via
-    #   ensembl-metadata-api
-    #   ensembl-py
-    #   pytest-dependency
-pytest-dependency==0.5.1
-    # via
-    #   ensembl-metadata-api
-    #   ensembl-py
-python-dotenv==0.19.2
-    # via
-    #   ensembl-metadata-api
-    #   ensembl-py
-pyyaml==6.0.1
-    # via
-    #   ensembl-metadata-api
-    #   ensembl-py
+pytest==8.3.3
+    # via ensembl-utils
+python-dotenv==1.0.1
+    # via ensembl-utils
+pyyaml==6.0.2
+    # via ensembl-utils
 requests==2.31.0
     # via
     #   -r requirements.in
-    #   ensembl-metadata-api
-    #   ensembl-py
-sqlalchemy==1.4.52
+    #   ensembl-utils
+sqlalchemy==2.0.35
     # via
-    #   ensembl-metadata-api
     #   ensembl-py
+    #   ensembl-utils
     #   sqlalchemy-utils
-sqlalchemy-utils==0.38.3
-    # via
-    #   ensembl-metadata-api
-    #   ensembl-py
+sqlalchemy-utils==0.41.2
+    # via ensembl-utils
 tomli==2.0.1
-    # via
-    #   ensembl-metadata-api
-    #   pytest
-types-pymysql==1.1.0.1
-    # via ensembl-metadata-api
+    # via pytest
 typing-extensions==4.10.0
-    # via pydantic
-urllib3==1.26.18
     # via
-    #   ensembl-metadata-api
-    #   requests
-
-# The following packages are considered to be unsafe in a requirements file:
-# setuptools
+    #   pydantic
+    #   sqlalchemy
+urllib3==1.26.18
+    # via requests

From 6f1c54c3a84c454b40f473fb55b35600482adc1c Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Sun, 22 Sep 2024 08:49:58 +0100
Subject: [PATCH 099/128] Fix Specified key was too long; max key length is
 1000 bytes Limit the index size

---
 modules/t/test-genome-DBs/multi/production/table.sql | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/t/test-genome-DBs/multi/production/table.sql b/modules/t/test-genome-DBs/multi/production/table.sql
index 6ccf981d4..b703720ad 100644
--- a/modules/t/test-genome-DBs/multi/production/table.sql
+++ b/modules/t/test-genome-DBs/multi/production/table.sql
@@ -91,7 +91,7 @@ CREATE TABLE `master_external_db` (
   `modified_by` int(11) DEFAULT NULL,
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`external_db_id`),
-  UNIQUE KEY `db_name_idx` (`db_name`,`db_release`,`is_current`)
+  UNIQUE KEY `db_name_idx` (`db_name(255)`,`db_release(100)`,`is_current`)
 ) ENGINE=MyISAM  ;
 
 CREATE TABLE `master_misc_set` (

From 8fe57dc875aba0598127ca0f032d9a7a212b2ad8 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Sun, 22 Sep 2024 09:54:21 +0100
Subject: [PATCH 100/128] Fix Specified key was too long; max key length is
 1000 bytes Limit the index size

---
 modules/t/test-genome-DBs/multi/production/table.sql | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/t/test-genome-DBs/multi/production/table.sql b/modules/t/test-genome-DBs/multi/production/table.sql
index b703720ad..66a59f0d9 100644
--- a/modules/t/test-genome-DBs/multi/production/table.sql
+++ b/modules/t/test-genome-DBs/multi/production/table.sql
@@ -77,7 +77,7 @@ CREATE TABLE `master_biotype` (
 CREATE TABLE `master_external_db` (
   `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `db_name` varchar(100) NOT NULL,
-  `db_release` varchar(255) DEFAULT NULL,
+  `db_release` varchar(100) DEFAULT NULL,
   `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
   `priority` int(11) NOT NULL,
   `db_display_name` varchar(255) NOT NULL,
@@ -91,7 +91,7 @@ CREATE TABLE `master_external_db` (
   `modified_by` int(11) DEFAULT NULL,
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`external_db_id`),
-  UNIQUE KEY `db_name_idx` (`db_name(255)`,`db_release(100)`,`is_current`)
+  UNIQUE KEY `db_name_idx` (`db_name`,`db_release`,`is_current`)
 ) ENGINE=MyISAM  ;
 
 CREATE TABLE `master_misc_set` (

From 963b1f1c89765192ac166e567a8dce73cc8757fd Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Sun, 22 Sep 2024 11:17:00 +0100
Subject: [PATCH 101/128] Fix Specified key was too long; max key length is
 1000 bytes Moved to InnoDB

---
 .../multi/production/table.sql                | 22 +++++++++----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/modules/t/test-genome-DBs/multi/production/table.sql b/modules/t/test-genome-DBs/multi/production/table.sql
index 66a59f0d9..c48b94465 100644
--- a/modules/t/test-genome-DBs/multi/production/table.sql
+++ b/modules/t/test-genome-DBs/multi/production/table.sql
@@ -13,7 +13,7 @@ CREATE TABLE `analysis_description` (
   `displayable` tinyint(1) NOT NULL,
   PRIMARY KEY (`analysis_description_id`),
   UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `master_attrib` (
   `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
@@ -26,7 +26,7 @@ CREATE TABLE `master_attrib` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`attrib_id`),
   UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
-) ENGINE=MyISAM ;
+) ENGINE=InnoDB ;
 
 CREATE TABLE `master_attrib_set` (
   `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
@@ -38,7 +38,7 @@ CREATE TABLE `master_attrib_set` (
   `modified_at` datetime DEFAULT NULL,
   UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
   KEY `attrib_idx` (`attrib_id`)
-) ENGINE=MyISAM ;
+) ENGINE=InnoDB ;
 
 CREATE TABLE `master_attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
@@ -52,7 +52,7 @@ CREATE TABLE `master_attrib_type` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `master_biotype` (
   `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -72,7 +72,7 @@ CREATE TABLE `master_biotype` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`biotype_id`),
   UNIQUE KEY `name_type_idx` (`name`,`object_type`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `master_external_db` (
   `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -92,7 +92,7 @@ CREATE TABLE `master_external_db` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`external_db_id`),
   UNIQUE KEY `db_name_idx` (`db_name`,`db_release`,`is_current`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `master_misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
@@ -107,7 +107,7 @@ CREATE TABLE `master_misc_set` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `code_idx` (`code`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `master_unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -119,7 +119,7 @@ CREATE TABLE `master_unmapped_reason` (
   `modified_by` int(11) DEFAULT NULL,
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -129,7 +129,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `meta_key` (
   `meta_key_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -145,7 +145,7 @@ CREATE TABLE `meta_key` (
   `is_multi_value` tinyint(1) NOT NULL DEFAULT '0',
   PRIMARY KEY (`meta_key_id`),
   KEY `name_type_idx` (`name`,`db_type`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE TABLE `web_data` (
   `web_data_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -157,7 +157,7 @@ CREATE TABLE `web_data` (
   `modified_at` datetime DEFAULT NULL,
   `description` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`web_data_id`)
-) ENGINE=MyISAM  ;
+) ENGINE=InnoDB  ;
 
 CREATE ALGORITHM=UNDEFINED DEFINER=CURRENT_USER() SQL SECURITY INVOKER VIEW `attrib` AS select `master_attrib`.`attrib_id` AS `attrib_id`,`master_attrib`.`attrib_type_id` AS `attrib_type_id`,`master_attrib`.`value` AS `value` from `master_attrib` where (`master_attrib`.`is_current` = 1) order by `master_attrib`.`attrib_id`;
 

From 153c7d6aefa25698acf68dba07fcd6f11ab5410b Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Sun, 22 Sep 2024 20:28:28 +0100
Subject: [PATCH 102/128] set travis dist to bionic to revert mysql version to
 5.7 similar to production staging server

---
 .travis.yml                                   |  2 +-
 .../multi/production/table.sql                | 24 +++++++++----------
 2 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0f7b7ca90..0f3c138ea 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,5 +1,5 @@
 language: perl
-dist: focal
+dist: bionic
 perl:
   - "5.14"
   - "5.26.2"
diff --git a/modules/t/test-genome-DBs/multi/production/table.sql b/modules/t/test-genome-DBs/multi/production/table.sql
index c48b94465..6ccf981d4 100644
--- a/modules/t/test-genome-DBs/multi/production/table.sql
+++ b/modules/t/test-genome-DBs/multi/production/table.sql
@@ -13,7 +13,7 @@ CREATE TABLE `analysis_description` (
   `displayable` tinyint(1) NOT NULL,
   PRIMARY KEY (`analysis_description_id`),
   UNIQUE KEY `logic_name_idx` (`logic_name`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `master_attrib` (
   `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
@@ -26,7 +26,7 @@ CREATE TABLE `master_attrib` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`attrib_id`),
   UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
-) ENGINE=InnoDB ;
+) ENGINE=MyISAM ;
 
 CREATE TABLE `master_attrib_set` (
   `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
@@ -38,7 +38,7 @@ CREATE TABLE `master_attrib_set` (
   `modified_at` datetime DEFAULT NULL,
   UNIQUE KEY `set_idx` (`attrib_set_id`,`attrib_id`),
   KEY `attrib_idx` (`attrib_id`)
-) ENGINE=InnoDB ;
+) ENGINE=MyISAM ;
 
 CREATE TABLE `master_attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
@@ -52,7 +52,7 @@ CREATE TABLE `master_attrib_type` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `code_idx` (`code`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `master_biotype` (
   `biotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -72,12 +72,12 @@ CREATE TABLE `master_biotype` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`biotype_id`),
   UNIQUE KEY `name_type_idx` (`name`,`object_type`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `master_external_db` (
   `external_db_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `db_name` varchar(100) NOT NULL,
-  `db_release` varchar(100) DEFAULT NULL,
+  `db_release` varchar(255) DEFAULT NULL,
   `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL,
   `priority` int(11) NOT NULL,
   `db_display_name` varchar(255) NOT NULL,
@@ -92,7 +92,7 @@ CREATE TABLE `master_external_db` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`external_db_id`),
   UNIQUE KEY `db_name_idx` (`db_name`,`db_release`,`is_current`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `master_misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
@@ -107,7 +107,7 @@ CREATE TABLE `master_misc_set` (
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `code_idx` (`code`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `master_unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -119,7 +119,7 @@ CREATE TABLE `master_unmapped_reason` (
   `modified_by` int(11) DEFAULT NULL,
   `modified_at` datetime DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -129,7 +129,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`(255)),
   KEY `species_value_idx` (`species_id`,`meta_value`(255))
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `meta_key` (
   `meta_key_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -145,7 +145,7 @@ CREATE TABLE `meta_key` (
   `is_multi_value` tinyint(1) NOT NULL DEFAULT '0',
   PRIMARY KEY (`meta_key_id`),
   KEY `name_type_idx` (`name`,`db_type`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE TABLE `web_data` (
   `web_data_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -157,7 +157,7 @@ CREATE TABLE `web_data` (
   `modified_at` datetime DEFAULT NULL,
   `description` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`web_data_id`)
-) ENGINE=InnoDB  ;
+) ENGINE=MyISAM  ;
 
 CREATE ALGORITHM=UNDEFINED DEFINER=CURRENT_USER() SQL SECURITY INVOKER VIEW `attrib` AS select `master_attrib`.`attrib_id` AS `attrib_id`,`master_attrib`.`attrib_type_id` AS `attrib_type_id`,`master_attrib`.`value` AS `value` from `master_attrib` where (`master_attrib`.`is_current` = 1) order by `master_attrib`.`attrib_id`;
 

From 8cd9826f409fa2f747ed304c8060485d36dffbd8 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Sun, 22 Sep 2024 21:31:45 +0100
Subject: [PATCH 103/128] set travis dist to default to revert mysql version to
 5.7 similar to production staging server

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 0f3c138ea..6013aff33 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,5 +1,4 @@
 language: perl
-dist: bionic
 perl:
   - "5.14"
   - "5.26.2"

From 928c0de3287830ddce657ee9eaece81516505676 Mon Sep 17 00:00:00 2001
From: jmgonzmart <jmgonzalez@ebi.ac.uk>
Date: Tue, 24 Sep 2024 16:48:50 +0100
Subject: [PATCH 104/128] Fixed analysis name

---
 .../EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
index 3a78ff9b1..128fe18fc 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
@@ -128,7 +128,7 @@ sub pipeline_analyses {
       -rc_name    => 'default'
     },
     {
-      -logic_name => 'checksum_W',
+      -logic_name => 'checksum',
       -module     => 'Bio::EnsEMBL::Production::Pipeline::Xrefs::Checksum',
       -comment    => 'Adds all checksum files into a single file and loads it into the checksum_xref table.',
       -parameters => {

From 6725416965ad186c4c17b6f154862eb2ad2fe99c Mon Sep 17 00:00:00 2001
From: jmgonzmart <jmgonzalez@ebi.ac.uk>
Date: Tue, 24 Sep 2024 16:51:01 +0100
Subject: [PATCH 105/128] Added new resource class as it was required by the
 XrefDownload pipeline

---
 modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index d57a14a70..c1ab410cf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -74,6 +74,7 @@ sub resource_classes {
     );
 
     my %memory = (
+        '100M'           => '100',
         '500M'           => '500',
         '1GB'            => '1000',
         '2GB'            => '2000',

From 7f0a5f1b9737842928ba9c42c9241aa4b15efc11 Mon Sep 17 00:00:00 2001
From: jmgonzmart <jmgonzalez@ebi.ac.uk>
Date: Tue, 24 Sep 2024 16:55:12 +0100
Subject: [PATCH 106/128] Updated file name in the URL for the UniParc data
 download

---
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json  | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json | 2 +-
 .../ensembl/production/xrefs/config/xref_all_sources.json       | 2 +-
 4 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
index b0910be58..f34e6f977 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/gencode_sources.json
@@ -16,7 +16,7 @@
     {
       "name" : "UniParc",
       "parser" : "ChecksumParser",
-      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis",
+      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis.gz",
       "db" : "checksum",
       "priority" : 1
     },
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
index 777e735b1..07c48e29a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_all_sources.json
@@ -9,7 +9,7 @@
     {
       "name" : "UniParc",
       "parser" : "ChecksumParser",
-      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis",
+      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis.gz",
       "db" : "checksum",
       "priority" : 1
     },
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
index d12edb9cf..0070a69d4 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/Xrefs/xref_sources.json
@@ -16,7 +16,7 @@
     {
       "name" : "UniParc",
       "parser" : "ChecksumParser",
-      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis",
+      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis.gz",
       "db" : "checksum",
       "priority" : 1
     },
diff --git a/src/python/ensembl/production/xrefs/config/xref_all_sources.json b/src/python/ensembl/production/xrefs/config/xref_all_sources.json
index e7b0065a4..a89f40d4a 100644
--- a/src/python/ensembl/production/xrefs/config/xref_all_sources.json
+++ b/src/python/ensembl/production/xrefs/config/xref_all_sources.json
@@ -16,7 +16,7 @@
     {
       "name" : "UniParc",
       "parser" : "ChecksumParser",
-      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis",
+      "file" : "https://ftp.ebi.ac.uk/pub/contrib/uniparc/upidump.lis.gz",
       "db" : "checksum",
       "priority" : 1
     },

From 1fd59825f006ef60ae36479ce01f1e98faba4cf7 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Mon, 14 Oct 2024 19:16:39 +0100
Subject: [PATCH 107/128] fix delete group param in dbcopy pipeline

---
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm  | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
index 11f63e43c..a1f3b4d71 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
@@ -39,6 +39,7 @@ sub default_options {
     # Database type factory
     groups => 1,
     group  => [],
+    delete_group => [], 
 
     # Named database factory
     dbname => [],
@@ -200,7 +201,7 @@ sub pipeline_analyses {
       -max_retry_count => 1,
       -parameters      => {
                             ensembl_release => $self->o('delete_release'),
-                            group           => $self->o('delete_group'),
+                            group           => (ref($self->o('delete_group')) eq 'ARRAY' && @{$self->o('delete_group')}) ? $self->o('delete_group') : $self->o('group'),
                             groups          => $self->o('groups'),
                           },
       -flow_into       => {

From e7955f9eee8246c5966bec8a8e717bb5e788c690 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Mon, 14 Oct 2024 19:33:23 +0100
Subject: [PATCH 108/128] remove exiting param delete group assigned to group

---
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm    | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
index a1f3b4d71..3cbb3c5b5 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
@@ -59,7 +59,6 @@ sub default_options {
     # Drop databases from target, by default the same set that will be copied
     delete_db          => 0,
     delete_release     => $self->o('ensembl_release'),
-    delete_group       => $self->o('group'),
     delete_dbname      => $self->o('dbname'),
     delete_marts       => $self->o('marts'),
     delete_compara     => $self->o('compara'),

From 62fc1cb4d1a8f5b988fafd9b75e37e07c4382614 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 15 Oct 2024 17:34:01 +0100
Subject: [PATCH 109/128] fix travis failures

---
 .travis.yml | 17 +++++++++++------
 1 file changed, 11 insertions(+), 6 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 57d78cef5..0502ffa97 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,7 +1,8 @@
 language: perl
+os: linux
+dist: focal
 perl:
-  - "5.14"
-  - "5.26.2"
+  - "5.26.4"
 services:
   - mysql
 env:
@@ -56,14 +57,18 @@ script:
 jobs:
   include:
     - language: python
-      python: 3.8
+      os: linux
+      dist: focal
+      python:
+        - '3.10'
+        - '3.11'
       install:
-        - pip install -e .
         - pip install -r requirements-test.txt
+        - pip install -e .
+      before_script:
+        - mysql -e "SET GLOBAL local_infile=1;"
       script:
         - pytest src/python/test
-
-
 notifications:
   email:
     on_success: always

From 80ff50803c514e5916114452aa00e8e1f673f8f2 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 15 Oct 2024 17:50:02 +0100
Subject: [PATCH 110/128] update travis to run bot the perl and python tests

---
 .travis.yml | 120 ++++++++++++++++++++++++++--------------------------
 1 file changed, 61 insertions(+), 59 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 0502ffa97..49da39005 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,67 +1,68 @@
 language: perl
 os: linux
 dist: focal
-perl:
-  - "5.26.4"
-services:
-  - mysql
-env:
-  - COVERALLS=true  DB=mysql
-addons:
-  apt:
-    update: true      
-    packages:
-      - unzip
-      - sendmail
-      - graphviz
-      - emboss
-      - libkyotocabinet-dev
-before_install:
-  - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
-  - export PATH=$PATH:$PWD/ensembl-git-tools/bin
-  - export ENSEMBL_BRANCH=master
-  - export SECONDARY_BRANCH=main
-  - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
-  - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
-  - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
-  - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
-  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
-  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
-  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
-  - git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
-  - git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
-  - cd htslib
-  - make
-  - export HTSLIB_DIR=$(pwd -P)
-  - mysql -e "SET GLOBAL local_infile=1;"
-  - cd ..
-install:
-  - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
-  - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
-  - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
-  - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
-  - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
-  - cpanm --sudo -v --installdeps --notest .
-  - cpanm --sudo -n Devel::Cover::Report::Coveralls
-  - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
-  - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
-script:
-  - ./travisci/harness.sh
+
 jobs:
   include:
-    - language: python
-      os: linux
-      dist: focal
+    - name: "Perl Job"
+      perl: "5.26.4"
+      services:
+        - mysql
+      env:
+        - COVERALLS=true  DB=mysql
+      addons:
+        apt:
+          update: true
+          packages:
+            - unzip
+            - sendmail
+            - graphviz
+            - emboss
+            - libkyotocabinet-dev
+      before_install:
+        - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
+        - export PATH=$PATH:$PWD/ensembl-git-tools/bin
+        - export ENSEMBL_BRANCH=master
+        - export SECONDARY_BRANCH=main
+        - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
+        - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
+        - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
+        - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
+        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
+        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
+        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
+        - git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
+        - git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
+        - cd htslib
+        - make
+        - export HTSLIB_DIR=$(pwd -P)
+        - mysql -e "SET GLOBAL local_infile=1;"
+        - cd ..
+      install:
+        - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
+        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
+        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
+        - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
+        - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
+        - cpanm --sudo -v --installdeps --notest .
+        - cpanm --sudo -n Devel::Cover::Report::Coveralls
+        - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
+        - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
+      script:
+        - ./travisci/harness.sh
+
+    - name: "Python Job"
+      language: python
       python:
-        - '3.10'
-        - '3.11'
+        - "3.10"
+        - "3.11"
       install:
         - pip install -r requirements-test.txt
         - pip install -e .
@@ -69,9 +70,10 @@ jobs:
         - mysql -e "SET GLOBAL local_infile=1;"
       script:
         - pytest src/python/test
+
 notifications:
   email:
     on_success: always
     on_failure: always
   slack:
-    secure: BkrSPAkOM5aTOpeyO9vZnHdZ0LF1PLk0r2HtcXN2eTMyiHoGXkl6VUjdAL8EkzI4gunW2GProdSIjHpf60WdiEmKAulMdJRI+xyUbuxnY31mwiikS9HYwqmPBbMTf0Mh2pMBngZRFs+gaFZDUMTfLfp+8MQfU1R54yb6hPuVt5I=
+    secure: BkrSPAkOM5aTOpeyO9vZnHdZ0LF1PLk0r2HtcXN2eTMyiHoGXkl6VUjdAL8EkzI4gunW2GProdSIjHpf60WdiEmKAulMdJRI+xyUbuxnY31mwiikS9HYwqmPBbMTf0Mh2pMBngZRFs+gaFZDUMTfLfp+8MQfU1R54yb6hPuVt5I=
\ No newline at end of file

From a4797ab2a2bca20f6010c558e185e6b8dd1e624c Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 15 Oct 2024 17:58:09 +0100
Subject: [PATCH 111/128] fix missing mysql service in python jobs for travis

---
 .travis.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.travis.yml b/.travis.yml
index 49da39005..1c409aa69 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -63,6 +63,10 @@ jobs:
       python:
         - "3.10"
         - "3.11"
+      services:
+        - mysql
+      env:
+        - COVERALLS=true  DB=mysql
       install:
         - pip install -r requirements-test.txt
         - pip install -e .

From 59cd63e2407a52bfea5bf4d9ba8b0e8defca2adc Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 15 Oct 2024 21:11:45 +0100
Subject: [PATCH 112/128] fix missing mysql service in python jobs for travis

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 1c409aa69..746361c80 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,7 +5,8 @@ dist: focal
 jobs:
   include:
     - name: "Perl Job"
-      perl: "5.26.4"
+      perl:
+      - "5.26.2"
       services:
         - mysql
       env:

From 5372422be105ab0fd6b6b6f7625d009a96711108 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 15 Oct 2024 21:11:45 +0100
Subject: [PATCH 113/128] fix missing mysql service in python jobs for travis

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 1c409aa69..746361c80 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,7 +5,8 @@ dist: focal
 jobs:
   include:
     - name: "Perl Job"
-      perl: "5.26.4"
+      perl:
+      - "5.26.2"
       services:
         - mysql
       env:

From 7fe42486b918766175210ff04354499735e91202 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 15 Oct 2024 21:20:17 +0100
Subject: [PATCH 114/128] fix missing mysql service in python jobs for travis

---
 .travis.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 746361c80..8ce5d480b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -5,8 +5,6 @@ dist: focal
 jobs:
   include:
     - name: "Perl Job"
-      perl:
-      - "5.26.2"
       services:
         - mysql
       env:
@@ -21,6 +19,10 @@ jobs:
             - emboss
             - libkyotocabinet-dev
       before_install:
+        - curl -L https://install.perlbrew.pl | bash
+        - source ~/perl5/perlbrew/etc/bashrc
+        - perlbrew install perl-5.26.4
+        - perlbrew use perl-5.26.4
         - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
         - export PATH=$PATH:$PWD/ensembl-git-tools/bin
         - export ENSEMBL_BRANCH=master

From ac5e7ab357a12026d2329972cb6405929d497205 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 15 Oct 2024 21:23:50 +0100
Subject: [PATCH 115/128] fix missing mysql service in python jobs for travis

---
 .travis.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 8ce5d480b..56f6fda11 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,7 +1,6 @@
 language: perl
 os: linux
 dist: focal
-
 jobs:
   include:
     - name: "Perl Job"

From a444f3275c161226cf73ae4231233364c119db12 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Wed, 16 Oct 2024 11:38:23 +0100
Subject: [PATCH 116/128] fix missing mysql service in python jobs for travis

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 56f6fda11..cf4cc9b3f 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -20,8 +20,8 @@ jobs:
       before_install:
         - curl -L https://install.perlbrew.pl | bash
         - source ~/perl5/perlbrew/etc/bashrc
-        - perlbrew install perl-5.26.4
-        - perlbrew use perl-5.26.4
+        - perlbrew install perl-5.26.2
+        - perlbrew use perl-5.26.2
         - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
         - export PATH=$PATH:$PWD/ensembl-git-tools/bin
         - export ENSEMBL_BRANCH=master

From 3d4a9df49c4eae68dd9617cd9e97a71bfe4b948d Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Wed, 16 Oct 2024 12:14:36 +0100
Subject: [PATCH 117/128] set perl version to 5.26.2

---
 .travis.yml | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index cf4cc9b3f..06368f4fd 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,4 +1,6 @@
 language: perl
+perl:
+  - "5.26.2"
 os: linux
 dist: focal
 jobs:
@@ -18,10 +20,6 @@ jobs:
             - emboss
             - libkyotocabinet-dev
       before_install:
-        - curl -L https://install.perlbrew.pl | bash
-        - source ~/perl5/perlbrew/etc/bashrc
-        - perlbrew install perl-5.26.2
-        - perlbrew use perl-5.26.2
         - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
         - export PATH=$PATH:$PWD/ensembl-git-tools/bin
         - export ENSEMBL_BRANCH=master

From f253f2872a1a2f86cab2dfc98928d4a5d2dc0b51 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Wed, 16 Oct 2024 12:44:42 +0100
Subject: [PATCH 118/128] revert the travis yml file and remove the perl
 version 5.14

---
 .travis.yml | 110 +++++++++++++++++++++++++---------------------------
 1 file changed, 53 insertions(+), 57 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 06368f4fd..01414e7aa 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,65 +1,61 @@
 language: perl
+dist: focal
 perl:
   - "5.26.2"
-os: linux
-dist: focal
+services:
+  - mysql
+env:
+  - COVERALLS=true  DB=mysql
+addons:
+  apt:
+    update: true
+    packages:
+      - unzip
+      - sendmail
+      - graphviz
+      - emboss
+      - libkyotocabinet-dev
+before_install:
+  - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
+  - export PATH=$PATH:$PWD/ensembl-git-tools/bin
+  - export ENSEMBL_BRANCH=master
+  - export SECONDARY_BRANCH=main
+  - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
+  - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
+  - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
+  - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
+  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
+  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
+  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
+  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
+  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
+  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
+  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
+  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
+  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
+  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
+  - git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
+  - git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
+  - cd htslib
+  - make
+  - export HTSLIB_DIR=$(pwd -P)
+  - mysql -e "SET GLOBAL local_infile=1;"
+  - cd ..
+install:
+  - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
+  - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
+  - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
+  - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
+  - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
+  - cpanm --sudo -v --installdeps --notest .
+  - cpanm --sudo -n Devel::Cover::Report::Coveralls
+  - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
+  - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
+script:
+  - ./travisci/harness.sh
 jobs:
   include:
-    - name: "Perl Job"
-      services:
-        - mysql
-      env:
-        - COVERALLS=true  DB=mysql
-      addons:
-        apt:
-          update: true
-          packages:
-            - unzip
-            - sendmail
-            - graphviz
-            - emboss
-            - libkyotocabinet-dev
-      before_install:
-        - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
-        - export PATH=$PATH:$PWD/ensembl-git-tools/bin
-        - export ENSEMBL_BRANCH=master
-        - export SECONDARY_BRANCH=main
-        - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
-        - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
-        - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
-        - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
-        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
-        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
-        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
-        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
-        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
-        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
-        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
-        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
-        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
-        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
-        - git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
-        - git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
-        - cd htslib
-        - make
-        - export HTSLIB_DIR=$(pwd -P)
-        - mysql -e "SET GLOBAL local_infile=1;"
-        - cd ..
-      install:
-        - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
-        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
-        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
-        - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
-        - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
-        - cpanm --sudo -v --installdeps --notest .
-        - cpanm --sudo -n Devel::Cover::Report::Coveralls
-        - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
-        - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
-      script:
-        - ./travisci/harness.sh
-
-    - name: "Python Job"
-      language: python
+    - language: python
       python:
         - "3.10"
         - "3.11"

From c69590eb171de1d8e25472d2bf3a9a44643cc572 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Wed, 16 Oct 2024 12:52:28 +0100
Subject: [PATCH 119/128] check perl test are running

---
 .travis.yml | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 01414e7aa..f2e944b92 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -56,9 +56,8 @@ script:
 jobs:
   include:
     - language: python
-      python:
-        - "3.10"
-        - "3.11"
+      python: 3.10
+
       services:
         - mysql
       env:

From a61bfe642d95ed2c5e212d508ece5e7ad4988f12 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Wed, 16 Oct 2024 13:33:31 +0100
Subject: [PATCH 120/128] Revert "fix missing mysql service in python jobs for
 travis"

This reverts commit 5372422b
---
 .travis.yml | 115 +++++++++++++++++++++++++++-------------------------
 1 file changed, 60 insertions(+), 55 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index f2e944b92..1c409aa69 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,63 +1,68 @@
 language: perl
+os: linux
 dist: focal
-perl:
-  - "5.26.2"
-services:
-  - mysql
-env:
-  - COVERALLS=true  DB=mysql
-addons:
-  apt:
-    update: true
-    packages:
-      - unzip
-      - sendmail
-      - graphviz
-      - emboss
-      - libkyotocabinet-dev
-before_install:
-  - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
-  - export PATH=$PATH:$PWD/ensembl-git-tools/bin
-  - export ENSEMBL_BRANCH=master
-  - export SECONDARY_BRANCH=main
-  - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
-  - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
-  - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
-  - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
-  - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
-  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
-  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
-  - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
-  - git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
-  - git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
-  - cd htslib
-  - make
-  - export HTSLIB_DIR=$(pwd -P)
-  - mysql -e "SET GLOBAL local_infile=1;"
-  - cd ..
-install:
-  - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
-  - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
-  - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
-  - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
-  - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
-  - cpanm --sudo -v --installdeps --notest .
-  - cpanm --sudo -n Devel::Cover::Report::Coveralls
-  - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
-  - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
-script:
-  - ./travisci/harness.sh
+
 jobs:
   include:
-    - language: python
-      python: 3.10
+    - name: "Perl Job"
+      perl: "5.26.4"
+      services:
+        - mysql
+      env:
+        - COVERALLS=true  DB=mysql
+      addons:
+        apt:
+          update: true
+          packages:
+            - unzip
+            - sendmail
+            - graphviz
+            - emboss
+            - libkyotocabinet-dev
+      before_install:
+        - git clone --depth 1 https://github.com/Ensembl/ensembl-git-tools.git
+        - export PATH=$PATH:$PWD/ensembl-git-tools/bin
+        - export ENSEMBL_BRANCH=master
+        - export SECONDARY_BRANCH=main
+        - echo "TRAVIS_BRANCH=$TRAVIS_BRANCH"
+        - if [[ $TRAVIS_BRANCH =~ ^release\/[0-9]+$ ]]; then export ENSEMBL_BRANCH=$TRAVIS_BRANCH; export SECONDARY_BRANCH=$TRAVIS_BRANCH; fi
+        - echo "ENSEMBL_BRANCH=$ENSEMBL_BRANCH"
+        - echo "SECONDARY_BRANCH=$SECONDARY_BRANCH"
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-test
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-compara
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-datacheck
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-variation
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-metadata
+        - git-ensembl --clone --branch $ENSEMBL_BRANCH --secondary_branch $SECONDARY_BRANCH --depth 1 ensembl-funcgen
+        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-hive
+        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-orm
+        - git-ensembl --clone --branch master --secondary_branch main --depth 1 ensembl-taxonomy
+        - git clone --branch 1.9 --depth 1 https://github.com/samtools/htslib.git
+        - git clone --branch release-1-6-924 --depth 1 https://github.com/bioperl/bioperl-live.git
+        - cd htslib
+        - make
+        - export HTSLIB_DIR=$(pwd -P)
+        - mysql -e "SET GLOBAL local_infile=1;"
+        - cd ..
+      install:
+        - cpanm --sudo -v --installdeps --with-recommends --notest --cpanfile ensembl/cpanfile .
+        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-hive/cpanfile .
+        - cpanm --sudo -v --installdeps --notest --cpanfile ensembl-datacheck/cpanfile .
+        - export PERL5LIB=$PERL5LIB:$PWD/bioperl-live
+        - cpanm travisci/kyotocabinet-perl-1.20.tar.gz
+        - cpanm --sudo -v --installdeps --notest .
+        - cpanm --sudo -n Devel::Cover::Report::Coveralls
+        - cp travisci/MultiTestDB.conf.travisci  modules/t/MultiTestDB.conf
+        - mysql -u root -h localhost -e 'GRANT ALL PRIVILEGES ON *.* TO "travis"@"%"'
+      script:
+        - ./travisci/harness.sh
 
+    - name: "Python Job"
+      language: python
+      python:
+        - "3.10"
+        - "3.11"
       services:
         - mysql
       env:

From 5781de67033f785dbe02deb0f9b6cdeb9a24e2b6 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Wed, 16 Oct 2024 13:34:21 +0100
Subject: [PATCH 121/128] check perl test are running

---
 .travis.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 1c409aa69..33c2fa8e3 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -1,11 +1,9 @@
 language: perl
 os: linux
-dist: focal
-
 jobs:
   include:
     - name: "Perl Job"
-      perl: "5.26.4"
+      perl: "5.26.2"
       services:
         - mysql
       env:

From b82e08afa51511d346740a98311093d144ae5fbb Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Wed, 16 Oct 2024 13:45:35 +0100
Subject: [PATCH 122/128] update hive version to 2.7 in core stats pipeline

---
 .../Production/Pipeline/PipeConfig/CoreStatistics_conf.pm       | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
index 909dbdcd9..1cf6a365a 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/CoreStatistics_conf.pm
@@ -38,7 +38,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::ApiVersion qw/software_version/;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 sub default_options {

From 68cc8f1dbfdc750c97b6ceaf7db09da1a15632d6 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Thu, 17 Oct 2024 17:27:10 +0100
Subject: [PATCH 123/128] update hive version to 2.7 in production pipeline

---
 .../Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm        | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm   | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/ChecksumLoader_conf.pm       | 2 +-
 .../Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm    | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm | 2 +-
 .../Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm | 2 +-
 .../Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm      | 2 +-
 .../Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm | 2 +-
 .../Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm   | 2 +-
 .../Production/Pipeline/PipeConfig/EnsemblSearchDumps_conf.pm   | 2 +-
 .../Production/Pipeline/PipeConfig/EnsemblThoasDumps_conf.pm    | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm        | 2 +-
 modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm | 2 +-
 .../Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm     | 2 +-
 .../Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm   | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/MVP_XrefProcess_conf.pm      | 2 +-
 .../Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm     | 2 +-
 .../Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm      | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm  | 2 +-
 .../Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm       | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm   | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm    | 2 +-
 .../Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm     | 2 +-
 .../Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm | 2 +-
 .../Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm   | 2 +-
 .../Production/Pipeline/PipeConfig/VariationStatistics_conf.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm  | 2 +-
 .../EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm  | 2 +-
 41 files changed, 41 insertions(+), 41 deletions(-)

diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
index b05614659..f16b1dfbe 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/AlphaDBImport_conf.pm
@@ -45,7 +45,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.6;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 
 =head2 default_options
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
index 2e51ffe33..54906c466 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BasePython_conf.pm
@@ -25,7 +25,7 @@ use strict;
 use warnings;
 use Data::Dumper;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 use base ('Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf');
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
index ae33dca99..4f0c0a558 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Base_conf.pm
@@ -24,7 +24,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Hive::PipeConfig::EnsemblGeneric_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 use File::Spec::Functions qw(catdir);
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
index 3c2bab042..b0503c433 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/BulkSQL_conf.pm
@@ -38,7 +38,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
index c7198cc3d..781f60416 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumGenerator_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumLoader_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumLoader_conf.pm
index a7e110a93..977ae0568 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumLoader_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ChecksumLoader_conf.pm
@@ -26,7 +26,7 @@ use warnings;
 use Data::Dumper;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
index 71d3b7655..de8aaffd0 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DataChecksNonCore_conf.pm
@@ -31,7 +31,7 @@ use warnings;
 use base ('Bio::EnsEMBL::DataCheck::Pipeline::DbDataChecks_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
index 3cbb3c5b5..627e0ab05 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DbCopy_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec::Functions qw(catdir);
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
index 89f38d607..02bbb9cc9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpCore_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
index 41a9ca74d..b0bd2e3a9 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_conf_strains.pm
@@ -24,7 +24,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::DumpOrtholog_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
 	my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
index ea3bcd8e4..fd730fc3e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_eg_conf.pm
@@ -24,7 +24,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::DumpOrtholog_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
 	my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
index a0e6ab38b..46f9513cf 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpOrtholog_ensembl_conf.pm
@@ -24,7 +24,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::DumpOrtholog_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
 	my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
index cd3b8e9a1..171494407 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/DumpSpeciesForGOA_conf.pm
@@ -34,7 +34,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec::Functions qw(catdir);
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
index 242743099..9d809f563 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EarlyDumps_conf.pm
@@ -26,7 +26,7 @@ use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 use Bio::EnsEMBL::Production::Pipeline::PipeConfig::FileDumpMySQL_conf;
 use Bio::EnsEMBL::Production::Pipeline::PipeConfig::DumpCore_conf;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec::Functions qw(catdir);
 
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblSearchDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblSearchDumps_conf.pm
index 8910c2531..7bd38728e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblSearchDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblSearchDumps_conf.pm
@@ -27,7 +27,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblThoasDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblThoasDumps_conf.pm
index e5153532e..61361da4c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblThoasDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/EnsemblThoasDumps_conf.pm
@@ -27,7 +27,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
index 5c8590d06..af53f5fd7 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FactoryTest_conf.pm
@@ -26,7 +26,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
index a6f5f3229..aff1a5ba6 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/FileDumpMySQL_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec::Functions qw(catdir);
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
index d5346d9f7..0f594487d 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GPAD_conf.pm
@@ -24,7 +24,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec::Functions qw(catdir);
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
index 59eeae96e..b31a3f0eb 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneAutoComplete_conf.pm
@@ -37,7 +37,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
index 075faf886..24d418067 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GeneTreeHighlighting_conf.pm
@@ -32,7 +32,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
index a81a2c03a..0a9d9fe4c 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/GrantMySQL_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
index 15c3a2486..793ec0d50 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadAppris_conf.pm
@@ -32,7 +32,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
index faab42885..c10601583 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadRefget_conf.pm
@@ -20,7 +20,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
index 670594711..184d5a82f 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/LoadTSL_conf.pm
@@ -32,7 +32,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MVP_XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MVP_XrefProcess_conf.pm
index 7c800054b..9826b1478 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MVP_XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/MVP_XrefProcess_conf.pm
@@ -24,7 +24,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
index 0b83cf992..66549db1e 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/OLSLoad_conf.pm
@@ -31,7 +31,7 @@ use warnings FATAL => 'all';
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
     my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
index 3b58fe283..002f8f271 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProductionDBSync_conf.pm
@@ -32,7 +32,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec::Functions qw(catdir);
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
index 3230814f0..55b1cea2e 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/ProteinFeatures_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 use File::Spec::Functions qw(catdir);
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
index 40c6c9b78..6d8fa3fc8 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/RNAGeneXref_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 use File::Spec::Functions qw(catdir);
 
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
index d02de7472..82778ac57 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleDataCopy_conf.pm
@@ -41,7 +41,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
index 79a860494..110f532dd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SampleData_conf.pm
@@ -43,7 +43,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
index 6b16ce2e4..adb3bcbbd 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/SearchDumps_conf.pm
@@ -37,7 +37,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
index 4df737ac6..dc30908ef 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/StableIDs_conf.pm
@@ -38,7 +38,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
index cb010d7ef..ec6141542 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TaxonomyInfoCore_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use File::Spec::Functions qw(catdir);
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
index b9426d30c..fdad0bde8 100755
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/TranscriptomeDomains_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::ProteinFeatures_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
index 8b02ae00d..b0a6c1460 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/UpdatePackedStatus_conf.pm
@@ -26,7 +26,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
index 0cb424cbf..a709f5b44 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/VariationStatistics_conf.pm
@@ -37,7 +37,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::CoreStatistics_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 sub default_options {
   my ($self) = @_;
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
index 128fe18fc..6bbe3fa04 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefDownload_conf.pm
@@ -24,7 +24,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
index f490d8722..d478fff24 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/XrefProcess_conf.pm
@@ -24,7 +24,7 @@ use warnings;
 
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
 
 sub default_options {
diff --git a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
index b72c803c2..69947d710 100644
--- a/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
+++ b/modules/Bio/EnsEMBL/Production/Pipeline/PipeConfig/Xref_update_conf.pm
@@ -25,7 +25,7 @@ use warnings;
 use base ('Bio::EnsEMBL::Production::Pipeline::PipeConfig::Base_conf');
 
 use Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf;
-use Bio::EnsEMBL::Hive::Version 2.5;
+use Bio::EnsEMBL::Hive::Version 2.7;
 
 
 sub default_options {

From c42b788917c5466b11bc2273d23d3373e8b51ea4 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 22 Oct 2024 10:27:59 +0100
Subject: [PATCH 124/128] update metadata-api to latest version

---
 requirements.in | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.in b/requirements.in
index db7fc5acc..4c5da5010 100755
--- a/requirements.in
+++ b/requirements.in
@@ -2,4 +2,4 @@ requests>=2.25.0,<3
 pydantic~=1.10.5
 ensembl-py>=2.1.0
 ensembl-utils>=0.4.4
-git+https://github.com/Ensembl/ensembl-metadata-api.git@3.0.1#egg=ensembl-metadata-api
\ No newline at end of file
+git+https://github.com/Ensembl/ensembl-metadata-api.git@3.3.3a1#egg=ensembl-metadata-api
\ No newline at end of file

From efa637cca99539bee40d9ec3e793dd2c28c8b8b9 Mon Sep 17 00:00:00 2001
From: vinay <vinay@ebi.ac.uk>
Date: Tue, 22 Oct 2024 10:47:39 +0100
Subject: [PATCH 125/128] update metadata-api to latest version 3.3.0a1

---
 requirements.in  | 2 +-
 requirements.txt | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/requirements.in b/requirements.in
index 4c5da5010..ff57a0d74 100755
--- a/requirements.in
+++ b/requirements.in
@@ -2,4 +2,4 @@ requests>=2.25.0,<3
 pydantic~=1.10.5
 ensembl-py>=2.1.0
 ensembl-utils>=0.4.4
-git+https://github.com/Ensembl/ensembl-metadata-api.git@3.3.3a1#egg=ensembl-metadata-api
\ No newline at end of file
+git+https://github.com/Ensembl/ensembl-metadata-api.git@3.3.0a1#egg=ensembl-metadata-api
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index 137c03abc..54aeade70 100755
--- a/requirements.txt
+++ b/requirements.txt
@@ -8,7 +8,7 @@ certifi==2024.2.2
     # via requests
 charset-normalizer==3.3.2
     # via requests
-ensembl-metadata-api @ git+https://github.com/Ensembl/ensembl-metadata-api.git@3.0.1
+ensembl-metadata-api @ git+https://github.com/Ensembl/ensembl-metadata-api.git@3.3.0a1
     # via -r requirements.in
 ensembl-py==2.1.3
     # via -r requirements.in

From 86da542ae4530d1e08959da764252f5b7e9ee5c9 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Tue, 5 Nov 2024 18:56:23 +0000
Subject: [PATCH 126/128] update MetadataUpdaterHiveCore to insert job details
 into result table

---
 .../MetadataUpdaterHiveCore.py                | 24 ++++++++++++-------
 1 file changed, 15 insertions(+), 9 deletions(-)

diff --git a/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py b/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
index 6a37efffc..05c9bbded 100644
--- a/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
+++ b/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
@@ -10,7 +10,7 @@
 #  See the License for the specific language governing permissions and
 #  limitations under the License.
 
-
+import json
 from ensembl.production.hive.BaseProdRunnable import BaseProdRunnable
 from ensembl.production.metadata.updater.core import CoreMetaUpdater
 
@@ -18,11 +18,17 @@
 class MetadataUpdaterHiveCore(BaseProdRunnable):
 
     def run(self):
-        if self.param("force") == 0 or self.param("force") is None:
-            run = CoreMetaUpdater(self.param("database_uri"), self.param("genome_metadata_uri"), self.param("taxonomy_uri"))
-        elif self.param("force") == 1:
-            run = CoreMetaUpdater(self.param("database_uri"), self.param("genome_metadata_uri"), self.param("taxonomy_uri"),
-                                  force=1)
-        else:
-            raise ValueError(f"Unable to figure out param {self.param('force')}")
-        run.process_core()
+        try:
+            run = CoreMetaUpdater(self.param("database_uri"), self.param("genome_metadata_uri"))
+            run.process_core()
+            output = { 'metadata_uri' : self.param("genome_metadata_uri"),
+             'database_uri' : self.param("database_uri"),
+             'email': self.param("email")
+            }
+            self.dataflow({
+			    'job_id' : self.input_job().dbID(),
+			    'output' : json.dumps(output)
+			}, 2);
+
+        except Exception as e : 
+            raise ValueError(str(e))

From fb31eff38c5c275006fc9cf3df178588b3ab7fb6 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Tue, 5 Nov 2024 19:30:43 +0000
Subject: [PATCH 127/128] test job_id

---
 .../hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py b/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
index 05c9bbded..e179945be 100644
--- a/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
+++ b/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
@@ -26,7 +26,7 @@ def run(self):
              'email': self.param("email")
             }
             self.dataflow({
-			    'job_id' : self.input_job().dbID(),
+			    'job_id' : 2,
 			    'output' : json.dumps(output)
 			}, 2);
 

From 6e4dfe7a36922885697167f9b5e9b936f9d586e2 Mon Sep 17 00:00:00 2001
From: vinay-ebi <59567245+vinay-ebi@users.noreply.github.com>
Date: Wed, 6 Nov 2024 07:29:33 +0000
Subject: [PATCH 128/128] set job id in output flow

---
 .../hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py    | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py b/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
index e179945be..e6c2a9a9c 100644
--- a/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
+++ b/src/python/ensembl/production/hive/ensembl_genome_metadata/MetadataUpdaterHiveCore.py
@@ -25,8 +25,9 @@ def run(self):
              'database_uri' : self.param("database_uri"),
              'email': self.param("email")
             }
+            
             self.dataflow({
-			    'job_id' : 2,
+			    'job_id' : self.input_job.dbID,
 			    'output' : json.dumps(output)
 			}, 2);