From efc07091a6691fb19742650855a97adad94064e6 Mon Sep 17 00:00:00 2001
From: Syphax Bouazzouni <gs_bouazzouni@esi.dz>
Date: Mon, 23 May 2022 18:44:06 +0200
Subject: [PATCH 1/4] add :ontologies to the serialize_default of the group
 model

---
 lib/ontologies_linked_data/models/group.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/lib/ontologies_linked_data/models/group.rb b/lib/ontologies_linked_data/models/group.rb
index 73ee8fd8..913d9ee3 100644
--- a/lib/ontologies_linked_data/models/group.rb
+++ b/lib/ontologies_linked_data/models/group.rb
@@ -8,6 +8,7 @@ class Group < LinkedData::Models::Base
       attribute :created, enforce: [:date_time], :default => lambda { |record| DateTime.now }
       attribute :ontologies, inverse: { on: :ontology, attribute: :group }
 
+      serialize_default :acronym, :name, :description, :created, :ontologies
       cache_timeout 86400
     end
   end

From db5a888eb392ac6f1f6b1dfed497aafcd1b8179d Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Wed, 22 May 2024 10:48:52 -0700
Subject: [PATCH 2/4] Revert "Feature: add :ontologies to the serialize_default
 of the group model"

---
 lib/ontologies_linked_data/models/group.rb | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/ontologies_linked_data/models/group.rb b/lib/ontologies_linked_data/models/group.rb
index 913d9ee3..73ee8fd8 100644
--- a/lib/ontologies_linked_data/models/group.rb
+++ b/lib/ontologies_linked_data/models/group.rb
@@ -8,7 +8,6 @@ class Group < LinkedData::Models::Base
       attribute :created, enforce: [:date_time], :default => lambda { |record| DateTime.now }
       attribute :ontologies, inverse: { on: :ontology, attribute: :group }
 
-      serialize_default :acronym, :name, :description, :created, :ontologies
       cache_timeout 86400
     end
   end

From 70fc2c8b377b9deabc838ecd56d3bc75ec764cc2 Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Tue, 11 Jun 2024 22:40:46 -0700
Subject: [PATCH 3/4] Gemfile update

---
 Gemfile      |  4 ++--
 Gemfile.lock | 36 +++++++++++++++++++-----------------
 2 files changed, 21 insertions(+), 19 deletions(-)

diff --git a/Gemfile b/Gemfile
index 23512929..b4bd6c44 100644
--- a/Gemfile
+++ b/Gemfile
@@ -34,5 +34,5 @@ group :development do
   gem 'rubocop', require: false
 end
 # NCBO gems (can be from a local dev path or from rubygems/git)
-gem 'goo', github: 'ncbo/goo', branch: 'develop'
-gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'develop'
+gem 'goo', github: 'ncbo/goo', branch: 'master'
+gem 'sparql-client', github: 'ncbo/sparql-client', branch: 'master'
diff --git a/Gemfile.lock b/Gemfile.lock
index 79d8e539..3b63c879 100644
--- a/Gemfile.lock
+++ b/Gemfile.lock
@@ -1,7 +1,7 @@
 GIT
   remote: https://github.com/ncbo/goo.git
-  revision: 70007faf43d0d96292809f89f15a27a757ccaa25
-  branch: develop
+  revision: 2cec53c2d84179171def81d7dc0a18e462e78fc2
+  branch: master
   specs:
     goo (0.0.2)
       addressable (~> 2.8)
@@ -16,8 +16,8 @@ GIT
 
 GIT
   remote: https://github.com/ncbo/sparql-client.git
-  revision: 1657f0dd69fd4b522d3549a6848670175f5e98cc
-  branch: develop
+  revision: e89c26aa96f184dbe9b52d51e04fb3d9ba998dbc
+  branch: master
   specs:
     sparql-client (1.0.1)
       json_pure (>= 1.4)
@@ -40,9 +40,9 @@ GEM
     base64 (0.2.0)
     bcrypt (3.1.20)
     bigdecimal (3.1.8)
-    builder (3.2.4)
+    builder (3.3.0)
     coderay (1.1.3)
-    concurrent-ruby (1.2.3)
+    concurrent-ruby (1.3.3)
     connection_pool (2.4.1)
     cube-ruby (0.0.3)
     daemons (1.4.1)
@@ -59,11 +59,13 @@ GEM
       faraday-net_http (>= 2.0, < 3.1)
       ruby2_keywords (>= 0.0.4)
     faraday-net_http (3.0.2)
-    ffi (1.16.3)
+    ffi (1.17.0-aarch64-linux-gnu)
+    ffi (1.17.0-x86_64-darwin)
+    ffi (1.17.0-x86_64-linux-gnu)
     hashie (5.0.0)
     htmlentities (4.3.4)
     http-accept (1.7.0)
-    http-cookie (1.0.5)
+    http-cookie (1.0.6)
       domain_name (~> 0.5)
     i18n (0.9.5)
       concurrent-ruby (~> 1.0)
@@ -84,7 +86,7 @@ GEM
     method_source (1.1.0)
     mime-types (3.5.2)
       mime-types-data (~> 3.2015)
-    mime-types-data (3.2024.0507)
+    mime-types-data (3.2024.0604)
     mini_mime (1.1.5)
     minitest (4.7.5)
     minitest-reporters (0.14.24)
@@ -94,7 +96,7 @@ GEM
       powerbar
     multi_json (1.15.0)
     net-http-persistent (2.9.4)
-    net-imap (0.4.11)
+    net-imap (0.4.12)
       date
       net-protocol
     net-pop (0.1.2)
@@ -104,12 +106,12 @@ GEM
     net-smtp (0.5.0)
       net-protocol
     netrc (0.11.0)
-    oj (3.16.3)
+    oj (3.16.4)
       bigdecimal (>= 3.0)
     omni_logger (0.1.4)
       logger
-    parallel (1.24.0)
-    parser (3.3.1.0)
+    parallel (1.25.1)
+    parser (3.3.2.0)
       ast (~> 2.4.1)
       racc
     pony (1.13.1)
@@ -130,7 +132,7 @@ GEM
       addressable (>= 2.2)
     redis (5.2.0)
       redis-client (>= 0.22.0)
-    redis-client (0.22.1)
+    redis-client (0.22.2)
       connection_pool
     regexp_parser (2.9.2)
     request_store (1.7.0)
@@ -140,12 +142,12 @@ GEM
       http-cookie (>= 1.0.2, < 2.0)
       mime-types (>= 1.16, < 4.0)
       netrc (~> 0.8)
-    rexml (3.2.8)
-      strscan (>= 3.0.9)
+    rexml (3.3.0)
+      strscan
     rsolr (2.6.0)
       builder (>= 2.1.2)
       faraday (>= 0.9, < 3, != 2.0.0)
-    rubocop (1.63.5)
+    rubocop (1.64.1)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)

From f32bc171e487b7c87fee28b80d9a411a7d45aa79 Mon Sep 17 00:00:00 2001
From: Alex Skrenchuk <alexskr@stanford.edu>
Date: Sun, 22 Sep 2024 10:59:47 -0700
Subject: [PATCH 4/4] disable debug logging (issue not fully resolved)

File/Dir permission issue is still unresolved, so anyone working on troubleshooting will need to manually re-enable logging when needed.
https://github.com/ncbo/bioportal-project/issues/323
---
 lib/ontologies_linked_data/models/ontology_submission.rb | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/lib/ontologies_linked_data/models/ontology_submission.rb b/lib/ontologies_linked_data/models/ontology_submission.rb
index 31a341a4..53b4b0a6 100644
--- a/lib/ontologies_linked_data/models/ontology_submission.rb
+++ b/lib/ontologies_linked_data/models/ontology_submission.rb
@@ -135,14 +135,15 @@ def self.copy_file_repository(acronym, submissionId, src, filename = nil)
         path_to_repo = File.join([LinkedData.settings.repository_folder, acronym.to_s, submissionId.to_s])
         name = filename || File.basename(File.new(src).path)
         # THIS LOGGER IS JUST FOR DEBUG - remove after NCBO-795 is closed
-        logger = Logger.new(Dir.pwd + "/create_permissions.log")
+        # https://github.com/ncbo/bioportal-project/issues/323
+        # logger = Logger.new(Dir.pwd + "/logs/create_permissions.log")
         if not Dir.exist? path_to_repo
           FileUtils.mkdir_p path_to_repo
-          logger.debug("Dir created #{path_to_repo} | #{"%o" % File.stat(path_to_repo).mode} | umask: #{File.umask}") # NCBO-795
+          # logger.debug("Dir created #{path_to_repo} | #{"%o" % File.stat(path_to_repo).mode} | umask: #{File.umask}") # NCBO-795
         end
         dst = File.join([path_to_repo, name])
         FileUtils.copy(src, dst)
-        logger.debug("File created #{dst} | #{"%o" % File.stat(dst).mode} | umask: #{File.umask}") # NCBO-795
+        # logger.debug("File created #{dst} | #{"%o" % File.stat(dst).mode} | umask: #{File.umask}") # NCBO-795
         if not File.exist? dst
           raise Exception, "Unable to copy #{src} to #{dst}"
         end