fixed a few bugs

uploadNeuroDB/NeuroDB/HRRT.pm

@@ -547,7 +547,7 @@ sub updateHrrtUploadInfo {
 
 
 sub getHrrtArchiveLocationFromHrrtArchiveID {
-    my ($dbh, $hrrt_archive_id, $dbh) = @_;
+    my ($hrrt_archive_id, $dbh) = @_;
 
     my $query = "SELECT ArchiveLocation FROM hrrt_archive WHERE HrrtArchiveID=?";
     my $sth   = $dbh->prepare($query);

uploadNeuroDB/NeuroDB/ImagingUpload.pm

@@ -648,7 +648,9 @@ sub CleanUpDataIncomingDir {
     ## Get config settings using ConfigOB
     # ----------------------------------------------------------------
     my $configOB          = $this->{configOB};
-    my $tarchive_location = $configOB->getTarchiveLibraryDir();
+    my $tarchive_location = $this->{'is_hrrt'}
+                                ? $configOB->getDataDirPath() . "/hrrtarchive"
+                                : $configOB->getTarchiveLibraryDir();
 
 
     ############################################################

uploadNeuroDB/NeuroDB/MRI.pm

@@ -1553,6 +1553,58 @@ sub isDicomImage {
 }
 
 
+=pod
+
+=head3 isEcatImage(@files_list)
+
+This method checks whether the files given as an argument are HRRT ECAT7 images or not.
+It will return a hash with the file path as keys and true or false as values (the
+value will be set to true if the file is an ECAT7 image, otherwise it will be set to
+false).
+
+INPUT: array with full path to the files
+
+RETURNS:
+  - %isEcatImage: hash with file path as keys and true or false as values (true
+                   if the file is a DICOM image file, false otherwise)
+
+=cut
+
+sub isEcatImage {
+    my (@files_list) = @_;
+
+    # For now, the files list need to be written in a temporary file so that the
+    # command does not fail on large amount of files. If doing directly
+    # `ls @files_list | xargs file` then the argument list is too long at it does
+    # not return one file per line but many files in one line. Writing in a
+    # temporary file on which we run the command `cat` seems to be the only option
+    # that works at the moment...
+    my $tmp_file = $ENV{'TMPDIR'} . "/tmp_list";
+    open(my $fh, '>', $tmp_file) or die "Could not open file '$tmp_file' $!";
+    foreach my $file (@files_list) {
+        printf $fh "%s\n", quotemeta($file);
+    }
+    close($fh);
+
+    my $cmd = "cat $tmp_file | xargs file";
+    my @file_types = `$cmd`;
+    unlink $tmp_file;
+
+    my %isEcatImage;
+    foreach my $line (@file_types) {
+        my ($file, $type) = split(':', $line);
+
+        if ($type =~ /data$/ && $file =~ /\.v$/) {
+            $isEcatImage{$file} = 1;
+        } else {
+            $isEcatImage{$file} = 0;
+        }
+    }
+
+    return \%isEcatImage;
+}
+
+
 =pod
 
 =head3 get_trashbin_file_rel_path($file)