Formatting.

Call set_release() for all relevant source IDs.

misc-scripts/xref_mapping/XrefParser/RefSeqParser.pm

@@ -33,28 +33,38 @@ sub run {
   my $file = shift;
   my $release_file = shift;
 
-  my $peptide_source_id = $self->get_source_id_for_source_name('RefSeq_peptide');
-  my $dna_source_id = $self->get_source_id_for_source_name('RefSeq_dna');
-  print "RefSeq_peptide source ID = $peptide_source_id; RefSeq_dna source ID = $dna_source_id\n";
+    my $peptide_source_id =
+      $self->get_source_id_for_source_name('RefSeq_peptide');
+    my $dna_source_id =
+      $self->get_source_id_for_source_name('RefSeq_dna');
 
-  my $pred_peptide_source_id = $self->get_source_id_for_source_name('RefSeq_peptide_predicted');
-  my $pred_dna_source_id = $self->get_source_id_for_source_name('RefSeq_dna_predicted');
-  print "RefSeq_peptide_predicted source ID = $pred_peptide_source_id; RefSeq_dna_predicted source ID = $pred_dna_source_id\n";
+    print "RefSeq_peptide source ID = $peptide_source_id\n";
+    print "RefSeq_dna source ID = $dna_source_id\n";
 
-  if(!defined($species_id)){
-    $species_id = $self->get_species_id_for_filename($file);
-  }
+    my $pred_peptide_source_id =
+      $self->get_source_id_for_source_name('RefSeq_peptide_predicted');
+    my $pred_dna_source_id =
+      $self->get_source_id_for_source_name('RefSeq_dna_predicted');
 
-  my $xrefs =
-    $self->create_xrefs( $peptide_source_id, $dna_source_id,
-      $pred_peptide_source_id, $pred_dna_source_id, $file, $species_id );
+    print "RefSeq_peptide_predicted source ID = "
+      . "$pred_peptide_source_id\n";
+    print "RefSeq_dna_predicted source ID = $pred_dna_source_id\n";
 
-  if(!defined($xrefs)){
-    return 1; #error
-  }
-  if(!defined($self->upload_xref_object_graphs($xrefs))){
-    return 1; # error
-  }
+    if ( !defined($species_id) ) {
+        $species_id = $self->get_species_id_for_filename($file);
+    }
+
+    my $xrefs =
+      $self->create_xrefs( $peptide_source_id, $dna_source_id,
+        $pred_peptide_source_id, $pred_dna_source_id, $file,
+        $species_id );
+
+    if ( !defined($xrefs) ) {
+        return 1;    #error
+    }
+    if ( !defined( $self->upload_xref_object_graphs($xrefs) ) ) {
+        return 1;    # error
+    }
 
     if ( defined $release_file ) {
         # Parse and set release info.
@@ -70,7 +80,11 @@ sub run {
 
         print "RefSeq release: '$release'\n";
 
-        $self->set_release( $source_id, $release );
+        $self->set_release( $source_id,              $release );
+        $self->set_release( $peptide_source_id,      $release );
+        $self->set_release( $dna_source_id,          $release );
+        $self->set_release( $pred_peptide_source_id, $release );
+        $self->set_release( $pred_dna_source_id,     $release );
     }
 
   return 0; # successfull