Remove getting source_id or species_id from filename if they are not set. As...

Remove getting source_id or species_id from filename if they are not set. As these have to be set or it dies before that bit is reached.

misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm

@@ -32,13 +32,6 @@ sub run {
 
   print "source_id = $source_id, species= $species_id, file = $file\n" if($verbose);
 
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
   my $added = 0;
   my $count = 0;
 

misc-scripts/xref_mapping/XrefParser/ImmunoDBParser.pm

@@ -23,13 +23,6 @@ sub run {
 
   print "source_id = $source_id, species = $species_id, file = $file\n" if($verbose);
 
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
   my $added = 0;
   my $count = 0;
 

misc-scripts/xref_mapping/XrefParser/InterproParser.pm

@@ -22,13 +22,6 @@ sub run {
 
   my $file = @{$files}[0];
 
-  if(!defined($source_id)){
-    $source_id = $self->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = $self->get_species_id_for_filename($file);
-  }
-
   my $add_interpro_sth =
     $self->dbi()
     ->prepare("INSERT INTO interpro (interpro, pfam, dbtype ) VALUES(?,?,?)");

misc-scripts/xref_mapping/XrefParser/MGDParser.pm

@@ -7,9 +7,6 @@ use File::Basename;
 
 use base qw( XrefParser::BaseParser );
 
-my $xref_sth ;
-my $dep_sth;
-
 sub run {
   my $self = shift;
   my $source_id = shift;
@@ -22,81 +19,5 @@ sub run {
 
   die "No longer used. MGI is taken form the uniprot file\n";
 }
-1;
-
-__END__
-
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
-  my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
-  my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};
-
-
-  my $count = 0;
-  my $mismatch = 0;
-  my %mgi_good;
-
-  my $file_io = $self->get_filehandle($file);
-
-  if ( !defined $file_io ) {
-    print "ERROR: Could not open file $file";
-    return 1;    # 1 is an error
-  }
-
-  while ( my $line = $file_io->getline() ) {
-    chomp $line;
-    my ($key,$label,$desc,$sps) = (split("\t",$line))[0,1,3,6];
-    my @sp = split(/\s/,$sps); 
-    foreach my $value (@sp){
-      if(defined($value) and $value and defined($swiss{$value})){
-	XrefParser::BaseParser->add_to_xrefs($swiss{$value},$key,'',$label,$desc,"",$source_id,$species_id);
-	$mgi_good{$key} = 1;
-	$count++;
-      }
-      elsif(defined($value) and $value and defined($refseq{$value})){
-	$mismatch++;
-      }
-    }
-
-  }
-  $file_io->close();
-
-  my $dir = dirname($file);
-  my $syn_file = $dir."/MRK_Synonym.sql.rpt";
-
-  $file_io = $self->get_filehandle($syn_file);
-
-  if ( !defined $file_io ) {
-    print "ERROR: Could not open file $syn_file";
-    return 1;
-  }
-
-  my $synonyms=0;
-
-  while ( $_ = $file_io->getline() ) {
-    if(/MGI:/){
-      chomp ;
-      my ($key,$syn) = (split)[0,4];
-      if(defined($mgi_good{$key})){
-	$self->add_to_syn($key, $source_id, $syn, $species_id);
-	$synonyms++;
-      }
-    }
-  }
-
-  $file_io->close();
-
-  print "\t$count xrefs succesfully loaded\n";
-  print "\t$synonyms synonyms successfully loaded\n";
-  print "\t$mismatch xrefs failed to load\n";
-     
-  return 0;
-}
 
 1;
-    

misc-scripts/xref_mapping/XrefParser/MGI_Desc_Parser.pm

@@ -26,15 +26,6 @@ sub run {
   my $file = @{$files}[0];
   my $syn_file = @{$files}[1];
 
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
-
-
   my $mgi_io = $self->get_filehandle($file);
 
   if ( !defined $mgi_io ) {

misc-scripts/xref_mapping/XrefParser/MIMParser.pm

@@ -28,14 +28,8 @@ sub run {
   my %removed;
   my $source_id;
   my @sources;
-  if(!defined($general_source_id)){
-    $general_source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
+
   push @sources, $general_source_id;
- 
 
   my $gene_source_id = XrefParser::BaseParser->get_source_id_for_source_name("MIM_GENE");
   push @sources, $gene_source_id;
@@ -43,7 +37,7 @@ sub run {
   push @sources, $morbid_source_id;
 
   print "sources are:- ".join(", ",@sources)."\n" if($verbose);
-    
+
   local $/ = "*RECORD*";
 
   my $mim_io = $self->get_filehandle($file);

misc-scripts/xref_mapping/XrefParser/PomBaseParser.pm

@@ -26,13 +26,6 @@ sub run {
 
   my $file = @{$files}[0];
 
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-  
   my $gene_source_id = XrefParser::BaseParser->get_source_id_for_source_name("PomBase_GENE");
   my $transcript_source_id = XrefParser::BaseParser->get_source_id_for_source_name("PomBase_TRANSCRIPT");
 

misc-scripts/xref_mapping/XrefParser/RGDParser.pm

@@ -24,13 +24,6 @@ sub run {
 
   my $file = @{$files}[0];
 
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
   my $dbi = $self->dbi();
 
   my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};

misc-scripts/xref_mapping/XrefParser/RefSeqGPFFParser.pm

@@ -44,14 +44,6 @@ sub run {
 
     my @xrefs;
     foreach my $file (@files) {
-        if ( $source_id < 1 ) {
-            $source_id =
-              $self->get_source_id_for_filename( basename($file) );
-        }
-        if ( !defined($species_id) ) {
-            $species_id = $self->get_species_id_for_filename($file);
-        }
-
         my $xrefs =
           $self->create_xrefs( $peptide_source_id,
                                $dna_source_id,

misc-scripts/xref_mapping/XrefParser/VBCommunitySymbolParser.pm

@@ -26,14 +26,6 @@ sub run {
 
   print "source_id = $source_id, species= $species_id, file = $file\n" if($verbose);
 
-
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
   my $added = 0;
   my $count = 0;
 

misc-scripts/xref_mapping/XrefParser/ZFINDescParser.pm

@@ -25,13 +25,6 @@ sub run {
 
   my $file = @{$files}[0];
 
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }
-
 #e.g.
 #ZDB-GENE-050102-6       WITHDRAWN:zgc:92147     WITHDRAWN:zgc:92147     0
 #ZDB-GENE-060824-3       apobec1 complementation factor  a1cf    0

misc-scripts/xref_mapping/XrefParser/ncRNAParser.pm

@@ -26,14 +26,6 @@ sub run {
 
   print "source_id = $source_id, species= $species_id, file = $file\n";
 
-
-  if(!defined($source_id)){
-    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
-  }
-  if(!defined($species_id)){
-    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
-  }                                                
-
   my %name_2_source_id=();
   my $added=0;