Set label to accession if it's not set otherwise (so that something gets...

Set label to accession if it's not set otherwise (so that something gets displayed on the web site).

Check all object_xrefs are unique.

Still problem with gene display_xrefs.

misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

@@ -926,9 +926,10 @@ sub dump_core_xrefs {
   # execute several queries with a max of 200 entries in each IN clause - more efficient
   my $batch_size = 200;
 
-  # keep track of what xref_ids have been written to prevent duplicates; e.g. several dependent
-  # xrefs my be dependent on the same master xref.
+  # keep track of what xref_id & object_xref_ids have been written to prevent 
+  # duplicates; e.g. several dependent xrefs may be dependent on the same master xref.
   my %xrefs_written;
+  my %object_xrefs_written;
 
   while(@xref_ids) {
 
@@ -959,6 +960,9 @@ sub dump_core_xrefs {
     # core database so we add on $xref_id_offset
     while ($xref_sth->fetch()) {
 
+      # make sure label is set to /something/ so that the website displays something
+      $label = $accession if (!$label);
+
       if (!$xrefs_written{$xref_id}) {
 	my $external_db_id = $source_to_external_db{$source_id};
 	print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\n";
@@ -977,6 +981,7 @@ sub dump_core_xrefs {
     while ($dep_sth->fetch()) {
 
       my $external_db_id = $source_to_external_db{$source_id};
+      $label = $accession if (!$label);
 
       if (!$xrefs_written{$xref_id}) {
 	print XREF ($xref_id+$xref_id_offset) . "\t" . $external_db_id . "\t" . $accession . "\t" . $label . "\t" . $version . "\t" . $description . "\tDEPENDENT\n";
@@ -991,11 +996,15 @@ sub dump_core_xrefs {
 	#print "xref $accession has " . scalar(@ensembl_object_ids) . " associated ensembl objects\n";
 	foreach my $object_id (@ensembl_object_ids) {
 	  my $type = $ensembl_object_types{$object_id};
-	  print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tDEPENDENT\n";
-	  $object_xref_id++;
-	  # Add this mapping to the list - note NON-OFFSET xref_id is used
-	  my $key = $type . ":" . $object_id;
-	  push @{$object_xref_mappings->{$key}}, $xref_id;
+	  my $full_key = $type.":".$object_id.":".$xref_id;
+	  if (!$object_xrefs_written{$full_key}) {
+	    print OBJECT_XREF "$object_xref_id\t$object_id\t$type\t" . ($xref_id+$xref_id_offset) . "\tDEPENDENT\n";
+	    $object_xref_id++;
+	    # Add this mapping to the list - note NON-OFFSET xref_id is used
+	    my $key = $type . ":" . $object_id;
+	    push @{$object_xref_mappings->{$key}}, $xref_id;
+	    $object_xrefs_written{$full_key} = 1;
+	  }
 	}
       }
     }
@@ -1382,12 +1391,12 @@ sub do_upload {
     }
 
     # is this nicer than using the mysql client?
+    print "Setting $table display_xrefs from $file\n";
     open(DISPLAY_XREF, $file);
     while(<DISPLAY_XREF>) {
 
       $sth = $self->dbi()->prepare($_);
-      print $_;
-      #$sth->execute();
+      $sth->execute();
 
     }