dump dependent xref synonyms

misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

@@ -1235,6 +1235,17 @@ sub dump_core_xrefs {
   # build cache of source id -> external_db id; note %source_to_external_db is global
   %source_to_external_db = $self->map_source_to_external_db();
 
+
+  my $sql_syn= "select s.xref_id, s.synonym ";
+  $sql_syn .= "   from xref x, synonym s, dependent_xref d ";
+  $sql_syn .= "     where d.dependent_xref_id = x.xref_id and ";
+  $sql_syn .= "            s.xref_id = x.xref_id and ";
+  $sql_syn .= "            x.xref_id = ?";
+
+  my $dep_syn_sth = $self->xref->dbc->prepare($sql_syn);
+
+
+
   # execute several queries with a max of 200 entries in each IN clause - more efficient
   my $batch_size = 200;
 
@@ -1299,6 +1310,7 @@ sub dump_core_xrefs {
       my $external_db_id = $source_to_external_db{$source_id};
       next if (!$external_db_id);
 
+
       $label = $accession if (!$label);
 
       if (!$xrefs_written{$xref_id}) {
@@ -1306,6 +1318,16 @@ sub dump_core_xrefs {
 	$xrefs_written{$xref_id} = 1;
 	$source_ids{$source_id} = $source_id;
       }
+      
+      #dump synonyms for dependent_xref
+      $dep_syn_sth->execute($xref_id);
+      
+      my ($syn_xref, $syn);
+      $dep_syn_sth->bind_columns(\$syn_xref, \$syn);
+      while ($dep_syn_sth->fetch()) {	
+	print EXTERNAL_SYNONYM ($syn_xref+$xref_id_offset) . "\t" .$syn."\n";
+      }
+      
 
       # create an object_xref linking this (dependent) xref with any objects it maps to
       # write to file and add to object_xref_mappings