Fix to SQL for storing dependent xrefs as part of large graphs, sometimes...

Fix to SQL for storing dependent xrefs as part of large graphs, sometimes wouldn't store linkage annotation (e.g. GO evidence code).

misc-scripts/xref_mapping/XrefParser/BaseParser.pm

@@ -582,7 +582,8 @@ sub get_existing_mappings {
   my $sth = dbi()->prepare($sql);
   $sth->execute($to_source, $from_source, $species_id, $species_id);
   while(my @row = $sth->fetchrow_array()){
-    $mappings{$row[1]} = $row[0];
+    $mappings{$row[1]} = $row[2];
+    #print "mgi_to_uniprot{" . $row[1] . "} = " . $row[2] . "\n";
   }
 
   print "Got " . scalar(keys(%mappings)) . " $from_source_name -> $to_source_name mappings\n";
@@ -611,7 +612,7 @@ sub upload_xref_object_graphs {
     my $pri_insert_sth = $dbi->prepare("INSERT INTO primary_xref VALUES(?,?,?,?)");
     my $pri_update_sth = $dbi->prepare("UPDATE primary_xref SET sequence=? WHERE xref_id=?");
     my $syn_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?)");
-    my $dep_sth = $dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)");
+    my $dep_sth = $dbi->prepare("INSERT INTO dependent_xref (master_xref_id, dependent_xref_id, linkage_annotation, linkage_source_id) VALUES(?,?,?,?)");
     my $xref_update_label_sth = $dbi->prepare("UPDATE xref SET label=? WHERE xref_id=?");
     my $xref_update_descr_sth = $dbi->prepare("UPDATE xref SET description=? WHERE xref_id=?");
     my $pair_sth = $dbi->prepare("INSERT INTO pairs VALUES(?,?,?)");
@@ -689,7 +690,6 @@ sub upload_xref_object_graphs {
 	  print STDERR "source = $dep{SOURCE_ID}\n";
 	}
 	$dep_sth->execute($xref_id, $dep_xref_id, $dep{LINKAGE_ANNOTATION}, $dep{LINKAGE_SOURCE_ID} ) || die $dbi->errstr;
-	# TODO linkage anntation?
 
       }	 # foreach dep
        
@@ -1133,10 +1133,12 @@ sub add_to_xrefs{
   if(!defined($dependent_id)){
     die "$acc\t$label\t\t$source_id\t$species_id\n";
   }
+  if ($master_xref == 48955) {
+    print "$master_xref\t$acc\t$dependent_id\t$linkage\t$source_id\n";
+  }
   $add_dependent_xref_sth->execute($master_xref, $dependent_id,  $linkage, $source_id)
     || die "$master_xref\t$dependent_id\t$linkage\t$source_id";
 
-
 }
 
 sub add_to_syn_for_mult_sources{