Check if an xref exists when inserting, if not use the new ID, if it does...

Check if an xref exists when inserting, if not use the new ID, if it does exist, use the existing xref_id.

misc-scripts/xref_mapping/BaseParser.pm

@@ -157,6 +157,9 @@ sub upload_xrefs {
     my $syn_sth = $dbi->prepare("INSERT INTO synonym VALUES(?,?,?)");
     my $dep_sth = $dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)");
 
+    local $xref_sth->{RaiseError}; # disable error handling here as we'll do it ourselves
+    local $xref_sth->{PrintError};
+
     foreach my $xref (@xrefs) {
 
       # Create entry in xref table and note ID
@@ -164,10 +167,11 @@ sub upload_xrefs {
 			 $xref->{LABEL},
 			 $xref->{DESCRIPTION},
 			 $xref->{SOURCE_ID},
-			 $xref->{SPECIES_ID}) || die $dbi->errstr;
+			 $xref->{SPECIES_ID});
 
-      # get ID of xref just inserted
-      my $xref_id = $xref_sth->{'mysql_insertid'};
+      # If there was an error, an xref with the same acc & source already exists.
+      # If so, find its ID, otherwise get ID of xref just inserted
+      my $xref_id = insert_or_select($xref_sth, $dbi->err, $xref->{ACCESSION}, $xref->{SOURCE_ID});
 
       # create entry in primary_xref table with sequence
       # TODO experimental/predicted????
@@ -184,9 +188,10 @@ sub upload_xrefs {
 			   $xref->{LABEL},
 			   $xref->{DESCRIPTION},
 			   $xref->{SOURCE_ID},
-			   $xref->{SPECIES_ID}) || die $dbi->errstr;
+			   $xref->{SPECIES_ID});
+
+	my $syn_xref_id = insert_or_select($xref_sth, $dbi->err, $syn, $xref->{SOURCE_ID});
 
-	my $syn_xref_id = $xref_sth->{'mysql_insertid'};
 	$syn_sth->execute($xref_id, $syn_xref_id, $xref->{SOURCE_ID} ) || die $dbi->errstr;
 
       }				# foreach syn
@@ -339,6 +344,46 @@ sub md5sum {
 
 }
 
+# --------------------------------------------------------------------------------
+
+sub get_xref_id_by_accession_and_source {
+
+  my ($acc, $source_id) = @_;
+
+  my $dbi = dbi();
+  my $sth = $dbi->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=?");
+  $sth->execute($acc, $source_id) || die $dbi->errstr;
+  my @row = $sth->fetchrow_array();
+  my $xref_id = $row[0];
+
+  return $xref_id;
+
+}
+
+# --------------------------------------------------------------------------------
+# If there was an error, an xref with the same acc & source already exists.
+# If so, find its ID, otherwise get ID of xref just inserted
+
+sub insert_or_select {
+
+  my ($sth, $error, $acc, $source) = @_;
+
+  my $id;
+
+  if ($error) {
+
+    $id = get_xref_id_by_accession_and_source($acc, $source);
+    print "Got existing xref id " . $id . " for " . $acc . " " . $source . "\n";
+
+  } else {
+	
+    $id = $sth->{'mysql_insertid'};
+
+  }
+
+  return $id;
+
+}
 
 # --------------------------------------------------------------------------------