diff --git a/misc-scripts/ontology/scripts/load_OBO_file.pl b/misc-scripts/ontology/scripts/load_OBO_file.pl
index 08f8ada64f9de8ae18cd54bd10ca08782d6279b4..75bb04caa5eca401d1910883aca3f067b503518f 100755
--- a/misc-scripts/ontology/scripts/load_OBO_file.pl
+++ b/misc-scripts/ontology/scripts/load_OBO_file.pl
@@ -43,8 +43,6 @@ sub write_ontology {
if ($truncate) { $dbh->do("TRUNCATE TABLE ontology") }
- $dbh->do("LOCK TABLE ontology WRITE");
-
my $statement = "INSERT INTO ontology (name, namespace) VALUES (?,?)";
my $sth = $dbh->prepare($statement);
@@ -63,7 +61,6 @@ sub write_ontology {
}
$dbh->do("OPTIMIZE TABLE ontology");
- $dbh->do("UNLOCK TABLES");
printf( "\tWrote %d entries\n", $count );
} ## end sub write_ontology
@@ -116,29 +113,61 @@ sub write_relation_type {
if ($truncate) { $dbh->do("TRUNCATE TABLE relation_type") }
- $dbh->do("LOCK TABLE relation_type WRITE");
+ my $select_stmt =
+ "SELECT relation_type_id FROM relation_type WHERE name = ?";
+ my $select_sth = $dbh->prepare($select_stmt);
- my $statement = "INSERT INTO relation_type (name) VALUES (?)";
-
- my $sth = $dbh->prepare($statement);
+ my $insert_stmt = "INSERT INTO relation_type (name) VALUES (?)";
+ my $insert_sth = $dbh->prepare($insert_stmt);
my $count = 0;
foreach my $relation_type ( keys( %{$relation_types} ) ) {
- $sth->bind_param( 1, $relation_type, SQL_VARCHAR );
+ $select_sth->bind_param( 1, $relation_type, SQL_VARCHAR );
+ $select_sth->execute();
- $sth->execute();
+ my $id;
+ my $found = 0;
- $relation_types->{$relation_type} = { 'id' => ++$count };
+ $select_sth->bind_columns( \$id );
+
+ while ( $select_sth->fetch() ) {
+ $relation_types->{$relation_type} = { 'id' => $id };
+ $found = 1;
+ }
+
+ if ( !$found ) {
+ $insert_sth->bind_param( 1, $relation_type, SQL_VARCHAR );
+ $insert_sth->execute();
+ $relation_types->{$relation_type} = {
+ 'id' => $dbh->last_insert_id(
+ undef, undef, 'relation_type', 'relation_type_id'
+ ) };
+ ++$count;
+ }
}
$dbh->do("OPTIMIZE TABLE relation_type");
- $dbh->do("UNLOCK TABLES");
printf( "\tWrote %d entries\n", $count );
} ## end sub write_relation_type
#-----------------------------------------------------------------------
+# Relation types to invert (from => to).
+# Extracted from http://www.obofoundry.org/ro/ro.obo (May 27, 2009)
+our %inverse_type = (
+ 'has_part' => 'part_of',
+ 'has_integral_part' => 'integral_part_of',
+ 'has_proper_part' => 'proper_part_of',
+ 'location_of' => 'located_in',
+ 'contains' => 'contained_in',
+ 'derived_into' => 'derives_from',
+ 'precedes' => 'preceded_by',
+ 'has_participant' => 'participates_in',
+ 'has_agent' => 'agent_in',
+ 'has_improper_part' => 'improper_part_of' # obsolete
+);
+
sub write_relation {
my ( $dbh, $truncate, $terms, $relation_types ) = @_;
@@ -162,10 +191,21 @@ sub write_relation {
foreach
my $parent_acc ( @{ $child_term->{'parents'}{$relation_type} } )
{
- $sth->bind_param( 1, $child_term->{'id'}, SQL_INTEGER );
- $sth->bind_param( 2, $terms->{$parent_acc}{'id'}, SQL_INTEGER );
- $sth->bind_param( 3, $relation_types->{$relation_type}{'id'},
- SQL_INTEGER );
+ if ( exists( $inverse_type{$relation_type} ) ) {
+ $relation_type = $inverse_type{$relation_type};
+
+ $sth->bind_param( 1, $terms->{$parent_acc}{'id'},
+ SQL_INTEGER );
+ $sth->bind_param( 2, $child_term->{'id'}, SQL_INTEGER );
+ $sth->bind_param( 3, $relation_types->{$relation_type}{'id'},
+ SQL_INTEGER );
+ } else {
+ $sth->bind_param( 1, $child_term->{'id'}, SQL_INTEGER );
+ $sth->bind_param( 2, $terms->{$parent_acc}{'id'},
+ SQL_INTEGER );
+ $sth->bind_param( 3, $relation_types->{$relation_type}{'id'},
+ SQL_INTEGER );
+ }
$sth->execute();
@@ -228,7 +268,7 @@ my ( %terms, %namespaces, %relation_types );
printf( "Reading OBO file '%s'...\n", $obo_file_name );
-my $date_is_checked = 0;
+my $default_namespace;
while ( defined( my $line = $obo->getline() ) ) {
chomp($line);
@@ -236,41 +276,49 @@ while ( defined( my $line = $obo->getline() ) ) {
if ( !defined($state) ) {
if ( $line =~ /^\[(\w+)\]$/ ) { $state = $1; next }
- if ( !$date_is_checked && $line =~ /^date: (.+)$/ ) {
- $obo_file_date = sprintf( "%s/%s", $obo_file_name, $1 );
-
- if ( defined($stored_obo_file_date) ) {
- if ( $stored_obo_file_date eq $obo_file_date ) {
- print("This OBO file has already been processed.\n");
- $obo->close();
- $dbh->disconnect();
- exit;
- } elsif ( index( $stored_obo_file_date, $obo_file_name ) != 1
- && $truncate == 0 )
- {
- print <<EOT;
+ if ( $line =~ /^([\w-]+): (.+)$/ ) {
+ my $type = $1;
+ my $data = $2;
+
+ if ( $type eq 'date' ) {
+ $obo_file_date = sprintf( "%s/%s", $obo_file_name, $data );
+
+ if ( defined($stored_obo_file_date) ) {
+ if ( $stored_obo_file_date eq $obo_file_date
+ && !$truncate )
+ {
+ print("This OBO file has already been processed.\n");
+ $obo->close();
+ $dbh->disconnect();
+ exit;
+ } elsif ( index( $stored_obo_file_date, $obo_file_name ) != -1
+ && !$truncate )
+ {
+ print <<EOT;
==> Trying to load a newer (?) OBO file that has already been loaded.
==> Please clean the database manually of data associated with this
==> file and try again... or use the -t (truncate) switch to empty the
==> tables completely (unless you want to preserve some of the data,
==> obviously).
EOT
- $obo->close();
- $dbh->disconnect();
- exit;
+ $obo->close();
+ $dbh->disconnect();
+ exit;
+ }
}
- }
-
- $date_is_checked = 1;
- } ## end if ( !$date_is_checked...
+ } elsif ( $type eq 'default-namespace' ) {
+ $default_namespace = $data;
+ }
+ } ## end if ( $line =~ /^(\w+): (.+)$/)
next;
} ## end if ( !defined($state) )
if ( $state eq 'Term' ) {
if ( $line eq '' ) {
- $namespaces{$namespace} = 'GO';
+ $namespace ||= $default_namespace;
+ ($namespaces{$namespace}) = $accession =~ /^([^:]+):/;
$terms{$accession} = {
'namespace' => $namespace,
'name' => $name,
@@ -330,6 +378,10 @@ write_relation( $dbh, $truncate, \%terms, \%relation_types );
print("Updating meta table...\n");
+if ($truncate) {
+ $dbh->do("TRUNCATE TABLE meta");
+}
+
my $sth =
$dbh->prepare( "DELETE FROM meta "
. "WHERE meta_key = 'OBO_file_date' "