diff --git a/misc-scripts/ontology/scripts/load_OBO_file.pl b/misc-scripts/ontology/scripts/load_OBO_file.pl
index 806230c1747355ab13d16a65f832be35df74e425..8bc6d30059f0d13b09c80716410ef32a680e16c2 100755
--- a/misc-scripts/ontology/scripts/load_OBO_file.pl
+++ b/misc-scripts/ontology/scripts/load_OBO_file.pl
@@ -15,10 +15,10 @@ use IO::File;
sub usage {
print("Usage:\n");
printf( "\t%s\t-h dbhost [-P dbport] \\\n"
- . "\t%s\t-u dbuser [-p dbpass] \\\n"
- . "\t%2\$s\t-d dbname [-t] \\\n"
- . "\t%2\$s\t-f file\n",
- $0, ' ' x length($0) );
+ . "\t%s\t-u dbuser [-p dbpass] \\\n"
+ . "\t%2\$s\t-d dbname [-t] \\\n"
+ . "\t%2\$s\t-f file\n",
+ $0, ' ' x length($0) );
print("\n");
printf( "\t%s\t-?\n", $0 );
print("\n");
@@ -52,7 +52,7 @@ sub write_ontology {
local $SIG{ALRM} = sub {
printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$namespaces} ) ) - $count );
+ $count, scalar( keys( %{$namespaces} ) ) - $count );
alarm(10);
};
alarm(10);
@@ -104,7 +104,7 @@ sub write_subset {
local $SIG{ALRM} = sub {
printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$subsets} ) ) - $count );
+ $count, scalar( keys( %{$subsets} ) ) - $count );
alarm(10);
};
alarm(10);
@@ -157,7 +157,7 @@ sub write_term {
local $SIG{ALRM} = sub {
printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$terms} ) ) - $count );
+ $count, scalar( keys( %{$terms} ) ) - $count );
alarm(10);
};
alarm(10);
@@ -169,13 +169,14 @@ sub write_term {
if ( exists( $term->{'subsets'} ) ) {
$term_subsets = join( ',',
- map { $subsets->{$_}{'name'} } @{ $term->{'subsets'} } );
+ map { $subsets->{$_}{'name'} }
+ @{ $term->{'subsets'} } );
}
$sth->bind_param( 1, $namespaces->{ $term->{'namespace'} }{'id'},
- SQL_INTEGER );
+ SQL_INTEGER );
$sth->bind_param( 2, $term_subsets, SQL_VARCHAR );
- $sth->bind_param( 3, $accession, SQL_VARCHAR );
+ $sth->bind_param( 3, $term->{'accession'}, SQL_VARCHAR );
$sth->bind_param( 4, $term->{'name'}, SQL_VARCHAR );
$sth->bind_param( 5, $term->{'definition'}, SQL_VARCHAR );
@@ -189,7 +190,7 @@ sub write_term {
$term->{'id'} = $id;
++$count;
- }
+ } ## end foreach my $accession ( sort...)
alarm(0);
$dbh->do("OPTIMIZE TABLE term");
@@ -218,7 +219,7 @@ sub write_relation_type {
local $SIG{ALRM} = sub {
printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$relation_types} ) ) - $count );
+ $count, scalar( keys( %{$relation_types} ) ) - $count );
alarm(10);
};
alarm(10);
@@ -241,12 +242,13 @@ sub write_relation_type {
$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'
- ) };
+ 'id' =>
+ $dbh->last_insert_id( undef, undef,
+ 'relation_type', 'relation_type_id'
+ ) };
++$count;
}
- }
+ } ## end foreach my $relation_type (...)
alarm(0);
$dbh->do("OPTIMIZE TABLE relation_type");
@@ -276,27 +278,32 @@ sub write_relation {
local $SIG{ALRM} = sub {
printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$terms} ) ) - $count );
+ $count, scalar( keys( %{$terms} ) ) - $count );
alarm(10);
};
alarm(10);
foreach my $child_term ( sort { $a->{'id'} <=> $b->{'id'} }
- values( %{$terms} ) )
+ values( %{$terms} ) )
{
foreach my $relation_type (
- sort( keys( %{ $child_term->{'parents'} } ) ) )
+ sort( keys( %{ $child_term->{'parents'} } ) ) )
{
foreach my $parent_acc (
- sort( @{ $child_term->{'parents'}{$relation_type} } ) )
+ sort( @{ $child_term->{'parents'}{$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 );
-
- $sth->execute();
-
+ if ( !defined( $terms->{$parent_acc} ) ) {
+ printf( "WARNING: Parent accession '%s' does not exist!\n",
+ $parent_acc );
+ } 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();
+ }
}
}
@@ -319,31 +326,28 @@ my ( $dbname, $truncate, $obo_file_name );
$dbport = '3306';
$truncate = 0;
-if (
- !GetOptions(
- 'dbhost|host|h=s' => \$dbhost,
- 'dbport|port|P=i' => \$dbport,
- 'dbuser|user|u=s' => \$dbuser,
- 'dbpass|pass|p=s' => \$dbpass,
- 'dbname|name|d=s' => \$dbname,
- 'truncate|t' => \$truncate,
- 'file|f=s' => \$obo_file_name,
- 'help|?' => sub { usage(); exit } )
- || !defined($dbhost)
- || !defined($dbuser)
- || !defined($dbname)
- || !defined($obo_file_name) )
+if ( !GetOptions( 'dbhost|host|h=s' => \$dbhost,
+ 'dbport|port|P=i' => \$dbport,
+ 'dbuser|user|u=s' => \$dbuser,
+ 'dbpass|pass|p=s' => \$dbpass,
+ 'dbname|name|d=s' => \$dbname,
+ 'truncate|t' => \$truncate,
+ 'file|f=s' => \$obo_file_name,
+ 'help|?' => sub { usage(); exit } )
+ || !defined($dbhost)
+ || !defined($dbuser)
+ || !defined($dbname)
+ || !defined($obo_file_name) )
{
usage();
exit;
}
my $dsn = sprintf( 'dbi:mysql:database=%s;host=%s;port=%s',
- $dbname, $dbhost, $dbport );
+ $dbname, $dbhost, $dbport );
-my $dbh =
- DBI->connect( $dsn, $dbuser, $dbpass,
- { 'RaiseError' => 1, 'PrintError' => 2 } );
+my $dbh = DBI->connect( $dsn, $dbuser, $dbpass,
+ { 'RaiseError' => 1, 'PrintError' => 2 } );
my $statement =
"SELECT meta_value FROM meta WHERE meta_key = 'OBO_file_date'";
@@ -364,6 +368,7 @@ my $default_namespace;
while ( defined( my $line = $obo->getline() ) ) {
chomp($line);
+ $line =~ s/\s+$//;
if ( !defined($state) ) { # IN OBO FILE HEADER
if ( $line =~ /^\[(\w+)\]$/ ) { $state = $1; next }
@@ -376,15 +381,13 @@ while ( defined( my $line = $obo->getline() ) ) {
$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 )
- {
+ 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 )
+ && !$truncate )
{
print <<EOT;
==> Trying to load a newer (?) OBO file that has already been loaded.
@@ -412,11 +415,19 @@ EOT
next;
} ## end if ( !defined($state) )
+ if ( $state eq 'Typedef' ) {
+ # Ignore this state.
+ if ( $line eq '' ) {
+ $state = 'clear';
+ }
+ }
+
if ( $state eq 'Term' ) { # IN OBO FILE BODY
if ( $line eq '' ) { # END OF PREVIOUS TERM
- $term{'namespace'} ||= $default_namespace;
- ( $namespaces{ $term{'namespace'} } ) =
- $term{'accession'} =~ /^([^:]+):/;
+ if ( !defined( $term{'namespace'} ) ) {
+ $term{'namespace'} = $default_namespace;
+ }
+ $namespaces{ $term{'namespace'} } = $term{'namespace'};
$terms{ $term{'accession'} } = {%term};
@@ -431,11 +442,15 @@ EOT
my $type = $1;
my $data = $2;
- if ( $type eq 'id' ) { $term{'accession'} = $data }
- elsif ( $type eq 'name' ) { $term{'name'} = $data }
- elsif ( $type eq 'namespace' ) { $term{'namespace'} = $data }
- elsif ( $type eq 'def' ) { $term{'definition'} = $data }
- elsif ( $type eq 'is_a' ) {
+ if ( $type eq 'id' ) {
+ ( $term{'accession'} ) = $data =~ /^([^ ]+)/;
+ } elsif ( $type eq 'name' ) {
+ $term{'name'} = $data;
+ } elsif ( $type eq 'namespace' ) {
+ $term{'namespace'} = $data;
+ } elsif ( $type eq 'def' ) {
+ $term{'definition'} = $data;
+ } elsif ( $type eq 'is_a' ) {
my ($parent_acc) = $data =~ /(\S+)/;
push( @{ $term{'parents'}{'is_a'} }, $parent_acc );
} elsif ( $type eq 'relationship' ) {
@@ -447,7 +462,7 @@ EOT
push( @{ $term{'subsets'} }, $data );
}
- }
+ } ## end elsif ( $line =~ /^(\w+): (.+)$/)
} ## end if ( $state eq 'Term' )
if ( $state eq 'clear' ) {
@@ -472,15 +487,15 @@ print("Updating meta table...\n");
if ($truncate) { $dbh->do("TRUNCATE TABLE meta") }
my $sth =
- $dbh->prepare( "DELETE FROM meta "
- . "WHERE meta_key = 'OBO_file_date' "
- . "AND meta_value LIKE ?" );
+ $dbh->prepare( "DELETE FROM meta "
+ . "WHERE meta_key = 'OBO_file_date' "
+ . "AND meta_value LIKE ?" );
$sth->bind_param( 1, sprintf( "%s/%%", $obo_file_name ), SQL_VARCHAR );
$sth->execute();
$sth->finish();
-$sth = $dbh->prepare( "INSERT INTO meta (meta_key, meta_value)"
- . "VALUES ('OBO_file_date', ?)" );
+$sth = $dbh->prepare( "INSERT INTO meta (meta_key, meta_value)"
+ . "VALUES ('OBO_file_date', ?)" );
$sth->bind_param( 1, $obo_file_date, SQL_VARCHAR );
$sth->execute();
$sth->finish();
@@ -489,15 +504,15 @@ my $obo_load_date =
sprintf( "%s/%s", $obo_file_name, scalar( localtime() ) );
$sth =
- $dbh->prepare( "DELETE FROM meta "
- . "WHERE meta_key = 'OBO_load_date' "
- . "AND meta_value LIKE ?" );
+ $dbh->prepare( "DELETE FROM meta "
+ . "WHERE meta_key = 'OBO_load_date' "
+ . "AND meta_value LIKE ?" );
$sth->bind_param( 1, sprintf( "%s/%%", $obo_file_name ), SQL_VARCHAR );
$sth->execute();
$sth->finish();
-$sth = $dbh->prepare( "INSERT INTO meta (meta_key, meta_value)"
- . "VALUES ('OBO_load_date', ?)" );
+$sth = $dbh->prepare( "INSERT INTO meta (meta_key, meta_value)"
+ . "VALUES ('OBO_load_date', ?)" );
$sth->bind_param( 1, $obo_load_date, SQL_VARCHAR );
$sth->execute();
$sth->finish();