diff --git a/misc-scripts/ontology/scripts/load_OBO_file.pl b/misc-scripts/ontology/scripts/load_OBO_file.pl
index 07cf673adb685081ed6b8456ce648f0ecf99ae62..840fb91c10ad4f476aef67ffc15fd7d3907d617c 100755
--- a/misc-scripts/ontology/scripts/load_OBO_file.pl
+++ b/misc-scripts/ontology/scripts/load_OBO_file.pl
@@ -45,7 +45,7 @@ USAGE
#-----------------------------------------------------------------------
sub write_ontology {
- my ( $dbh, $namespaces ) = @_;
+ my ($dbh, $namespaces) = @_;
print("Writing to 'ontology' table...\n");
@@ -57,28 +57,27 @@ sub write_ontology {
my $count = 0;
local $SIG{ALRM} = sub {
- printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$namespaces} ) ) - $count );
+ printf("\t%d entries, %d to go...\n", $count, scalar(keys(%{$namespaces})) - $count);
alarm(10);
};
alarm(10);
- foreach my $namespace ( sort( keys( %{$namespaces} ) ) ) {
+ foreach my $namespace (sort(keys(%{$namespaces}))) {
my $ontology = $namespaces->{$namespace};
- $sth->bind_param( 1, $ontology, SQL_VARCHAR );
- $sth->bind_param( 2, $namespace, SQL_VARCHAR );
+ $sth->bind_param(1, $ontology, SQL_VARCHAR);
+ $sth->bind_param(2, $namespace, SQL_VARCHAR);
$sth->execute();
- if ( !defined($id) ) {
- $id =
- $dbh->last_insert_id( undef, undef, 'ontology', 'ontology_id' );
- } else {
+ if (!defined($id)) {
+ $id = $dbh->last_insert_id(undef, undef, 'ontology', 'ontology_id');
+ }
+ else {
++$id;
}
- $namespaces->{$namespace} = { 'id' => $id, 'name' => $ontology };
+ $namespaces->{$namespace} = {'id' => $id, 'name' => $ontology};
++$count;
}
@@ -86,18 +85,18 @@ sub write_ontology {
#if unknown ontology not found, store it
my ($unknown_onto_id) = $dbh->selectrow_array("SELECT ontology_id from ontology WHERE name = 'UNKNOWN'");
-
+
if (!defined($unknown_onto_id)) {
my $statement = "INSERT INTO ontology (name, namespace) VALUES ('UNKNOWN','unknown ontology')";
- my $sth = $dbh->prepare($statement);
+ my $sth = $dbh->prepare($statement);
$sth->execute();
- $unknown_onto_id = $dbh->last_insert_id( undef, undef, 'ontology', 'ontology_id' );
+ $unknown_onto_id = $dbh->last_insert_id(undef, undef, 'ontology', 'ontology_id');
}
$dbh->do("OPTIMIZE TABLE ontology");
- printf( "\tWrote %d entries\n", $count );
+ printf("\tWrote %d entries\n", $count);
return $unknown_onto_id;
} ## end sub write_ontology
@@ -105,14 +104,13 @@ sub write_ontology {
#-----------------------------------------------------------------------
sub write_subset {
- my ( $dbh, $subsets ) = @_;
+ my ($dbh, $subsets) = @_;
print("Writing to 'subset' table...\n");
$dbh->do("LOCK TABLE subset WRITE");
- my $statement =
- "INSERT INTO subset " . "(name, definition) " . "VALUES (?,?)";
+ my $statement = "INSERT INTO subset " . "(name, definition) " . "VALUES (?,?)";
my $sth = $dbh->prepare($statement);
@@ -120,29 +118,28 @@ sub write_subset {
my $count = 0;
local $SIG{ALRM} = sub {
- printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$subsets} ) ) - $count );
+ printf("\t%d entries, %d to go...\n", $count, scalar(keys(%{$subsets})) - $count);
alarm(10);
};
alarm(10);
- foreach my $subset_name ( sort( keys( %{$subsets} ) ) ) {
+ foreach my $subset_name (sort(keys(%{$subsets}))) {
my $subset = $subsets->{$subset_name};
- if (!( defined($subset->{'name'}) && defined($subset->{'definition'}) ))
- {
- print "Null value encountered: subset name " . $subset->{'name'}." subset definition ". $subset->{'definition'} . "\n";
- exit;
+ if (!(defined($subset->{'name'}) && defined($subset->{'definition'}))) {
+ print "Null value encountered: subset name " . $subset->{'name'} . " subset definition " . $subset->{'definition'} . "\n";
+ exit;
}
- $sth->bind_param( 1, $subset->{'name'}, SQL_VARCHAR );
- $sth->bind_param( 2, $subset->{'definition'}, SQL_VARCHAR );
+ $sth->bind_param(1, $subset->{'name'}, SQL_VARCHAR);
+ $sth->bind_param(2, $subset->{'definition'}, SQL_VARCHAR);
$sth->execute();
- if ( !defined($id) ) {
- $id = $dbh->last_insert_id( undef, undef, 'subset', 'subset_id' );
- } else {
+ if (!defined($id)) {
+ $id = $dbh->last_insert_id(undef, undef, 'subset', 'subset_id');
+ }
+ else {
++$id;
}
$subset->{'id'} = $id;
@@ -154,22 +151,19 @@ sub write_subset {
$dbh->do("OPTIMIZE TABLE term");
$dbh->do("UNLOCK TABLES");
- printf( "\tWrote %d entries\n", $count );
+ printf("\tWrote %d entries\n", $count);
} ## end sub write_subset
#-----------------------------------------------------------------------
sub write_term {
- my ( $dbh, $terms, $subsets, $namespaces, $unknown_onto_id ) = @_;
+ my ($dbh, $terms, $subsets, $namespaces, $unknown_onto_id) = @_;
print("Writing to 'term' and 'synonym' tables...\n");
$dbh->do("LOCK TABLES term WRITE, synonym WRITE");
- my $statement =
- "INSERT INTO term "
- . "(ontology_id, subsets, accession, name, definition) "
- . "VALUES (?,?,?,?,?)";
+ my $statement = "INSERT INTO term " . "(ontology_id, subsets, accession, name, definition) " . "VALUES (?,?,?,?,?)";
my $syn_stmt = "INSERT INTO synonym (term_id, name) VALUES (?,?)";
@@ -177,109 +171,110 @@ sub write_term {
my $update_stmt = "UPDATE term SET ontology_id = ?, subsets = ?, name = ?, definition = ? WHERE term_id = ?";
- my $sth = $dbh->prepare($statement);
- my $update_sth = $dbh->prepare($update_stmt);
- my $syn_sth = $dbh->prepare($syn_stmt);
+ my $sth = $dbh->prepare($statement);
+ my $update_sth = $dbh->prepare($update_stmt);
+ my $syn_sth = $dbh->prepare($syn_stmt);
my $existing_term_sth = $dbh->prepare($existing_term_st);
my $id;
- my $count = 0;
+ my $count = 0;
my $updated_count = 0;
- my $syn_count = 0;
+ my $syn_count = 0;
local $SIG{ALRM} = sub {
- printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$terms} ) ) - $count );
+ printf("\t%d entries, %d to go...\n", $count, scalar(keys(%{$terms})) - $count);
alarm(10);
};
alarm(10);
- foreach my $accession ( sort( keys( %{$terms} ) ) ) {
+ foreach my $accession (sort(keys(%{$terms}))) {
my $term = $terms->{$accession};
my $term_subsets;
- if ( exists( $term->{'subsets'} ) ) {
- $term_subsets = join( ',',
- map { $subsets->{$_}{'name'} }
- @{ $term->{'subsets'} } );
+ if (exists($term->{'subsets'})) {
+ $term_subsets = join(',', map { $subsets->{$_}{'name'} } @{$term->{'subsets'}});
+ }
+
+ if (!defined($term->{'name'})) {
+
+ #check if we have this term in the db already
+ $existing_term_sth->execute($term->{'accession'});
+ my ($existing_term_id, $ontology_id) = $existing_term_sth->fetchrow_array;
+ if (defined($existing_term_id)) {
+ $term->{'id'} = $existing_term_id;
+ }
+ else {
+
+ #if not link it to Unknown ontology
+
+ $sth->bind_param(1, $unknown_onto_id, SQL_INTEGER);
+ $sth->bind_param(2, $term_subsets, SQL_VARCHAR);
+ $sth->bind_param(3, $term->{'accession'}, SQL_VARCHAR);
+ $sth->bind_param(4, 'UNKNOWN NAME', SQL_VARCHAR);
+ $sth->bind_param(5, 'UNKNOWN DEFINITION', SQL_VARCHAR);
+
+ $sth->execute();
+
+ if (!defined($id)) {
+ $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
+ }
+ else {
+ ++$id;
+ }
+ $term->{'id'} = $id;
+ ++$count;
+ }
+
}
+ else {
+
+ #we have the term name, check if the term is linked to unknown ontology in the ontology db
+ #if so, update it
+ $existing_term_sth->execute($term->{'accession'});
+ my ($existing_term_id, $ontology_id) = $existing_term_sth->fetchrow_array;
+ if (defined($existing_term_id) && $ontology_id == $unknown_onto_id) {
+
+ $update_sth->bind_param(1, $namespaces->{$term->{'namespace'}}{'id'}, SQL_INTEGER);
+ $update_sth->bind_param(2, $term_subsets, SQL_VARCHAR);
+ $update_sth->bind_param(3, $term->{'name'}, SQL_VARCHAR);
+ $update_sth->bind_param(4, $term->{'definition'}, SQL_VARCHAR);
+ $update_sth->bind_param(5, $existing_term_id, SQL_INTEGER);
+
+ $update_sth->execute();
+
+ $term->{'id'} = $existing_term_id;
+ ++$updated_count;
+ }
+ else {
- if (!defined($term->{'name'}))
- {
- #check if we have this term in the db already
- $existing_term_sth->execute($term->{'accession'});
- my ($existing_term_id, $ontology_id) = $existing_term_sth->fetchrow_array;
- if (defined($existing_term_id)) {
- $term->{'id'} = $existing_term_id;
- } else {
- #if not link it to Unknown ontology
-
- $sth->bind_param( 1, $unknown_onto_id, SQL_INTEGER );
- $sth->bind_param( 2, $term_subsets, SQL_VARCHAR );
- $sth->bind_param( 3, $term->{'accession'}, SQL_VARCHAR );
- $sth->bind_param( 4, 'UNKNOWN NAME', SQL_VARCHAR );
- $sth->bind_param( 5, 'UNKNOWN DEFINITION', SQL_VARCHAR );
-
- $sth->execute();
-
- if ( !defined($id) ) {
- $id = $dbh->last_insert_id( undef, undef, 'term', 'term_id' );
- } else {
- ++$id;
- }
- $term->{'id'} = $id;
- ++$count;
- }
-
- } else {
-
- #we have the term name, check if the term is linked to unknown ontology in the ontology db
- #if so, update it
- $existing_term_sth->execute($term->{'accession'});
- my ($existing_term_id, $ontology_id) = $existing_term_sth->fetchrow_array;
- if (defined($existing_term_id) && $ontology_id == $unknown_onto_id) {
-
- $update_sth->bind_param( 1, $namespaces->{ $term->{'namespace'} }{'id'},
- SQL_INTEGER );
- $update_sth->bind_param( 2, $term_subsets, SQL_VARCHAR );
- $update_sth->bind_param( 3, $term->{'name'}, SQL_VARCHAR );
- $update_sth->bind_param( 4, $term->{'definition'}, SQL_VARCHAR );
- $update_sth->bind_param( 5, $existing_term_id, SQL_INTEGER );
-
- $update_sth->execute();
-
- $term->{'id'} = $existing_term_id;
- ++$updated_count;
- } else {
-
- $sth->bind_param( 1, $namespaces->{ $term->{'namespace'} }{'id'},
- SQL_INTEGER );
- $sth->bind_param( 2, $term_subsets, 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 );
-
- $sth->execute();
-
- if ( !defined($id) ) {
- $id = $dbh->last_insert_id( undef, undef, 'term', 'term_id' );
- } else {
- ++$id;
- }
- $term->{'id'} = $id;
-
- ++$count;
- }
-
- foreach my $syn ( @{ $term->{'synonyms'} } ) {
- $syn_sth->bind_param( 1, $id, SQL_INTEGER );
- $syn_sth->bind_param( 2, $syn, SQL_VARCHAR );
-
- $syn_sth->execute();
-
- ++$syn_count;
- }
+ $sth->bind_param(1, $namespaces->{$term->{'namespace'}}{'id'}, SQL_INTEGER);
+ $sth->bind_param(2, $term_subsets, 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);
+
+ $sth->execute();
+
+ if (!defined($id)) {
+ $id = $dbh->last_insert_id(undef, undef, 'term', 'term_id');
+ }
+ else {
+ ++$id;
+ }
+ $term->{'id'} = $id;
+
+ ++$count;
+ }
+
+ foreach my $syn (@{$term->{'synonyms'}}) {
+ $syn_sth->bind_param(1, $id, SQL_INTEGER);
+ $syn_sth->bind_param(2, $syn, SQL_VARCHAR);
+
+ $syn_sth->execute();
+
+ ++$syn_count;
+ }
}
} ## end foreach my $accession ( sort...)
alarm(0);
@@ -288,21 +283,18 @@ sub write_term {
$dbh->do("OPTIMIZE TABLE synonym");
$dbh->do("UNLOCK TABLES");
- printf(
- "\tWrote %d entries into 'term', updated %d entries in 'term' and wrote %d entries into 'synonym'\n",
- $count, $updated_count, $syn_count );
+ printf("\tWrote %d entries into 'term', updated %d entries in 'term' and wrote %d entries into 'synonym'\n", $count, $updated_count, $syn_count);
} ## end sub write_term
#-----------------------------------------------------------------------
sub write_relation_type {
- my ( $dbh, $relation_types ) = @_;
+ my ($dbh, $relation_types) = @_;
print("Writing to 'relation_type' table...\n");
- my $select_stmt =
- "SELECT relation_type_id FROM relation_type WHERE name = ?";
- my $select_sth = $dbh->prepare($select_stmt);
+ my $select_stmt = "SELECT relation_type_id FROM relation_type WHERE name = ?";
+ my $select_sth = $dbh->prepare($select_stmt);
my $insert_stmt = "INSERT INTO relation_type (name) VALUES (?)";
my $insert_sth = $dbh->prepare($insert_stmt);
@@ -310,34 +302,29 @@ sub write_relation_type {
my $count = 0;
local $SIG{ALRM} = sub {
- printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$relation_types} ) ) - $count );
+ printf("\t%d entries, %d to go...\n", $count, scalar(keys(%{$relation_types})) - $count);
alarm(10);
};
alarm(10);
- foreach my $relation_type ( sort( keys( %{$relation_types} ) ) ) {
- $select_sth->bind_param( 1, $relation_type, SQL_VARCHAR );
+ foreach my $relation_type (sort(keys(%{$relation_types}))) {
+ $select_sth->bind_param(1, $relation_type, SQL_VARCHAR);
$select_sth->execute();
my $id;
my $found = 0;
- $select_sth->bind_columns( \$id );
+ $select_sth->bind_columns(\$id);
- while ( $select_sth->fetch() ) {
- $relation_types->{$relation_type} = { 'id' => $id };
+ while ($select_sth->fetch()) {
+ $relation_types->{$relation_type} = {'id' => $id};
$found = 1;
}
- if ( !$found ) {
- $insert_sth->bind_param( 1, $relation_type, SQL_VARCHAR );
+ if (!$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'
- ) };
+ $relation_types->{$relation_type} = {'id' => $dbh->last_insert_id(undef, undef, 'relation_type', 'relation_type_id')};
++$count;
}
} ## end foreach my $relation_type (...)
@@ -345,87 +332,67 @@ sub write_relation_type {
$dbh->do("OPTIMIZE TABLE relation_type");
- printf( "\tWrote %d entries\n", $count );
+ printf("\tWrote %d entries\n", $count);
} ## end sub write_relation_type
#-----------------------------------------------------------------------
sub write_relation {
- my ( $dbh, $terms, $relation_types ) = @_;
+ my ($dbh, $terms, $relation_types) = @_;
print("Writing to 'relation' table...\n");
$dbh->do("LOCK TABLE relation WRITE");
- my $statement =
- "INSERT INTO relation "
- . "(child_term_id, parent_term_id, relation_type_id, intersection_of) "
- . "VALUES (?,?,?,?)";
+ my $statement = "INSERT INTO relation " . "(child_term_id, parent_term_id, relation_type_id, intersection_of) " . "VALUES (?,?,?,?)";
my $sth = $dbh->prepare($statement);
my $count = 0;
local $SIG{ALRM} = sub {
- printf( "\t%d entries, %d to go...\n",
- $count, scalar( keys( %{$terms} ) ) - $count );
+ printf("\t%d entries, %d to go...\n", $count, scalar(keys(%{$terms})) - $count);
alarm(10);
};
alarm(10);
- foreach my $child_term ( sort { $a->{'id'} <=> $b->{'id'} }
- values( %{$terms} ) )
- {
- foreach my $relation_type (
- sort( keys( %{ $child_term->{'parents'} } ) ) )
- {
- foreach my $parent_acc (
- sort( @{ $child_term->{'parents'}{$relation_type} } ) )
- {
- if ( !defined( $terms->{$parent_acc} ) ) {
- printf( "WARNING: Parent accession '%s' does not exist!\n",
- $parent_acc );
- } else {
-
- if ( !( defined($child_term->{'id'}) && defined($terms->{$parent_acc}{'id'}) && defined($relation_types->{$relation_type}{'id'}) ) )
- {
- print "Null value encountered: child term id " . $child_term->{'id'} ." parent term id ". $terms->{$parent_acc}{'id'} . " relationship type " . $relation_types->{$relation_type}{'id'} . "\n";
- exit;
- }
-
- $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->bind_param( 4, 0, SQL_INTEGER );
+ foreach my $child_term (sort { $a->{'id'} <=> $b->{'id'} } values(%{$terms})) {
+ foreach my $relation_type (sort(keys(%{$child_term->{'parents'}}))) {
+ foreach my $parent_acc (sort(@{$child_term->{'parents'}{$relation_type}})) {
+ if (!defined($terms->{$parent_acc})) {
+ printf("WARNING: Parent accession '%s' does not exist!\n", $parent_acc);
+ }
+ else {
+
+ if (!(defined($child_term->{'id'}) && defined($terms->{$parent_acc}{'id'}) && defined($relation_types->{$relation_type}{'id'}))) {
+ print "Null value encountered: child term id " . $child_term->{'id'} . " parent term id " . $terms->{$parent_acc}{'id'} . " relationship type " . $relation_types->{$relation_type}{'id'} . "\n";
+ exit;
+ }
+
+ $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->bind_param(4, 0, SQL_INTEGER);
$sth->execute();
}
}
}
- foreach my $relation_type (
- sort( keys( %{ $child_term->{'intersection_of_parents'} } ) ) )
- {
- foreach my $parent_acc (
- sort( @{ $child_term->{'intersection_of_parents'}{$relation_type} } ) )
- {
- if ( !defined( $terms->{$parent_acc} ) ) {
- printf( "WARNING: Parent accession '%s' does not exist!\n",
- $parent_acc );
- } else {
-
- if ( !( defined($child_term->{'id'}) && defined($terms->{$parent_acc}{'id'}) && defined($relation_types->{$relation_type}{'id'}) ) )
- {
- print "Null value encountered: child term id " . $child_term->{'id'} ." parent term id ". $terms->{$parent_acc}{'id'} . " relationship type " . $relation_types->{$relation_type}{'id'} . "\n";
- exit;
- }
-
- $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->bind_param( 4, 1, SQL_INTEGER );
+ foreach my $relation_type (sort(keys(%{$child_term->{'intersection_of_parents'}}))) {
+ foreach my $parent_acc (sort(@{$child_term->{'intersection_of_parents'}{$relation_type}})) {
+ if (!defined($terms->{$parent_acc})) {
+ printf("WARNING: Parent accession '%s' does not exist!\n", $parent_acc);
+ }
+ else {
+
+ if (!(defined($child_term->{'id'}) && defined($terms->{$parent_acc}{'id'}) && defined($relation_types->{$relation_type}{'id'}))) {
+ print "Null value encountered: child term id " . $child_term->{'id'} . " parent term id " . $terms->{$parent_acc}{'id'} . " relationship type " . $relation_types->{$relation_type}{'id'} . "\n";
+ exit;
+ }
+
+ $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->bind_param(4, 1, SQL_INTEGER);
$sth->execute();
}
}
@@ -437,107 +404,105 @@ sub write_relation {
$dbh->do("OPTIMIZE TABLE relation");
$dbh->do("UNLOCK TABLES");
- printf( "\tWrote %d entries\n", $count );
+ printf("\tWrote %d entries\n", $count);
} ## end sub write_relation
#-----------------------------------------------------------------------
-my ( $dbhost, $dbport );
-my ( $dbuser, $dbpass );
-my ( $dbname, $obo_file_name );
+my ($dbhost, $dbport);
+my ($dbuser, $dbpass);
+my ($dbname, $obo_file_name);
my $ontology_name;
my $delete_unknown;
-$dbport = '3306';
-
-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,
- 'file|f=s' => \$obo_file_name,
- 'ontology|o=s' => \$ontology_name,
- 'delete_unknown' => \$delete_unknown,
- 'help|?' => sub { usage(); exit }
+$dbport = '3306';
+
+GetOptions(
+ 'dbhost|host|h=s' => \$dbhost,
+ 'dbport|port|P=i' => \$dbport,
+ 'dbuser|user|u=s' => \$dbuser,
+ 'dbpass|pass|p=s' => \$dbpass,
+ 'dbname|name|d=s' => \$dbname,
+ 'file|f=s' => \$obo_file_name,
+ 'ontology|o=s' => \$ontology_name,
+ 'delete_unknown' => \$delete_unknown,
+ 'help|?' => sub { usage(); exit }
);
-if (!defined($dbhost) || !defined($dbuser) || !defined($dbname) ) {
- usage();
- exit;
+if (!defined($dbhost) || !defined($dbuser) || !defined($dbname)) {
+ usage();
+ exit;
}
-if (!$delete_unknown && (!defined($obo_file_name) || !defined($ontology_name)) ) {
- usage();
- exit;
+if (!$delete_unknown && (!defined($obo_file_name) || !defined($ontology_name))) {
+ usage();
+ exit;
}
-my $dsn = sprintf( 'dbi:mysql:database=%s;host=%s;port=%s',
- $dbname, $dbhost, $dbport );
-
-my $dbh = DBI->connect( $dsn, $dbuser, $dbpass,
- { 'RaiseError' => 1, 'PrintError' => 2 } );
+my $dsn = sprintf('dbi:mysql:database=%s;host=%s;port=%s', $dbname, $dbhost, $dbport);
+my $dbh = DBI->connect($dsn, $dbuser, $dbpass, {'RaiseError' => 1, 'PrintError' => 2});
#delete the 'UNKNOWN' ontology and exit
if ($delete_unknown) {
- my ($unknown_onto_id) = $dbh->selectrow_array("SELECT ontology_id from ontology WHERE name = 'UNKNOWN'");
-
- if (!defined($unknown_onto_id)) {
- print "'UNKNOWN' ontology doesn\'t exist - nothing to delete.\n";
- } else {
- my ($unknown_term_count) = $dbh->selectrow_array("select count(1) from term t join ontology o using(ontology_id) where o.name = 'UNKNOWN'");
+ my ($unknown_onto_id) = $dbh->selectrow_array("SELECT ontology_id from ontology WHERE name = 'UNKNOWN'");
- if ($unknown_term_count > 0) {
- print ("Cannot delete ontology 'UNKNOWN' as $unknown_term_count terms are linked to this ontology.\n");
+ if (!defined($unknown_onto_id)) {
+ print "'UNKNOWN' ontology doesn\'t exist - nothing to delete.\n";
+ }
+ else {
+ my ($unknown_term_count) = $dbh->selectrow_array("select count(1) from term t join ontology o using(ontology_id) where o.name = 'UNKNOWN'");
- } else {
-
- my $delete_unknown_sth = $dbh->prepare("delete from ontology where ontology_id = $unknown_onto_id");
- $delete_unknown_sth->execute();
- $delete_unknown_sth->finish();
- print ("0 terms linked to 'UNKNOWN' ontology - ontology deleted.\n");
- }
+ if ($unknown_term_count > 0) {
+ print("Cannot delete ontology 'UNKNOWN' as $unknown_term_count terms are linked to this ontology.\n");
}
+ else {
- $dbh->disconnect();
- exit;
-}
+ my $delete_unknown_sth = $dbh->prepare("delete from ontology where ontology_id = $unknown_onto_id");
+ $delete_unknown_sth->execute();
+ $delete_unknown_sth->finish();
+ print("0 terms linked to 'UNKNOWN' ontology - ontology deleted.\n");
+ }
+ }
+
+ $dbh->disconnect();
+ exit;
+}
#if parsing an EFO obo file delete xref lines - not compatible with OBO:Parser
my @returncode = `grep "default-namespace: efo" $obo_file_name`;
my $returncode = @returncode;
if ($returncode > 0) {
- open (OBO_FILE, "$obo_file_name") or die;
- my $terminator = $/;
- undef $/;
- my $buf = <OBO_FILE>;
- $buf =~ s/\cM\cJ/\n/g;
- $/ = $terminator;
- my @file_lines = split(/\n/, $buf);
- my $no_of_lines = @file_lines;
- my $new_obo_file_name = "new" . $obo_file_name;
- open (NEW_OBO_FILE, ">$new_obo_file_name");
- for (my $i = 0; $i < $no_of_lines; $i++) {
- my $line = shift(@file_lines);
- if ($line !~ /^xref/) {
- print NEW_OBO_FILE $line, "\n";
- }
- }
- close OBO_FILE;
- close NEW_OBO_FILE;
- $obo_file_name = $new_obo_file_name;
-
-}
-
+ open(OBO_FILE, "$obo_file_name") or die;
+ my $terminator = $/;
+ undef $/;
+ my $buf = <OBO_FILE>;
+ $buf =~ s/\cM\cJ/\n/g;
+ $/ = $terminator;
+ my @file_lines = split(/\n/, $buf);
+ my $no_of_lines = @file_lines;
+ my $new_obo_file_name = "new" . $obo_file_name;
+ open(NEW_OBO_FILE, ">$new_obo_file_name");
+
+ for (my $i = 0 ; $i < $no_of_lines ; $i++) {
+ my $line = shift(@file_lines);
+ if ($line !~ /^xref/) {
+ print NEW_OBO_FILE $line, "\n";
+ }
+ }
+ close OBO_FILE;
+ close NEW_OBO_FILE;
+ $obo_file_name = $new_obo_file_name;
+}
my $my_parser = OBO::Parser::OBOParser->new;
-printf( "Reading OBO file '%s'...\n", $obo_file_name );
+printf("Reading OBO file '%s'...\n", $obo_file_name);
my $ontology = $my_parser->work($obo_file_name) or die;
@@ -545,163 +510,158 @@ my $statement = "SELECT name from ontology where name = ? group by name";
my $select_sth = $dbh->prepare($statement);
-$select_sth->bind_param(1,$ontology_name,SQL_VARCHAR);
+$select_sth->bind_param(1, $ontology_name, SQL_VARCHAR);
$select_sth->execute();
-if ( $select_sth->fetch() ) {
- print("This ontology name already exists in the database.\nPlease run the program again with a new name.\n");
- $select_sth->finish();
- $dbh->disconnect();
- exit;
+if ($select_sth->fetch()) {
+ print("This ontology name already exists in the database.\nPlease run the program again with a new name.\n");
+ $select_sth->finish();
+ $dbh->disconnect();
+ exit;
}
-$statement =
- "SELECT meta_value FROM meta WHERE meta_key = 'OBO_file_date'";
+$statement = "SELECT meta_value FROM meta WHERE meta_key = 'OBO_file_date'";
my $stored_obo_file_date = $dbh->selectall_arrayref($statement)->[0][0];
my $obo_file_date = $ontology->date();
-$obo_file_date = sprintf( "%s/%s", $obo_file_name, $obo_file_date );
+$obo_file_date = sprintf("%s/%s", $obo_file_name, $obo_file_date);
-if ( defined($stored_obo_file_date) ) {
- if ( $stored_obo_file_date eq $obo_file_date ){
- print("This OBO file has already been processed.\n");
- $dbh->disconnect();
- exit;
- } elsif ( index( $stored_obo_file_date, $obo_file_name ) != -1)
- {
- print <<EOT;
+if (defined($stored_obo_file_date)) {
+ if ($stored_obo_file_date eq $obo_file_date) {
+ print("This OBO file has already been processed.\n");
+ $dbh->disconnect();
+ exit;
+ }
+ elsif (index($stored_obo_file_date, $obo_file_name) != -1) {
+ 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...
EOT
- $dbh->disconnect();
- exit;
- }
+ $dbh->disconnect();
+ exit;
+ }
}
-my ( %terms, %namespaces, %relation_types, %subsets );
+my (%terms, %namespaces, %relation_types, %subsets);
my $default_namespace = $ontology->default_namespace();
my @subsets;
if ($OBO::Core::Ontology::VERSION <= 1.31) {
- my $set = $ontology->subset_def_set();
- @subsets = $set->get_set();
-} else {
- @subsets = $ontology->subset_def_map()->values();
+ my $set = $ontology->subset_def_set();
+ @subsets = $set->get_set();
+}
+else {
+ @subsets = $ontology->subset_def_map()->values();
}
foreach my $subs (@subsets) {
- $subsets{$subs->name()}{'name'} = $subs->name();
- $subsets{$subs->name()}{'definition'} = $subs->description();
+ $subsets{$subs->name()}{'name'} = $subs->name();
+ $subsets{$subs->name()}{'definition'} = $subs->description();
}
# get all non obsolete terms
foreach my $t (@{$ontology->get_terms()}) {
- if (!($t->is_obsolete())) {
-
- my %term;
-
- my @t_namespace = $t->namespace();
- my $t_namespace_elm = @t_namespace;
- if ($t_namespace_elm > 0){
- $term{'namespace'} = $t_namespace[0];
- }else {
- $term{'namespace'} = $default_namespace;
+ if (!($t->is_obsolete())) {
+
+ my %term;
+
+ my @t_namespace = $t->namespace();
+ my $t_namespace_elm = @t_namespace;
+ if ($t_namespace_elm > 0) {
+ $term{'namespace'} = $t_namespace[0];
+ }
+ else {
+ $term{'namespace'} = $default_namespace;
+ }
+ $namespaces{$term{'namespace'}} = $ontology_name;
+
+ $term{'accession'} = $t->id();
+ $term{'name'} = $t->name();
+ $term{'definition'} = $t->def_as_string();
+
+ my $rels = $ontology->get_relationships_by_source_term($t);
+ foreach my $r (@{$rels}) {
+
+ #get parent term
+ my $pterm = $r->head();
+ push(@{$term{'parents'}{$r->type()}}, $pterm->id());
+ }
+
+ my @intersection_of = $t->intersection_of();
+ foreach my $r (@intersection_of) {
+
+ if ($r->isa('OBO::Core::Relationship')) {
+
+ #get parent term for relationship
+ my $pterm = $r->head();
+ my $type = $r->type();
+ if (!defined($type) || $type eq 'nil') {
+ $type = 'is_a';
}
- $namespaces{ $term{'namespace'} } = $ontology_name;
-
- $term{'accession'} = $t->id();
- $term{'name'} = $t->name();
- $term{'definition'} = $t->def_as_string();
-
- my $rels = $ontology->get_relationships_by_source_term($t);
- foreach my $r (@{$rels}) {
- #get parent term
- my $pterm = $r->head();
- push( @{ $term{'parents'}{$r->type()} }, $pterm->id() );
- }
-
- my @intersection_of = $t->intersection_of();
- foreach my $r (@intersection_of) {
-
- if ($r->isa('OBO::Core::Relationship') ){
- #get parent term for relationship
- my $pterm = $r->head();
- my $type = $r->type();
- if (!defined($type) || $type eq 'nil') {
- $type = 'is_a';
- }
- push( @{ $term{'intersection_of_parents'}{$type} }, $pterm->id() );
- } else {
- #this is a term
- push( @{ $term{'intersection_of_parents'}{'is_a'} }, $r->id() );
- }
-
- }
-
- my @term_subsets = $t->subset();
- foreach my $term_subset (@term_subsets) {
- push( @{ $term{'subsets'} }, $term_subset );
- }
- my @t_synonyms = $t->synonym_set();
- foreach my $t_synonym (@t_synonyms) {
- push( @{ $term{'synonyms'} }, $t_synonym->def_as_string() );
- }
-
-
- $terms{ $term{'accession'} } = {%term};
-
- }
+ push(@{$term{'intersection_of_parents'}{$type}}, $pterm->id());
+ }
+ else {
+
+ #this is a term
+ push(@{$term{'intersection_of_parents'}{'is_a'}}, $r->id());
+ }
+
+ }
+
+ my @term_subsets = $t->subset();
+ foreach my $term_subset (@term_subsets) {
+ push(@{$term{'subsets'}}, $term_subset);
+ }
+ my @t_synonyms = $t->synonym_set();
+ foreach my $t_synonym (@t_synonyms) {
+ push(@{$term{'synonyms'}}, $t_synonym->def_as_string());
+ }
+
+ $terms{$term{'accession'}} = {%term};
+
+ }
}
#get all relationship types
foreach my $rel_type (@{$ontology->get_relationship_types()}) {
- my $rel_type_name = $rel_type->id();
- if ( !exists( $relation_types{$rel_type_name} ) ) {
- $relation_types{$rel_type_name} = 1;
- }
+ my $rel_type_name = $rel_type->id();
+ if (!exists($relation_types{$rel_type_name})) {
+ $relation_types{$rel_type_name} = 1;
+ }
}
print("Finished reading OBO file, now writing to database...\n");
-my $unknown_onto_id = write_ontology( $dbh, \%namespaces );
-write_subset( $dbh, \%subsets );
-write_term( $dbh, \%terms, \%subsets, \%namespaces, $unknown_onto_id);
-write_relation_type( $dbh, \%relation_types );
-write_relation( $dbh, \%terms, \%relation_types );
+my $unknown_onto_id = write_ontology($dbh, \%namespaces);
+write_subset($dbh, \%subsets);
+write_term($dbh, \%terms, \%subsets, \%namespaces, $unknown_onto_id);
+write_relation_type($dbh, \%relation_types);
+write_relation($dbh, \%terms, \%relation_types);
print("Updating meta table...\n");
-my $sth =
- $dbh->prepare( "DELETE FROM meta "
- . "WHERE meta_key = 'OBO_file_date' "
- . "AND meta_value LIKE ?" );
-$sth->bind_param( 1, sprintf( "%s/%%", $obo_file_name ), SQL_VARCHAR );
+my $sth = $dbh->prepare("DELETE FROM meta " . "WHERE meta_key = 'OBO_file_date' " . "AND meta_value LIKE ?");
+$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->bind_param( 1, $obo_file_date, SQL_VARCHAR );
+$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();
-my $obo_load_date =
- sprintf( "%s/%s", $obo_file_name, scalar( localtime() ) );
+my $obo_load_date = sprintf("%s/%s", $obo_file_name, scalar(localtime()));
-$sth =
- $dbh->prepare( "DELETE FROM meta "
- . "WHERE meta_key = 'OBO_load_date' "
- . "AND meta_value LIKE ?" );
-$sth->bind_param( 1, sprintf( "%s/%%", $obo_file_name ), SQL_VARCHAR );
+$sth = $dbh->prepare("DELETE FROM meta " . "WHERE meta_key = 'OBO_load_date' " . "AND meta_value LIKE ?");
+$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->bind_param( 1, $obo_load_date, SQL_VARCHAR );
+$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();
@@ -709,5 +669,4 @@ $dbh->disconnect();
print("Done.\n");
-
# $Id$