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Commit 18df072b authored by Andreas Kusalananda Kähäri's avatar Andreas Kusalananda Kähäri
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When creating the aux_XX_YY_map tables, map XX ontology terms to *all* 

ancestors within the YY subset (not just the closest one(s)).  Suggested
by Paul K.
parent 89fefbab
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misc-scripts/ontology/scripts/add_subset_maps.pl
+ 41
− 108
View file @ 18df072b
......@@ -13,9 +13,9 @@ use Data::Dumper;
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\n",
$0, ' ' x length($0) );
. "\t%s\t-u dbuser [-p dbpass] \\\n"
. "\t%2\$s\t-d dbname\n",
$0, ' ' x length($0) );
print("\n");
printf( "\t%s\t-?\n", $0 );
print("\n");
......@@ -37,34 +37,32 @@ my $dbname;
$dbport = '3306';
if (
!GetOptions(
'dbhost|host|h=s' => \$dbhost,
'dbport|port|P=i' => \$dbport,
'dbuser|user|u=s' => \$dbuser,
'dbpass|pass|p=s' => \$dbpass,
'dbname|name|d=s' => \$dbname,
'help|?' => sub { usage(); exit } )
|| !defined($dbhost)
|| !defined($dbuser)
|| !defined($dbname) )
!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,
'help|?' => sub { usage(); exit } )
|| !defined($dbhost)
|| !defined($dbuser)
|| !defined($dbname) )
{
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' => 0, 'PrintError' => 0 } );
my $dbh = DBI->connect( $dsn, $dbuser, $dbpass,
{ 'RaiseError' => 0, 'PrintError' => 0 } );
# Associate all subsets in the ontology database with their respective
# ontology.
my %subsets;
{
my $statement = q(
my $statement = q(
SELECT DISTINCT
ontology.name,
subset.name
......@@ -75,25 +73,15 @@ WHERE ontology.ontology_id = term.ontology_id
AND FIND_IN_SET(subset.name, term.subsets) > 0
);
my $sth = $dbh->prepare($statement);
$sth->execute();
my ( $ontology_name, $subset_name );
$sth->bind_columns( \( $ontology_name, $subset_name ) );
while ( $sth->fetch() ) {
push( @{ $subsets{$ontology_name} }, $subset_name );
}
}
{
my $select_statement = q(
my $table_template = q(
CREATE TABLE %s (
term_id INT UNSIGNED NOT NULL,
subset_term_id INT UNSIGNED NOT NULL,
UNIQUE INDEX map_idx (term_id, subset_term_id)
)
SELECT DISTINCT
child_term.term_id,
parent_term.term_id,
closure.distance
child_term.term_id
parent_term.term_id
FROM ontology
JOIN term parent_term
ON (parent_term.ontology_id = ontology.ontology_id)
......@@ -101,87 +89,32 @@ FROM ontology
ON (closure.parent_term_id = parent_term.term_id)
JOIN term child_term
ON (child_term.term_id = closure.child_term_id)
WHERE FIND_IN_SET(?, parent_term.subsets) > 0
AND ontology.name = ?
ORDER BY child_term.accession, closure.distance;
WHERE ontology.name = %s
AND FIND_IN_SET(%s, parent_term.subsets) > 0
);
my $select_sth = $dbh->prepare($select_statement);
foreach my $ontology_name ( keys(%subsets) ) {
foreach my $subset_name ( @{ $subsets{$ontology_name} } ) {
my $sth = $dbh->prepare($statement);
my $aux_table_name = $dbh->quote_identifier(
sprintf( "aux_%s_%s_map", $ontology_name, $subset_name ) );
$sth->execute();
$dbh->do(
sprintf(
"CREATE TABLE %s ( "
. "term_id INT UNSIGNED NOT NULL, "
. "subset_term_id INT UNSIGNED NOT NULL, "
. "UNIQUE INDEX map_idx (term_id, subset_term_id) )",
$aux_table_name
) );
my ( $ontology_name, $subset_name );
if ( $dbh->err() ) {
printf( "MySQL error, \"%s\", skipping...\n", $dbh->errstr() );
next;
}
$sth->bind_columns( \( $ontology_name, $subset_name ) );
printf( "%s...\n", $aux_table_name );
while ( $sth->fetch() ) {
$select_sth->bind_param( 1, $subset_name, SQL_VARCHAR );
$select_sth->bind_param( 2, $ontology_name, SQL_VARCHAR );
my $aux_table_name = $dbh->quote_identifier(
sprintf( "aux_%s_%s_map", $ontology_name, $subset_name ) );
$select_sth->execute();
$dbh->do(
sprintf( $table_template,
$aux_table_name, $ontology_name, $subset_name ) );
my ( $child_id, $parent_id, $distance );
$select_sth->bind_columns(
\( $child_id, $parent_id, $distance ) );
$dbh->do( sprintf( "LOCK TABLE %s WRITE", $aux_table_name ) );
my $insert_statement = sprintf(
"INSERT IGNORE INTO %s "
. "(term_id, subset_term_id) "
. "VALUES (?, ?)",
$aux_table_name
);
my $insert_sth = $dbh->prepare($insert_statement);
my $last_child_id;
my $the_distance;
while ( $select_sth->fetch() ) {
if ( !defined($last_child_id)
|| $child_id != $last_child_id )
{
$last_child_id = $child_id;
$the_distance = $distance;
}
if ( $child_id == $last_child_id && $distance != $the_distance )
{
next;
}
if ( $child_id == $last_child_id
&& $distance == $the_distance )
{
$insert_sth->bind_param( 1, $child_id, SQL_INTEGER );
$insert_sth->bind_param( 2, $parent_id, SQL_INTEGER );
$insert_sth->execute();
}
}
$dbh->do( sprintf( "OPTIMIZE TABLE %s", $aux_table_name ) );
$dbh->do("UNLOCK TABLES");
if ( $dbh->err() ) {
printf( "MySQL error, \"%s\", skipping...\n", $dbh->errstr() );
next;
}
} ## end foreach my $subset_name ( @...)
} ## end foreach my $ontology_name (...)
}
# $Id$
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