Script to add auxiliary mapping tables.

The script adds one table by subset previously added to the database and
maps all terms to the closest term within that subset.  The tables are
named "aux_XX_YY_map" where "XX" is the ontology ("GO" or "SO"), and
"YY" is the subset name (e.g., "goslim_goa").

The schema for each of the subset map tables is simply as follows:

  +----------------+------------------+------+-----+---------+-------+
  | Field          | Type             | Null | Key | Default | Extra |
  +----------------+------------------+------+-----+---------+-------+
  | term_id        | int(10) unsigned | NO   | PRI | NULL    |       |
  | subset_term_id | int(10) unsigned | NO   | PRI | NULL    |       |
  +----------------+------------------+------+-----+---------+-------+

... where both fields refers into the 'term' table.

misc-scripts/ontology/scripts/add_subset_maps.pl

+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+use DBI qw( :sql_types );
+use Getopt::Long qw( :config no_ignore_case );
+
+#-----------------------------------------------------------------------
+
+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) );
+  print("\n");
+  printf( "\t%s\t-?\n", $0 );
+  print("\n");
+  print("Arguments:\n");
+  print("\t-h/--host dbhost\tDatabase server host name\n");
+  print("\t-P/--port dbport\tDatabase server port (optional)\n");
+  print("\t-u/--user dbuser\tDatabase user name\n");
+  print("\t-p/--pass dbpass\tUser password (optional)\n");
+  print("\t-d/--name dbname\tDatabase name\n");
+  print("\t-?/--help\t\tDisplays this information\n");
+}
+
+#-----------------------------------------------------------------------
+
+my ( $dbhost, $dbport );
+my ( $dbuser, $dbpass );
+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) )
+{
+  usage();
+  exit;
+}
+
+my $dsn = sprintf( "DBI:mysql:database=%s;host=%s;port=%s",
+  $dbname, $dbhost, $dbport );
+
+my $dbh =
+  DBI->connect( $dsn, $dbuser, $dbpass,
+  { 'RaiseError' => 0, 'PrintError' => 0 } );
+
+my %subsets;
+{
+  my $statement = q(
+SELECT DISTINCT
+        ontology.name,
+        subset.name
+FROM    ontology,
+        term,
+        subset
+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 );
+  }
+
+  $sth->finish();
+}
+
+{
+  my $select_statement = q(
+SELECT  child_term.term_id,
+        parent_term.term_id,
+        closure.distance
+FROM    closure,
+        term child_term,
+        term parent_term,
+        ontology
+WHERE   closure.parent_term_id = parent_term.term_id
+  AND   closure.child_term_id = child_term.term_id
+  AND   FIND_IN_SET(?, parent_term.subsets) > 0
+  AND   parent_term.ontology_id = ontology.ontology_id
+  AND   ontology.name = ?
+ORDER BY child_term.accession, closure.distance;
+);
+
+  my $select_sth = $dbh->prepare($select_statement);
+
+  foreach my $ontology_name ( keys(%subsets) ) {
+    foreach my $subset_name ( @{ $subsets{$ontology_name} } ) {
+
+      my $aux_table_name = $dbh->quote_identifier(
+        sprintf( "aux_%s_%s_map", $ontology_name, $subset_name ) );
+
+      $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
+        ) );
+
+      if ( $dbh->err() ) {
+        printf( "MySQL error, \"%s\", skipping...\n", $dbh->errstr() );
+        next;
+      }
+
+      $select_sth->bind_param( 1, $subset_name,   SQL_VARCHAR );
+      $select_sth->bind_param( 2, $ontology_name, SQL_VARCHAR );
+
+      $select_sth->execute();
+
+      my ( $child_id, $parent_id, $distance );
+
+      $select_sth->bind_columns(
+        \( $child_id, $parent_id, $distance ) );
+
+      my $insert_statement = sprintf(
+        "INSERT IGNORE INTO %s "
+          . "(term_id, subset_term_id) "
+          . "VALUES (?, ?)",
+        $aux_table_name
+      );
+
+      $dbh->do( sprintf( "LOCK TABLE %s WRITE", $aux_table_name ) );
+
+      my $insert_sth = $dbh->prepare($insert_statement);
+
+      printf( "%s...\n", $aux_table_name );
+
+      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();
+        }
+      }
+
+      $select_sth->finish();
+
+      $dbh->do( sprintf( "OPTIMIZE TABLE %s", $aux_table_name ) );
+      $dbh->do("UNLOCK TABLES");
+
+    } ## end foreach my $subset_name ( @...)
+  } ## end foreach my $ontology_name (...)
+}
+
+# $Id$