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File

tripal_feature/includes/gff_loader.inc, line 1184

@todo Add file header description

Code

function tripal_feature_load_gff3_ontology($feature, $dbxrefs) {

  // iterate through each of the dbxrefs
  foreach ($dbxrefs as $dbxref) {

    // get the database name from the reference.  If it doesn't exist then create one.
    $ref = explode(":", $dbxref);
    $dbname = $ref[0];
    $accession = $ref[1];

    // first look for the database name
    $options = array('statement_name' => 'sel_db_name');
    $db = tripal_core_chado_select('db', array('db_id'), array('name' => "DB:$dbname"), $options);
    if (sizeof($db) == 0) {
      // now look for the name without the 'DB:' prefix.
      $db = tripal_core_chado_select('db', array('db_id'), array('name' => "$dbname"), $options);
      if (sizeof($db) == 0) {
        watchdog("T_gff3_loader", "Database, $dbname, is not present. Cannot associate term: $dbname:$accession", array(), WATCHDOG_WARNING);
        return 0;
      }
    }
    $db = $db[0];

    // now check to see if the accession exists
    $options = array('statement_name' => 'sel_dbxref_accession_dbid');
    $dbxref = tripal_core_chado_select('dbxref', array('dbxref_id'), 
    array('accession' => $accession, 'db_id' => $db->db_id), $options);
    if (sizeof($dbxref) == 0) {
      watchdog("T_gff3_loader", "Accession, $accession is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
      return 0;
    }
    $dbxref = $dbxref[0];

    // now check to see if the cvterm exists
    $options = array('statement_name' => 'sel_cvterm_dbxrefid');
    $cvterm = tripal_core_chado_select('cvterm', array('cvterm_id'), array(
      'dbxref_id' => $dbxref->dbxref_id), $options);
    // if it doesn't exist in the cvterm table, look for an alternate id
    if (sizeof($cvterm) == 0) {
      $options = array('statement_name' => 'sel_cvtermdbxref_dbxrefid');
      $cvterm = tripal_core_chado_select('cvterm_dbxref', array('cvterm_id'), array(
        'dbxref_id' => $dbxref->dbxref_id), $options);
      if (sizeof($cvterm) == 0) {
        watchdog("T_gff3_loader", "CV Term is missing for reference: $dbname:$accession", array(), WATCHDOG_WARNING);
        return 0;
      }
    }
    $cvterm = $cvterm[0];


    // check to see if this feature cvterm already exists
    $options = array('statement_name' => 'sel_featurecvterm_cvtermid_featureid');
    $fcvt = tripal_core_chado_select('feature_cvterm', array('feature_cvterm_id'), 
    array('cvterm_id' => $cvterm->cvterm_id, 'feature_id' => $feature->feature_id), 
    $options);

    // now associate this feature with the cvterm if it doesn't already exist
    if (sizeof($fcvt) == 0) {
      $values = array(
        'cvterm_id' => $cvterm->cvterm_id,
        'feature_id' => $feature->feature_id,
        'pub_id' => array(
          'uniquename' => 'null',
        ),
      );
      $options = array('statement_name' => 'ins_featurecvterm_cvtermid_featureid_pubid');
      $success = tripal_core_chado_insert('feature_cvterm', $values, $options);

      if (!$success) {
        watchdog("T_gff3_loader", "Failed to insert ontology term: $dbname:$accession", array(), WATCHDOG_WARNING);
        return 0;
      }
    }
  }
  return 1;
}