File

tripal_feature/api/tripal_feature.api.inc, line 1031

Provides an application programming interface (API) for working with features

Code

function tripal_feature_add_dbxref($feature_id, $dbname, $accession) {

  // make sure the db exists. If it doesn't, then add it
  $values = array('name' => $dbname);
  $options = array('statement_name' => 'sel_db_na');
  $db = tripal_core_chado_select('db', array('db_id'), $values, $options);
  if (!$db or count($db) == 0) {
    $options = array('statement_name' => 'ins_db_na');
    $success = tripal_core_chado_insert('db', $values, $options);
    if (!$success) {
      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, ". 
        "could not be added because the database, %dbname, does not exist and cannot be added.', 
      array('%feature_id' => $feature_id, '%dbname' => $dbname), WATCHDOG_WARNING);
      return FALSE;
    }
  }

  // first make sure that the record doesn't already exist
  $values = array(
    'dbxref_id' => array(
      'accession' => $accession,
      'db_id' => array(
        'name' => $dbname
      ),
    ),
    'feature_id' => $feature_id,
  );
  $options = array('statement_name' => 'sel_featuredbxref_dbfe');
  $xref = tripal_core_chado_select('feature_dbxref', array('feature_dbxref_id'), $values, $options);
  if (count($xref) == 0) {
    // if the record doesn't exist then add it.
    $options = array('statement_name' => 'ins_featuredbxref_dbfe');
    $success = tripal_core_chado_insert('feature_dbxref', $values, $options);
    if (!$success) {
      watchdog('tripal_feature', 'tripal_feature_add_dbxref: The feature dbxref entry for feature, %feature_id, ' .
        'could not be added: %db:%accession.', array('%feature_id' => $feature_id, '%db' => $dbname,
        '%accession' => $accession), WATCHDOG_WARNING);
      return FALSE;
    }
  }
  return TRUE;
}