See also

chado_associate_dbxref().

File

tripal_featuremap/api/tripal_featuremap.DEPRECATED.inc, line 140

Wrapper functions to provide backwards compatibility for the tripal featuremap api

Code

function tripal_featuremap_add_featuremap_dbxref($featuremap_id, $featuremap_dbxref) {

  tripal_report_error(
  'tripal_deprecated', 
  TRIPAL_NOTICE, 
  "DEPRECATED: %old_function has been replaced with %new_function. Please update your code.", 
  array(
    '%old_function' => 'tripal_featuremap_add_featuremap_dbxref',
    '%new_function' => 'chado_associate_dbxref'
  )
  );

  // break apart the dbxref
  $dbname = '';
  $accession = '';
  if (preg_match('/^(.*?):(.*?)$/', $featuremap_dbxref, $matches)) {
    $dbname = $matches[1];
    $accession = $matches[2];
  }
  else {
    return FALSE;
  }

  // check to see if the featuremap_dbxref record already exist
  $values = array(
    'dbxref_id' => array(
      'accession' => $accession,
      'db_id' => array(
        'name' => $dbname,
      ),
    ),
    'featuremap_id' => $featuremap_id,
  );
  $options = array('statement_name' => 'sel_featuremapdbxref_dbpu');
  $results = chado_select_record('featuremap_dbxref', array('*'), $values, $options);

  // if the featuremap_dbxref record  exist then we don't need to re-add it.
  if (count($results) > 0) {
    return $results[0];
  }

  // make sure our database already exists
  $db = tripal_db_add_db($dbname);

  // get the database cross-reference
  $dbxvalues = array(
    'accession' => $accession,
    'db_id' => $db->db_id,
  );
  $dbxoptions = array('statement_name' => 'sel_dbxref_acdb');
  $results = chado_select_record('dbxref', array('dbxref_id'), $dbxvalues, $dbxoptions);
  // if the accession doesn't exist then add it
  if (count($results) == 0) {
    $dbxref = tripal_db_add_dbxref($db->db_id, $accession);
  }
  else {
    $dbxref = $results[0];
  }

  // now add the record
  $options = array('statement_name' => 'ins_featuremapdbxref_dbpu');
  $results = chado_insert_record('featuremap_dbxref', $values, $options);
  if (!$results) {
    tripal_report_error('t_featuremap', TRIPAL_ERROR, "Cannot add map dbxref: %db:%accession.", 
    array('%db' => $dbname, '%accession' => $accession));
    return FALSE;
  }
  return $results;
}