Implements hook_vocab_get_vocabulary().

This hook is created by the Tripal module and is not a Drupal hook.

File

tripal_chado/includes/tripal_chado.vocab_storage.inc, line 78

Code

function tripal_chado_vocab_get_vocabulary($vocabulary) {
  // It's possible that Chado is not available (i.e. it gets renamed
  // for copying) but Tripal has already been prepared and the
  // entities exist.  If this is the case we don't want to run the
  // commands below.
  if (!chado_table_exists('cv')) {
    return FALSE;
  }

  // Make sure the materiailzd view is present.
  if (!chado_table_exists('db2cv_mview')) {
    drupal_set_message('Please update the database using "drush updatedb" before continuing');
    return FALSE;
  }

  $sql = "
     SELECT DB.name as short_name, DB.description, DB.url, DB.urlprefix,
       SUM(DBCVM.num_terms) as num_terms,
       array_to_string(array_agg(DBCVM.cvname), ', ') as name
     FROM {db} DB
      INNER JOIN {db2cv_mview} DBCVM ON DBCVM.db_id = DB.db_id
     WHERE DB.name = :name
     GROUP BY DB.name, DB.description, DB.url, DB.urlprefix
  ";
  $result = chado_query($sql, array(':name' => $vocabulary));
  $result = $result->fetchAssoc();
  if (!$result) {
    return FALSE;
  }

  if (!$result['name']) {
    $result['name'] = $result['short_name'];
  }
  $sw_url = $result['urlprefix'];
  if ($sw_url) {
    $sw_url = preg_replace('/\{db\}/', $result['short_name'], $sw_url);
    $sw_url = preg_replace('/\{accession\}/', '', $sw_url);
    $sw_url = url($sw_url, array('absolute' => TRUE));
  }
  $result['sw_url'] = $sw_url;
  return $result;
}