Implements hook_vocab_get_terms().

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

File

tripal_chado/includes/tripal_chado.vocab_storage.inc, line 167

Code

function tripal_chado_vocab_get_terms($vocabulary, $limit = 25, $element = 0) {
  // 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('cvterm')) {
    return FALSE;
  }

  $sql = "
    SELECT CVT.cvterm_id
    FROM {cvterm} CVT
      INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
      INNER JOIN {db} DB on DB.db_id = DBX.db_id
    WHERE db.name = :dbname
    ORDER BY CVT.name
  ";
  $csql = "
    SELECT COUNT(CVT.cvterm_id)
    FROM {cvterm} CVT
      INNER JOIN {dbxref} DBX on DBX.dbxref_id = CVT.dbxref_id
      INNER JOIN {db} DB on DB.db_id = DBX.db_id
    WHERE db.name = :dbname
  ";
  $results = chado_pager_query($sql, array(':dbname' => $vocabulary), $limit, $element, $csql);

  $terms = array();
  while ($cvterm_id = $results->fetchField()) {
    $match = array('cvterm_id' => $cvterm_id);
    $cvterm = chado_generate_var('cvterm', $match);
    $terms[] = _tripal_chado_format_term_description($cvterm);
  }
  return $terms;
}