This function uses organism_id's of all drupal organism nodes as input and pull the organism information (genus, species, common_name, comment) from chado database. The return type is an object array that stores $organism objects sorted by common_name

Related topics

File

tripal_organism/tripal_organism.module, line 592

tripal_organism Organism Module

Code

function get_chado_organisms() {
  $sql_drupal = "SELECT COUNT (organism_id) FROM {chado_organism}";
  $no_orgs = db_result(db_query($sql_drupal));
  if ($no_orgs != 0) {
    $sql = "SELECT organism_id, nid FROM {chado_organism}";
    $result = chado_query($sql);
    $sql = "SELECT genus, species, common_name, comment " .
      "FROM {Organism} " .
      "WHERE organism_id=%d";
    $organisms = array();
    $count = 0;
    while ($data = db_fetch_object($result)) {
      $organism = db_fetch_object(chado_query($sql, $data->organism_id));
      $organism->node_id = $data->nid;
      // Use common_name plus $count as the key so we can sort by common
      // name later. Since common_name is not unique, we need to add $count
      // to the key
      $key = drupal_strtolower($organism->common_name) . $count;
      $organisms[$key] = $organism;
      $count++;
    }

    //Sort organisms by common name
    ksort($organisms, SORT_STRING);
    return $organisms;
  }
}