Adds a new organism record to Chado.

Parameters

sci_name: The scientific name as provied by NCBI Taxonomy.

$rank: The rank of the organism as provied by NCBI Taxonomy.

File

tripal_chado/includes/TripalImporter/TaxonomyImporter.inc, line 580

Class

TaxonomyImporter

Code

private function addOrganism($sci_name, $rank) {

  $organism = NULL;
  $matches = array();
  $genus = '';
  $species = '';
  $infra = '';
  $values = array();

  // Check if the scientific name has an infraspecific part or is just
  // a species name.
  if (preg_match('/^(.+?)\s+(.+?)\s+(.+)$/', $sci_name, $matches)) {
    $genus = $matches[1];
    $species = $matches[2];
    $infra = $matches[3];

    // Get the CV term for the rank.
    $type = chado_get_cvterm(array(
      'name' => preg_replace('/ /', '_', $rank),
      'cv_id' => array('name' => 'taxonomic_rank')
    ));

    // Remove the rank from the infraspecific name.
    $abbrev = chado_abbreviate_infraspecific_rank($rank);
    $infra = preg_replace("/$abbrev/", "", $infra);
    $infra = trim($infra);

    $values = array(
      'genus' => $genus,
      'species' => $species,
      'abbreviation' => $genus[0] . '. ' . $species,
      'type_id' => $type->cvterm_id,
      'infraspecific_name' => $infra,
    );
    $organism = chado_insert_record('organism', $values);
    $organism = (object) $organism;
    $organism->type = $rank;
  }
  else if (preg_match('/^(.+?)\s+(.+?)$/', $sci_name, $matches)) {
    $genus = $matches[1];
    $species = $matches[2];
    $infra = '';
    $values = array(
      'genus' => $genus,
      'species' => $species,
      'abbreviation' => $genus[0] . '. ' . $species,
    );
    $organism = chado_insert_record('organism', $values);
    $organism = (object) $organism;
  }
  if ($organism) {
    $organism->is_new = TRUE;
    $this->all_orgs[] = $organism;
  }

  return $organism;
}