Adds a cvterm relationship

@object_is_relationship Set to 1 if this term is a relationship term @default_db The name of the default database.

Parameters

$cvterm: A database object for the cvterm

$rel: The relationship name

$objname: The relationship term name

$defaultcv: A database object containing a record from the cv table for the default controlled vocabulary

File

tripal_chado/includes/TripalImporter/OBOImporter.inc, line 956

Class

OBOImporter

Code

private function addRelationship($cvterm, $defaultcv, $rel, 
$objname, $object_is_relationship = 0, $default_db = 'OBO_REL') {
  // If an accession was passed we need to see if we can find the actual label.
  if (strpos($rel, ':')) {
    $pair = explode(":", $rel);
    $ontology_id = $pair[0];
    $accession_num = $pair[1];
    if (is_numeric($accession_num)) {
      $results = $this->oboEbiLookup($rel, 'query');
      if (!empty($results)) {
        if (array_key_exists('docs', $results)) {
          if (!empty($results['docs'])) {
            $rel = $results['docs']['label'];
          }
          else {
            // The first search doesn't work, so let's try a broader one.
            $results = $this->oboEbiLookup($rel, 'query-non-local');
            if (!empty($results)) {
              if (array_key_exists('docs', $results)) {
                if (!empty($results['docs'])) {
                  $accession = $rel;
                  $accession_underscore = str_replace(":", "_", $accession);
                  foreach ($results['docs'] as $item) {
                    if ($item['label'] != $accession && $item['label'] != $accession_underscore) {
                      //Found the first place a label is other than the accession is used, so take
                      // that info and then end the loop.
                      $rel = $item['label'];
                      break;
                    }
                  }
                }
              }
            }
          }
        }
      }
    }
  }
  // Make sure the relationship cvterm exists.
  $term = array(
    'name' => $rel,
    'id' => "$default_db:$rel",
    'definition' => '',
    'is_obsolete' => 0,
    'cv_name' => $defaultcv,
    'is_relationship' => TRUE,
    'db_name' => $default_db
  );
  $relcvterm = chado_insert_cvterm($term, array('update_existing' => FALSE));

  if (!$relcvterm) {
    // If the relationship term couldn't be found in the default_db provided
    // then do on more check to find it in the relationship ontology
    $term = array(
      'name' => $rel,
      'id' => "OBO_REL:$rel",
      'definition' => '',
      'is_obsolete' => 0,
      'cv_name' => $defaultcv,
      'is_relationship' => TRUE,
      'db_name' => 'OBO_REL'
    );
    $relcvterm = chado_insert_cvterm($term, array('update_existing' => FALSE));
    if (!$relcvterm) {
      throw new Exception("Cannot find the relationship term in the current ontology or in the relationship ontology: $rel\n");
    }
  }

  // Get the object term.
  $oterm = $this->getTerm($objname);
  if (!$oterm) {
    throw new Exception("Could not find object term $objname\n");
  }

  $objterm = array();
  $objterm['id'] = $oterm['id'][0];
  $objterm['name'] = $oterm['name'][0];
  if (array_key_exists('def', $oterm)) {
    $objterm['definition'] = $oterm['def'][0];
  }
  if (array_key_exists('subset', $oterm)) {
    $objterm['subset'] = $oterm['subset'][0];
  }
  if (array_key_exists('namespace', $oterm)) {
    $objterm['namespace'] = $oterm['namespace'][0];
  }
  if (array_key_exists('is_obsolete', $oterm)) {
    $objterm['is_obsolete'] = $oterm['is_obsolete'][0];
  }

  $objterm['cv_name'] = $defaultcv;
  $objterm['is_relationship'] = $object_is_relationship;
  $objterm['db_name'] = $default_db;

  $objcvterm = chado_insert_cvterm($objterm, array('update_existing' => TRUE));
  if (!$objcvterm) {
    throw new Exception("Cannot add cvterm " . $oterm['name'][0]);
  }

  // check to see if the cvterm_relationship already exists, if not add it
  $values = array(
    'type_id' => $relcvterm->cvterm_id,
    'subject_id' => $cvterm->cvterm_id,
    'object_id' => $objcvterm->cvterm_id
  );
  $result = chado_select_record('cvterm_relationship', array('*'), $values);
  if (count($result) == 0) {
    $options = array('return_record' => FALSE);
    $success = chado_insert_record('cvterm_relationship', $values, $options);
    if (!$success) {
      throw new Exception("Cannot add term relationship: '$cvterm->name' $rel '$objcvterm->name'");
    }
  }

  return TRUE;
}