Add database reference to cvterm

Related topics

File

tripal_cv/includes/obo_loader.inc, line 940

Tripal Ontology Loader

Code

function tripal_cv_obo_add_cvterm_dbxref($cvterm, $xref) {

  $dbname = preg_replace('/^(.+?):.*$/', '$1', $xref);
  $accession = preg_replace('/^.+?:\s*(.*?)(\{.+$|\[.+$|\s.+$|\".+$|$)/', '$1', $xref);
  $description = preg_replace('/^.+?\"(.+?)\".*?$/', '$1', $xref);
  $dbxrefs = preg_replace('/^.+?\[(.+?)\].*?$/', '$1', $xref);

  if (!$accession) {
    tripal_cv_obo_quiterror();
    watchdog("T_obo_loader", "Cannot add a dbxref without an accession: '$xref'", NULL, WATCHDOG_WARNING);
    return FALSE;
  }

  // if the xref is a database link, handle that specially
  if (strcmp($dbname, 'http') == 0) {
    $accession = $xref;
    $dbname = 'URL';
  }

  // add the database
  $db = tripal_db_add_db($dbname);
  if (!$db) {
    tripal_cv_obo_quiterror("Cannot find database '$dbname' in Chado.");
  }

  // now add the dbxref
  $dbxref = tripal_cv_obo_add_dbxref($db->db_id, $accession, '', $description);
  if (!$dbxref) {
    tripal_cv_obo_quiterror("Cannot find or add the database reference (dbxref)");
  }

  // finally add the cvterm_dbxref but first check to make sure it exists
  $values = array(
    'cvterm_id' => $cvterm->cvterm_id,
    'dbxref_id' => $dbxref->dbxref_id,
  );
  $options = array('statement_name' => 'sel_cvtermdbxref_cvdb');
  $result = tripal_core_chado_select('cvterm_dbxref', array('*'), $values, $options);
  if (count($result) == 0) {
    $ins_options = array(
      'statement_name' => 'ins_cvtermdbxref_cvdb',
      'return_record' => FALSE
    );
    $result = tripal_core_chado_insert('cvterm_dbxref', $values, $ins_options);
    if (!$result) {
      tripal_cv_obo_quiterror("Cannot add cvterm_dbxref: $xref");
      return FALSE;
    }
  }

  return TRUE;
}