Adds a database reference to a cvterm

Parameters

cvterm: The database object of the cvterm to which the synonym will be added.

xref: The cross refernce. It should be of the form from the OBO specification

Related topics

File

tripal_cv/includes/tripal_cv.obo_loader.inc, line 1265

Functions to aid in loading ontologies into the chado cv module

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 (!$accession) {
    tripal_cv_obo_quiterror();
    tripal_report_error("T_obo_loader", TRIPAL_WARNING, "Cannot add a dbxref without an accession: '$xref'", NULL);
    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_insert_db(array('name' => $dbname));
  if (!$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,
  );
  $result = chado_select_record('cvterm_dbxref', array('*'), $values);
  if (count($result) == 0) {
    $ins_options = array('return_record' => FALSE);
    $result = chado_insert_record('cvterm_dbxref', $values, $ins_options);
    if (!$result) {
      tripal_cv_obo_quiterror("Cannot add cvterm_dbxref: $xref");
      return FALSE;
    }
  }

  return TRUE;
}