File

tripal_cv/includes/obo_loader.inc, line 352

Tripal Ontology Loader

Code

function tripal_cv_obo_load_typedefs($defaultcv, $newcvs, $default_db, $jobid) {
  $sql = "
    SELECT * 
    FROM tripal_obo_temp
    WHERE type = 'Typedef' 
  ";
  $typedefs = chado_query($sql);

  $sql = "
    SELECT count(*) as num_terms
    FROM tripal_obo_temp
    WHERE type = 'Typedef'     
  ";
  $result = db_fetch_object(chado_query($sql));
  $count = $result->num_terms;

  // calculate the interval for updates
  $interval = intval($count * 0.0001);
  if ($interval < 1) {
    $interval = 1;
  }
  $i = 0;
  while ($typedef = db_fetch_object($typedefs)) {
    $term = unserialize(base64_decode($typedef->stanza));

    // update the job status every interval
    if ($jobid and $i % $interval == 0) {
      $complete = ($i / $count) * 33.33333333;
      tripal_job_set_progress($jobid, intval($complete + 33.33333333));
      printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
    }

    tripal_cv_obo_process_term($term, $defaultcv->name, 1, $newcvs, $default_db);

    $i++;
  }
  // set the final status
  if ($jobid) {
    if ($count > 0) {
      $complete = ($i / $count) * 33.33333333;
    }
    else {
      $complete = 33.33333333;
    }
    tripal_job_set_progress($jobid, intval($complete + 33.33333333));
    printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
  }
  return 1;
}