OBO files are divided into a typedefs terms section and vocabulary terms section. This function loads the typedef terms from the OBO.

Parameters

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

$newcvs: An associative array of controlled vocabularies for this OBO. The key must be the name of the vocabulary and the value the cv_id from the cv table of chado.

$default_db: The name of the default database.

$jobid: The job_id of the job from the Tripal jobs management system.

Related topics

File

tripal_cv/includes/tripal_cv.obo_loader.inc, line 627

Functions to aid in loading ontologies into the chado cv module

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'
  ";
  $result = chado_query($sql)->fetchObject();
  $count = $result->num_terms;

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

    // update the job status every interval
    if ($jobid and $i % $interval == 0) {
      $complete = ($i / $count) * 33.33333333;
      tripal_set_job_progress($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 {
      $complete = 33.33333333;
    }
    tripal_set_job_progress($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;
}