OBO files are divided into a typedefs section and a 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

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

$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.

Related topics

File

tripal_cv/includes/tripal_cv.obo_loader.inc, line 689

Functions to aid in loading ontologies into the chado cv module

Code

function tripal_cv_obo_process_terms($defaultcv, $jobid = NULL, &$newcvs, $default_db) {

  $i = 0;

  // iterate through each term from the OBO file and add it
  $sql = "
    SELECT * FROM {tripal_obo_temp}
    WHERE type = 'Term'
    ORDER BY id
  ";
  $terms = chado_query($sql);

  $sql = "
    SELECT count(*) as num_terms
    FROM {tripal_obo_temp}
    WHERE type = 'Term'
  ";
  $result = chado_query($sql)->fetchObject();
  $count = $result->num_terms;

  // calculate the interval for updates
  $interval = intval($count * 0.0001);
  if ($interval < 1) {
    $interval = 1;
  }
  foreach ($terms as $t) {
    $term = unserialize(base64_decode($t->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 + 66.666666));
      printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
    }

    // add/update this term
    if (!tripal_cv_obo_process_term($term, $defaultcv->name, 0, $newcvs, $default_db)) {
      tripal_cv_obo_quiterror("Failed to process terms from the ontology");
    }

    $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 + 66.666666));
    printf("%d of %d records. (%0.2f%%) Memory: %s bytes\r", $i, $count, $complete * 3, number_format(memory_get_usage()));
  }

  return 1;
}