File

tripal_pub/api/tripal_pub.api.inc, line 359

The Tripal Pub API

Code

function tripal_pub_add_publications($pubs, $do_contact, $update = FALSE) {
  $report = array();
  $report['error'] = 0;
  $report['inserted'] = array();
  $report['skipped'] = array();
  $total_pubs = count($pubs);

  // iterate through the publications and add each one
  $i = 1;
  foreach ($pubs as $pub) {
    $memory = number_format(memory_get_usage()) . " bytes";
    print "Processing $i of $total_pubs. Memory usage: $memory.\r";

    // add the publication to Chado
    $action = '';

    // make sure the publication has a citation before trying to add. The citation
    // becomes the uniquename for the pub.  If it doesn't exist then the importer
    // couldn't create one because the pub type is not handled, so skip it
    if (!$pub['Citation']) {
      $action = 'skipped';
    }
    else {
      $pub_id = tripal_pub_add_publication($pub, $action, $do_contact, $update);
    }

    if ($pub_id) {
      // add the publication cross reference (e.g. to PubMed)
      if ($pub['Publication Dbxref']) {
        $pub_dbxref = tripal_pub_add_pub_dbxref($pub_id, $pub['Publication Dbxref']);
      }
      $pub['pub_id'] = $pub_id;
    }

    switch ($action) {
      case 'error':
        $report['error']++;
        break;
      case 'inserted':
        $report['inserted'][] = $pub;
        break;
      case 'updated':
        $report['updated'][] = $pub;
        break;
      case 'skipped':
        $report['skipped'][] = $pub;
        break;
    }
    $i++;
  }
  print "\n";
  return $report;
}