Adds publications that have been retrieved from a remote database and consolidated into an array of details.

Parameters

$pubs: An array containing a list of publications to add to Chado. The array contains a set of details for the publication.

$do_contact: Set to TRUE if authors should automatically have a contact record added to Chado.

$update: If set to TRUE then publications that already exist in the Chado database will be updated, whereas if FALSE only new publications will be added

Return value

Returns an array containing the number of publications that were inserted, updated, skipped and which had an error during import.

Related topics

File

tripal_pub/includes/tripal_pub.pub_importers.inc, line 873

Management of importers

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 = '';
    $pub_id = tripal_pub_add_publication($pub, $action, $do_contact, $update);
    if ($pub_id) {
      // add the publication cross reference (e.g. to PubMed)
      if ($pub_id and $pub['Publication Dbxref']) {
        $dbxref = array();
        if (preg_match('/^(.*?):(.*?)$/', trim($pub['Publication Dbxref']), $matches)) {
          $dbxref['db_name'] = $matches[1];
          $dbxref['accession'] = $matches[2];
        }
        else {
          tripal_report_error(
          'tripal_pub', 
          TRIPAL_ERROR, 
          'Unable to extract the dbxref to be associated with the publication (pub ID=@pub_id) from @dbxref. This reference should be [database-name]:[accession]', 
          array('@pub_id' => $pub_id, '@dbxref' => $pub['Publication Dbxref'])
          );
        }
        $pub_dbxref = tripal_associate_dbxref('pub', $pub_id, $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;
}