Imports a singe publication specified by a remote database cross reference.

Parameters

$pub_dbxref: The unique database ID for the record to update. This value must be of the format DB_NAME:ACCESSION where DB_NAME is the name of the database (e.g. PMID or AGL) and the ACCESSION is the unique identifier for the record in the database.

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

$do_update: If set to TRUE then the publication will be updated if it already exists in the database.

Related topics

File

tripal_chado/api/modules/tripal_chado.pub.api.inc, line 340

Provides API functions specificially for managing publication records in Chado.

Code

function chado_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update = TRUE) {
  $num_to_retrieve = 1;
  $pager_id = 0;
  $page = 0;
  $num_pubs = 0;
  $pub_id = NULL;

  module_load_include('inc', 'tripal_chado', 'includes/loaders/tripal_chado.pub_importers');

  print "\nNOTE: Loading of publications is performed using a database transaction. \n" .
    "If the load fails or is terminated prematurely then the entire set of \n" .
    "insertions/updates is rolled back and will not be found in the database\n\n";

  $transaction = db_transaction();
  try {
    if (preg_match('/^(.*?):(.*?)$/', $pub_dbxref, $matches)) {
      $dbname = $matches[1];
      $accession = $matches[2];

      $criteria = array(
        'num_criteria' => 1,
        'remote_db' => $dbname,
        'criteria' => array(
          '1' => array(
            'search_terms' => "$dbname:$accession",
            'scope' => 'id',
            'operation' => '',
            'is_phrase' => 0,
          ),
        ),
      );
      $remote_db = $criteria['remote_db'];
      $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
      $pubs = $results['pubs'];
      $search_str = $results['search_str'];
      $total_records = $results['total_records'];
      tripal_pub_add_publications($pubs, $do_contact, $do_update);
    }

    // For backwards compatibility check to see if the legacy pub module
    // is enabled. If so, then sync the nodes.
    if (module_exists('tripal_pub')) {

      // Sync the newly added publications with Drupal.
      print "Syncing publications with Drupal...\n";
      chado_node_sync_records('pub');

      // If any of the importers wanted to create contacts from the authors 
      // then sync them.
      if ($do_contact) {
        print "Syncing contacts with Drupal...\n";
        chado_node_sync_records('contact');
      }
    }
  }
  catch (Exception $e) {
    $transaction->rollback();
    print "\n"; // make sure we start errors on new line
    watchdog_exception('T_pub_import', $e);
    print "FAILED: Rolling back database changes...\n";
    return;
  }
}