function tripal_import_pub_by_dbxref

2.x tripal_pub.pub_importers.inc tripal_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update)
3.x tripal_chado.module.DEPRECATED.api.inc tripal_import_pub_by_dbxref($pub_dbxref, $do_contact = false, $do_update = true)

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

Publication Module
Integrates the Chado Publication module with Drupal Nodes & Views, as well as, provides the ability to import publication from PubMed
2 calls to tripal_import_pub_by_dbxref()
drush_tripal_pub_trp_import_pubs in tripal_pub/tripal_pub.drush.inc
Imports publications into Chado
tripal_pub_import_by_dbxref in tripal_pub/api/tripal_pub.DEPRECATED.inc

File

tripal_pub/includes/tripal_pub.pub_importers.inc, line 1746
Management of importers

Code

function tripal_import_pub_by_dbxref($pub_dbxref, $do_contact = FALSE, $do_update) {
  $num_to_retrieve = 1;
  $pager_id = 0;
  $page = 0;
  $num_pubs = 0;

  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'];
      $pub_id = tripal_pub_add_publications($pubs, $do_contact, $do_update);
    }

    // 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;
  }

  print "Done.\n";
}