function tripal_execute_active_pub_importers

2.x tripal_pub.pub_importers.inc tripal_execute_active_pub_importers($report_email = FALSE, $do_update = FALSE)
3.x tripal_chado.module.DEPRECATED.api.inc tripal_execute_active_pub_importers($report_email = false, $do_update = false)

Imports all publications for all active import setups.

Parameters

$report_email: A list of email address, separated by commas, that should be notified once importing has completed

$do_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

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_execute_active_pub_importers()
drush_tripal_pub_trp_import_pubs in tripal_pub/tripal_pub.drush.inc
Imports publications into Chado
tripal_pub_import_publications in tripal_pub/api/tripal_pub.DEPRECATED.inc
1 string reference to 'tripal_execute_active_pub_importers'
tripal_pub_import_publications in tripal_pub/api/tripal_pub.DEPRECATED.inc

File

tripal_pub/includes/tripal_pub.pub_importers.inc, line 1471
Management of importers

Code

function tripal_execute_active_pub_importers($report_email = FALSE, $do_update = FALSE) {
  $num_to_retrieve = 100;
  $page = 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";

  // start the transaction
  $transaction = db_transaction();

  try {
    // get all of the loaders
    $args = array();
    $sql = "SELECT * FROM {tripal_pub_import} WHERE disabled = 0 ";
    $results = db_query($sql, $args);
    $do_contact = FALSE;
    $reports = array();
    foreach ($results as $import) {
      $page = 0;
      print "Executing importer: '" . $import->name . "'\n";
      // keep track if any of the importers want to create contacts from authors
      if ($import->do_contact == 1) {
        $do_contact = TRUE;
      }
      $criteria = unserialize($import->criteria);
      $remote_db = $criteria['remote_db'];
      do {
        // retrieve the pubs for this page. We'll retreive 100 at a time
        $results = tripal_get_remote_pubs($remote_db, $criteria, $num_to_retrieve, $page);
        $pubs = $results['pubs'];
        $reports[$import->name] = tripal_pub_add_publications($pubs, $import->do_contact, $do_update);
        $page++;
      } 
      // continue looping until we have a $pubs array that does not have
      // our requested numer of records.  This means we've hit the end
       while (count($pubs) == $num_to_retrieve);
    }

    // sync the newly added publications with Drupal. If the user
    // requested a report then we don't want to print any syncing information
    // so pass 'FALSE' to the sync call
    print "Syncing publications with Drupal...\n";
    chado_node_sync_records('pub');

    // Iterate through each of the reports and generate a final report with
    // HTML links.
    $HTML_report = '';
    if ($report_email) {
      $HTML_report .= "<html>";
      global $base_url;
      foreach ($reports as $importer => $report) {
        $total = count($report['inserted']);
        $HTML_report .= "<b>$total new publications from importer: $importer</b><br><ol>\n";
        foreach ($report['inserted'] as $pub) {
          $item = $pub['Title'];
          if (array_key_exists('pub_id', $pub)) {
            $item = l($pub['Title'], "$base_url/pub/" . $pub['pub_id']);
          }
          $HTML_report .= "<li>$item</li>\n";
        }
        $HTML_report .= "</ol>\n";
      }
      $HTML_report .= "</html>";
      $site_email = variable_get('site_mail', '');
      $params = array(
        'message' => $HTML_report
      );
      drupal_mail('tripal_pub', 'import_report', $report_email, language_default(), $params, $site_email, TRUE);
    }

    // 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";
}