function chado_execute_active_pub_importers

3.x tripal_chado.pub.api.inc chado_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

Chado Publication
Provides API functions specificially for managing publication records in Chado.
2 calls to chado_execute_active_pub_importers()
drush_tripal_chado_trp_import_pubs in tripal_chado/tripal_chado.drush.inc
Imports publications into Chado
tripal_execute_active_pub_importers in tripal_chado/api/modules/tripal_chado.module.DEPRECATED.api.inc
Imports all publications for all active import setups.

File

tripal_chado/api/modules/tripal_chado.pub.api.inc, line 416
Provides API functions specificially for managing publication records in Chado.

Code

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

    // For backwards compatibility check to see if the legacy pub module
    // is enabled. If so, then sync the nodes.
    if (module_exists('tripal_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";
}