File

tripal_pub/includes/pub_importers.inc, line 52

Code

function tripal_pub_importer_setup($action = 'new', $pub_import_id = NULL) {
  global $pager_total, $pager_total_items;

  $pager_id = 0;
  $limit = 20;

  // make sure the tripal_pub and tripal_contact ontologies are loaded
  $values = array('name' => 'tripal_pub');
  $tpub_cv = tripal_core_chado_select('cv', array('cv_id'), $values);
  if (count($tpub_cv) == 0) {
    drupal_set_message(t('Before importing publications you must first ') . l(t('load the Tripal Pub Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
  }
  $values = array('name' => 'tripal_contact');
  $tpub_cv = tripal_core_chado_select('cv', array('cv_id'), $values);
  if (count($tpub_cv) == 0) {
    drupal_set_message(t('If you want to create contact pages for authors, you must first ') . l(t('load the Tripal Contact Ontology'), 'admin/tripal/tripal_cv/obo_loader'), 'error');
  }

  // generate the search form
  $form = drupal_get_form('tripal_pub_importer_setup_form', $pub_import_id, $action);

  $output = l("Return to publication importers list", "admin/tripal/tripal_pub/import_list");
  $output .= $form;

  // retrieve any results
  $remote_db = $_SESSION['tripal_pub_import']['remote_db'];
  $num_criteria = $_SESSION['tripal_pub_import']['num_criteria'];
  $days = $_SESSION['tripal_pub_import']['days'];

  $search_array = array();
  $search_array['remote_db'] = $remote_db;
  $search_array['num_criteria'] = $num_criteria;
  $search_array['days'] = $days;
  for ($i = 1; $i <= $num_criteria; $i++) {
    $search_array['criteria'][$i]['search_terms'] = $_SESSION['tripal_pub_import']['criteria'][$i]['search_terms'];
    $search_array['criteria'][$i]['scope'] = $_SESSION['tripal_pub_import']['criteria'][$i]['scope'];
    $search_array['criteria'][$i]['is_phrase'] = $_SESSION['tripal_pub_import']['criteria'][$i]['is_phrase'];
    $search_array['criteria'][$i]['operation'] = $_SESSION['tripal_pub_import']['criteria'][$i]['operation'];
  }


  if ($_SESSION['tripal_pub_import']['perform_search']) {
    // get the list of publications from the remote database using the search criteria.
    $pubs = tripal_pub_get_remote_search_results($remote_db, $search_array, $limit, $pager_id);
    //dpm($pubs);

    // generate the pager
    $total_pages = $pager_total[$pager_id];
    $total_items = $pager_total_items[$pager_id];
    $page = isset($_GET['page']) ? $_GET['page'] : '0';
    $pager = theme('pager');

    // iterate through the results and construct the table displaying the publications
    $rows = array();
    $i = $page * $limit + 1;
    if (count($pubs) > 0) {
      foreach ($pubs as $pub) {
        $citation = htmlspecialchars($pub['Citation']);
        $raw_link = '';
        if ($pub['Publication Dbxref']) {
          $raw_link = l('raw', 'admin/tripal/tripal_pub/import/raw/' . $pub['Publication Dbxref'], array('attributes' => array('target' => '_blank')));
        }
        $rows[] = array(
          number_format($i),
          $citation,
          $raw_link,
        );
        $i++;
      }
    }
    $headers = array('', 'Publication', '');
    $table = theme('table', $headers, $rows);

    // join all to form the results
    $output .= "<br><p><b>Found " . number_format($total_items) .
      ". Page " . ($page + 1) . " of $total_pages. " .
      " Results</b></br>" . $table . '</p>' . $pager;
  }
  return $output;
}