/7.x/modules/cdm_dataportal/cdm_dataportal.module - EDIT - EDIT Project Management

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cdm-dataportal/7.x/modules/cdm_dataportal/cdm_dataportal.module @ c9ffb64e

       <?php
       /**
        * @file
        * Module to provide a CDM Dataportal.
+       *
        * @copyright
        *   (C) 2007-2012 EDIT
        *   European Distributed Institute of Taxonomy
        *   http://www.e-taxonomy.eu
+       *
        *   The contents of this module are subject to the Mozilla
        *   Public License Version 1.1.
        * @see http://www.mozilla.org/MPL/MPL-1.1.html
+       *
        * @author
        *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
        *   - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
        */
       module_load_include('php', 'cdm_dataportal', 'node_types');
       module_load_include('php', 'cdm_dataportal', 'settings');
       module_load_include('php', 'cdm_dataportal', 'help');
       module_load_include('php', 'cdm_dataportal', 'cdm_dataportal.search');
       module_load_include('inc', 'cdm_dataportal', 'includes/pages');
       module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
       module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
       module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
       module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
       module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.bibliography');
       module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
       module_load_include('php', 'cdm_dataportal', 'classes/footnote');
       module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
       module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
       /**
       * loads external java script files asynchronously.
+      *
       * @param unknown_type $script_url
       */
       function drupal_add_js_async($script_url, $callback){
         drupal_add_js("
               jQuery(document).ready(function() {
                 jQuery.ajax({
                   url: '" . $script_url . "',
                   dataType: 'script',
                   cache: true, // otherwise will get fresh copy every page load
                   success: function() {
                         " . $callback . "
+                  }
                 });
               });"
         , 'inline');
+      }
       /**
        * @param unknown_type $link_element_selector
        * @param unknown_type $progress_element_selector
        */
       function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
         $callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
         drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
         //   drupal_add_js("
         //   	  if (Drupal.jsEnabled) {
         //         $(document).ready(function() {
         //       		$('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
         //         });
         //       }", 'inline');
+        }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _add_js_treeselector() {
         // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
         drupal_add_js("
             jQuery(document).ready(function() {
                jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
                     jQuery('#cdm-taxonomictree-selector-form').submit();
                 });
             });
           ",
           array(
             'type' => 'inline',
             'scope' => 'footer'
+          )
         );
+      }
       function _add_js_openlayers() {
         $openlayers = '/js/OpenLayers-2.11/OpenLayers.js';
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers, array(
             'type' => 'file',
             'weight' => JS_LIBRARY,
             'cache' => FALSE,
         ));
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _add_js_openlayers_map() {
         _add_js_openlayers();
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/openlayers_map.js');
         $gmap_api_key = variable_get('gmap_api_key', 'ABQIAAAAFho6eHAcUOTHLmH9IYHAeBRi_j0U6kJrkFvY4-OX2XYmEAa76BTsyMmEq-tn6nFNtD2UdEGvfhvoCQ');
         $baseLayers = variable_get('baselayers', array());
         if (!is_array($baseLayers) || count($baseLayers) == 0) {
           $baseLayers = array(
             'metacarta_vmap0' => 'Metacarta Vmap0',
             'PREFERRED' => 'metacarta_vmap0',
           );
+        }
         $layerNames = '';
         foreach ($baseLayers as $layerName => $layerLabel) {
           if ($layerName == 'PREFERRED') {
             $preferredLayer = $baseLayers['PREFERRED'];
+          }
           else {
             $layerNames .= ($layerNames ? ', ' : '') . "'$layerName'";
+          }
+        }
         if (isset($baseLayers['gmap']) || isset($baseLayers['gsat']) || isset($baseLayers['ghyb'])) {
           drupal_add_html_head('<script src=http://maps.google.com/maps?file=api&amp;v=2&amp;sensor=false&amp;key=' . $gmap_api_key . '" type="text/javascript"></script>', $key = NULL /* TODO Set this variable. */);
           drupal_add_js('http://dev.virtualearth.net/mapcontrol/mapcontrol.ashx?v=6.1', array('type' => 'external'));
+        }
         $edit_map_service = get_edit_map_service_settings();
         // window.onload - is executed when the document and images etc is fully loaded
         // Query(document).ready - is executed much earlier, when the DOM is loaded
         drupal_add_js("
                 jQuery(document).ready(function() {
                       window.onload = function () {
           			  // ---
                         jQuery('#openlayers_map').cdm_openlayers_map(
                          '" . $edit_map_service['base_uri'] . "',
                          '" . $edit_map_service['version'] . "',
+                         {
                           legendPosition: 3,
                           displayWidth: '" . variable_get('cdm_dataportal_geoservice_display_width', FALSE) . "',
                           boundingBox: '" . variable_get('cdm_dataportal_geoservice_bounding_box', FALSE) . "',
                           distributionOpacity: '" . variable_get('cdm_dataportal_geoservice_distributionOpacity', '0.5') . "',
                           legendOpacity: '" . variable_get('cdm_dataportal_geoservice_legendOpacity', '0.5') . "',
                           showLayerSwitcher: " . (variable_get('cdm_dataportal_geoservice_showLayerSwitcher', TRUE) ? 'true' : 'false') . ",
                           baseLayerNames: [" . $layerNames . "],
                           defaultBaseLayerName: '" . $preferredLayer . "',
+                     	  }
                       );
                      	// ---
       			  };
                 });
               ", array('type' => 'inline'));
+      }
       /**
        * @todo Enter description here ...
+       *
        * @param unknown_type $width
        * @param unknown_type $bounding_box
        * @param unknown_type $occurrenceQuery
        * @param unknown_type $distributionQuery
        * @param unknown_type $legendFormatQuery
        * @param unknown_type $map_caption
+       *
        * @return unknown
        */
       function get_image_map($width, $bounding_box = FALSE, $occurrenceQuery = FALSE, $distributionQuery = FALSE, $legendFormatQuery = FALSE, $map_caption = FALSE) {
         // Additional query parameters as set in the data portal admin section.
         $labels_on = variable_get('cdm_dataportal_geoservice_labels_on', 0);
         $query_string = '&image=true&recalculate=false&legend=1&ms=' . $width
           . ($bounding_box ? '&bbox=' . $bounding_box : '')
           . ($labels_on ? '&label=' . $labels_on : '');
         if ($map_caption) {
           $query_string .= '&mlp=3&mc_s=Georgia,15,blue&mc=' . $map_caption;
+        }
         if (get_edit_map_service_version_number() >= 1.1) {
           // Either occurrence or distribution - combined maps will be possible
           // in the future.
           if ($occurrenceQuery) {
             // @todo Fix $occurrenceQuery.
             $occurrenceQuery = str_replace("&image=false", "", $occurrenceQuery);
             // $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
             // Will be replaced below.. HACK!!!
             $occurrenceQuery .= '&l=tdwg4&as=';
             $query_string .= "&" . $occurrenceQuery;
+          }
           elseif ($distributionQuery) {
             $query_string .= "&" . $distributionQuery;
+          }
           // Apply Plain Image map settings special for version >= 1.1.
           /*
           example : title=a:Naturalized++non-invasive
           &ad=cyprusdivs:bdcode:a:5&as=a:ff9900,,0.1,&l=tdwg4
           &ms=500&bbox=32,34,35,36&img=true&legend=1&mlp=3
           &mc_s=Georgia,15,blue&mc=&recalculate=false
           http://edit.br.fgov.be/edit_wp5/v1/rest_gen.php?
           l=background_gis:b,cyprusdivs&ad=cyprusdivs%3Abdcode%3Aa%3A8%2C4
           &as=a%3A339966%2C%2C0.1%2C|b:0000ff,,
           &bbox=32%2C34%2C35%2C36&img=true&legend=1&mc=&mc_s=Georgia%2C15%2Cblue
           &mlp=3&ms=500&recalculate=false&title=a%3Aindigenous
           */
           $map_service_script_name = "rest_gen.php";
           $bgcolor_areaStyleId = "y";
           $baselayer_areaStyleId = "z";
           $bgcolor_layer = '';
           $additional_area_styles = array();
           // Background color:
           if (variable_get('map_bg_color', '')) {
             $bgcolor_layer = "background_gis:" . $bgcolor_areaStyleId;
             $additional_area_styles[] = $bgcolor_areaStyleId . ":" . variable_get('map_bg_color', '') . ",,";
+          }
           // TODO HACK to replace the default base layer which currently is tdwg4 !!!
           // only needed for distribution maps.
           if (strpos($query_string, "?l=") !== FALSE) {
             $layer_param_token = "?l=";
+          }
           else {
             $layer_param_token = "&l=";
+          }
           if (strpos($query_string, "?as=") !== FALSE) {
             $areystyle_param_token = "?as=";
+          }
           else {
             $areystyle_param_token = "&as=";
+          }
           if (variable_get('map_base_layer', '')) {
             $query_string = str_replace($layer_param_token . "tdwg4", "$layer_param_token" . variable_get('map_base_layer', '') . ":" . $baselayer_areaStyleId, $query_string);
+          }
           else {
             $query_string = str_replace($layer_param_token . "tdwg4", $layer_param_token . "tdwg4:" . $baselayer_areaStyleId . ",", $query_string);
+          }
           if ($bgcolor_layer) {
             $query_string = str_replace($layer_param_token, $layer_param_token . $bgcolor_layer . ",", $query_string);
+          }
           if (variable_get('map_base_layer_style', '')) {
             $additional_area_styles[] = $baselayer_areaStyleId . ":" . variable_get('map_base_layer_style', '');
+          }
           foreach ($additional_area_styles as $as) {
             $query_string = str_replace($areystyle_param_token, $areystyle_param_token . $as . "|", $query_string);
+          }
+        }
         else {
           // Pre 1.1. version of map service.
           if ($occurrenceQuery) {
             $map_service_script_name = "point.php";
             // Fix $occurrenceQuery.
             $occurrenceQuery = str_replace("&image=false", "", $occurrenceQuery);
             // $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
             $occurrenceQuery .= '&l=v:e_w_0';
             $query_string .= "&" . $occurrenceQuery;
+          }
           elseif ($distributionQuery) {
             $query_string .= "&" . $distributionQuery;
             $map_service_script_name = "areas.php";
+          }
+        }
         $mapUri = url(get_edit_map_service_full_uri() . '/' . $map_service_script_name . '?' .  $query_string);
         $out = '<img class="distribution_map" src="' . $mapUri . '" alt="Map" />';
         // Showing map caption.
         if ($map_caption) {
           // FIXME: replace <br> by according css style.
           $out .= '<div class="distribution_map_caption">' . $map_caption . '</div>' . '<br />';
           $out .= '</div>';
+        }
         return $out;
+      }
       /**
        * @todo Enter description here ...
+       *
        * @param unknown_type $width
        * @param unknown_type $bounding_box
        * @param unknown_type $occurrenceQuery
        * @param unknown_type $distributionQuery
        * @param unknown_type $legendFormatQuery
        * @param unknown_type $map_caption
+       *
        * @return unknown
        */
       function get_openlayers_map($width, $bounding_box = FALSE, $occurrenceQuery = FALSE, $distributionQuery = FALSE, $legendFormatQuery = FALSE, $map_caption = FALSE) {
         _add_js_openlayers_map();
         $out = '<div id="openlayers">';
         $out .= '<div id="openlayers_map" class="smallmap"';
         if($width) {
           $out .= ' style="width: ' . $width . 'px; height:' . ($width / 2) . 'px"';
+        }
         // Additional query parameters as set in the data portal admin section.
         $labels_on = variable_get('cdm_dataportal_geoservice_labels_on', 0);
         $openlayers_map_query_string = '&img=false&ms=' . $width
           . ($bounding_box ? '&bbox=' . $bounding_box : '')
           . ($labels_on ? '&label=' . $labels_on : '');
         if ($occurrenceQuery) {
           // @todo Fix $occurrenceQuery.
       //     $occurrenceQuery .= '&bbox=-180,-90,180,90';
           $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
           // $occurrenceQuery .= '&l=v:e_w_0';
           // TODO add to cdm service?
           $occurrenceQuery .= '&legend=0';
           $out .= ' occurrenceQuery="' . $occurrenceQuery . '&' . $openlayers_map_query_string . '"';
+        }
         if ($distributionQuery) {
           $out .= ' distributionQuery="' . $distributionQuery . '&' . $openlayers_map_query_string . '"';
+        }
         if ($legendFormatQuery) {
           $out .= ' legendFormatQuery="' . $legendFormatQuery . '"';
+        }
         $out .= '></div></div>';
         // Showing map caption.
         if ($map_caption) {
           // FIXME: replace <br> by according css style.
           $out .= '<div class="distribution_map_caption">' . $map_caption . '</div>' . '<br />';
           $out .= '</div>';
+        }
         return $out;
+      }
       /* ====================== hook implementations ====================== */
       /**
        * Implements hook_permission().
+       *
        * Valid permissions for this module.
+       *
        * @return array
        *   An array of valid permissions for the portfolio module.
        */
       function cdm_dataportal_permission() {
         return array(
           'administer cdm_dataportal' => array(
             'title' => t('administer cdm_dataportal'),
             'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
           ),
           'cdm_dataportal view notes' => array(
             'title' => t('cdm_dataportal view notes'),
             'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
           ),
           // TODO Which other permissions are required?
           // -> check the WP6 requirements document.
         );
+      }
       /**
        * Implements hook_menu().
        */
       function cdm_dataportal_menu() {
         $items = array();
         // @see settings.php.
         cdm_dataportal_menu_admin($items);
         cdm_dataportal_menu_help($items);
         $items['cdm_dataportal/names'] = array(
           'page callback' => 'cdm_dataportal_view_names',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
         );
         // Optional callback arguments: page.
         $items['cdm_dataportal/taxon'] = array(
           'page callback' => 'cdm_dataportal_taxon_page_view',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/name'] = array(
           'page callback' => 'cdm_dataportal_name_page_view',
             /*
           'page arguments' => array(
              'taxon_name_uuid',
              'taxon_to_hide_uuid',
              'synonym_uuid' => NULL
             ),
             */
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/reference'] = array(
           'page callback' => 'cdm_dataportal_view_reference',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/reference/list'] = array(
           'page callback' => 'cdm_dataportal_view_reference_list',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/media'] = array(
           'page callback' => 'cdm_dataportal_view_media',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments:
           // uuid, mediarepresentation_uuid, part_uuid or part#.
         );
         $items['cdm_dataportal/polytomousKey'] = array(
           'page callback' => 'cdm_dataportal_view_polytomousKey',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: polytomousKey->uuid.
         );
         $items['cdm_dataportal/search'] = array(
           'page callback' => 'cdm_dataportal_view_search_advanced',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
         );
         $items['cdm_dataportal/search/advanced'] = array(
           'title' => 'Advanced',
           'page callback' => 'cdm_dataportal_view_search_advanced',
           'access arguments' => array('access content'),
           'type' => MENU_DEFAULT_LOCAL_TASK,
         );
         $items['cdm_dataportal/search/taxon_by_description'] = array(
           'title' => 'By description full text',
           'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
           'access arguments' => array('access content'),
           'type' => MENU_LOCAL_TASK,
         );
         $items['cdm_dataportal/search/results/taxon'] = array(
           'page callback' => 'cdm_dataportal_view_search_results_taxon',
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
         );
         /*
          $items['cdm/xml2json'] = array(
          'page callback' => 'cdm_view_xml2json',
          'access arguments' => array('access content'),
          'type' => MENU_CALLBACK,
          );
          */
         // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
         // User configuration of cdm_dataportal.
         $items['user/%/cdm_dataportal'] = array(
           'title' => 'cdm_dataportal',
           'access arguments' => array('access content'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_dataportal_user_form'),
           'type' => MENU_LOCAL_TASK,
           'weight' => 10,
         );
         // }
         // 'May not cache' in D5.
         // --- Local tasks for Taxon.
         $items['cdm_dataportal/name/%'] = array(
           // 'page callback' => 'cdm_dataportal_view_name',
           'page callback' => 'cdm_dataportal_name_page_view',
           'page arguments' => array(2, 3, 4),
           'access arguments' => array('access content'),
           'type' => MENU_CALLBACK,
         );
         if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
           $items['cdm_dataportal/taxon/%'] = array(
             'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access content'),
             'type' => MENU_CALLBACK,
             'weight' => 1,
             'page arguments' => array(2, "description")
             , // Expected callback arguments: name_uuid.
           );
           $items['cdm_dataportal/taxon/%/all'] = array(
             'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access content'),
             'type' => MENU_CALLBACK,
             'weight' => 2,
             'page arguments' => array(2, "all")
             , // Expected callback arguments: name_uuid.
           );
           $items['cdm_dataportal/taxon/%/description'] = array(
             'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access content'),
             'type' => MENU_DEFAULT_LOCAL_TASK,
             'weight' => 2,
             'page arguments' => array(2, "description")
             , // Expected callback arguments: name_uuid.
           );
           $items['cdm_dataportal/taxon/%/synonymy'] = array(
             'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy')),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 4,
             'page arguments' => array(2, "synonymy", 4)
             , // Expected callback arguments: name_uuid.
           );
           $items['cdm_dataportal/taxon/%/images'] = array(
             'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Images')),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 5,
             'page arguments' => array(2, "images")
             , // Expected callback arguments: name_uuid.
           );
           $items['cdm_dataportal/taxon/%/specimens'] = array(
             'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens')),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 6,
             'page arguments' => array(2, "specimens")
             , // Expected callback arguments: name_uuid.
           );
           $items['cdm_dataportal/taxon/%/keys'] = array(
             'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys')),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 6,
             'page arguments' => array(2, "keys")
             , // Expected callback arguments: name_uuid.
           );
+        }
         return $items;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_init() {
         drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
         // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
         drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
+      }
       /**
        * The function generate form for own user cdm dataportal configurations.
        */
       function cdm_dataportal_user_form($form, &$form_state) {
         global $user;
         $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
         $form['check'] = array(
           '#type' => 'checkbox',
           '#title' => t('Activate user default configuration'),
           '#default_value' => variable_get($checkbox_value, 0),
           '#description' => t('Check this if you want configure your own default tab from the below menu.'),
         );
         $form['cdm_dataportal_user_form'] = array(
           '#type' => 'select',
           '#title' => t('Default tab to display'),
           '#default_value' => get_default_taxon_tab(TRUE),
           '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
           '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
                     <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
                     to be renderized will be the synonymy of the accepted taxon and not the above selected tab.'),
         );
         $form['submit'] = array(
           '#type' => 'submit',
           '#value' => t('Submit'),
         );
         return $form;
+      }
       /**
        * Form submission handler for user_form().
+       *
        * Submits the user cdm dataportal configurations.
        */
       function cdm_dataportal_user_form_submit($form, &$form_state) {
         global $user;
         $msg_type = 'status';
         $username = $user->name;
         $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
         // If is the right user the variables are setted.
         if (arg(0) == 'user' && ($uid = arg(1)) && is_numeric($uid) && $user->uid == $uid) {
           $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
           variable_set($variable_to_use . '_active', $form_state['values']['check']);
           variable_set($variable_to_use, $form_state['values']['cdm_dataportal_user_form']);
           if ($form_state['values']['check']) {
             drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
             drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
               '!tab' => $variable[variable_get($variable_to_use, 0)],
               '!user' => $username,
             ))), $msg_type);
+          }
           else {
             drupal_set_message(check_plain(t('The user default tab wont be used for
               the next taxon site, check the box if you want to use the user default configuration.')));
+          }
           // Problem with the user id => variables wont be saved.
+        }
         else {
           $msg_type = 'warning';
           drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
+        }
+      }
       /**
        * Implements hook_block_info().
        */
       function cdm_dataportal_block_info() {
           // $block[0]["info"] = t("CDM DataPortal DevLinks");
           // $block[1]["info"] = t("CDM DataPortal Credits");
           $block["2"]["info"] = t("CDM Search Taxa");
           // $block[3]["info"] = t("CDM Filters");
           $block["4"]["info"] = t("CDM Dataportal Print");
           $block["keys"]["info"] = t("CDM identification keys");
           $block["uses"]["info"] = t("CDM Uses");
           $block["fundedByEDIT"]["info"] = t('Funded by EDIT');
           return $block;
+      }
       /**
        * Implements hook_block_view().
        */
       function cdm_dataportal_block_view($delta) {
         // TODO Rename block deltas (e.g. '2') to readable strings.
         switch ($delta) {
           // case 'delta-1':
           // $block['subject'] = t('Credits');
           // $block['content'] = theme('cdm_credits');
           // return $block;
           case '2':
             $block['subject'] = t('Search taxa');
             $form = drupal_get_form('cdm_dataportal_search_taxon_form');
             $block['content'] = drupal_render($form);
             if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
               $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
+            }
             return $block;
           case '4':
             $block['subject'] = t('<none>');
             $block['content'] = theme('cdm_print_button');
             return $block;
           case "keys":
             $block['subject'] = t('Identification Keys');
             $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
             return $block;
             // Creating a block specific for the Use Interface.
           case "uses":
             $block['subject'] = t('Uses');
             $block['content'] = theme('cdm_block_uses', array('taxonUuid' => NULL));
             return $block;
           case "fundedByEDIT":
             // t('Funded by EDIT');
             $text = '<none>';
             $block['subject'] = $text;
             $img_tag = '<img src="' . drupal_get_path('module', 'cdm_dataportal') . '/images/funded_by_EDIT.png' . '" alt="' . $text . '"/>';
             $block['content'] = l($img_tag, "http://www.e-taxonomy.eu/", array(
               'attributes' => array("target" => "EDIT"),
               'absolute' => TRUE,
               'html' => TRUE,
             ));
             return $block;
+        }
+      }
       /*
        function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
        $_SESSION['cdm'] = NULL;
        if(is_string($cdm_ws_uri_update)){
        $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
+       }
+       }
        function cdm_dataportal_session_validate(){
        if(!isset($_SESSION['cdm']['ws_uri'])){
        $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
        } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
        cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
+       }
+       }
        */
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_taxonomictree_selector() {
         _add_js_treeselector();
         $form = drupal_get_form('cdm_taxonomictree_selector_form');
         $out = drupal_render($form);
         return $out;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_taxonomictree_selector_form($form, &$form_state) {
         $url = url('cdm_api/setvalue/session', array('query' => NULL));
         $form['#action'] = $url;
         $form['var'] = array(
           '#weight' => -3,
           '#type' => 'hidden',
           '#value' => '[cdm][taxonomictree_uuid]',
         );
         $destination_array = drupal_get_destination();
         $destination = $destination_array['destination'];
         $form['destination'] = array(
           '#weight' => -3,
           '#type' => 'hidden',
           '#value' =>  $destination,
         );
         $form['val'] = array(
           '#type' => 'select',
           '#title' => t('Available classifications'),
           '#default_value' => get_taxonomictree_uuid_selected(),
           '#options' => cdm_get_taxontrees_as_options(),
         );
         return $form;
+      }
       /* UNREACHABLE since action of form directly links to view.
        function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
        $_SESSION['cdm']['search'] = $form_values;
        //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
        return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
        //$paramstr = compose_url_prameterstr($form_values);
        //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
+       }
        */
       /* ====================== menu callback functions ====================== */
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       /*
       function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
         static $comment_node_disabled =  0;
         static $comment_node_read_only =  1;
         static $comment_node_read_write =  2;
         if ($form_id == 'node_type_form'
          && isset($form['identity']['type'])
          && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
         ) {
           $form['workflow']['comment'] = array(
             '#type' => 'radios',
             '#title' => t('Default comment setting'),
             '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
             '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
             '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
           );
+        }
+      }
       */
       /**
        * Displays a list of the known taxonomic names.
+       *
        * When the list of taxonomic names is displayed, long lists are split up into
        * multiple pages.
+       *
        * TODO: Parameters are still preliminary.
+       *
        * @param string $beginsWith
        * @param string $page
        *   Page number to diplay defaults to page 1.
        * @param bool $onlyAccepted
        */
       function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
         $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
         /*
         // FIXME the filter for accepted names will be a form element, thus this
         // widget should be generated via form api preferably as block.
         $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
         $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
         $out .= theme('cdm_listof_taxa', $taxonPager);
         return $out;
         */
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
         $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
         return theme('cdm_reference_page', array('reference' => $reference));
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_view_reference_list($pageNumber) {
         $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
         return theme('cdm_reference_pager', array(
           'referencePager' => $referencePager,
           'path' => 'cdm_dataportal/reference/list/',
           ));
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
         $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
         return theme('cdm_media_page', array(
           'media' => $media,
           'mediarepresentation_uuid' => $mediarepresentation_uuid,
           'partId' => $part,
           ));
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _load_taxonBase(&$taxonBase) {
         if (isset($taxonBase->uuid)) {
           $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
           $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
           $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
+        }
+      }
       /**
        * Loads the media associated to the given taxon from the cdm server.
        * The aggregation settings regarding taxon relathionships and
        * taxonnomic childen are taken into account.
+       *
        * The media lists are cached in a static variable.
+       *
        * @param Taxon $taxon
        *   A CDM Taxon entitiy
+       *
        * @return array
        *   An array of CDM Media entities
+       *
        */
       function _load_media_for_taxon($taxon) {
         static $media = NULL;
         if(!isset($media)) {
           $media = array();
+        }
         if (!isset($media[$taxon->uuid])) {
           // --- GET Images --- //
           $mediaQueryParameters = array(
               "type" => "ImageFile",
           );
           $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
           $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
           $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
           $ws_endpoint = NULL;
           if ( variable_get('cdm_images_include_children', 0) == 0) {
             $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
           } else {
             $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
+          }
           $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
               array(
                   $taxon->uuid,
               ),
               queryString($mediaQueryParameters)
              );
+        }
         return $media[$taxon->uuid];
+      }
       /**
+       *
        * @param Taxon $taxon
        *   A CDM Taxon entitiy
+       *
        * @return array
        *   An array of CDM SpecimenOrObservation entities
+       *
       function _load_occurences_for_taxon($taxon){
         static $occurences = NULL;
         if(!isset($occurences)) {
           $occurences = array();
+        }
         if (!isset($occurences[$taxon->uuid])){
           $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
           $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
           $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
           $by_associatedtaxon_query = http_build_query(array(
               'relationshipsInvers' => implode(',', $relationship_choice['invers']),
               'relationships' => implode(',', $relationship_choice['direct']),
               'pageSize' => null // all hits in one page
+          )
           );
           $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
               null,
               $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
           );
           if(isset($pager->records[0])){
             $occurences[$taxon->uuid] =  $pager->records;
+          }
+        }
         return $occurences[$taxon->uuid];
+      }
        */
       /**
        * Gets a Drupal variable, string or array and returns it.
+       *
        * Similar to the variable_get() function of Drupal, except that this function
        * is able to handle arrays correctly. This function is especially useful
        * when dealing with collections of setting form elements (#tree = TRUE).
+       *
        * @param string $variableKey
        *   The Unique key of the Drupal variable in the Drupal variables table.
        * @param string $defaultValueString
        *   A string as for example derived from a CONSTANT.
+       *
        * @return mixed
        *   Returns usally an array, depending on the nature of the variable.
        */
       function mixed_variable_get($variableKey, $defaultValueString) {
         $systemDefaults = unserialize($defaultValueString);
         $storedSettings = variable_get($variableKey, array());
         if (is_array($storedSettings)) {
           $settings = array_merge($systemDefaults, $storedSettings);
+        }
         else {
           $settings = $systemDefaults;
+        }
         return $settings;
+      }
       /**
        * Wrapps the given $html string into a reder array suitable for drupal_render()
+       *
        * @param string $html
        *   the html string, see
        *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
        * @param number $weight
        *   A positive or negative number (integer or decimal).
        *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
+       *
        * @return
        *   A render array
+       *
        */
       function markup_to_render_array($html, $weight = 0) {
         return array(
                 '#markup' => $html,
                 '#weight' => $weight,
             );
+      }
       /**
        * Loads the subgraph of a given PolytomousKeyNode.
+       *
        * Loads the subgraph of the given PolytomousKeyNode recursively from
        * the CDM REST service.
+       *
        * @param mixed $polytomousKeyNode
        *   PolytomousKeyNode passed by reference.
+       *
        * @return void
        */
       function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
         if (!$polytomousKeyNode) {
           return;
+        }
         if ($polytomousKeyNode->class != "PolytomousKeyNode") {
           drupal_set_message(_load_polytomousKeySubGraph() . t('invalid type given.'), 'error');
           return;
+        }
         if (!is_uuid($polytomousKeyNode->uuid)) {
           drupal_set_message(_load_polytomousKeySubGraph() . t('invalid type given.'), 'error');
           return;
+        }
         $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
         if (!$polytomousKeyNode) {
           // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
           return;
+        }
         // Load children.
         foreach ($polytomousKeyNode->children as &$childNode) {
           _load_polytomousKeySubGraph($childNode);
+        }
         // Load subkey.
         $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
         // Load taxon.
         $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
         _load_taxonBase($polytomousKeyNode->taxon);
         return;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
         $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
         $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
         if (is_array($sourcePager->records)) {
           $polytomousKey->sources = $sourcePager->records;
           // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
+        }
         $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
         if (is_array($annotationPager->records)) {
           $polytomousKey->annotations = $annotationPager->records;
+        }
         _load_polytomousKeySubGraph($polytomousKey->root);
         return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
+      }
       /**
        * Creates a taxon page view or a chapter of it.
+       *
        * The taxon page gives detailed information on a taxon, it shows:
        *  - Taxon name.
        *  - Full list of synonyms homotypic synonyms on top, followed by the
        *    heterotypic and finally followed by misapplied names.
        *    The list is ordered historically.
        *  - All description associated with the taxon.
+       *
        * @param string $uuid
        * @param string $chapter
        *   Name of the part to display, valid values are:
        *   'description', 'images', 'synonymy', 'specimens', 'all'.
+       *
        * @return unknown_type
        */
       function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
         // Display the page for the taxon defined by $uuid.
         // set_last_taxon_page_tab(arg(3));
         $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
         if (!empty($taxonpage)) {
           return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
+        }
         else {
           return '';
+        }
+      }
       /**
        * This function will genreate the taxon page part ($chapter) and returns a taxonpage object
        * which has two fields, one for the page title and one for the content. Later on in the
        * process chain the value contained in these fields will be passed to the cdm_node_show()
        * function as the function parameters $title and $content.
+       *
        * @param string $uuid
        *   the uuid of the taxon to show
        * @param string $chapter
        *   Name of the part to display, valid values are:
        *   'description', 'images', 'synonymy', 'all'.
+       *
        * @return taxonpage object with the following fields:
        *   - title : the title of the page
        *   - content: the content of the page
+       *
        */
       function cdm_dataportal_taxon_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
         // Taxon object.
         $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
         if (empty($taxon)) {
           drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
           return FALSE;
+        }
         $taxonpage = new stdClass();
         $taxonpage->title = theme('cdm_taxon_page_title', array(
           'taxon' => $taxon,
           'uuid' => $uuid,
           'synonym_uuid' => $synonym_uuid,
         ));
         // Check if the taxon id contained in the currently selected tree.
         $taxon_in_current_tree = taxon_in_current_tree($uuid);
         if (!$taxon_in_current_tree) {
           $classifications = get_classifications_for_taxon($taxon);
           if (count($classifications) == 0) {
             drupal_set_message(check_plain(t('This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification.', array(
               '!taxonname' => theme('cdm_taxonName', array('taxonName' => $taxon->name)),
             ))), 'warning');
+          }
           else {
             $trees = '';
             foreach ($classifications as $classification) {
               if (isset($classification->titleCache)) {
                 $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
+              }
+            }
             drupal_set_message(format_plural(count($taxon_nodes),
                 'This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification, but in this one: !trees',
                 'This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification, but in one of these: !trees',
                 array('!taxonname' => theme('cdm_taxonName', array('taxonName' => $taxon->name)), '!trees' => $trees)) , 'warning');
+          }
+        }
         // Render the taxon page.
         $taxonpage->content = theme('cdm_taxon_page', array(
           'taxon' => $taxon,
           'page_part' => $chapter,
         ));
         return $taxonpage;
+      }
       /**
        * Returns a name page as a Drupal node ready to be renderized by Drupal.
+       *
        * The node page shows the taxon name title and the list of taxon related
        * with such taxon. Name on the tree already in use.
+       *
        * @param string $taxon_name_uuid
        *   A taxon name UUID.
+       *
        * @return mixed
        *   The formatted name page as node.
        */
       function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
         $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
         if (!empty($taxonname_page)) {
           return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
+        }
         else {
           return '';
+        }
+      }
       /**
        * Generates an object ready to be transformated to a node.
+       *
        * This is a preparation in order to show it as a Drupal node.
+       *
        * @param string $taxon_name_uuid
+       *
        * @return mixed
        *   The object with the page content and title.
        */
       function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
         // Getting the full taxonname object from the server.
         $taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
         if (!$taxon_name) {
           drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
           return FALSE;
+        }
         // Searching for all the taxa connected with the taxon name on the tree
         // in use.
         $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
         $request_params = array();
         $request_params['query'] = $name_cache;
         $request_params['tree'] = get_taxonomictree_uuid_selected();
         $request_params['doTaxa'] = 1;
         $request_params['doSynonyms'] = 1;
         $request_params['doTaxaByCommonNames'] = 0;
         $request_params['matchMode'] = "EXACT";
         $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
         // Removing the name where we come from.
         foreach ($taxon_pager->records as $k => &$taxon) {
           if ($taxon->uuid == $taxon_to_hide_uuid) {
             unset($taxon_pager->records[$k]);
+          }
+        }
         // Show the taxa list or go to the singular taxon.
         if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
           reset($taxon_pager->records);
           $singleTaxon = $taxon_pager->records[0];
           if ($singleTaxon->class != "Taxon") {
             // It is a Synonym -> look for the accepted.
             $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_taxonomictree_uuid_selected()));
             if (!empty($synonym_uuid)) {
               drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', array('query' => array('highlite' => $synonym_uuid)));
+            }
             else {
               drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
+            }
+          }
           else {
             // It is an accepted taxon.
             if (!empty($synonym_uuid)) {
               drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $synonym_uuid)));
+            }
             else {
               drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
+            }
+          }
+        }
         else {// More than one taxa case.
           $taxon_name_page = new stdClass();
           $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
           if ($taxon_pager->records) {
             $taxon_name_page->content = theme_cdm_list_of_taxa($taxon_pager->records, FALSE);
+          }
           else {
             $taxon_name_page->content = 'This name has no taxa';
+          }
           return $taxon_name_page;
+        }
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_view_search_advanced() {
         drupal_set_title(t('Advanced search'), PASS_THROUGH);
         $form = array();
         $form_state = array();
         $searchForm = cdm_dataportal_search_taxon_form($form, $form_state, TRUE);
         return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_dataportal_view_search_taxon_by_description() {
         drupal_set_title(t('Search by description full text'), PASS_THROUGH);
         // $form_state = false;
         // $searchForm = cdm_dataportal_search_taxon_by_description_form($form_state);
         $searchForm = cdm_dataportal_search_taxon_by_description_form();
         return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
+      }
       /**
        * Executes the search and generates the result list of taxa.
        */
       function cdm_dataportal_view_search_results_taxon() {
         $taxonPager = cdm_dataportal_search_execute();
         $showThumbnails = do_showThumbnails();
         $setSessionUri = url('cdm_api/setvalue/session', array(
             'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
         ));
         drupal_add_js('jQuery(document).ready(function() {
             // init
             if(' . $showThumbnails . ' == 1){
             jQuery(\'.media_gallery\').show(20);
         } else {
             jQuery(\'.media_gallery\').hide(20);
+        }
             // add change hander
             jQuery(\'#showThumbnails\').change(
             function(event){
             var state = 0;
             if(jQuery(this).is(\':checked\')){
             jQuery(\'.media_gallery\').show(20);
             state = 1;
         } else {
             jQuery(\'.media_gallery\').hide(20);
+        }
             // store state in session variable
             var uri = \'' . $setSessionUri . '\' + state;
             jQuery.get(uri);
         });
         });',
         array('type' => "inline", 'scope' => JS_DEFAULT));
         drupal_set_title(t('Search results'), PASS_THROUGH);
         return theme('cdm_search_results', array(
           'pager' => $taxonPager,
           'path' => 'cdm_dataportal/search/results/taxon',
           'query_parameters' => $_REQUEST,
           ));
+      }
       /**
        * Returns the state of the the showThumbnails flag set in the
        * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
+       *
        * @return Ambigous <boolean, number>
        *    returns 1 if the flag is set
        */
       function do_showThumbnails() {
         static $showThumbnails = null;
         if($showThumbnails == null) {
           $showThumbnails = FALSE;
           if (isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
             $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
+          }
           if (!is_numeric($showThumbnails)) {
             $showThumbnails = 1;
+          }
+        }
         return $showThumbnails;
+      }
       /**
        * View which transforms XML output from a given webservice endpoint into JSON.
        */
       /*
        function cdm_view_xml2json(){
        $file = arg(2);
        $datastr = file_get_contents(variable_get('cdm_webservice_url', '').$file);
        return  xml2json::transformXmlStringToJson($datastr);
+       }
        */
       /* ====================== other functions ====================== */
       /**
        * Creates a URL to the taxon page specified by the $uuid parameter.
+       *
        * The URL will be prepended with a path element to a specific taxon page tab.
+       *
        * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
        * be set globally in the administrative settings or individually in the user
        * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
        * the last portal will stay on this last tab.
+       *
        * A third option is offerered by the $page_tab parameter which allows overwriting this
        * internal mechanism by a specific value.
+       *
        * @param string $uuid
        *   The UUID of the taxon.
        * @param string $page_tab
        *   Overwriting the preset mechanism by defining specific value for the
        *   taxon page tab.
+       *
        * @return string
        *   The created URL.
        */
       function path_to_taxon($uuid, $page_tab = FALSE) {
         $tab = get_default_taxon_tab();
         $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
         if (!$uuid) {
           return FALSE;
+        }
         if ($page_tab) {
           return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
+        }
         elseif (!$tab || strtolower($tab) == 'general') {
           return 'cdm_dataportal/taxon/' . $uuid;
+        }
         elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
           return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
+        }
         else {
           return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
+        }
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function uri_to_synonym($synonymUuid, $acceptedUuid) {
         $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
         return url($acceptedPath, array('query' => array('highlite' => $synonymUuid)));
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function path_to_key($keyType, $keyUuid) {
         if (!$keyUuid || !$keyType) {
           return FALSE;
+        }
         $keyType{0} = strtolower($keyType{0});
         return "cdm_dataportal/" . $keyType . "/$keyUuid";
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function path_to_reference($uuid) {
         if (!$uuid) {
           return FALSE;
+        }
         return 'cdm_dataportal/reference/' . $uuid;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function path_to_name($name_uuid) {
         $res = FALSE;
         if ($name_uuid) {
           $res = 'cdm_dataportal/name/' . $name_uuid;
+        }
         return $res;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
         if (!$uuid) {
           return FALSE;
+        }
         $out = 'cdm_dataportal/media/' . $uuid;
         if ($representaion_uuid) {
           $out .= '/' . $representaion_uuid;
           if ($partId !== FALSE) {
             $out .= '/' . $partId;
+          }
+        }
         return $out;
+      }
       /**
        * Compares thisRank with thatRank.
+       *
        * Returns a negative integer, zero, or a positive integer
        * as the of thisRank is higher than, equal to, or lower than thatRank.
        * e.g:
        * <ul>
        * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
        * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
        * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
        * </ul>
        * <p>
        * This compare logic of the underlying webservice is the
        * <b>inverse logic</b> of the the one implemented in
        * java.lang.Comparable#compareTo(java.lang.Object)
+       *
        * @param $thisRankUuid
        * @param $thatRankUuid
+       *
        * @return int
        *   A negative integer, zero, or a positive integer
        *   as the thisRank is lower than, equal to, or higher than thatRank.
        */
       function rank_compare($thisRankUuid, $thatRankUuid) {
         $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
         return $result->Integer;
+      }
       /**
        * Composes an HTML element class attribute value composed of
        * the shortname of the cdm class and the uuid of the entity.
        * This class attribute should be used whereever an cdm-entity is rendered.
+       *
        * These according class selectors in css must be escaped, eg:
        *    .cdm\:TextData
+       *
        * @param $cdmEntity
        */
       function html_class_atttibute_ref($cdmEntity) {
         if (is_cdm_entity($cdmEntity)) {
           return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
+        }
+      }
       /**
        * Preprocess the taggedName to normalize newly introduced
        * tagtypes like hybridSign, separator, .. more?
+       *
        * @param unknown_type $taggedTextList
        */
       function normalize_TaggedName(&$taggedTextList) {
         if (is_array($taggedTextList)) {
           // First pass: rename.
           for ($i = 0; $i < count($taggedTextList); $i++) {
             if ($taggedTextList[$i]->type == "hybridSign") {
               $taggedTextList[$i]->type = "name";
+            }
+          }
           // Second pass: resolve separators.
           $taggedNameListNew = array();
           for ($i = 0; $i < count($taggedTextList); $i++) {
             if ($i + 1 < count($taggedTextList) && $taggedTextList[$i + 1]->type == "separator") {
               if ($taggedTextList[$i]->type == $taggedTextList[$i + 2]->type) {
                 $taggedName = $taggedTextList[$i];
                 $taggedName->text = $taggedName->text . $taggedTextList[$i + 1]->text . $taggedTextList[$i + 2]->text;
                 $taggedNameListNew[] = $taggedName;
                 ++$i;
                 ++$i;
+              }
+            }
             else {
               $taggedNameListNew[] = $taggedTextList[$i];
+            }
+          }
           $taggedTextList = $taggedNameListNew;
+        }
+      }
       /**
        * Creates a short taxonname.
+       *
        * The short name is created by using the taggename field of
        * NameSTO or NameTO instances.
        * If the taggename if empty the fullname will be returned.
+       *
        * @param unknown_type $name
        *   Name or TreeNode.
+       *
        * @return string
        */
       function cdm_dataportal_shortname_of($name) {
         $nameStr = '';
         normalize_TaggedName($name->taggedTitle);
         // Get all tagged text tokens of the scientific name.
         foreach ($name->taggedTitle as $tagtxt) {
           if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
             $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
+          }
+        }
         $nameStr = trim($nameStr);
         if ($nameStr) {
           // Do not return short names for these.
           if ($name->unplaced || $name->excluded) {
             return $nameStr;
+          }
           /*
 st capture group (^[a-zA-Z]): First letter of uninomial.
           Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
           Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
           but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
           OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
           */
           $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
           if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
             return $matches[1][0] . "." . $matches[3][0];
+          }
           else {
             return $nameStr;
+          }
+        }
         else {
           return $name->titleCache;
+        }
+      }
       /**
        * Check if a taxon is accepted by the current taxonomic tree.
+       *
        * @param mixed $taxon
        *   The Taxon obkect to check.
+       *
        * @return bool
        *   Returns TRUE if $taxon is accepted, FALSE otherwise.
        */
       function _cdm_dataportal_acceptedByCurrentView($taxon) {
         $defaultTreeUuid = get_taxonomictree_uuid_selected();
         if (isset($taxon->taxonNodes)) {
           $taxonNodes = $taxon->taxonNodes;
+        }
         else {
           $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
+        }
         if ($taxon->class == "Taxon" && isset($taxonNodes)) {
           foreach ($taxonNodes as $node) {
             if (is_object($node->classification)) {
               if ($node->classification->uuid == $defaultTreeUuid) {
                 return TRUE;
+              }
+            }
             else {
               if ($node->classification == $defaultTreeUuid) {
                 return TRUE;
+              }
+            }
+          }
+        }
         return FALSE;
+      }
       /**
        * Workaround for missing original source type.
+       *
        * idNamespace is always set in these cases.
        * @todo improve documentation of this function.
+       *
        * @param unknown_type $source
+       *
        * @return unknown_type
        */
       function _is_original_source_type($source) {
         return !$source->idNamespace && strlen($source->idNamespace) == 0;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
         return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
+      }
       /**
        * Gets the metadata info such as title or artist of a media file.
+       *
        * The function tries at first to get all the info from the file metadata
        * and if it is not avaible look at the media file info stored at the database.
+       *
        * @param mixed $media
        *   The media file object for which to get the metadata.
+       *
        * @return array
        *   The array with the available specified metadata info.
        * TODO rename to read_media_metadata() and move to *.module.
        */
       function cdm_read_media_metadata($media) {
         $metadata_caption = array(
           'title' => '',// Media_metadata and media.
           'artist' => '',// Media_metadata and media.
           'rights',// Media_metadata and media.
           'location',// Media_metadata.
           'filename' => '',// Media.
           'mediacreated' => '',// Media.
           'description' => '',
         );// Media.
         // Getting the media metadata.
         $media_metadata = cdm_ws_get(CDM_WS_MEDIA_METADATA, array($media->uuid));
         $media_metadata_aux = (array) $media_metadata;
         // Filename.
         if (!empty($media->representations[0]->parts[0]->uri)) {
           $fileUri = $media->representations[0]->parts[0]->uri;
           $filename = substr($fileUri, strrpos($fileUri, "/") + 1);
           $metadata_caption['filename'] = $filename;
+        }
         else {
           $metadata_caption['filename'] = '';
+        }
         // Title.
         if (!empty($media_metadata->ObjectName)) {
           $metadata_caption['title'] = $media_metadata->ObjectName;
+        }
         elseif (!empty($media_metadata_aux['Object Name'])) {
           $metadata_caption['title'] = $media_metadata_aux['Object Name'];
+        }
         elseif (!empty($media->title_L10n)) {
           $metadata_caption['title'] = $media->title_L10n;
+        }
         elseif (!empty($media->titleCache)) {
           $metadata_caption['title'] = $media->titleCache;
+        }
         // Append description to title.
         if (!empty($media->description_L10n)) {
           $metadata_caption['title'] .= '<span class="media-description">' . $media->description_L10n . '<span>';
+        }
         // Artist.
         if ($media_metadata->Artist) {
           $metadata_caption['artist'] = ($media_metadata->Artist ? '' . $media_metadata->Artist : '');
+        }
         elseif (!empty($media->artist->titleCache)) {
           $metadata_caption['artist'] = $media->artist->titleCache;
+        }
         // Copyright.
         $metadata_caption['rights'] = array(
           'copyright' => array('agentNames' => array()),
           'license' => array(
             'agentNames' => array(),
             'types' => array(),
             'abbreviatedTexts' => array(),
             'uris' => array(),
           ),
         );
         if (!empty($media_metadata->Copyright)) {
           $metadata_caption['rights']['copyright']['agentNames'][] = $media_metadata->Copyright;
+        }
         elseif (isset($media->rights) && is_array($media->rights)) {
           foreach ($media->rights as $right) {
             switch ($right->term->uuid) {
               case UUID_RIGHTS_LICENCE:
                 $metadata_caption['rights']['license']['agentNames'][] = ($right->agent ? '' . $right->agent->firstname . ' ' . $right->agent->lastname : '');
                 $metadata_caption['rights']['license']['types'][] = ($right->representation_L10n ? '' . $right->representation_L10n : '');
                 $metadata_caption['rights']['license']['abbreviatedTexts'][] = ($right->abbreviatedText ? '' . $right->abbreviatedText : '');
                 $metadata_caption['rights']['license']['uris'][] = ($right->uri ? '' . $right->uri : '');
                 break;
               case UUID_RIGHTS_COPYRIGHT:
                 $metadata_caption['rights']['copyright']['agentNames'][] = $right->agent->firstname . ' ' . $right->agent->lastname;
                 break;
+            }
+          }
+        }
         else {
           $metadata_caption['rights']['agentNames'][] = '';
+        }
         // Filling the description (though there is no description in the db???).
         // $metadata_caption['description'] = $media->description_L10n;
         // Location.
         $metadata_caption['location'] = array();
         $metadata_caption['location']['sublocation'] = !empty($media_metadata->Sublocation) ? $media_metadata->Sublocation : FALSE;
         $metadata_caption['location']['city'] = !empty($media_metadata->City) ? $media_metadata->City : FALSE;
         $metadata_caption['location']['province'] = !empty($media_metadata->Province) ? $media_metadata->Province : FALSE;
         $metadata_caption['location']['country'] = !empty($media_metadata->Country)? $media_metadata->Country : FALSE;
         /*
          // Creation date.
          if($media_metadata["Modify Date"])
          $metadata_caption['mediacreated'] = $media_metadata["Modify Date"];
          else
          $metadata_caption['mediacreated'] = $media->created;
          */
         // Returned value.
         return $metadata_caption;
+      }
       /**
        * Collects all the media from a list of description elements.
+       *
        * @param array $descriptionElements
        *   The description elements from which to collect the media.
+       *
        * @return array
        *   The output with all the collected media.
        */
       function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
         $outArrayOfMedia = array();
         // Avoiding a warning box in Drupal for Flora Malesiana.
         if (isset($descriptionElements) && is_array($descriptionElements)) {
           foreach ($descriptionElements as $descriptionElement) {
             if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
               foreach ($descriptionElement->media as $media) {
                 if (is_object($media)) {
                   $outArrayOfMedia[] = $media;
+                }
+              }
+            }
+          }
+        }
         return $outArrayOfMedia;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
+       *
        * @param array $cdmBase_list
        *   An array of CdmBase instances or a single instance.
        * @param string $footnote_list_key
+       *
        * @return unknown
        */
       function cdm_annotations_as_footnotekeys($cdmBase_list, $footnote_list_key = NULL) {
         // Comment @WA: undefined variable.
         /*
          static $annotations_types_filter;
          if(!$annotations_types_filter) {
          unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
+         }
          */
         unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
         $footNoteKeys = array();
         // Is argument cdmBase an array?
         if (!is_array($cdmBase_list)) {
           $cdmBase_array = array();
           $cdmBase_array[] = $cdmBase_list;
+        }
         else {
           $cdmBase_array = $cdmBase_list;
+        }
         // Getting the key for the footnotemanager.
         if (isset($footnote_list_key)) {
           $footnoteListKey = $footnote_list_key;
+        }
         else {
           $footnoteListKey = RenderHints::getFootnoteListKey() . '-annotations';
+        }
         // Adding the footnotes keys.
         $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
         foreach ($cdmBase_array as $cdmBase_element) {
           $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
           if (is_array($annotations)) {
             foreach ($annotations as $annotation) {
               $footNoteKeys[] = FootnoteManager::addNewFootnote($footnoteListKey, $annotation->text);
+            }
+          }
+        }
         return $footNoteKeys;
+      }
       // @WA Comment: should this not be a theme function?
       /**
        *  Creates a CDM Dynabox.
        * @param string $dynabox_id
        *   a uninque name for tha dynabox, using a cdm entity uuid herefore is good pratice
        * @param string $label
        *   The clickable text to show.
        * @param string $content_url
        *   The cdm REST service request url wich will deliver the content to be shown
        *   once the dynabox toggles open.
        * @param string $theme
        *   The theme to be used for rendering the cdm REST service reponse with is
        *   returned from the $content_url.
        * @param string $link_alt_text
        *   The value for the alt attribute of the dynabox link.
        * @param array $enclosingtags
        *   An array with two elements: $enclosingtags[0] will be used for the dynabox
        *   element itself, $enclosingtags[1] is the tag to be used for the
        *   dynabox_content (optional)
        * @param string $open_callback
        *   optional javascript call back function to be triggered after toggeling the box to
        *   the open state.
        * @param string $close_callback
        *   optional javascript call back function to be triggered after toggeling the box to
        *   the closed state.
+       *
        * @return string
        *   Returns HTML for a dynabox.
        */
       function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text, $enclosingtags = array('li', 'ul'), $open_callback = 'function(){}', $close_callback = 'function(){}') {
         $out = '';
         // check for plain class attribute string
         $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
         drupal_add_js("
             jQuery(document).ready(
       		function() {
       			dynabox('". $dynabox_id ."',
+      			{
                     open_callback: " . $open_callback .",
                     close_callback: " . $close_callback .",
+                  }
                 );
+      		}
             );",
             array(
               'type'=>'inline',
               'scope'=>'footer'
+            )
           );
         $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
         $out .= '<!-- ' . $content_url . ' -->';
         $out .= '<' . $enclosingtags[0] . ' class="dynabox-' . $dynabox_id . '"><a href="#" class="label" alt="' . t($link_alt_text) . '">' . $label . '</a>';
         $out .= '<' . $enclosingtags[1] . ' class="dynabox-' . $dynabox_id . '-content" title="' . $cdm_proxy_url . '"><' . $enclosingtags[0] . '><img class="loading" src="' . drupal_get_path('module', 'cdm_dataportal') . '/images/loading_circle_grey_16.gif" style="display:none;"></' . $enclosingtags[0] . '></' . $enclosingtags[1] . '>';
         $out .= '</' . $enclosingtags[0] . '>';
         return $out;
+      }
       /**
        * Checks whether a feature has any description elements.
+       *
        * @param mixed $featureNode
        *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
+       *
        * @see _mergeFeatureTreeDescriptions()
+       *
        * @return bool
        *   Returns TRUE if the given $featureNode or any of its subordinate nodes
        *   contains at least one non empty TextData or at least one DescriptionElement
        *   of an other type. A TextData element holding a multilanguageText or a
        *   source reference is considered to be not empty.
        */
       function hasFeatureNodeDescriptionElements($featureNode) {
         if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
           foreach ($featureNode->descriptionElements as $descriptionElement) {
             if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text) && $descriptionElement->multilanguageText_L10n->text != '' || isset($descriptionElement->sources[0]) || isset($descriptionElement->media[0]) ) {
               return TRUE;
+            }
+          }
+        }
         elseif (isset($featureNode->children) && is_array($featureNode->children)) {
           foreach ($featureNode->children as $child) {
             if (hasFeatureNodeDescriptionElements($child)) {
               return TRUE;
+            }
+          }
+        }
         return FALSE;
+      }

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cdm-dataportal/7.x/modules/cdm_dataportal/cdm_dataportal.module @ c9ffb64e