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

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ e0d3e148

       <?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/common');
         module_load_include('inc', 'cdm_dataportal', 'includes/name');
         module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
         module_load_include('inc', 'cdm_dataportal', 'includes/references');
         module_load_include('inc', 'cdm_dataportal', 'includes/pages');
         module_load_include('inc', 'cdm_dataportal', 'includes/media');
         module_load_include('inc', 'cdm_dataportal', 'includes/maps');
         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('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');
         /* ============================ java script functions ============================= */
         /**
         * 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() {
                           " . $callback . "
+                    }
                   });
                 });"
           , 'inline');
+        }
         /**
          */
         function drupal_add_js_rowToggle($tableId){
             drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');
             drupal_add_js('jQuery(document).ready(function(){
                 addRowToggle("' . $tableId . '");
             });
             ', array('type' => '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('" . $progress_element_selector . "');
           //         });
           //       }", 'inline');
+          }
         /**
          * @todo Please document this function.
          * @see http://drupal.org/node/1354
          */
         function _add_js_treeselector() {
           // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
           drupal_add_js("
               jQuery(document).ready(function() {
                  jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
                       jQuery('#cdm-taxonomictree-selector-form').submit();
                   });
               });
             ",
             array(
               'type' => 'inline',
               'scope' => 'footer'
+            )
           );
+        }
         function _add_js_resizable_element($selector, $y_axis_only) {
           _add_jquery_ui();
           $options = "";
           if($y_axis_only) {
             $options = "resize: function(event, ui) {
               ui.size.width = ui.originalSize.width;
               },
               handles: \"s\"";
+          }
           drupal_add_js("
                 jQuery(document).ready(function() {
                    jQuery('" . $selector . "').resizable({". $options ."});
                 });
               ",
             array(
               'type' => 'inline',
               'scope' => 'footer'
+            )
           );
+        }
         function _add_js_openlayers() {
           $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
           $proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
           if(variable_get('cdm_js_devel_mode', FALSE)){
             // develooper mode libs
         //     $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
             $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
             $proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
+          }
           drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
             array(
               'type' => 'file',
               'group' => JS_LIBRARY,
               'weight' => 0,
               'cache' => TRUE,
               'preprocess' => FALSE
+            )
           );
           // see https://github.com/proj4js/proj4js
           // http://openlayers.org/dev/examples/using-proj4js.html
           drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
             array(
               'type' => 'file',
               'group' => JS_LIBRARY,
               'weight' => -1, // before open layers
               'cache' => TRUE,
+            )
           );
           // configure the theme
           $openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
           $openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
           drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
               'type' => 'inline',
               'group' => JS_LIBRARY,
               'weight' => 1, // after openlayers
               'cache' => TRUE,
               'preprocess' => FALSE
             ));
           drupal_add_css($openlayers_theme_path . 'style.tidy.css',
             array(
               'type' => 'file',
               'cache' => TRUE,
               'preprocess' => FALSE
+            )
           );
+        }
         /**
          * @todo Please document this function.
          * @see http://drupal.org/node/1354
          */
         function _add_js_thickbox() {
           // ---- jQuery thickbox:
           /*
           * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
           * not triggered because of problems with compat-1.0.js' see INSTALL.txt
           */
           // drupal_add_js(drupal_get_path('module',
           // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
           //
           // Add a setting for the path to cdm_dataportal module, used to find the path
           // for the loading animation image in thickbox.
           drupal_add_js(array(
           'cdm_dataportal' => array(
           'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
+          )
           ),
           'setting'
               );
               drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
               drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
+        }
         /**
          * @todo Please document this function.
          * @see http://drupal.org/node/1354
          */
         function _add_js_lightbox($galleryID) {
           /*
            * Important Notice: The jquery.lightbox-0.5.js has been modified in order to
            * allow using the "alt" attribute for captions instead of the "title"
            * attribute
            */
           $lightbox_base_path =  drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
           $lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
           drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
           drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
           drupal_add_js('jQuery(document).ready(function() {
               jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
                 fixedNavigation:  true,
                 imageLoading:     \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
                 imageBtnPrev:     \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
                 imageBtnNext:     \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
                 imageBtnClose:    \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
                 imageBlank:       \'' . $lightbox_image_path . 'lightbox-blank.gif\',
                 adjustToWindow: true
               });
             });
             ', array('type' => 'inline'));
+        }
         /**
          * @todo Please document this function.
          * @see http://drupal.org/node/1354
          */
         function _add_js_footnotes() {
           _add_js_domEvent();
           drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
+        }
         /**
          * @todo Please document this function.
          * @see http://drupal.org/node/1354
          */
         function _add_js_ahah() {
           _add_js_domEvent(); // requires domEvent.js
           drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
+        }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _add_js_taxonomic_children($jquery_selector) {
         global $base_url;
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
         drupal_add_js('jQuery(document).ready(function() {
               jQuery(\'' . $jquery_selector . '\').taxonomic_children({
                 // hoverClass: "fa-rotate-90",
                 // activeClass: "fa-rotate-90",
                 classificationUuid: "' . get_current_classification_uuid() . '",
                 taxonUuid: "' . get_current_taxon_uuid() . '",
                 cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
                 proxyBaseUri: "' . $base_url . '",
               });
             });
             ', array('type' => 'inline'));
+      }
         /**
          * Adds the external javascript file for domEvent.js.
+         *
          * @see drupal_add_js()
          */
         function _add_js_domEvent() {
           drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
+        }
         function _add_jquery_ui()
+        {
           drupal_add_css(drupal_get_path('module',
               'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
           drupal_add_js(drupal_get_path('module',
               'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
             array(
               'type' => 'file',
               'weight' => JS_LIBRARY,
               'cache' => TRUE,
               'preprocess' => FALSE
+            )
           );
+        }
         /**
          * Provides the markup for an font awesome icon.
+         *
          * The icons is created in default size without any extra features.
+         *
          * The available icons are listed here http://fontawesome.io/cheatsheet/
          * fontawesome icons have much more features than implemented here in this function,
          * for spinning icons, fixed width icons, rotation, etc please checkout the
          * examples at http://fontawesome.io/examples/
+         *
          * @parameter $icon_name
          *  The name of the icon which starts with 'fa-'
+         *
          * @return String
          *    the markup for the icon in an <i> tag
+         *
          */
         function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
           //<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
           $font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal').'/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
           //$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
           drupal_add_html_head_link(
             array(
               'href' => $font_awesome_css_uri,
               'rel' => 'stylesheet'
+            )
           );
           if($icon_name){
             if(!isset($attributes['class'])){
               $attributes['class'] = array();
+            }
             $attributes['class'][] = 'fa';
             $attributes['class'][] = $icon_name;
             return '<i ' . drupal_attributes($attributes) . '></i>';
+          }
           return '';
+        }
         /* ====================== hook implementations ====================== */
         /**
          * Implements hook_permission().
+         *
          * Valid permissions for this module.
+         *
          * @return array
          *   An array of valid permissions for the cdm_dataportal module.
          */
         function cdm_dataportal_permission() {
           return array(
             'administer cdm_dataportal' => array(
               'title' => t('Administer CDM DataPortal settings'),
               'description' => t("Access the settings pages specific for the cdm_dataportal module"),
             ),
             'access cdm content' => array(
               'title' => t('Access CDM content'),
               'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
             ),
           );
+        }
       /**
        * 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 cdm content'),
           'type' => MENU_CALLBACK,
         );
         // Optional callback arguments: page.
         $items['cdm_dataportal/taxon'] = array(
           'page callback' => 'cdm_dataportal_taxon_page_view',
           'access arguments' => array('access cdm content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/specimen'] = array(
             'page callback' => 'cdm_dataportal_specimen_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_CALLBACK,
             // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/named_area'] = array(
           'page callback' => 'cdm_dataportal_named_area_page_view',
           'access arguments' => array('access cdm 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 cdm content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/reference'] = array(
           'page callback' => 'cdm_dataportal_view_reference',
           'access arguments' => array('access cdm 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 cdm content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         $items['cdm_dataportal/media'] = array(
           'page callback' => 'cdm_dataportal_view_media',
           'access arguments' => array('access cdm 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 cdm 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 cdm content'),
           'type' => MENU_CALLBACK,
         );
         $items['cdm_dataportal/search/advanced'] = array(
           'title' => 'Advanced', // will be passed through t()
           'page callback' => 'cdm_dataportal_view_search_advanced',
           'access arguments' => array('access cdm content'),
           'type' => MENU_DEFAULT_LOCAL_TASK,
         );
         $items['cdm_dataportal/search/taxon_by_description'] = array(
           'title' => 'By content category', // will be passed through t()
           'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
           'access arguments' => array('access cdm content'),
           'type' => MENU_LOCAL_TASK,
         );
         $items['cdm_dataportal/search/results/taxon'] = array(
           'page callback' => 'cdm_dataportal_view_search_results_taxon',
           'access arguments' => array('access cdm content'),
           'type' => MENU_CALLBACK,
         );
         $items['cdm_dataportal/search/registration'] = array(
           'page callback' => 'cdm_dataportal_view_search_registrations_results',
           'access arguments' => array('access cdm content'),
           'type' => MENU_CALLBACK,
         );
         // Optional callback arguments: page.
         $items['cdm_dataportal/registration'] = array(
           'page callback' => 'cdm_dataportal_registration_page_view',
           'access arguments' => array('access cdm content'),
           'type' => MENU_CALLBACK,
           // Expected callback arguments: uuid.
         );
         /*
          $items['cdm/xml2json'] = array(
          'page callback' => 'cdm_view_xml2json',
          'access arguments' => array('access cdm content'),
          'type' => MENU_CALLBACK,
          );
          */
         // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
         // User configuration of cdm_dataportal.
         $items['user/%/cdm_dataportal'] = array(
           'title' => 'cdm_dataportal',
           'access arguments' => array('access cdm content'),
           'page callback' => 'drupal_get_form',
           'page arguments' => array('cdm_dataportal_user_form'),
           'type' => MENU_LOCAL_TASK,
           'weight' => 10,
         );
         // }
         // 'May not cache' in D5.
         $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 cdm content'),
           'type' => MENU_CALLBACK,
         );
         // --- Local tasks for Taxon.
         // --- tabbed taxon page
         if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
           $items['cdm_dataportal/taxon/%'] = array(
             'title' => cdm_taxonpage_tab_label('General'),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_CALLBACK,
             'weight' => 1,
             'page arguments' => array(2, "description")
             , // Expected callback arguments: taxon_uuid.
           );
           $items['cdm_dataportal/taxon/%/all'] = array(
             'title' => cdm_taxonpage_tab_label('General'),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_CALLBACK,
             'weight' => 2,
             'page arguments' => array(2, "all")
             , // Expected callback arguments: taxon_uuid.
           );
           $items['cdm_dataportal/taxon/%/description'] = array(
             'title' => cdm_taxonpage_tab_label('General'),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_DEFAULT_LOCAL_TASK,
             'weight' => 2,
             'page arguments' => array(2, "description")
             , // Expected callback arguments: taxon_uuid.
           );
           $items['cdm_dataportal/taxon/%/synonymy'] = array(
             'title' => cdm_taxonpage_tab_label('Synonymy'),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 4,
             'page arguments' => array(2, "synonymy", 4)
             , // Expected callback arguments: taxon_uuid and ...
           );
           $items['cdm_dataportal/taxon/%/images'] = array( // Images
             'title' => cdm_taxonpage_tab_label('Images'),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 5,
             'page arguments' => array(2, "images")
             , // Expected callback arguments: taxon_uuid.
           );
           $items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
             'title' => cdm_taxonpage_tab_label('Specimens'),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 6,
             'page arguments' => array(2, "specimens")
             , // Expected callback arguments: taxon_uuid.
           );
           $items['cdm_dataportal/taxon/%/keys'] = array( // Keys
             'title' => cdm_taxonpage_tab_label('Keys'),
             'page callback' => 'cdm_dataportal_taxon_page_view',
             'access arguments' => array('access cdm content'),
             'type' => MENU_LOCAL_TASK,
             'weight' => 6,
             'page arguments' => array(2, "keys")
             , // Expected callback arguments: taxon_uuid.
           );
           $items['cdm_dataportal/taxon/%/experts'] = array( // Experts
             'title' => cdm_taxonpage_tab_label('Experts'),
               'page callback' => 'cdm_dataportal_taxon_page_view',
               'access arguments' => array('access cdm content'),
               'type' => MENU_LOCAL_TASK,
               'weight' => 6,
               'page arguments' => array(2, "experts")
           , // Expected callback arguments: taxon_uuid.
           );
           $items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
               'page callback' => 'cdm_dataportal_taxon_autosuggest',
               'access arguments' => array('access cdm content'),
               'page arguments' => array(3,4,5),
               'type' => MENU_CALLBACK
           );
+        }
         // --- refresh link for all cdmnode types
         foreach (cdm_get_nodetypes() as $type=>$name) {
           $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
               'title' => 'Refresh',
               'page callback' => 'cdm_dataportal_refresh_node',
               'access arguments' => array('administer cdm_dataportal'),
               'type' => MENU_LOCAL_TASK,
               'weight' => 100,
               'page arguments' => array($name, 2)
           );
+        }
         return $items;
+      }
       /**
        * Implements hook_init().
+       *
        */
       function cdm_dataportal_init() {
         if (!path_is_admin(current_path())) {
           //FIXME To add CSS or JS that should be present on all pages, modules
           //      should not implement this hook, but declare these files in their .info file.
           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'));
         } else {
           drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
+        }
         if(variable_get('cdm_debug_mode', FALSE)){
           $file = 'temporary://drupal_debug.txt';
           file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
+        }
         $bibliography_settings = get_bibliography_settings();
         $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
         FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
+      }
       function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
         $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
         if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
           // force reloading of all and notify user about this special loading
           drupal_set_message(t('The level 2 cache has been cleared for all tabs of this taxon page at once, please click here to return to the tabbed page: ')
               . l('Back to tabbed taxon page', $base_path));
           $base_path .= '/all';
         } else {
           drupal_set_message(t('The level 2 cache has been cleared for this page'));
+        }
         $parameters['cacheL2_refresh'] ='1';
         drupal_goto($base_path, array('query' => $parameters));
+      }
       /**
        * Implements hook_requirements($phase)
        */
       function cdm_dataportal_requirements($phase) {
           $requirements = array();
           if($phase == 'runtime'){
+          }
           return $requirements;
+      }
       /**
        * The function generate form for own user cdm dataportal configurations.
        */
       function cdm_dataportal_user_form($form, &$form_state) {
         global $user;
         $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
         $form['taxon_page_tabs'] = array(
             '#type' => 'fieldset',
             '#tree' => true,
             '#title' => t('Taxon page tabs'),
         );
         $form['taxon_page_tabs']['user_defined'] = array(
           '#type' => 'checkbox',
           '#title' => t('Activate user default configuration'),
           '#default_value' => variable_get($checkbox_value, 0),
           '#description' => t('Check this if you want configure your own default tab from the below menu.'),
         );
         $form['taxon_page_tabs']['default_tab'] = 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 rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
         );
         if(false){
           $form['developer_options'] = array(
               '#type' => 'fieldset',
               '#tree' => true,
               '#title' => t('Developer options'),
           );
           $form['developer_options']['show_render_path'] = array(
             '#type' => 'checkbox',
             '#title' => t('Display the render path for each taxon name.'),
             '#default_value' => variable_get($checkbox_value, 0),
             '#description' => t('This option is very helpful if you are editing the !link for taxon names.',
               array(
                   '!link' => l(
                     'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
+                  )
               ),
           );
+        }
         $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';
         // FIXME: this is completely wrong, see user_profile_form_submit()
         // it is only possible to change own user settings
         if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
           // DEFAULT_TAXON_TAB
           $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
           variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
           variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
           if ($form_state['values']['taxon_page_tabs']['user_defined']) {
             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.')));
+          }
+        }
         else {
           // Problem with the user id => variables wont be saved.
           $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"] = array(
               "info" => t("CDM - Search Taxa"),
               "cache" => DRUPAL_NO_CACHE
             );
           // $block[3]["info"] = t("CDM Filters");
           $block["4"]["info"] = t("CDM  - Dataportal Print");
           $block["keys"]["info"] = t("CDM - Identification keys");
           $block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
           $block["classification_breadcrumbs"] =  array(
               'info' => t('CDM - Classification breadcrumbs'),
               'cache' => DRUPAL_CACHE_PER_PAGE
             );
           $block["taxonomic_children"] =  array(
             'info' => t('CDM - Taxonomic children'),
             'cache' => DRUPAL_CACHE_PER_PAGE
           );
           $block["back_to_search_results"] =  array(
             'title' => '<none>',
             'info' => t('CDM - Back to search Results'),
             'cache' => DRUPAL_CACHE_PER_PAGE,
             'visibility' => BLOCK_VISIBILITY_LISTED,
             'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
           );
         $block['registrations_search_filter'] =  array(
           'title' => '<none>',
           'info' => t('CDM - Registrations search filter'),
           'cache' => DRUPAL_CACHE_PER_PAGE,
           'visibility' => BLOCK_VISIBILITY_LISTED,
           'pages' => "cdm_dataportal/search/registration\ncdm_dataportal/search/registration/*", // multiple page paths separated by "\n"!!!
         );
           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'] = '';
             $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;
           case "fundedByEDIT":
             // t('Funded by EDIT');
             $text = '<none>';
             $block['subject'] = $text;
             $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
             $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
               'attributes' => array("target" => "EDIT"),
               'absolute' => TRUE,
               'html' => TRUE,
             ));
             return $block;
           case 'classification_breadcrumbs':
             $taxon_uuid = get_current_taxon_uuid();
             $block['subject'] = '<none>';
             $block['content'] = compose_classification_breadcrumbs($taxon_uuid);
             return $block;
           case 'taxonomic_children':
             $taxon_uuid = get_current_taxon_uuid();
             $block['subject'] = '<none>';
             $block['content'] = compose_taxonomic_children($taxon_uuid);
             return $block;
           case 'back_to_search_results':
             $block['subject'] = '<none>';
             if (isset($_SESSION['cdm']['search'])) {
               $block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
+            }
             return $block;
           case 'registrations_search_filter':
             $block['subject'] = '<none>';
             $block['content'] = $form = drupal_get_form('cdm_dataportal_search_registration_form'); // see cdm_dataportal_search_registration_form($form, &$form_state)
             return $block;
           default:
             return null;
+        }
+      }
       /**
        * Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
+       *
        * @return string
        *   the taxon uuid or NULL
        */
       function get_current_taxon_uuid()
+      {
         static $taxon_uuid;
         if(!isset($taxon_uuid)){
           if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
             $taxon_uuid = $_REQUEST['currentTaxon'];
           } else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
             $taxon_uuid = arg(2);
           } else {
             $taxon_uuid = null;
+          }
+        }
         return $taxon_uuid;
+      }
       /**
        * Returns the currently classification tree in use.
+       *
        * @return string
        *   The uuid of the currently focused classification
        */
       function get_current_classification_uuid() {
         if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
           return $_SESSION['cdm']['taxonomictree_uuid'];
+        }
         else {
           return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
+        }
+      }
       /*
        function cdm_dataportal_session_clear($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));
+       }
+       }
        */
       /**
        * creates a  selector form for taxonomic trees.
+       *
        * @return array
        *  a drupal form array
        */
       function cdm_taxonomictree_selector() {
         _add_js_treeselector();
         $form = drupal_get_form('cdm_taxonomictree_selector_form');
         return $form;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
+       *
        * @deprecated use compose_classification_selector instead
        */
       function cdm_taxonomictree_selector_form($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,
         );
         $options = cdm_get_taxontrees_as_options();
         $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
         if($taxontree_includes){
           $filtered_options = array();
           foreach($options as $uuid=>$label){
             if(!empty($taxontree_includes[$uuid])){
               $filtered_options[$uuid] = $label;
+            }
+          }
           $options = $filtered_options;
+        }
         $form['val'] = array(
           '#type' => 'select',
           '#title' => t('Available classifications'),
           '#default_value' => get_current_classification_uuid(),
           '#options' => $options,
           '#attributes' => array('class' => array('highlite-first-child')),
         );
         return $form;
+      }
       /**
+       *
        * @ingroup compose
        */
       function compose_classification_selector() {
         $destination_array = drupal_get_destination();
         $destination = $destination_array['destination'];
         $options = cdm_get_taxontrees_as_options();
         $items = array();
         $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
         $current_classification_uuid = get_current_classification_uuid();
         foreach($options as $uuid=>$label){
           if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
             $class_attributes = '';
             if($current_classification_uuid == $uuid){
               $class_attributes  = array('focused');
+            }
             $items[] = array(
               'data' => l($label,
                 'cdm_api/setvalue/session',
                 array(
                   'query' => array(
                     'destination' => $destination,
                     'val' => $uuid,
                     'var' => '[cdm][taxonomictree_uuid]'
                   ),
+                )
               ),
               'class' => $class_attributes
             );
+          }
+        }
         $render_array = array(
           '#theme' => 'item_list',
           '#type' => 'ul',
           '#items' => $items
         );
         return $render_array;
+      }
       /* UNREACHABLE since action of form directly links to view.
        function cdm_dataportal_search_taxon_form_submit($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) {
         cdm_check_valid_portal_page();
         $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
         return theme('cdm_reference_page', array('reference' => $reference));
+      }
       /**
        * Creates a view on a all references contained in the portal.
+       *
        * This function is used at the path cdm_dataportal/reference/list
        */
       function cdm_dataportal_view_reference_list($pageNumber) {
         $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
         cdm_reference_pager($referencePager, '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) {
         cdm_check_valid_portal_page();
         $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']));
           $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
           $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
           $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
           $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
           $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 settings form elements (#tree = TRUE).
+       *
        * @param string $variableKey
        *   The Unique key of the Drupal variable in the Drupal variables table.
        * @param string $defaultValueString
        *   A string as for example derived from a CONSTANT.
+       *
        * @return mixed
        *   usually an array, depending on the nature of the variable.
+       *
        * TODO compare with get_array_variable_merged() duplicate functions?
        * @deprecated rather use get_array_variable_merged() since this function
        * used an array as second parameter
        */
       function mixed_variable_get($variableKey, $defaultValueString) {
         $systemDefaults = unserialize($defaultValueString);
         $storedSettings = variable_get($variableKey, array());
         if (is_array($storedSettings)) {
           // TODO better use drupal_array_merge_deep() ?
           $settings = array_merge($systemDefaults, $storedSettings);
+        }
         else {
           $settings = $systemDefaults;
+        }
         return $settings;
+      }
       /**
        * Recursive function to convert an object into an array.
        * also subordinate objects will be converted.
+       *
        * @param object $object
        * @return the array
        */
       function convert_to_array($object) {
         if(is_object($object) || is_array($object)) {
           $array = (array)$object;
           foreach ($array as $key=>$value){
             $array[$key] = convert_to_array($value);
+          }
           return $array;
         } else {
           return $object;
+        }
+      }
       /**
        * Searches the $collection for the cdm entitiy given as $element.
+       *
        * The elements are compared by their UUID.
+       *
        * @param $element
        *  the CDM entitiy to search for
        * @param $collection
        *  the list of CDM entities to search in
+       *
        * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
+       *
        */
       function contains_cdm_entitiy($element, $collection) {
         $result = FALSE;
         foreach ($collection as $a) {
           if ($a->uuid == $element->uuid) {
             $result = TRUE;
+          }
+        }
         return $result;
+      }
       /**
        * Fiters the array $entity_list of CDM entities by the list
        * of $excludes. Any element contained in the $excludes will be removed
        * from included int the retuned list.
+       *
        * If the $entity_list is not an array the $excludes will be returned.
        */
       function filter_cdm_entity_list($entity_list, $excludes) {
         if (is_array($entity_list)) {
           $result = $entity_list;
           if ($excludes) {
             foreach ($excludes as $exclude) {
               if (!contains_cdm_entitiy($exclude, $entity_list)) {
                 $result[] = $exclude;
+              }
+            }
+          }
+        }
         else {
           $result = $excludes;
+        }
         return $result;
+      }
       /**
        * Wraps the given $html string into a render array suitable for drupal_render()
+       *
        * @param $html
        *   the html string, see
        *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
        * @param $weight
        *   A positive or negative number (integer or decimal).
        *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
        * @param $prefix
        *   Optional markup for the '#prefix' element of the render array
        * @param $suffix
        *   Optional markup for the '#suffix' element of the render array
+       *
        * @return array
        *   A render array
+       *
        */
       function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
         $render_array = array(
           '#markup' => $html
             );
         if (is_numeric($weight)) {
           $render_array['#weight'] = $weight;
+        }
         if($prefix){
           $render_array['#prefix'] = $prefix;
+        }
         if($suffix) {
           $render_array['#suffix'] = $suffix;
+        }
         return $render_array;
+      }
       /**
        * 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) {
         cdm_check_valid_portal_page();
         $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 $chapter
        *   Name of the part to display, valid values are:
        *   'description', 'images', 'synonymy', 'specimens', 'all'.
+       *
        * @return string
        */
       function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
         cdm_check_valid_taxon_page($chapter);
         cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
         // show a warning in case the javascript development mode is anabled
         if(variable_get('cdm_js_devel_mode', FALSE)) {
           drupal_set_message(t('The !url1 is enabled.
               WARNING: this is a performance penalty and must be turned off on production websites.', array(
                 '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
           )),
           'warning'
               );
+        }
         // Display the page for the taxon defined by $uuid.
         // set_last_taxon_page_tab(arg(3));
         $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
         if (!empty($taxonpage)) {
           cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
           return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
+        }
         else {
           cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
           return '';
+        }
+      }
       /**
        * This function will genreate the taxon page part ($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 $chapter
        *   Name of the part to display, valid values are:
        *   'description', 'images', 'synonymy', 'all'.
+       *
        * @return object with the following fields:
        *   - title : the title of the page
        *   - content: the content of the page
+       *
        */
       function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
         // 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
         ));
         // Check if the taxon id contained in the currently selected tree.
         $taxon_in_current_classification = taxon_in_current_classification($uuid);
         if (!$taxon_in_current_classification) {
           $classifications = get_classifications_for_taxon($taxon);
           RenderHints::pushToRenderStack('not_in_current_classification');
           $taxon_name_markup = render_taxon_or_name($taxon);
           if (count($classifications) == 0) {
             drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
               array(
               '!taxonname' => $taxon_name_markup,
+              )
             ), 'warning');
+          }
           else {
             $trees = '';
             foreach ($classifications as $classification) {
               if (isset($classification->titleCache)) {
                 $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
+              }
+            }
             drupal_set_message(format_plural(count($trees),
                 'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
                 'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
                 array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
               ) ,
               'warning');
+          }
           RenderHints::popFromRenderStack();
+        }
         // Render the taxon page.
         $render_array = compose_cdm_taxon_page($taxon, $chapter);
         $taxonpage->content = drupal_render($render_array);
         return $taxonpage;
+      }
       /**
        * Creates a specimen page view.
        * @param string $uuid the UUID of the specimen
        * @return array|string
        */
       function cdm_dataportal_specimen_page_view($uuid) {
           //cdm_check_valid_taxon_page($chapter);
           //cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
           // show a warning in case the javascript development mode is anabled
           if(variable_get('cdm_js_devel_mode', FALSE)) {
               drupal_set_message(t('The !url1 is enabled.
               WARNING: this is a performance penalty and must be turned off on production websites.', array(
                   '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
               )),
                   'warning'
               );
+          }
           // Display the page for the specimen defined by $uuid.
           $specimenpage = cdm_dataportal_specimen_view($uuid);
           if (!empty($specimenpage)) {
               return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
+          }
           else {
               return '';
+          }
+      }
       /**
+       *
        * Creates a specimen view.
        * @param string $uuid the UUID of the specimen
        * @return array|string
        */
       function cdm_dataportal_specimen_view($uuid) {
           $specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
           if (empty($specimen)) {
               drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
               return FALSE;
+          }
           $specimenpage = new stdClass();
           $specimenpage->title = theme('cdm_specimen_page_title', array(
               'specimen' => $specimen
           ));
           // Render the specimen page.
           $render_array = compose_cdm_specimen_page($uuid);
           $specimenpage->content = drupal_render($render_array);
           return $specimenpage;
+      }
       /**
+       *
        * Creates a named area view.
        * @param string $uuid the UUID of the specimen
        *  * @return object
        *   An object with two fields:
        *     - title: the page title
        *     - content: the page content
        */
       function cdm_dataportal_named_area_view($uuid) {
         $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
         if (empty($named_area) || $named_area->class !== 'NamedArea') {
           drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
           return FALSE;
+        }
         $named_area_page = new stdClass();
         $named_area_page->title = $named_area->representation_L10n;
         // Render the specimen page.
         $render_array = compose_cdm_named_area_page($uuid);
         $named_area_page->content = drupal_render($render_array);
         return $named_area_page;
+      }
       function cdm_dataportal_named_area_page_view($uuid) {
         cdm_check_valid_portal_page();
         $named_area_page = cdm_dataportal_named_area_view($uuid);
         if (!empty($named_area_page)) {
           return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
+        }
         else {
           return '';
+        }
+      }
       /**
        * 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 UUID $taxon_name_uuid
        *   The uuid of the CDM TaxonName to show a name page for
        * @param UUID $taxon_to_hide_uuid
        *   A taxon which should not be displayed in the taxon list
        * @param UUID $highlite_synonym_uuid
        *   Optinal parameter wich takes another taxon uuid, if given the
        *   target taxon pages will show the syonymy tab where the taxon
        *   refenrenced by the $highlite_synonym_uuid will be highlighted
        *   in case it is found on this page.
+       *
        * @return mixed
        *   The formatted name page as node.
        */
       function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
         cdm_check_valid_portal_page();
         $taxonname_page = cdm_dataportal_name_view($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 '';
+        }
+      }
       /**
        * View function for a TaxonName page.
+       *
        * The name page lists all taxa for which the name specified by the
        * $taxon_name_uuid is being used. I case there is only one name the
        * page automatically redirects ti the according taxon page. Otherwise
        * the list of names is displayed.
+       *
        * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
        * list of taxa. This is useful for example when referencing from a taxon
        * to the name page and the referring taxon should not be repeaded in the
        * name page.
+       *
+       *
        * @param UUID $taxon_name_uuid
        *   The uuid of the CDM TaxonName to show a name page for
        * @param UUID $taxon_to_hide_uuid
        *   A taxon which should not be displayed in the taxon list
        * @param UUID $highlite_synonym_uuid
        *   Optinal parameter wich takes another taxon uuid, if given the
        *   target taxon pages will show the syonymy tab where the taxon
        *   refenrenced by the $highlite_synonym_uuid will be highlighted
        *   in case it is found on this page.
+       *
        * @return object
        *   An object with two fields:
        *     - title: the page title
        *     - content: the page content
        */
       function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
         // Getting the full taxonname object from the server.
         $taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($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_current_classification_uuid();
         $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 came 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.
           $singleTaxon = array_pop($taxon_pager->records);
           if ($singleTaxon->class != "Taxon") {
             // It is a Synonym -> look for the accepted.
             $accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
             if (!empty($highlite_synonym_uuid)) {
               drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
+            }
             else {
               drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
+            }
+          }
           else {
             // It is an accepted taxon.
             if (!empty($highlite_synonym_uuid)) {
               drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $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) {
             $taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
+          }
           else {
             $taxon_name_page->content = 'This name is not assigned to a taxon.';
+          }
           return $taxon_name_page;
+        }
+      }
       /**
        * Returns a registration page as a Drupal node to be rendered by Drupal.
+       *
        * @param string  $registration_identifier_encoded
        *   The persistent identifier of the registration urlencoded.
        * @return mixed
        *   The formatted registration page as node.
        */
       function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
         cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
         $registration_page = cdm_dataportal_registration_view($registration_identifier_encoded);
         return cdm_node_show_simulate($registration_page);
+      }
       function cdm_dataportal_registration_view($registration_identifier_encoded) {
         $registration_identifier = urldecode($registration_identifier_encoded);
         $render_array = array();
         $registration_dto = cdm_ws_get("registrationDTO/identifier/" . $registration_identifier_encoded);
         if($registration_dto){
           drupal_set_title(t('Registration') . ' ' . $registration_identifier, PASS_THROUGH);
           $render_array['citation'] = markup_to_render_array("<div class=\"" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
             . l($registration_dto->bibliographicCitationString, path_to_registration_workingset($registration_dto->citationUuid))
             . "</br>&nbsp;</div>");
           $render_array['summary'] = markup_to_render_array("<div>" . cdm_tagged_text_to_markup($registration_dto->summaryTaggedText) . "</div>");
       //    $registration = cdm_ws_get("registration/identifier/" . $registration_identifier_encoded);
       //    if(is_array($registration->typeDesignations)){
       //      $type_designations_markup = "";
       //      foreach ($registration->typeDesignations as $type_designation){
       //        $type_designations_markup .= render_cdm_specimen($type_designation);
       //      }
       //      $render_array['type_designations'] = markup_to_render_array($type_designations_markup);
       //    }
         } else {
           drupal_set_title(t('Registration not found'), PASS_THROUGH);
           $render_array['error'] = markup_to_render_array("A registration with the identifier  " . $registration_identifier . " does not exist.");
+        }
         return $render_array ;
+      }
       /**
        * Creates a page with the advance search form.
+       *
        * NOTE: The advance search form allows searching for taxa.
        */
       function cdm_dataportal_view_search_advanced() {
         drupal_set_title(t('Advanced search'), PASS_THROUGH);
         return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
+      }
       /**
        * Creates a page with the search form for searching by taxon descriptions.
        */
       function cdm_dataportal_view_search_taxon_by_description() {
         drupal_set_title(t('Search by factual data'), PASS_THROUGH);
         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_taxon_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 handler
             jQuery(\'#showThumbnails input.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_taxa_results', array(
           'pager' => $taxonPager,
           'path' => 'cdm_dataportal/search/results/taxon',
           ));
+      }
       /**
        * Executes the search for registrations and generates the result list..
        */
       function cdm_dataportal_view_search_registrations_results() {
         $block = block_load('cdm_dataportal', 'registrations_search_filter');
         $render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
         $registration_pager = cdm_dataportal_search_registrations_execute();
         drupal_set_title(t('Search registrations'), PASS_THROUGH);
         $registrations_pager_array = compose_registrations_search_results($registration_pager);
         $render_array = array_merge($render_array, $registrations_pager_array);
         return $render_array;
+      }
       /**
        * Provides the standart image wich indicated a loading process
+       *
        * @return string
        *  The img html tag
        */
       function loading_image_html() {
         return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
           . '/images/loading_circle_grey_16.gif" style="display:none;">';
+      }
       /**
        * Returns the state of the the showThumbnails flag set in the
        * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
+       *
        * @return boolean
        *    returns 1 if the flag is set
        */
       function do_showThumbnails() {
         static $showThumbnails = null;
         if($showThumbnails == null) {
           $showThumbnails = 0;
           if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
             $showThumbnails = 0;
             $search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
             $showThumbnails = is_array($search_gallery_settings)
               && isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
               && (
                   $search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
                   $search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
                   $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
+                  )
                ? 1 : 0;
              drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
+          }
           $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
           if (!is_numeric($showThumbnails)) {
             $showThumbnails = 1;
+          }
+        }
         return $showThumbnails;
+      }
       /* ====================== 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);
+        }
+      }
       function path_to_specimen($uuid) {
           if (!$uuid) {
               return FALSE;
+          }
           else {
               return 'cdm_dataportal/specimen/' . $uuid;
+          }
+      }
       function path_to_named_area($uuid) {
         if (!$uuid) {
           return FALSE;
+        }
         else {
           return 'cdm_dataportal/named_area/' . $uuid;
+        }
+      }
       /**
        * Creates a URL to show a synonmy in the according taxon page.
+       *
        * The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
        * The resulting URI will include query parameters to highlight the synonym, and to optionally display
        * the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
        * include the sysnonym uuid as fragment in order to let the browser scroll to the according location
        * in the page
+       *
        * @param string $synonymUuid
        *    The uuid of the synonym
        * @param string $acceptedUuid
        *    The uuid of the according accepted taxon
        * @return string
        *    The URL to show a synonmy in the according taxon page
        */
       function uri_to_synonym($synonymUuid, $acceptedUuid) {
         $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
         return url($acceptedPath, array(
             'query' => array(
               // highlite the synony in the synonymy
               'highlite' => $synonymUuid,
               // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
               // see theme_taxon_page_title()
               'acceptedFor' => $synonymUuid
             ),
             'fragment' => $synonymUuid
         ));
+      }
       /**
        * Composes the drupal path to the key identified by the uuid.
+       *
        * @param string $keyType
        *    the key typer corresponds to the specific class of the CDM
        *    IdentificationKey. Possible values are
        *      -PolytomousKey
        *      -MultimediaKey
        *      - ...
        * @param string $keyUuid
        *   The UUID of the key
        */
       function path_to_key($keyType, $keyUuid) {
         if (!$keyUuid || !$keyType) {
           return FALSE;
+        }
         $keyType{0} = strtolower($keyType{0});
         return "cdm_dataportal/" . $keyType . "/$keyUuid";
+      }
       /**
        * Composes the drupal path to the reference identified by the uuid.
+       *
        * @param $uuid string String representation of the registration entity uuid.
+       *
        * @return string
        *  The drupal path
+       *
        */
       function path_to_reference($uuid) {
         if (!$uuid) {
           return FALSE;
+        }
         return 'cdm_dataportal/reference/' . $uuid;
+      }
       /**
        * Composes the drupal path to the reference identified by the uuid.
+       *
        * @param string $identifier
        *  The persistent identifier of the registration entity (Registration.identifier).
        * @return string
        *  The drupal path
        */
       function path_to_registration($identifier) {
         return 'cdm_dataportal/registration/' . urlencode($identifier);
+      }
       /**
        * Composes the drupal path to the reference identified by the uuid.
+       *
        * @param $uuid string
        *    The uuid of the reference which is the base entity for registration workingset..
+       *
        * @return string
        *  The drupal path
        */
       function path_to_registration_workingset($identifier) {
         return 'cdm_dataportal/reference/' . urlencode($identifier);
+      }
       /**
        * Creates the path to a cdm_dataportal taxon name page.
+       *
        * @param string $taxon_name_uuid
        *   The uuid as string of the CDM TaxonName to show a name page for
        * @param string $taxon_to_hide_uuid
        *   The uuid as string of a taxon which should not be displayed in the taxon list
        * @param string $highlite_synonym_uuid
        *   Optional parameter which takes another taxon uuid, if given the
        *   target taxon pages will show the synonymy tab where the taxon
        *   referenced by the $highlite_synonym_uuid will be highlighted
        *   in case it is found on this page.
+       *
        * @return string
        *  URI path element as string
        */
       function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid  = NULL) {
         $res = FALSE;
         if ($name_uuid) {
           $res = 'cdm_dataportal/name/' . $name_uuid;
+        }
         if($taxon_to_hide_uuid){
           $res .= '/' . $taxon_to_hide_uuid;
           if($synonym_uuid){
             $res .= '/' . $synonym_uuid;
+          }
+        }
         return $res;
+      }
       /**
        * Composes the drupal path to the media entity identified by the uuid.
+       *
        * @param string $uuid
        *  The persistent identifier of the entity entity
        * @return string
        *  The drupal path
        */
       function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
         if (!$uuid) {
           return FALSE;
+        }
         $out = 'cdm_dataportal/media/' . $uuid;
         if ($representaion_uuid) {
           $out .= '/' . $representaion_uuid;
           if (is_numeric($partId)) {
             $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 short-name of the cdm class and the uuid of the entity.
        * This class attribute should be used wherever an cdm-entity is rendered.
+       *
        * In case of Taxon entities or TaxonNodeDTOs the secReference is also added
        * to the class attributes as 'sec_uuid:<uuid>'. In case of TaxonNodeDTOs the
        * Taxon uuid is added also as taxon_uuid:<uuid>
+       *
        * These according class selectors in css must be escaped, eg:
        *    .cdm\:TextData
+       *
        * @param $cdm_entity
        *    A CDM entity, TaxonNodeDTO or TypedEntityReference
        */
       function html_class_attribute_ref($cdm_entity) {
         $attributes = '';
         if (is_cdm_entity($cdm_entity)) {
           $attributes =  "cdm:" . $cdm_entity->class . " uuid:" . $cdm_entity->uuid;
         } else if($cdm_entity->class == 'TypedEntityReference') {
           $attributes =  "cdm:" . $cdm_entity->type . " uuid:" . $cdm_entity->uuid;
+        }
         if($cdm_entity->class == 'TaxonNodeDto'){
           $attributes .= " taxon_uuid:"  . $cdm_entity->taxonUuid . " sec_uuid:"  . $cdm_entity->secUuid;;
+        }
         if($cdm_entity->class == 'Taxon' && isset($cdm_entity->sec->uuid)){
           $attributes .= " sec_uuid:"  . $cdm_entity->sec->uuid;
+        }
         return $attributes;
+      }
       /**
        * Creates a short version of a taxonname.
+       *
        * The short name is created by using the taggedTitle field of
        * TaxonNodeDTO instances.
        * If the taggedTitle if empty the fullname will be returned.
+       *
        * @param object $taxonNodeDTO
        *   A TaxonNodeDTO object
+       *
        * @return string
        */
       function cdm_dataportal_shortname_of($taxonNodeDTO) {
         $nameStr = '';
         normalize_tagged_text($taxonNodeDTO->taggedTitle);
         // Get all tagged text tokens of the scientific name.
         foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
           if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
             $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
+          }
+        }
         $nameStr = trim($nameStr);
         if ($nameStr) {
           // Do not return short names for these.
           if ($taxonNodeDTO->unplaced || $taxonNodeDTO->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 $taxonNodeDTO->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) {
         $defaultTreeUuid = get_current_classification_uuid();
         if (isset($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 $node) {
             if (isset($node->classification)){
               if(is_object($node->classification)) {
                 if ($node->classification->uuid == $defaultTreeUuid) {
                   return TRUE;
+                }
+              }
               else {
                 if ($node->classification == $defaultTreeUuid) {
                   return TRUE;
+                }
+              }
+            }
+          }
+        }
         return FALSE;
+      }
       /**
        * Checks is the source has one of the given types.
+       *
        * @param object $source
        *   The original source entity
        * @param array $types
        *   An array of elementd of the OriginalSourceType enumeration
        *   If not set the default will be used which is:
        *    - Lineage
        *    - PrimaryMediaSource
        *    - PrimaryTaxonomicSource
        *    - Unknown
        *    - Other
        * @return boolean
        */
         function _is_original_source_type($source, $types = null) {
           // this is the default
           // maybe this should also be put into the settings
           static $default = array(
             OriginalSourceType::Lineage,
             OriginalSourceType::PrimaryMediaSource,
             OriginalSourceType::PrimaryTaxonomicSource,
             OriginalSourceType::Unknown,
             OriginalSourceType::Other,
           );
           if(!$types){
             $types = $default;
+          }
           return isset($source->type) && in_array($source->type, $types);
+        }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
         return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
+      }
       /**
        * 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 $cdm_entities
        *   An array of CdmBase instances or a single instance.
        * @param string $footnote_list_key_suggestion
+       *
        * @return unknown
        */
       function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
          static $annotations_types_filter = null;
          if(!$annotations_types_filter) {
            $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
+         }
         $footNoteKeys = array();
         // Is argument cdmBase an array?
         if (!is_array($cdm_entities)) {
           $cdmBase_array = array();
           $cdmBase_array[] = $cdm_entities;
+        }
         else {
           $cdmBase_array = $cdm_entities;
+        }
         // Getting the key for the footnotemanager.
         if (isset($footnote_list_key_suggestion)) {
           $footnote_list_key = $footnote_list_key_suggestion;
+        }
         else {
           $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
+        }
         // Adding the footnotes keys.
         foreach ($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) {
               $footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
+            }
+          }
+        }
         return $footNoteKeys;
+      }
       /**
        * Creates a CDM Dynabox.
+       *
        * @param string $dynabox_id
        *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
        * @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 response 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 array $attributes
        * @param $content_element_selector
        *   Optional jQuery selector which can be used to reference a dom element which should
        *   be used as container for the content to be shown. The dynabox-<dynabox id>-content
        *  element will be placed in this container.
+       *
        * @param string $open_callback
        *   optional javascript call back function to be triggered after toggling the box to
        *   the open state.
        * @param string $close_callback
        *   optional javascript call back function to be triggered after toggling the box to
        *   the closed state.
        * @return string Returns HTML for a dynabox.
        * Returns HTML for a dynabox.
        */
       function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
                            $enclosingtags = array('li', 'ul'), $attributes = array(),
                            $content_element_selector = null,
                            $open_callback = 'function(){}', $close_callback = 'function(){}' ) {
         $out = '';
         // check for plain class attribute string
         $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
         if(!array_key_exists('class', $attributes)) {
           $attributes['class'] = array();
+        }
         $attributes['id'][] = 'dynabox-' . $dynabox_id;
         $dynabox_attributes = drupal_attributes($attributes);
         _add_js_domEvent(); // requires domEvent.js
         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: " . $close_callback .
                   ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
+                }
               );
+            }
          );",
          array(
           'type'=>'inline',
           'scope'=>'footer'
+          )
         );
         $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
         $out .= '<!-- dynabox for ' . $content_url . ' -->';
         $out .= '<' . $enclosingtags[0] . ' ' .  $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t('@link-alt-text', array('@link-alt-text' => $link_alt_text)) . '">' . $label . '</a>';
         $out .= '  <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
         $out .= '    <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
         $out .= '    </' . $enclosingtags[1] . '>';
         $out .= '  </' . $enclosingtags[0] . '>';
         $out .= '<!-- dynabox end -->';
         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.
+       *
        * @TODO this function may have become obsolete by the new method of detecting empty blocks,
        *       see $block_content_is_not_empty in make_feature_block_list() and
        *       $feature_block_has_content in compose_feature_block_items_generic
        */
       function has_feature_node_description_elements($featureNode) {
         if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
           if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
             foreach ($featureNode->descriptionElements as $descriptionElement) {
               if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
                 && $descriptionElement->multilanguageText_L10n->text != ''
                 || isset($descriptionElement->sources[0])
                 || isset($descriptionElement->media[0]) ) {
                 return TRUE;
+              }
+            }
+          }
+        }
         else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
           foreach ($featureNode->childNodes as $child) {
             if (has_feature_node_description_elements($child)) {
               return TRUE;
+            }
+          }
+        }
         return FALSE;
+      }
       /**
        * Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
+       *
        * @param $chapter
        *   The taxon page chapter or part
        */
       function cdm_check_valid_taxon_page($chapter){
         static $taxon_tabs = null;
         cdm_check_valid_portal_page();
         if($taxon_tabs == null){
           $taxon_tabs = array('all', 'description');
           foreach(get_taxon_tabs_list() as $tab){
             $taxon_tabs[] = strtolower($tab);
+          }
+        }
         if(!in_array($chapter, $taxon_tabs)){
           // oops this is not a valid chapter name
           http_response_code(404); // 404 = Not Found
+        }
+      }
       /**
        * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
        * The test applied by default it a check for the query parameter 'q' ending with a file suffix like '*.*'
+       *
        * @param $preg_pattern
        *   Optional regular expression pattern to be used in preg_match().
        */
       function cdm_check_valid_portal_page($preg_pattern = null){
         $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
         if($preg_pattern === null){
           $preg_pattern = $ends_with_file_suffix_pattern;
+        }
         if(preg_match($preg_pattern, $_GET['q'])){
           // oops this urls ends with a file_suffix and thus does not refer to a portal page
           http_response_code(404); // 404 = Not Found
           exit('HTTP 404');
+        }
+      }
       /**
        * Generates the diff of the texts and presents it in a HTML diff viewer.
+       *
        * @param $text_a
        * @param $text_b
        * @return string
        */
       function diff_viewer($text_a, $text_b) {
         static $diff_viewer_count = 0;
         $element_id = 'part_definitions_diff_' . $diff_viewer_count++;
         // http://code.stephenmorley.org/php/diff-implementation/
         module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
         drupal_add_css(drupal_get_path('module',
             'cdm_dataportal') . '/css/diff.css');
         _add_jquery_ui();
         drupal_add_js(
           'jQuery(document).ready( function(){
               jQuery(\'#' . $element_id . '\').accordion({
               collapsible: true,
               active: false,
               fillSpace: true,
               }).children(\'div\').css({ \'height\': \'auto\' });
               jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
            });'
           , array(
           'type' => 'inline',
           'scope' => 'footer'
         ));
         $diff = Diff::compare($text_a,
           $text_b);
         $diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
           . Diff::toTable($diff, '', '')
           . '</div></div>';
         return $diff_viewer_markup;
+      }

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ e0d3e148