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

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cdm-dataportal/modules/cdm_dataportal/cdm_dataportal.module @ 93ae67cc

-            6657531f
+<?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)
  */
-b27a36
+  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');
-e31ea9e
+  module_load_include('inc', 'cdm_dataportal', 'includes/name');
-            b7a20282
+  module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
   module_load_include('inc', 'cdm_dataportal', 'includes/references');
-b27a36
+  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() {
                     " . $callback . "
+              }
             });
           });"
     , 'inline');
-            6657531f
+            Andreas Kohlbecker
-b27a36
+  /**
    */
   function drupal_add_js_rowToggle($tableId){
-            6657531f
+            Andreas Kohlbecker
-b27a36
+      drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');
       drupal_add_js('jQuery(document).ready(function(){
           addRowToggle("' . $tableId . '");
-            6657531f
+      });
-b27a36
+      ', array('type' => 'inline'));
+  }
-            d2fd2a4c
+            Andreas Kohlbecker
-b27a36
+  /**
    * @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'
+      )
     );
-ea8b301
+            Andreas Kohlbecker
-b27a36
+  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',
         'weight' => JS_LIBRARY,
         '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',
         'weight' => JS_LIBRARY,
         '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() . $openlayers_imp_path . '";', array(
         'type' => 'inline',
         'weight' => JS_LIBRARY,
         'cache' => TRUE,
         'preprocess' => FALSE
       ));
     drupal_add_css($openlayers_theme_path . 'style.tidy.css',
       array(
         'type' => 'file',
         'cache' => TRUE,
         'preprocess' => FALSE
+      )
     );
-            e3026d72
+            Andreas Kohlbecker
-b27a36
+            Andreas Kohlbecker
-            e3026d72
+            Andreas Kohlbecker
-b27a36
+  /**
    * @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'),
-f6aa4b
+            Andreas Kohlbecker
-b27a36
+    ),
     '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');
+  }
-ff9
+            Andreas Kohlbecker
-b27a36
+  /**
    * @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
         });
-ff9
+      });
-b27a36
+      ', array('type' => 'inline'));
+  }
-ff9
+            Andreas Kohlbecker
-b27a36
+  /**
    * @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');
+  }
-ff9
+            Andreas Kohlbecker
-b27a36
+  /**
    * @todo Please document this function.
    * @see http://drupal.org/node/1354
    */
   function _add_js_cluetip() {
     // TODO replace by
     // @see http://www.socialembedded.com/labs/jQuery-Tooltip-Plugin/jQuery-Tooltip-Plugin.html
     drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.min.js');
     drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.dimensions.js');
     drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.hoverIntent.js');
     if(variable_get('cdm_js_devel_mode', FALSE)){
       drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.js');
+    }
     drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.css');
     drupal_add_js("jQuery(document).ready(function(){
         jQuery('.cluetip').css({color: '#0062C2'}).cluetip({
           splitTitle: '|',
           showTitle: true,
           activation: 'hover',
           sicky: true,
           arrows: true,
           dropShadow: false,
           cluetipClass: 'rounded'
         });
-            d0d23caa
+      });",
       array(
         'type' => 'inline',
         'scope' => 'footer'
+      )
     );
-ea8b301
+            Andreas Kohlbecker
-ff9
+            Andreas Kohlbecker
-b27a36
+  /**
    * @todo Please document this function.
    * @see http://drupal.org/node/1354
    */
   function _add_js_ahah() {
-            b386ae48
+            Andreas Kohlbecker
-b27a36
+    _add_js_domEvent(); // requires domEvent.js
     drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
+  }
-ff9
+            Andreas Kohlbecker
-            d0d23caa
+/**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_taxonomic_children($jquery_selector) {
-            b0adfd32
+            Andreas Kohlbecker
   global $base_url;
   drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
-            faf4f771
+            Andreas Kohlbecker
-            d0d23caa
+  drupal_add_js('jQuery(document).ready(function() {
-            b0adfd32
+        jQuery(\'' . $jquery_selector . '\').taxonomic_children({
           hoverClass: "fa-rotate-90",
           activeClass: "fa-rotate-90",
           classificationUuid: "' . get_current_classification_uuid() . '",
-af3ce28
+          taxonUuid: "' . get_current_taxon_uuid() . '",
-da4e54
+          cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
-            b0adfd32
+          proxyBaseUri: "' . $base_url . '",
         });
-            d0d23caa
+      });
       ', array('type' => 'inline'));
+}
-b27a36
+  /**
    * 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');
+  }
-            b386ae48
+            Andreas Kohlbecker
-bb473
+  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
+      )
     );
+  }
-b27a36
+  /**
    * 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/
-            ef12d0c6
+   * fontawesome icons have much more features than implemented here in this function,
    * for spinning icons, fixed width icons, rotation, etc please checkout the
-b27a36
+   * examples at http://fontawesome.io/examples/
+   *
    * @parameter $icon_name
    *  The name of the icon which starts with 'fa-'
+   *
    * @return String
    *    the markup for the icon in an <i> tag
+   *
    */
-            b0aa9a8f
+  function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
-b27a36
+            Andreas Kohlbecker
     //<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
-            b0aa9a8f
+    $font_awesome_css_uri=drupal_get_path('module', 'cdm_dataportal').'/font-awesome/4.5.0/css/font-awesome.min.css';
     $font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
-b27a36
+            Andreas Kohlbecker
     drupal_add_html_head_link(
       array(
         'href' => $font_awesome_css_uri,
         'rel' => 'stylesheet'
+      )
     );
-            b0aa9a8f
+    if($icon_name){
       if(!isset($attributes['class'])){
         $attributes['class'] = array();
+      }
       $attributes['class'][] = 'fa';
       $attributes['class'][] = $icon_name;
       return '<i ' . drupal_attributes($attributes) . '></i>';
-b27a36
+            Andreas Kohlbecker
-            b0aa9a8f
+    return '';
-b27a36
+            Andreas Kohlbecker
-ff9
+            Andreas Kohlbecker
-b27a36
+            Andreas Kohlbecker
   /* ====================== hook implementations ====================== */
   /**
    * Implements hook_permission().
+   *
    * Valid permissions for this module.
+   *
    * @return array
    *   An array of valid permissions for the portfolio module.
    */
   function cdm_dataportal_permission() {
     return array(
       'administer cdm_dataportal' => array(
         'title' => t('administer cdm_dataportal'),
         'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
       ),
       'cdm_dataportal view notes' => array(
         'title' => t('cdm_dataportal view notes'),
         'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
       ),
       // TODO Which other permissions are required?
       // -> check the WP6 requirements document.
     );
+  }
-            6657531f
+            Andreas Kohlbecker
 /**
-            f19f47fa
+ * Implements hook_menu().
  */
-            6657531f
+function cdm_dataportal_menu() {
   $items = array();
   // @see settings.php.
   cdm_dataportal_menu_admin($items);
   cdm_dataportal_menu_help($items);
   $items['cdm_dataportal/names'] = array(
     'page callback' => 'cdm_dataportal_view_names',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
   // Optional callback arguments: page.
   $items['cdm_dataportal/taxon'] = array(
     'page callback' => 'cdm_dataportal_taxon_page_view',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
-d37c9d9
+   // Optional callback arguments: page.
-            d6d4cc03
+    //FIXME point to view/page method in this module
-d37c9d9
+    $items['cdm_dataportal/specimen'] = array(
-            b810158e
+        'page callback' => 'cdm_dataportal_specimen_page_view',
-d37c9d9
+        'access arguments' => array('access content'),
         'type' => MENU_CALLBACK,
         // Expected callback arguments: uuid.
     );
-            6657531f
+  $items['cdm_dataportal/name'] = array(
     'page callback' => 'cdm_dataportal_name_page_view',
       /*
     'page arguments' => array(
        'taxon_name_uuid',
        'taxon_to_hide_uuid',
        'synonym_uuid' => NULL
       ),
       */
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
   $items['cdm_dataportal/reference'] = array(
     'page callback' => 'cdm_dataportal_view_reference',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
   $items['cdm_dataportal/reference/list'] = array(
     'page callback' => 'cdm_dataportal_view_reference_list',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
   $items['cdm_dataportal/media'] = array(
     'page callback' => 'cdm_dataportal_view_media',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments:
     // uuid, mediarepresentation_uuid, part_uuid or part#.
   );
   $items['cdm_dataportal/polytomousKey'] = array(
     'page callback' => 'cdm_dataportal_view_polytomousKey',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: polytomousKey->uuid.
   );
   $items['cdm_dataportal/search'] = array(
     'page callback' => 'cdm_dataportal_view_search_advanced',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
   $items['cdm_dataportal/search/advanced'] = array(
-ee5
+    'title' => 'Advanced', // will be passed through t()
-            6657531f
+    'page callback' => 'cdm_dataportal_view_search_advanced',
     'access arguments' => array('access content'),
     'type' => MENU_DEFAULT_LOCAL_TASK,
   );
   $items['cdm_dataportal/search/taxon_by_description'] = array(
-ee5
+    'title' => 'By factual data', // will be passed through t()
-            6657531f
+    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
     'access arguments' => array('access content'),
     'type' => MENU_LOCAL_TASK,
   );
   $items['cdm_dataportal/search/results/taxon'] = array(
     'page callback' => 'cdm_dataportal_view_search_results_taxon',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
   /*
    $items['cdm/xml2json'] = array(
    'page callback' => 'cdm_view_xml2json',
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
    );
    */
   // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
   // User configuration of cdm_dataportal.
   $items['user/%/cdm_dataportal'] = array(
     'title' => 'cdm_dataportal',
     'access arguments' => array('access content'),
     'page callback' => 'drupal_get_form',
     'page arguments' => array('cdm_dataportal_user_form'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10,
   );
   // }
   // 'May not cache' in D5.
   $items['cdm_dataportal/name/%'] = array(
     // 'page callback' => 'cdm_dataportal_view_name',
     'page callback' => 'cdm_dataportal_name_page_view',
     'page arguments' => array(2, 3, 4),
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
-f1a217c
+  // --- Local tasks for Taxon.
   // --- tabbed taxon page
-            6657531f
+  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
     $items['cdm_dataportal/taxon/%'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_CALLBACK,
       'weight' => 1,
       'page arguments' => array(2, "description")
-cd0b
+      , // Expected callback arguments: taxon_uuid.
-            6657531f
+    );
     $items['cdm_dataportal/taxon/%/all'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_CALLBACK,
       'weight' => 2,
       'page arguments' => array(2, "all")
-cd0b
+      , // Expected callback arguments: taxon_uuid.
-            6657531f
+    );
     $items['cdm_dataportal/taxon/%/description'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_DEFAULT_LOCAL_TASK,
       'weight' => 2,
       'page arguments' => array(2, "description")
-cd0b
+      , // Expected callback arguments: taxon_uuid.
-            6657531f
+    );
     $items['cdm_dataportal/taxon/%/synonymy'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 4,
       'page arguments' => array(2, "synonymy", 4)
-cd0b
+      , // Expected callback arguments: taxon_uuid and ...
-            6657531f
+    );
     $items['cdm_dataportal/taxon/%/images'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Images')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 5,
       'page arguments' => array(2, "images")
-cd0b
+      , // Expected callback arguments: taxon_uuid.
-            6657531f
+    );
     $items['cdm_dataportal/taxon/%/specimens'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 6,
       'page arguments' => array(2, "specimens")
-cd0b
+      , // Expected callback arguments: taxon_uuid.
-            6657531f
+    );
     $items['cdm_dataportal/taxon/%/keys'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 6,
       'page arguments' => array(2, "keys")
-cd0b
+      , // Expected callback arguments: taxon_uuid.
     );
     $items['cdm_dataportal/taxon/%/experts'] = array(
         'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Experts')),
         'page callback' => 'cdm_dataportal_taxon_page_view',
         'access arguments' => array('access content'),
         'type' => MENU_LOCAL_TASK,
         'weight' => 6,
         'page arguments' => array(2, "experts")
     , // Expected callback arguments: taxon_uuid.
-            6657531f
+    );
-ae67cc
+            Patrick Plitzner
     $items['cdm_dataportal/taxonSearch/autocomplete'] = array(
         'page callback' => 'cdm_dataportal_taxaon_search_autocomplete',
         'access arguments' => array('access taxon search autocomplete'),
         'type' => MENU_CALLBACK
     );
-            6657531f
+            Andreas Kohlbecker
-f1a217c
+  // --- refresh link for all cdmnode types
   foreach (cdm_get_nodetypes() as $type=>$name) {
     $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
         'title' => t('Refresh'),
         'page callback' => 'cdm_dataportal_refresh_node',
-db26
+        'access arguments' => array('administer cdm_dataportal'),
-f1a217c
+        'type' => MENU_LOCAL_TASK,
         'weight' => 100,
         'page arguments' => array($name, 2)
     );
+  }
-            6657531f
+  return $items;
+}
 /**
-            b85ab055
+ * Implements hook_init().
+ *
-            6657531f
+ */
 function cdm_dataportal_init() {
-ea8b301
+  //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.
-            6657531f
+  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'));
-dd59bb5
+            Andreas Kohlbecker
   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
+  }
-d467
+            Andreas Kohlbecker
   $bibliography_settings = get_bibliography_settings();
-d513cb
+  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
   FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
-            6657531f
+            Andreas Kohlbecker
-f1a217c
+function cdm_dataportal_refresh_node($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' => $parameters));
+}
-            6657531f
+/**
  * The function generate form for own user cdm dataportal configurations.
  */
 function cdm_dataportal_user_form($form, &$form_state) {
-            36818236
+            Andreas Kohlbecker
-            6657531f
+  global $user;
   $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
-e1dc7ec
+  $form['taxon_page_tabs'] = array(
       '#type' => 'fieldset',
-            36818236
+      '#tree' => true,
-e1dc7ec
+      '#title' => t('Taxon page tabs'),
   );
-            36818236
+            Andreas Kohlbecker
   $form['taxon_page_tabs']['user_defined'] = array(
-            6657531f
+    '#type' => 'checkbox',
     '#title' => t('Activate user default configuration'),
     '#default_value' => variable_get($checkbox_value, 0),
     '#description' => t('Check this if you want configure your own default tab from the below menu.'),
   );
-            36818236
+  $form['taxon_page_tabs']['default_tab'] = array(
-            6657531f
+    '#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
-            36818236
+              to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
   );
-            f695daf4
+  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'))
+            )
         ),
     );
+  }
-            6657531f
+            Andreas Kohlbecker
   $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';
-            36818236
+  // 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
-            6657531f
+    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
-            36818236
+    variable_set($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']) {
-            6657531f
+      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.')));
+    }
-            36818236
+            Andreas Kohlbecker
-            6657531f
+            Andreas Kohlbecker
   else {
-            36818236
+    // Problem with the user id => variables wont be saved.
-            6657531f
+    $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");
-            fc13aa30
+    $block["2"] = array(
         "info" => t("CDM Search Taxa"),
         "cache" => DRUPAL_NO_CACHE
       );
-            6657531f
+    // $block[3]["info"] = t("CDM Filters");
     $block["4"]["info"] = t("CDM Dataportal Print");
     $block["keys"]["info"] = t("CDM identification keys");
     $block["fundedByEDIT"]["info"] = t('Funded by EDIT');
-            f9a3d0f6
+    $block["classification_breadcrumbs"] =  array(
         'info' => t('Classification breadcrumbs'),
         'cache' => DRUPAL_CACHE_PER_PAGE
       );
-            6657531f
+            Andreas Kohlbecker
     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');
-f88fd
+      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
       $block['content'] = drupal_render($form);
-            6657531f
+            Andreas Kohlbecker
       if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
         $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
+      }
       return $block;
     case '4':
-            c8234bdf
+      $block['subject'] = '';
-            6657531f
+      $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;
-c74b7
+      $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(
-            6657531f
+        'attributes' => array("target" => "EDIT"),
         'absolute' => TRUE,
         'html' => TRUE,
       ));
       return $block;
-            f9a3d0f6
+    case 'classification_breadcrumbs':
-af3ce28
+      $taxon_uuid = get_current_taxon_uuid();
-da4e54
+      $block['subject'] = '<none>';
       $block['content'] = compose_classification_breadcrumbs($taxon_uuid);
       return $block;
-            6657531f
+            Andreas Kohlbecker
+}
-af3ce28
+/**
  * 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 $_SESSION['cdm']['taxonomictree_uuid'];
+  }
   else {
     return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
+  }
+}
-            6657531f
+/*
  function cdm_dataportal_session_clear($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));
+ }
+ }
  */
 /**
-            d7588d36
+ * creates a  selector form for taxonomic trees.
+ *
-af3ce28
+ * @return array
  *  a drupal form array
-            6657531f
+ */
 function cdm_taxonomictree_selector() {
   _add_js_treeselector();
-            a8a8f23c
+  $form = drupal_get_form('cdm_taxonomictree_selector_form');
-            d7588d36
+  return $form;
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
-af3ce28
+            Andreas Kohlbecker
  * @deprecated use compose_classification_selector instead
-            6657531f
+ */
 function cdm_taxonomictree_selector_form($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,
   );
-fb3778
+  $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;
+  }
-            6657531f
+  $form['val'] = array(
     '#type' => 'select',
     '#title' => t('Available classifications'),
-cd0b
+    '#default_value' => get_current_classification_uuid(),
-fb3778
+    '#options' => $options,
-af3ce28
+    '#attributes' => array('class' => array('highlite-first-child')),
-            6657531f
+  );
   return $form;
+}
-af3ce28
+/**
+ *
  * @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 $render_array;
+}
-            6657531f
+/* UNREACHABLE since action of form directly links to view.
  function cdm_dataportal_search_taxon_form_submit($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) {
-            f26245c8
+            Andreas Kohlbecker
   cdm_check_valid_portal_page();
-            6657531f
+  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
   return theme('cdm_reference_page', array('reference' => $reference));
+}
 /**
-            b2ebf0d3
+ * Creates a view on a all references contained in the portal.
-            b5dca1e2
+            Andreas Kohlbecker
  * This function is used at the path cdm_dataportal/reference/list
-            6657531f
+ */
 function cdm_dataportal_view_reference_list($pageNumber) {
   $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
-            b2ebf0d3
+  cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
-            f26245c8
+            Andreas Kohlbecker
   cdm_check_valid_portal_page();
-            6657531f
+  $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"));
+  }
+}
-ad3a
+/**
  * 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])) {
-            f19f47fa
+    // --- 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']));
-            a950f2f9
+    $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($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;
-ad3a
+            Andreas Kohlbecker
-            f19f47fa
+    $ws_endpoint = NULL;
-ad3a
+    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;
+    }
-            f19f47fa
+            Andreas Kohlbecker
     $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
         array(
             $taxon->uuid,
         ),
-ad3a
+        queryString($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 $occurences = NULL;
-            f19f47fa
+            Andreas Kohlbecker
   if(!isset($occurences)) {
     $occurences = array();
+  }
-ad3a
+            Andreas Kohlbecker
   if (!isset($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']);
-            f19f47fa
+    $relationship_choice['invers'] = get_selection($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;
+    }
+  }
-ad3a
+  return $occurences[$taxon->uuid];
+}
  */
-            6657531f
+/**
  * 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
-c962983
+ * when dealing with collections of settings form elements (#tree = TRUE).
-            6657531f
+            Andreas Kohlbecker
  * @param string $variableKey
  *   The Unique key of the Drupal variable in the Drupal variables table.
  * @param string $defaultValueString
  *   A string as for example derived from a CONSTANT.
+ *
  * @return mixed
-c962983
+ *   usually an array, depending on the nature of the variable.
+ *
  * TODO compare with get_array_variable_merged() duplicate functions?
-f7c9d15
+ * @deprecated rather use get_array_variable_merged() since this function
  * used an array as second parameter
-            6657531f
+ */
 function mixed_variable_get($variableKey, $defaultValueString) {
   $systemDefaults = unserialize($defaultValueString);
   $storedSettings = variable_get($variableKey, array());
   if (is_array($storedSettings)) {
-c962983
+    // TODO better use drupal_array_merge_deep() ?
-            6657531f
+    $settings = array_merge($systemDefaults, $storedSettings);
+  }
   else {
     $settings = $systemDefaults;
+  }
   return $settings;
+}
-            b5519d3a
+/**
-f7c9d15
+ * Recursive function to convert an object into an array.
-            b5519d3a
+ * 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;
+  }
+}
-fd6da0b
+/**
  * 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;
+}
-a1151a4
+/**
-f5c7f2a
+ * Wraps the given $html string into a render array suitable for drupal_render()
-a1151a4
+            Andreas Kohlbecker
-            65345976
+ * @param $html
-a1151a4
+ *   the html string, see
  *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
-            65345976
+ * @param $weight
-a1151a4
+ *   A positive or negative number (integer or decimal).
  *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
-            65345976
+ * @param $prefix
  *   Optional markup for the '#prefix' element of the render array
  * @param $suffix
  *   Optional markup for the '#suffix' element of the render array
-a1151a4
+            Andreas Kohlbecker
-            65345976
+ * @return array
-a1151a4
+ *   A render array
+ *
  */
-            65345976
+function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
-f5c7f2a
+  $render_array = array(
     '#markup' => $html
-ce9afb7
+      );
-f5c7f2a
+  if (is_numeric($weight)) {
     $render_array['#weight'] = $weight;
-            65345976
+            Andreas Kohlbecker
   if($prefix){
     $render_array['#prefix'] = $prefix;
+  }
   if($suffix) {
     $render_array['#suffix'] = $suffix;
+  }
-f5c7f2a
+  return $render_array;
-a1151a4
+            Andreas Kohlbecker
-            6657531f
+/**
  * 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") {
-            f19f47fa
+    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
-            6657531f
+    return;
+  }
   if (!is_uuid($polytomousKeyNode->uuid)) {
-            f19f47fa
+    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
-            6657531f
+    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) {
-            f26245c8
+            Andreas Kohlbecker
   cdm_check_valid_portal_page();
-            6657531f
+  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
   $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
   if (is_array($sourcePager->records)) {
     $polytomousKey->sources = $sourcePager->records;
     // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
+  }
   $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
   if (is_array($annotationPager->records)) {
     $polytomousKey->annotations = $annotationPager->records;
+  }
   _load_polytomousKeySubGraph($polytomousKey->root);
   return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
+}
 /**
  * Creates a taxon page view or a chapter of it.
+ *
  * The taxon page gives detailed information on a taxon, it shows:
  *  - Taxon name.
  *  - Full list of synonyms homotypic synonyms on top, followed by the
  *    heterotypic and finally followed by misapplied names.
  *    The list is ordered historically.
  *  - All description associated with the taxon.
+ *
  * @param string $uuid
  * @param string $chapter
  *   Name of the part to display, valid values are:
  *   'description', 'images', 'synonymy', 'specimens', 'all'.
+ *
  * @return unknown_type
  */
 function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
-ea8b301
+            Andreas Kohlbecker
-            f26245c8
+  cdm_check_valid_taxon_page($chapter);
-dd59bb5
+  cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
-ea8b301
+  // 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'
         );
+  }
-            6657531f
+  // Display the page for the taxon defined by $uuid.
   // set_last_taxon_page_tab(arg(3));
   $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
   if (!empty($taxonpage)) {
-dd59bb5
+    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
-            6657531f
+    return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
+  }
   else {
-dd59bb5
+    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
-            6657531f
+    return '';
+  }
+}
 /**
-f6da42
+ * This function will genreate the taxon page part ($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.
-            6657531f
+            Andreas Kohlbecker
  * @param string $uuid
-f6da42
+ *   the uuid of the taxon to show
-            6657531f
+ * @param string $chapter
  *   Name of the part to display, valid values are:
  *   'description', 'images', 'synonymy', 'all'.
+ *
-f6da42
+ * @return taxonpage object with the following fields:
  *   - title : the title of the page
  *   - content: the content of the page
+ *
-            6657531f
+ */
-cf9238f
+function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
-            6657531f
+  // 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(
-cf9238f
+    'taxon' => $taxon
-            6657531f
+  ));
   // Check if the taxon id contained in the currently selected tree.
-cd0b
+  $taxon_in_current_classification = taxon_in_current_classification($uuid);
-b6ee11
+            Andreas Kohlbecker
-cd0b
+  if (!$taxon_in_current_classification) {
-b6ee11
+    $classifications = get_classifications_for_taxon($taxon);
-            e24d373b
+    RenderHints::pushToRenderStack('not_in_current_classification');
     $taxon_name_markup = render_taxon_or_name($taxon);
-b6ee11
+    if (count($classifications) == 0) {
-            e24d373b
+      drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
-            fba00a4f
+        array(
-            e24d373b
+        '!taxonname' => $taxon_name_markup,
-            fba00a4f
+            Andreas Kohlbecker
       ), 'warning');
-            6657531f
+            Andreas Kohlbecker
     else {
       $trees = '';
-b6ee11
+      foreach ($classifications as $classification) {
         if (isset($classification->titleCache)) {
           $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
-            6657531f
+            Andreas Kohlbecker
+      }
-b7c460
+      drupal_set_message(format_plural(count($trees),
-            e24d373b
+          '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)
-            fba00a4f
+        ) ,
         'warning');
-            6657531f
+            Andreas Kohlbecker
-            e24d373b
+    RenderHints::popFromRenderStack();
-            6657531f
+            Andreas Kohlbecker
   // Render the taxon page.
-a607f17
+  $render_array = compose_cdm_taxon_page($taxon, $chapter);
   $taxonpage->content = drupal_render($render_array);
-            6657531f
+            Andreas Kohlbecker
   return $taxonpage;
+}
-d37c9d9
+/**
  * 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_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
     ));
-            b810158e
+    // Render the specimen page.
     $render_array = compose_cdm_specimen_page($uuid);
-d37c9d9
+    $specimenpage->content = drupal_render($render_array);
     return $specimenpage;
+}
-            6657531f
+/**
  * 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.
+ *
-b04faf
+ * @param UUID $taxon_name_uuid
  *   The uuid of the CDM TaxonNameBase 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 $highlite_synonym_uuid will be highlighted
  *   in case it is found on this page.
-            6657531f
+            Andreas Kohlbecker
  * @return mixed
  *   The formatted name page as node.
  */
 function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
-            f26245c8
+  cdm_check_valid_portal_page();
-            6657531f
+  $taxonname_page = cdm_dataportal_name_view($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 '';
+  }
+}
 /**
-            e3001c8d
+ * View function for a TaxonNameBase page.
-            6657531f
+            Andreas Kohlbecker
-            e3001c8d
+ * 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.
-            6657531f
+            Andreas Kohlbecker
-            e3001c8d
+ * 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.
-            6657531f
+            Andreas Kohlbecker
-            e3001c8d
+            Andreas Kohlbecker
  * @param UUID $taxon_name_uuid
  *   The uuid of the CDM TaxonNameBase 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 $highlite_synonym_uuid will be highlighted
  *   in case it is found on this page.
+ *
  * @return object
  *   An object with two fields:
  *     - title: the page title
  *     - content: the page content
-            6657531f
+ */
-            e3001c8d
+function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
-            6657531f
+  // Getting the full taxonname object from the server.
-            d0d068e9
+  $taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
-            6657531f
+  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;
-cd0b
+  $request_params['tree'] = get_current_classification_uuid();
-            6657531f
+  $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));
-            d0d068e9
+  // Removing the name where we came from.
-            6657531f
+  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.
-            e3001c8d
+    $singleTaxon = array_pop($taxon_pager->records);
-            6657531f
+    if ($singleTaxon->class != "Taxon") {
       // It is a Synonym -> look for the accepted.
-cd0b
+      $accepted_taxa = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_current_classification_uuid()));
-            e3001c8d
+      if (!empty($highlite_synonym_uuid)) {
-            f0bf24e7
+        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
-            6657531f
+            Andreas Kohlbecker
       else {
-            f0bf24e7
+        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
-            6657531f
+            Andreas Kohlbecker
+    }
     else {
       // It is an accepted taxon.
-            e3001c8d
+      if (!empty($highlite_synonym_uuid)) {
         drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
-            6657531f
+            Andreas Kohlbecker
       else {
         drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
+      }
+    }
+  }
   else {// More than one taxa case.
     $taxon_name_page = new stdClass();
-f225a0f
+    $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
-            6657531f
+    if ($taxon_pager->records) {
-d19c
+      $taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
-            6657531f
+            Andreas Kohlbecker
     else {
       $taxon_name_page->content = 'This name has no taxa';
+    }
     return $taxon_name_page;
+  }
+}
 /**
-b13813
+ * Creates a page with the advance search form.
+ *
  * NOTE: The advance search form allows searching for taxa.
-            6657531f
+ */
 function cdm_dataportal_view_search_advanced() {
   drupal_set_title(t('Advanced search'), PASS_THROUGH);
   return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
+}
 /**
-b13813
+ * Creates a page with the search form for searching by taxon descriptions.
-            6657531f
+ */
 function cdm_dataportal_view_search_taxon_by_description() {
-ddfb
+  drupal_set_title(t('Search by factual data'), PASS_THROUGH);
-            6657531f
+  return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
+}
 /**
  * Executes the search and generates the result list of taxa.
  */
 function cdm_dataportal_view_search_results_taxon() {
   $taxonPager = cdm_dataportal_search_execute();
-            f19f47fa
+  $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){
-d69a96c
+          jQuery(\'.media_gallery\').show(20);
       } else {
           jQuery(\'.media_gallery\').hide(20);
+      }
       // add change handler
       jQuery(\'#showThumbnails input.showThumbnails\').change(
-            f19f47fa
+      function(event){
-d69a96c
+        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);
       });
-e178e2
+  });',
-            f19f47fa
+  array('type' => "inline", 'scope' => JS_DEFAULT));
-e178e2
+  drupal_set_title(t('Search results'), PASS_THROUGH);
-            6657531f
+  return theme('cdm_search_results', array(
     'pager' => $taxonPager,
     'path' => 'cdm_dataportal/search/results/taxon',
     ));
+}
-ff9
+/**
  * Provides the standart image wich indicated a loading process
+ *
  * @return string
  *  The img html tag
  */
 function loading_image_html() {
   return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
     . '/images/loading_circle_grey_16.gif" style="display:none;">';
+}
-e178e2
+/**
  * Returns the state of the the showThumbnails flag set in the
  * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
+ *
-            c5ed6357
+ * @return boolean
-e178e2
+ *    returns 1 if the flag is set
  */
 function do_showThumbnails() {
   static $showThumbnails = null;
   if($showThumbnails == null) {
-            c5ed6357
+    $showThumbnails = 0;
     if (!isset($_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'] +
             $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
+            )
          ? 1 : 0;
-            f19f47fa
+            Andreas Kohlbecker
-            c5ed6357
+       drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
+    }
-            f19f47fa
+    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
     if (!is_numeric($showThumbnails)) {
       $showThumbnails = 1;
+    }
-e178e2
+            Andreas Kohlbecker
   return $showThumbnails;
+}
-            6657531f
+            Andreas Kohlbecker
 /* ====================== 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);
+  }
+}
-d37c9d9
+function path_to_specimen($uuid) {
     if (!$uuid) {
         return FALSE;
+    }
     else {
         return 'cdm_dataportal/specimen/' . $uuid;
+    }
+}
-            6657531f
+/**
-c7044
+ * 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 $acceptedUuid
  *    The uuid of the according accepted taxon
  * @return string
  *    The URL to show a synonmy in the according taxon page
-            6657531f
+ */
 function uri_to_synonym($synonymUuid, $acceptedUuid) {
   $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
-            d071bed7
+  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
-c7044
+      ),
       'fragment' => $synonymUuid
-            d071bed7
+  ));
-            6657531f
+            Andreas Kohlbecker
 /**
-            b8bfa4bd
+ * Compses 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 UUID $keyUuid
  *   The UUID of the key
-            6657531f
+ */
 function path_to_key($keyType, $keyUuid) {
   if (!$keyUuid || !$keyType) {
     return FALSE;
+  }
   $keyType{0} = strtolower($keyType{0});
   return "cdm_dataportal/" . $keyType . "/$keyUuid";
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function path_to_reference($uuid) {
   if (!$uuid) {
     return FALSE;
+  }
   return 'cdm_dataportal/reference/' . $uuid;
+}
 /**
-b04faf
+ * Creates the path to a cdm_dataportal taxon name page.
+ *
  * @param UUID $taxon_name_uuid
  *   The uuid of the CDM TaxonNameBase 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 $highlite_synonym_uuid will be highlighted
  *   in case it is found on this page.
+ *
  * @return a URI path element as string
-            6657531f
+ */
-b04faf
+function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid  = NULL) {
-            6657531f
+  $res = FALSE;
   if ($name_uuid) {
     $res = 'cdm_dataportal/name/' . $name_uuid;
+  }
-b04faf
+  if($taxon_to_hide_uuid){
     $res .= '/' . $taxon_to_hide_uuid;
     if($synonym_uuid){
       $res .= '/' . $synonym_uuid;
+    }
+  }
-            6657531f
+  return $res;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
   if (!$uuid) {
     return FALSE;
+  }
   $out = 'cdm_dataportal/media/' . $uuid;
   if ($representaion_uuid) {
     $out .= '/' . $representaion_uuid;
     if ($partId !== FALSE) {
       $out .= '/' . $partId;
+    }
+  }
   return $out;
+}
 /**
  * Compares thisRank with thatRank.
+ *
  * Returns a negative integer, zero, or a positive integer
  * as the of thisRank is higher than, equal to, or lower than thatRank.
  * e.g:
  * <ul>
  * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
  * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
  * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
  * </ul>
  * <p>
  * This compare logic of the underlying webservice is the
  * <b>inverse logic</b> of the the one implemented in
  * java.lang.Comparable#compareTo(java.lang.Object)
+ *
  * @param $thisRankUuid
  * @param $thatRankUuid
+ *
  * @return int
  *   A negative integer, zero, or a positive integer
  *   as the thisRank is lower than, equal to, or higher than thatRank.
  */
 function rank_compare($thisRankUuid, $thatRankUuid) {
   $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
   return $result->Integer;
+}
 /**
  * Composes an HTML element class attribute value composed of
  * the shortname of the cdm class and the uuid of the entity.
  * This class attribute should be used whereever an cdm-entity is rendered.
+ *
  * These according class selectors in css must be escaped, eg:
  *    .cdm\:TextData
+ *
  * @param $cdmEntity
  */
-            f19f47fa
+function html_class_attribute_ref($cdmEntity) {
-            6657531f
+            Andreas Kohlbecker
   if (is_cdm_entity($cdmEntity)) {
     return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
+  }
+}
 /**
  * Creates a short taxonname.
+ *
-            e90899ac
+ * The short name is created by using the taggedTitle field of
-            6657531f
+ * NameSTO or NameTO instances.
-            e90899ac
+ * If the taggedTitle if empty the fullname will be returned.
-            6657531f
+            Andreas Kohlbecker
  * @param unknown_type $name
  *   Name or TreeNode.
+ *
  * @return string
  */
 function cdm_dataportal_shortname_of($name) {
   $nameStr = '';
-            e90899ac
+  normalize_tagged_text($name->taggedTitle);
-            6657531f
+            Andreas Kohlbecker
   // Get all tagged text tokens of the scientific name.
   foreach ($name->taggedTitle as $tagtxt) {
     if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
       $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
+    }
+  }
   $nameStr = trim($nameStr);
   if ($nameStr) {
     // Do not return short names for these.
     if ($name->unplaced || $name->excluded) {
       return $nameStr;
+    }
     /*
 st capture group (^[a-zA-Z]): First letter of uninomial.
     Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
     Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
     but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
     OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
     */
     $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
     if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
       return $matches[1][0] . "." . $matches[3][0];
+    }
     else {
       return $nameStr;
+    }
+  }
   else {
     return $name->titleCache;
+  }
+}
 /**
  * Check if a taxon is accepted by the current taxonomic tree.
+ *
  * @param mixed $taxon
  *   The Taxon obkect to check.
+ *
  * @return bool
  *   Returns TRUE if $taxon is accepted, FALSE otherwise.
  */
 function _cdm_dataportal_acceptedByCurrentView($taxon) {
-cd0b
+  $defaultTreeUuid = get_current_classification_uuid();
-            6657531f
+            Andreas Kohlbecker
   if (isset($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 $node) {
-fc780
+      if (isset($node->classification)){
         if(is_object($node->classification)) {
           if ($node->classification->uuid == $defaultTreeUuid) {
             return TRUE;
+          }
-            6657531f
+            Andreas Kohlbecker
-fc780
+        else {
           if ($node->classification == $defaultTreeUuid) {
             return TRUE;
+          }
-            6657531f
+            Andreas Kohlbecker
+      }
+    }
+  }
   return FALSE;
+}
 /**
-cfa718
+ * Checks is the source has one of the given types.
+ *
  * @param object $source
  *   The original source entity
  * @param array $types
  *   An array of elementd of the OriginalSourceType enumeration
  *   If not set the default will be used which is:
  *    - Lineage
  *    - PrimaryMediaSource
  *    - PrimaryTaxonomicSource
  *    - Unknown
  *    - Other
  * @return boolean
-            6657531f
+ */
-cfa718
+  function _is_original_source_type($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, $types);
+  }
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _is_invers_taxonRelationship($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
+ *
-            65345976
+ * @param array $cdm_entities
-            6657531f
+ *   An array of CdmBase instances or a single instance.
-c5c87a
+ * @param string $footnote_list_key_suggestion
-            6657531f
+            Andreas Kohlbecker
  * @return unknown
  */
-            65345976
+function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
-e37
+            Andreas Kohlbecker
    static $annotations_types_filter = null;
-            6657531f
+   if(!$annotations_types_filter) {
-e37
+     $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
-            6657531f
+            Andreas Kohlbecker
   $footNoteKeys = array();
   // Is argument cdmBase an array?
-            65345976
+  if (!is_array($cdm_entities)) {
-            6657531f
+    $cdmBase_array = array();
-            65345976
+    $cdmBase_array[] = $cdm_entities;
-            6657531f
+            Andreas Kohlbecker
   else {
-            65345976
+    $cdmBase_array = $cdm_entities;
-            6657531f
+            Andreas Kohlbecker
   // Getting the key for the footnotemanager.
-c5c87a
+  if (isset($footnote_list_key_suggestion)) {
     $footnote_list_key = $footnote_list_key_suggestion;
-            6657531f
+            Andreas Kohlbecker
   else {
-c5c87a
+    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
-            6657531f
+            Andreas Kohlbecker
   // Adding the footnotes keys.
   foreach ($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) {
-c5c87a
+        $footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
-            6657531f
+            Andreas Kohlbecker
+    }
+  }
   return $footNoteKeys;
+}
-            d9763fd3
+            Andreas Kohlbecker
-            6657531f
+/**
-            d9763fd3
+ * Creates a CDM Dynabox.
+ *
-            c1f5d897
+ * @param string $dynabox_id
-            d9763fd3
+ *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
-            6657531f
+ * @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
-ce9afb7
+ *   The theme to be used for rendering the cdm REST service response with is
-            6657531f
+ *   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
-            c1f5d897
+ *   dynabox_content (optional)
-            d9763fd3
+ * @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.
+ *
-            c1f5d897
+ * @param string $open_callback
-ce9afb7
+ *   optional javascript call back function to be triggered after toggling the box to
-            c1f5d897
+ *   the open state.
  * @param string $close_callback
-ce9afb7
+ *   optional javascript call back function to be triggered after toggling the box to
-            c1f5d897
+ *   the closed state.
-            d9763fd3
+ * @return string Returns HTML for a dynabox.
  * Returns HTML for a dynabox.
-            6657531f
+ */
-            d9763fd3
+function cdm_dynabox($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(){}' ) {
-            6657531f
+  $out = '';
-            c1f5d897
+            Andreas Kohlbecker
   // check for plain class attribute string
   $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
-c9d11f7
+  if(!array_key_exists('class', $attributes)) {
     $attributes['class'] = array();
+  }
-            d9763fd3
+  $attributes['id'][] = 'dynabox-' . $dynabox_id;
-c9d11f7
+  $dynabox_attributes = drupal_attributes($attributes);
-            b386ae48
+  _add_js_domEvent(); // requires domEvent.js
-            6657531f
+  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
-            c1f5d897
+  drupal_add_js("
-bb8db6
+  jQuery(document).ready(
       function() {
         dynabox('". $dynabox_id ."',
+          {
             open_callback: " . $open_callback .",
-            d9763fd3
+            close_callback: " . $close_callback .
             ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
-bb8db6
+            Andreas Kohlbecker
         );
+      }
    );",
    array(
     'type'=>'inline',
     'scope'=>'footer'
+    )
   );
-            6657531f
+            Andreas Kohlbecker
-c9d11f7
+            Andreas Kohlbecker
-            6657531f
+  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
-c9d11f7
+  $out .= '<!-- dynabox for ' . $content_url . ' -->';
-            dcd1f0e0
+  $out .= '<' . $enclosingtags[0] . ' ' .  $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t($link_alt_text) . '">' . $label . '</a>';
-            d9763fd3
+  $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] . '>';
-c9d11f7
+  $out .= '<!-- dynabox end -->';
-            6657531f
+  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.
-cd9bb
+            Andreas Kohlbecker
  * @TODO this function may have become obsolete by the new method of detecting empty blocks,
-            aa26f9f0
+ *       see $block_content_is_not_empty in compose_feature_blocks() and
-ebb6efc
+ *       $feature_block_has_content in compose_feature_block_items_generic
-            6657531f
+ */
-            f19f47fa
+function has_feature_node_description_elements($featureNode) {
-            6657531f
+            Andreas Kohlbecker
   if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
-e1
+    if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
       foreach ($featureNode->descriptionElements as $descriptionElement) {
-cd9bb
+        if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
           && $descriptionElement->multilanguageText_L10n->text != ''
           || isset($descriptionElement->sources[0])
           || isset($descriptionElement->media[0]) ) {
-e1
+          return TRUE;
+        }
-            6657531f
+            Andreas Kohlbecker
+    }
+  }
-e1
+  else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
-            fae36a2a
+    foreach ($featureNode->childNodes as $child) {
-            f19f47fa
+      if (has_feature_node_description_elements($child)) {
-            6657531f
+        return TRUE;
+      }
+    }
+  }
   return FALSE;
+}
-            f26245c8
+            Andreas Kohlbecker
 /**
  * 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
-            b4a5c2be
+    http_response_code(404); // 404 = Not Found
-            f26245c8
+            Andreas Kohlbecker
+}
 /**
  * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise
+ *
  * @param $chapter
  *   The taxon page chapter or part
  */
 function cdm_check_valid_portal_page(){
-de9f0
+  $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
-            f26245c8
+  if(preg_match($ends_with_file_suffix_pattern, $_GET['q'])){
     // oops this urls ends with a file_suffix and thus does not refer to a portal page
-            b4a5c2be
+    http_response_code(404); // 404 = Not Found
-de9f0
+    exit('HTTP 404');
-            f26245c8
+            Andreas Kohlbecker
+}
-            b2b9e057
+            Andreas Kohlbecker
 /**
  * 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');
-bb473
+  _add_jquery_ui();
-            b2b9e057
+  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 @ 93ae67cc