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

| Branch: | Tag: | Revision:

cdm-dataportal/7.x/modules/cdm_dataportal/cdm_dataportal.module @ c8234bdf

-            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)
  */
 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');
-ae6064e
+module_load_include('inc', 'cdm_dataportal', 'includes/common');
-            eeb98da8
+module_load_include('inc', 'cdm_dataportal', 'includes/pages');
 module_load_include('inc', 'cdm_dataportal', 'includes/media');
-            3445600f
+module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
 module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
-            c4f1eee9
+module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
-f6da42
+            Andreas Kohlbecker
-ab8d4a
+module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
-            6657531f
+module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
 module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.bibliography');
 module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
 module_load_include('php', 'cdm_dataportal', 'classes/footnote');
 module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
 module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
-ff9
+            Andreas Kohlbecker
 /* ============================ java script functions ============================= */
-            6657531f
+/**
 * loads external java script files asynchronously.
+*
 * @param unknown_type $script_url
 */
 function drupal_add_js_async($script_url, $callback){
   drupal_add_js("
         jQuery(document).ready(function() {
           jQuery.ajax({
             url: '" . $script_url . "',
             dataType: 'script',
             cache: true, // otherwise will get fresh copy every page load
             success: function() {
                   " . $callback . "
+            }
           });
         });"
   , 'inline');
+}
 /**
  * @param unknown_type $link_element_selector
  * @param unknown_type $progress_element_selector
  */
 function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
   $callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
   drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
   //   drupal_add_js("
   //   	  if (Drupal.jsEnabled) {
   //         $(document).ready(function() {
   //       		$('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
   //         });
   //       }", 'inline');
+  }
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_treeselector() {
   // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
   drupal_add_js("
       jQuery(document).ready(function() {
          jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
               jQuery('#cdm-taxonomictree-selector-form').submit();
           });
       });
-e178e2
+    ",
     array(
       'type' => 'inline',
       'scope' => 'footer'
+    )
   );
-            6657531f
+            Andreas Kohlbecker
-dfc9
+function _add_js_openlayers() {
   $openlayers = '/js/OpenLayers-2.11/OpenLayers.js';
   drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers, array(
       'type' => 'file',
       'weight' => JS_LIBRARY,
       'cache' => FALSE,
   ));
+}
-            6657531f
+/**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_openlayers_map() {
-dfc9
+  _add_js_openlayers();
-            e7505114
+            Andreas Kohlbecker
-            6657531f
+  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/openlayers_map.js');
   $gmap_api_key = variable_get('gmap_api_key', 'ABQIAAAAFho6eHAcUOTHLmH9IYHAeBRi_j0U6kJrkFvY4-OX2XYmEAa76BTsyMmEq-tn6nFNtD2UdEGvfhvoCQ');
   $baseLayers = variable_get('baselayers', array());
   if (!is_array($baseLayers) || count($baseLayers) == 0) {
     $baseLayers = array(
       'metacarta_vmap0' => 'Metacarta Vmap0',
       'PREFERRED' => 'metacarta_vmap0',
     );
+  }
   $layerNames = '';
   foreach ($baseLayers as $layerName => $layerLabel) {
     if ($layerName == 'PREFERRED') {
       $preferredLayer = $baseLayers['PREFERRED'];
+    }
     else {
       $layerNames .= ($layerNames ? ', ' : '') . "'$layerName'";
+    }
+  }
   if (isset($baseLayers['gmap']) || isset($baseLayers['gsat']) || isset($baseLayers['ghyb'])) {
     drupal_add_html_head('<script src=http://maps.google.com/maps?file=api&amp;v=2&amp;sensor=false&amp;key=' . $gmap_api_key . '" type="text/javascript"></script>', $key = NULL /* TODO Set this variable. */);
     drupal_add_js('http://dev.virtualearth.net/mapcontrol/mapcontrol.ashx?v=6.1', array('type' => 'external'));
+  }
-            ba706bf0
+  $edit_map_service = get_edit_map_service_settings();
-            e7505114
+  // window.onload - is executed when the document and images etc is fully loaded
   // Query(document).ready - is executed much earlier, when the DOM is loaded
-            6657531f
+  drupal_add_js("
           jQuery(document).ready(function() {
-            e7505114
+            Andreas Kohlbecker
                 window.onload = function () {
-            eeb98da8
+            // ---
-            ba706bf0
+                  jQuery('#openlayers_map').cdm_openlayers_map(
                    '" . $edit_map_service['base_uri'] . "',
                    '" . $edit_map_service['version'] . "',
+                   {
-            e7505114
+                    legendPosition: 3,
                     displayWidth: '" . variable_get('cdm_dataportal_geoservice_display_width', FALSE) . "',
                     boundingBox: '" . variable_get('cdm_dataportal_geoservice_bounding_box', FALSE) . "',
                     distributionOpacity: '" . variable_get('cdm_dataportal_geoservice_distributionOpacity', '0.5') . "',
                     legendOpacity: '" . variable_get('cdm_dataportal_geoservice_legendOpacity', '0.5') . "',
                     showLayerSwitcher: " . (variable_get('cdm_dataportal_geoservice_showLayerSwitcher', TRUE) ? 'true' : 'false') . ",
                     baseLayerNames: [" . $layerNames . "],
-bb8db6
+                    defaultBaseLayerName: '" . $preferredLayer . "'
-            eeb98da8
+            Andreas Kohlbecker
-            ba706bf0
+                );
-            eeb98da8
+                 // ---
         };
-bb8db6
+      });
     ", array('type' => 'inline'));
-            6657531f
+            Andreas Kohlbecker
+}
-ff9
+/**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_thickbox() {
   // ---- jQuery thickbox:
   /*
   * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
   * not triggered because of problems with compat-1.0.js' see INSTALL.txt
   */
   // drupal_add_js(drupal_get_path('module',
   // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
   //
   // Add a setting for the path to cdm_dataportal module, used to find the path
   // for the loading animation image in thickbox.
   drupal_add_js(array(
   'cdm_dataportal' => array(
   'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
+  )
   ),
   'setting'
       );
       drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
       drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_lightbox($galleryID) {
   /*
    * Important Notice: The jquery.lightbox-0.5.js has been modified in order to
   * allow using the "alt" attribute for captions instead of the "title"
   * attribute
   */
-            b386ae48
+  $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');
-ff9
+  drupal_add_js('jQuery(document).ready(function() {
       jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
         fixedNavigation:  true,
-            b386ae48
+        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\',
-ff9
+        adjustToWindow: true
       });
     });
     ', array('type' => 'inline'));
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_footnotes() {
-            b386ae48
+  _add_js_domEvent();
-ff9
+  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_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.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');
   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'
       });
     });", array('type' => 'inline'));
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_js_ahah() {
-            b386ae48
+            Andreas Kohlbecker
   _add_js_domEvent(); // requires domEvent.js
-ff9
+  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
+}
-            b386ae48
+/**
  * 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');
+}
-ff9
+            Andreas Kohlbecker
-            6657531f
+/**
  * @todo Enter description here ...
+ *
  * @param unknown_type $width
  * @param unknown_type $bounding_box
  * @param unknown_type $occurrenceQuery
  * @param unknown_type $distributionQuery
  * @param unknown_type $legendFormatQuery
  * @param unknown_type $map_caption
+ *
  * @return unknown
  */
 function get_image_map($width, $bounding_box = FALSE, $occurrenceQuery = FALSE, $distributionQuery = FALSE, $legendFormatQuery = FALSE, $map_caption = FALSE) {
   // Additional query parameters as set in the data portal admin section.
   $labels_on = variable_get('cdm_dataportal_geoservice_labels_on', 0);
   $query_string = '&image=true&recalculate=false&legend=1&ms=' . $width
     . ($bounding_box ? '&bbox=' . $bounding_box : '')
     . ($labels_on ? '&label=' . $labels_on : '');
   if ($map_caption) {
     $query_string .= '&mlp=3&mc_s=Georgia,15,blue&mc=' . $map_caption;
+  }
-            ba706bf0
+  if (get_edit_map_service_version_number() >= 1.1) {
-            6657531f
+            Andreas Kohlbecker
     // Either occurrence or distribution - combined maps will be possible
     // in the future.
     if ($occurrenceQuery) {
       // @todo Fix $occurrenceQuery.
       $occurrenceQuery = str_replace("&image=false", "", $occurrenceQuery);
       // $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
       // Will be replaced below.. HACK!!!
       $occurrenceQuery .= '&l=tdwg4&as=';
       $query_string .= "&" . $occurrenceQuery;
+    }
     elseif ($distributionQuery) {
       $query_string .= "&" . $distributionQuery;
+    }
     // Apply Plain Image map settings special for version >= 1.1.
     /*
     example : title=a:Naturalized++non-invasive
     &ad=cyprusdivs:bdcode:a:5&as=a:ff9900,,0.1,&l=tdwg4
     &ms=500&bbox=32,34,35,36&img=true&legend=1&mlp=3
     &mc_s=Georgia,15,blue&mc=&recalculate=false
     http://edit.br.fgov.be/edit_wp5/v1/rest_gen.php?
     l=background_gis:b,cyprusdivs&ad=cyprusdivs%3Abdcode%3Aa%3A8%2C4
     &as=a%3A339966%2C%2C0.1%2C|b:0000ff,,
     &bbox=32%2C34%2C35%2C36&img=true&legend=1&mc=&mc_s=Georgia%2C15%2Cblue
     &mlp=3&ms=500&recalculate=false&title=a%3Aindigenous
     */
     $map_service_script_name = "rest_gen.php";
     $bgcolor_areaStyleId = "y";
     $baselayer_areaStyleId = "z";
     $bgcolor_layer = '';
     $additional_area_styles = array();
     // Background color:
     if (variable_get('map_bg_color', '')) {
       $bgcolor_layer = "background_gis:" . $bgcolor_areaStyleId;
       $additional_area_styles[] = $bgcolor_areaStyleId . ":" . variable_get('map_bg_color', '') . ",,";
+    }
     // TODO HACK to replace the default base layer which currently is tdwg4 !!!
     // only needed for distribution maps.
     if (strpos($query_string, "?l=") !== FALSE) {
       $layer_param_token = "?l=";
+    }
     else {
       $layer_param_token = "&l=";
+    }
     if (strpos($query_string, "?as=") !== FALSE) {
       $areystyle_param_token = "?as=";
+    }
     else {
       $areystyle_param_token = "&as=";
+    }
     if (variable_get('map_base_layer', '')) {
       $query_string = str_replace($layer_param_token . "tdwg4", "$layer_param_token" . variable_get('map_base_layer', '') . ":" . $baselayer_areaStyleId, $query_string);
+    }
     else {
       $query_string = str_replace($layer_param_token . "tdwg4", $layer_param_token . "tdwg4:" . $baselayer_areaStyleId . ",", $query_string);
+    }
     if ($bgcolor_layer) {
       $query_string = str_replace($layer_param_token, $layer_param_token . $bgcolor_layer . ",", $query_string);
+    }
     if (variable_get('map_base_layer_style', '')) {
       $additional_area_styles[] = $baselayer_areaStyleId . ":" . variable_get('map_base_layer_style', '');
+    }
     foreach ($additional_area_styles as $as) {
       $query_string = str_replace($areystyle_param_token, $areystyle_param_token . $as . "|", $query_string);
+    }
+  }
   else {
     // Pre 1.1. version of map service.
     if ($occurrenceQuery) {
       $map_service_script_name = "point.php";
       // Fix $occurrenceQuery.
       $occurrenceQuery = str_replace("&image=false", "", $occurrenceQuery);
       // $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
       $occurrenceQuery .= '&l=v:e_w_0';
       $query_string .= "&" . $occurrenceQuery;
+    }
     elseif ($distributionQuery) {
       $query_string .= "&" . $distributionQuery;
       $map_service_script_name = "areas.php";
+    }
+  }
-            ba706bf0
+  $mapUri = url(get_edit_map_service_full_uri() . '/' . $map_service_script_name . '?' .  $query_string);
-            6657531f
+  $out = '<img class="distribution_map" src="' . $mapUri . '" alt="Map" />';
   // Showing map caption.
   if ($map_caption) {
     // FIXME: replace <br> by according css style.
     $out .= '<div class="distribution_map_caption">' . $map_caption . '</div>' . '<br />';
     $out .= '</div>';
+  }
   return $out;
+}
 /**
  * @todo Enter description here ...
+ *
  * @param unknown_type $width
  * @param unknown_type $bounding_box
  * @param unknown_type $occurrenceQuery
  * @param unknown_type $distributionQuery
  * @param unknown_type $legendFormatQuery
  * @param unknown_type $map_caption
+ *
  * @return unknown
  */
 function get_openlayers_map($width, $bounding_box = FALSE, $occurrenceQuery = FALSE, $distributionQuery = FALSE, $legendFormatQuery = FALSE, $map_caption = FALSE) {
   _add_js_openlayers_map();
   $out = '<div id="openlayers">';
   $out .= '<div id="openlayers_map" class="smallmap"';
-            cdb6af36
+  if($width) {
     $out .= ' style="width: ' . $width . 'px; height:' . ($width / 2) . 'px"';
+  }
-            6657531f
+            Andreas Kohlbecker
   // Additional query parameters as set in the data portal admin section.
   $labels_on = variable_get('cdm_dataportal_geoservice_labels_on', 0);
   $openlayers_map_query_string = '&img=false&ms=' . $width
     . ($bounding_box ? '&bbox=' . $bounding_box : '')
     . ($labels_on ? '&label=' . $labels_on : '');
   if ($occurrenceQuery) {
     // @todo Fix $occurrenceQuery.
-            d04720ed
+//     $occurrenceQuery .= '&bbox=-180,-90,180,90';
-            6657531f
+    $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
     // $occurrenceQuery .= '&l=v:e_w_0';
     // TODO add to cdm service?
     $occurrenceQuery .= '&legend=0';
     $out .= ' occurrenceQuery="' . $occurrenceQuery . '&' . $openlayers_map_query_string . '"';
+  }
   if ($distributionQuery) {
     $out .= ' distributionQuery="' . $distributionQuery . '&' . $openlayers_map_query_string . '"';
+  }
   if ($legendFormatQuery) {
     $out .= ' legendFormatQuery="' . $legendFormatQuery . '"';
+  }
   $out .= '></div></div>';
   // Showing map caption.
   if ($map_caption) {
     // FIXME: replace <br> by according css style.
     $out .= '<div class="distribution_map_caption">' . $map_caption . '</div>' . '<br />';
     $out .= '</div>';
+  }
   return $out;
+}
 /* ====================== hook implementations ====================== */
 /**
  * Implements hook_permission().
+ *
  * Valid permissions for this module.
+ *
  * @return array
  *   An array of valid permissions for the portfolio module.
  */
 function cdm_dataportal_permission() {
   return array(
     'administer cdm_dataportal' => array(
       'title' => t('administer cdm_dataportal'),
       'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
     ),
     'cdm_dataportal view notes' => array(
       'title' => t('cdm_dataportal view notes'),
       'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
     ),
     // TODO Which other permissions are required?
     // -> check the WP6 requirements document.
   );
+}
 /**
  * Implements hook_menu().
  */
 function cdm_dataportal_menu() {
   $items = array();
   // @see settings.php.
   cdm_dataportal_menu_admin($items);
   cdm_dataportal_menu_help($items);
   $items['cdm_dataportal/names'] = array(
     'page callback' => 'cdm_dataportal_view_names',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
   // Optional callback arguments: page.
   $items['cdm_dataportal/taxon'] = array(
     'page callback' => 'cdm_dataportal_taxon_page_view',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
   $items['cdm_dataportal/name'] = array(
     'page callback' => 'cdm_dataportal_name_page_view',
       /*
     'page arguments' => array(
        'taxon_name_uuid',
        'taxon_to_hide_uuid',
        'synonym_uuid' => NULL
       ),
       */
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
   $items['cdm_dataportal/reference'] = array(
     'page callback' => 'cdm_dataportal_view_reference',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
   $items['cdm_dataportal/reference/list'] = array(
     'page callback' => 'cdm_dataportal_view_reference_list',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: uuid.
   );
   $items['cdm_dataportal/media'] = array(
     'page callback' => 'cdm_dataportal_view_media',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments:
     // uuid, mediarepresentation_uuid, part_uuid or part#.
   );
   $items['cdm_dataportal/polytomousKey'] = array(
     'page callback' => 'cdm_dataportal_view_polytomousKey',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
     // Expected callback arguments: polytomousKey->uuid.
   );
   $items['cdm_dataportal/search'] = array(
     'page callback' => 'cdm_dataportal_view_search_advanced',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
   $items['cdm_dataportal/search/advanced'] = array(
     'title' => 'Advanced',
     'page callback' => 'cdm_dataportal_view_search_advanced',
     'access arguments' => array('access content'),
     'type' => MENU_DEFAULT_LOCAL_TASK,
   );
   $items['cdm_dataportal/search/taxon_by_description'] = array(
     'title' => 'By description full text',
     'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
     'access arguments' => array('access content'),
     'type' => MENU_LOCAL_TASK,
   );
   $items['cdm_dataportal/search/results/taxon'] = array(
     'page callback' => 'cdm_dataportal_view_search_results_taxon',
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
   /*
    $items['cdm/xml2json'] = array(
    'page callback' => 'cdm_view_xml2json',
    'access arguments' => array('access content'),
    'type' => MENU_CALLBACK,
    );
    */
   // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
   // User configuration of cdm_dataportal.
   $items['user/%/cdm_dataportal'] = array(
     'title' => 'cdm_dataportal',
     'access arguments' => array('access content'),
     'page callback' => 'drupal_get_form',
     'page arguments' => array('cdm_dataportal_user_form'),
     'type' => MENU_LOCAL_TASK,
     'weight' => 10,
   );
   // }
   // 'May not cache' in D5.
   // --- Local tasks for Taxon.
   $items['cdm_dataportal/name/%'] = array(
     // 'page callback' => 'cdm_dataportal_view_name',
     'page callback' => 'cdm_dataportal_name_page_view',
     'page arguments' => array(2, 3, 4),
     'access arguments' => array('access content'),
     'type' => MENU_CALLBACK,
   );
   if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
     $items['cdm_dataportal/taxon/%'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_CALLBACK,
       'weight' => 1,
       'page arguments' => array(2, "description")
       , // Expected callback arguments: name_uuid.
     );
     $items['cdm_dataportal/taxon/%/all'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_CALLBACK,
       'weight' => 2,
       'page arguments' => array(2, "all")
       , // Expected callback arguments: name_uuid.
     );
     $items['cdm_dataportal/taxon/%/description'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_DEFAULT_LOCAL_TASK,
       'weight' => 2,
       'page arguments' => array(2, "description")
       , // Expected callback arguments: name_uuid.
     );
     $items['cdm_dataportal/taxon/%/synonymy'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 4,
       'page arguments' => array(2, "synonymy", 4)
       , // Expected callback arguments: name_uuid.
     );
     $items['cdm_dataportal/taxon/%/images'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Images')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 5,
       'page arguments' => array(2, "images")
       , // Expected callback arguments: name_uuid.
     );
     $items['cdm_dataportal/taxon/%/specimens'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 6,
       'page arguments' => array(2, "specimens")
       , // Expected callback arguments: name_uuid.
     );
     $items['cdm_dataportal/taxon/%/keys'] = array(
       'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys')),
       'page callback' => 'cdm_dataportal_taxon_page_view',
       'access arguments' => array('access content'),
       'type' => MENU_LOCAL_TASK,
       'weight' => 6,
       'page arguments' => array(2, "keys")
       , // Expected callback arguments: name_uuid.
     );
+  }
   return $items;
+}
-            b85ab055
+            Andreas Kohlbecker
 /**
-da88db
+ * Implements hook_init().
-            6657531f
+            Andreas Kohlbecker
  * can be removed after fixing the FIXME below
-da88db
+ */
-            6657531f
+function cdm_dataportal_init() {
   //FIXME To add CSS or JS that should be present on all pages, modules should not implement this hook, but declare these files in their .info file.
   drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
   // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
   drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
+}
 /**
  * The function generate form for own user cdm dataportal configurations.
  */
 function cdm_dataportal_user_form($form, &$form_state) {
   global $user;
   $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
   $form['check'] = array(
     '#type' => 'checkbox',
     '#title' => t('Activate user default configuration'),
     '#default_value' => variable_get($checkbox_value, 0),
     '#description' => t('Check this if you want configure your own default tab from the below menu.'),
   );
   $form['cdm_dataportal_user_form'] = array(
     '#type' => 'select',
     '#title' => t('Default tab to display'),
     '#default_value' => get_default_taxon_tab(TRUE),
     '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
     '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
               <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
               to be renderized will be the synonymy of the accepted taxon and not the above selected tab.'),
   );
   $form['submit'] = array(
     '#type' => 'submit',
     '#value' => t('Submit'),
   );
   return $form;
+}
 /**
  * Form submission handler for user_form().
+ *
  * Submits the user cdm dataportal configurations.
  */
 function cdm_dataportal_user_form_submit($form, &$form_state) {
   global $user;
   $msg_type = 'status';
   $username = $user->name;
   $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
   // If is the right user the variables are setted.
   if (arg(0) == 'user' && ($uid = arg(1)) && is_numeric($uid) && $user->uid == $uid) {
     $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
     variable_set($variable_to_use . '_active', $form_state['values']['check']);
     variable_set($variable_to_use, $form_state['values']['cdm_dataportal_user_form']);
     if ($form_state['values']['check']) {
       drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
       drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
         '!tab' => $variable[variable_get($variable_to_use, 0)],
         '!user' => $username,
       ))), $msg_type);
+    }
     else {
       drupal_set_message(check_plain(t('The user default tab wont be used for
         the next taxon site, check the box if you want to use the user default configuration.')));
+    }
     // Problem with the user id => variables wont be saved.
+  }
   else {
     $msg_type = 'warning';
     drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
+  }
+}
 /**
  * Implements hook_block_info().
  */
 function cdm_dataportal_block_info() {
-            fc13aa30
+    // $block[0]["info"] = t("CDM DataPortal DevLinks");
     // $block[1]["info"] = t("CDM DataPortal Credits");
     $block["2"] = array(
         "info" => t("CDM Search Taxa"),
-            6657531f
+        "cache" => DRUPAL_NO_CACHE
       );
     // $block[3]["info"] = t("CDM Filters");
     $block["4"]["info"] = t("CDM Dataportal Print");
     $block["keys"]["info"] = t("CDM identification keys");
     $block["uses"]["info"] = t("CDM Uses");
     $block["fundedByEDIT"]["info"] = t('Funded by EDIT');
     return $block;
+}
 /**
  * Implements hook_block_view().
  */
 function cdm_dataportal_block_view($delta) {
   // TODO Rename block deltas (e.g. '2') to readable strings.
   switch ($delta) {
     // case 'delta-1':
     // $block['subject'] = t('Credits');
     // $block['content'] = theme('cdm_credits');
     // return $block;
-f88fd
+    case '2':
       $block['subject'] = t('Search taxa');
-            6657531f
+      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
       $block['content'] = drupal_render($form);
       if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
         $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
+      }
-            c8234bdf
+      return $block;
-            6657531f
+    case '4':
       $block['subject'] = '';
       $block['content'] = theme('cdm_print_button');
       return $block;
     case "keys":
       $block['subject'] = t('Identification Keys');
       $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
       return $block;
       // Creating a block specific for the Use Interface.
     case "uses":
       $block['subject'] = t('Uses');
       $block['content'] = theme('cdm_block_uses', array('taxonUuid' => NULL));
       return $block;
     case "fundedByEDIT":
       // t('Funded by EDIT');
-            d5f0e39e
+      $text = '<none>';
-            6657531f
+      $block['subject'] = $text;
       $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/funded_by_EDIT.png' . '" alt="' . $text . '"/>';
       $block['content'] = l($img_tag, "http://www.e-taxonomy.eu/", array(
         'attributes' => array("target" => "EDIT"),
         'absolute' => TRUE,
         'html' => TRUE,
       ));
       return $block;
+  }
+}
 /*
  function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
  $_SESSION['cdm'] = NULL;
  if(is_string($cdm_ws_uri_update)){
  $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
+ }
+ }
  function cdm_dataportal_session_validate(){
  if(!isset($_SESSION['cdm']['ws_uri'])){
  $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
  } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
  cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
+ }
+ }
  */
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_taxonomictree_selector() {
-            a8a8f23c
+  _add_js_treeselector();
-            6657531f
+  $form = drupal_get_form('cdm_taxonomictree_selector_form');
   $out = drupal_render($form);
   return $out;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_taxonomictree_selector_form($form, &$form_state) {
   $url = url('cdm_api/setvalue/session', array('query' => NULL));
   $form['#action'] = $url;
   $form['var'] = array(
     '#weight' => -3,
     '#type' => 'hidden',
     '#value' => '[cdm][taxonomictree_uuid]',
   );
   $destination_array = drupal_get_destination();
   $destination = $destination_array['destination'];
   $form['destination'] = array(
     '#weight' => -3,
     '#type' => 'hidden',
     '#value' =>  $destination,
   );
   $form['val'] = array(
     '#type' => 'select',
     '#title' => t('Available classifications'),
     '#default_value' => get_taxonomictree_uuid_selected(),
     '#options' => cdm_get_taxontrees_as_options(),
   );
   return $form;
+}
 /* UNREACHABLE since action of form directly links to view.
  function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
  $_SESSION['cdm']['search'] = $form_values;
  //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
  return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
  //$paramstr = compose_url_prameterstr($form_values);
  //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
+ }
  */
 /* ====================== menu callback functions ====================== */
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 /*
 function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
   static $comment_node_disabled =  0;
   static $comment_node_read_only =  1;
   static $comment_node_read_write =  2;
   if ($form_id == 'node_type_form'
    && isset($form['identity']['type'])
    && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
   ) {
     $form['workflow']['comment'] = array(
       '#type' => 'radios',
       '#title' => t('Default comment setting'),
       '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
       '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
       '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
     );
+  }
+}
 */
 /**
  * Displays a list of the known taxonomic names.
+ *
  * When the list of taxonomic names is displayed, long lists are split up into
  * multiple pages.
+ *
  * TODO: Parameters are still preliminary.
+ *
  * @param string $beginsWith
  * @param string $page
  *   Page number to diplay defaults to page 1.
  * @param bool $onlyAccepted
  */
 function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
   $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
   /*
   // FIXME the filter for accepted names will be a form element, thus this
   // widget should be generated via form api preferably as block.
   $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
   $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
   $out .= theme('cdm_listof_taxa', $taxonPager);
   return $out;
   */
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
   $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
   return theme('cdm_reference_page', array('reference' => $reference));
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_dataportal_view_reference_list($pageNumber) {
   $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
   return theme('cdm_reference_pager', array(
     'referencePager' => $referencePager,
     'path' => 'cdm_dataportal/reference/list/',
     ));
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
   $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
   return theme('cdm_media_page', array(
     'media' => $media,
     'mediarepresentation_uuid' => $mediarepresentation_uuid,
     'partId' => $part,
     ));
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _load_taxonBase(&$taxonBase) {
   if (isset($taxonBase->uuid)) {
     $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
     $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
     $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
+  }
-ad3a
+            Andreas Kohlbecker
 /**
  * Loads the media associated to the given taxon from the cdm server.
  * The aggregation settings regarding taxon relathionships and
  * taxonnomic childen are taken into account.
+ *
  * The media lists are cached in a static variable.
+ *
  * @param Taxon $taxon
  *   A CDM Taxon entitiy
+ *
  * @return array
  *   An array of CDM Media entities
+ *
  */
 function _load_media_for_taxon($taxon) {
   static $media = NULL;
   if(!isset($media)) {
     $media = array();
+  }
   if (!isset($media[$taxon->uuid])) {
     // --- GET Images --- //
     $mediaQueryParameters = array(
         "type" => "ImageFile",
     );
-            a950f2f9
+    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
     $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
     $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
     $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
     $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
-ad3a
+    $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
     $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
     $ws_endpoint = NULL;
     if ( variable_get('cdm_images_include_children', 0) == 0) {
       $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
     } else {
       $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
+    }
     $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
         array(
             $taxon->uuid,
         ),
         queryString($mediaQueryParameters)
        );
+  }
   return $media[$taxon->uuid];
+}
 /**
+ *
  * @param Taxon $taxon
  *   A CDM Taxon entitiy
+ *
  * @return array
  *   An array of CDM SpecimenOrObservation entities
+ *
 function _load_occurences_for_taxon($taxon){
   static $occurences = NULL;
   if(!isset($occurences)) {
     $occurences = array();
+  }
   if (!isset($occurences[$taxon->uuid])){
     $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
     $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
     $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
     $by_associatedtaxon_query = http_build_query(array(
         'relationshipsInvers' => implode(',', $relationship_choice['invers']),
         'relationships' => implode(',', $relationship_choice['direct']),
         'pageSize' => null // all hits in one page
+    )
     );
     $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
         null,
         $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
     );
     if(isset($pager->records[0])){
       $occurences[$taxon->uuid] =  $pager->records;
+    }
+  }
   return $occurences[$taxon->uuid];
+}
-            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
  * when dealing with collections of setting form elements (#tree = TRUE).
+ *
  * @param string $variableKey
  *   The Unique key of the Drupal variable in the Drupal variables table.
  * @param string $defaultValueString
  *   A string as for example derived from a CONSTANT.
+ *
  * @return mixed
  *   Returns usally an array, depending on the nature of the variable.
  */
 function mixed_variable_get($variableKey, $defaultValueString) {
   $systemDefaults = unserialize($defaultValueString);
   $storedSettings = variable_get($variableKey, array());
   if (is_array($storedSettings)) {
     $settings = array_merge($systemDefaults, $storedSettings);
+  }
   else {
     $settings = $systemDefaults;
+  }
   return $settings;
-            b5519d3a
+            Andreas Kohlbecker
 /**
  * Recusive funciton to convert an object into an array.
  * also subordinate objects will be converted.
+ *
  * @param object $object
  * @return the array
  */
 function convert_to_array($object) {
   if(is_object($object) || is_array($object)) {
     $array = (array)$object;
     foreach ($array as $key=>$value){
       $array[$key] = convert_to_array($value);
+    }
     return $array;
   } else {
     return $object;
+  }
-a1151a4
+            Andreas Kohlbecker
 /**
  * Wrapps the given $html string into a reder array suitable for drupal_render()
+ *
  * @param string $html
  *   the html string, see
  *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
  * @param number $weight
  *   A positive or negative number (integer or decimal).
  *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
+ *
  * @return
  *   A render array
+ *
  */
 function markup_to_render_array($html, $weight = 0) {
   return array(
           '#markup' => $html,
           '#weight' => $weight,
       );
-            6657531f
+            Andreas Kohlbecker
 /**
  * Loads the subgraph of a given PolytomousKeyNode.
+ *
  * Loads the subgraph of the given PolytomousKeyNode recursively from
  * the CDM REST service.
+ *
  * @param mixed $polytomousKeyNode
  *   PolytomousKeyNode passed by reference.
+ *
  * @return void
  */
 function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
   if (!$polytomousKeyNode) {
     return;
+  }
   if ($polytomousKeyNode->class != "PolytomousKeyNode") {
     drupal_set_message(_load_polytomousKeySubGraph() . t('invalid type given.'), 'error');
     return;
+  }
   if (!is_uuid($polytomousKeyNode->uuid)) {
     drupal_set_message(_load_polytomousKeySubGraph() . t('invalid type given.'), 'error');
     return;
+  }
   $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
   if (!$polytomousKeyNode) {
     // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
     return;
+  }
   // Load children.
   foreach ($polytomousKeyNode->children as &$childNode) {
     _load_polytomousKeySubGraph($childNode);
+  }
   // Load subkey.
   $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
   // Load taxon.
   $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
   _load_taxonBase($polytomousKeyNode->taxon);
   return;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
   $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
   $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
   if (is_array($sourcePager->records)) {
     $polytomousKey->sources = $sourcePager->records;
     // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
+  }
   $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
   if (is_array($annotationPager->records)) {
     $polytomousKey->annotations = $annotationPager->records;
+  }
   _load_polytomousKeySubGraph($polytomousKey->root);
   return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
+}
 /**
  * Creates a taxon page view or a chapter of it.
+ *
  * The taxon page gives detailed information on a taxon, it shows:
  *  - Taxon name.
  *  - Full list of synonyms homotypic synonyms on top, followed by the
  *    heterotypic and finally followed by misapplied names.
  *    The list is ordered historically.
  *  - All description associated with the taxon.
+ *
  * @param string $uuid
  * @param string $chapter
  *   Name of the part to display, valid values are:
  *   'description', 'images', 'synonymy', 'specimens', 'all'.
+ *
  * @return unknown_type
  */
 function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
   // Display the page for the taxon defined by $uuid.
   // set_last_taxon_page_tab(arg(3));
   $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
   if (!empty($taxonpage)) {
     return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
+  }
   else {
     return '';
+  }
+}
-f6da42
+            Andreas Kohlbecker
 /**
  * This function will genreate the taxon page part ($chapter) and returns a taxonpage object
  * which has two fields, one for the page title and one for the content. Later on in the
-            6657531f
+ * process chain the value contained in these fields will be passed to the cdm_node_show()
  * function as the function parameters $title and $content.
-f6da42
+            Andreas Kohlbecker
-            6657531f
+ * @param string $uuid
  *   the uuid of the taxon to show
  * @param string $chapter
  *   Name of the part to display, valid values are:
-f6da42
+ *   'description', 'images', 'synonymy', 'all'.
+ *
  * @return taxonpage object with the following fields:
  *   - title : the title of the page
-            6657531f
+ *   - content: the content of the page
-cf9238f
+            Andreas Kohlbecker
-            6657531f
+ */
 function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
   // Taxon object.
   $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
   if (empty($taxon)) {
     drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
     return FALSE;
+  }
   $taxonpage = new stdClass();
-cf9238f
+            Andreas Kohlbecker
-            6657531f
+  $taxonpage->title = theme('cdm_taxon_page_title', array(
     'taxon' => $taxon
   ));
-b6ee11
+  // Check if the taxon id contained in the currently selected tree.
-            6657531f
+  $taxon_in_current_tree = taxon_in_current_tree($uuid);
-b6ee11
+            Andreas Kohlbecker
   if (!$taxon_in_current_tree) {
-c55
+    $classifications = get_classifications_for_taxon($taxon);
-            6657531f
+    if (count($classifications) == 0) {
       drupal_set_message(check_plain(t('This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification.', array(
         '!taxonname' => theme('cdm_taxonName', array('taxonName' => $taxon->name)),
       ))), 'warning');
+    }
-b6ee11
+    else {
       $trees = '';
       foreach ($classifications as $classification) {
-            6657531f
+        if (isset($classification->titleCache)) {
           $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
+        }
-b7c460
+            Andreas Kohlbecker
-c55
+            Andreas Kohlbecker
       drupal_set_message(format_plural(count($trees),
-            6657531f
+          'This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification, but in this one: !trees',
           'This concept of the taxon !taxonname is not contained as an accepted taxon in currently chosen classification, but in one of these: !trees',
           array('!taxonname' => theme('cdm_taxonName', array('taxonName' => $taxon->name)), '!trees' => $trees)) , 'warning');
+    }
+  }
   // Render the taxon page.
   $taxonpage->content = theme('cdm_taxon_page', array(
     'taxon' => $taxon,
     'page_part' => $chapter,
   ));
   return $taxonpage;
+}
 /**
  * Returns a name page as a Drupal node ready to be renderized by Drupal.
+ *
  * The node page shows the taxon name title and the list of taxon related
  * with such taxon. Name on the tree already in use.
+ *
  * @param string $taxon_name_uuid
  *   A taxon name UUID.
+ *
  * @return mixed
  *   The formatted name page as node.
  */
 function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
   $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
   if (!empty($taxonname_page)) {
     return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
+  }
   else {
     return '';
+  }
+}
-            e3001c8d
+            Andreas Kohlbecker
-            6657531f
+/**
-            e3001c8d
+ * View function for a TaxonNameBase page.
+ *
  * The name page lists all taxa for which the name specified by the
  * $taxon_name_uuid is being used. I case there is only one name the
-            6657531f
+ * page automatically redirects ti the according taxon page. Otherwise
-            e3001c8d
+ * the list of names is displayed.
+ *
  * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
  * list of taxa. This is useful for example when referencing from a taxon
-            6657531f
+ * to the name page and the referring taxon should not be repeaded in the
-            e3001c8d
+ * 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 $highlite_synonym_uuid will be highlighted
  *   in case it is found on this page.
+ *
  * @return object
  *   An object with two fields:
-            6657531f
+ *     - title: the page title
-            e3001c8d
+ *     - content: the page content
-            6657531f
+ */
 function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
   // Getting the full taxonname object from the server.
   $taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
   if (!$taxon_name) {
     drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
     return FALSE;
+  }
   // Searching for all the taxa connected with the taxon name on the tree
   // in use.
   $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
   $request_params = array();
   $request_params['query'] = $name_cache;
   $request_params['tree'] = get_taxonomictree_uuid_selected();
   $request_params['doTaxa'] = 1;
   $request_params['doSynonyms'] = 1;
   $request_params['doTaxaByCommonNames'] = 0;
   $request_params['matchMode'] = "EXACT";
   $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
   // Removing the name where we come from.
   foreach ($taxon_pager->records as $k => &$taxon) {
     if ($taxon->uuid == $taxon_to_hide_uuid) {
       unset($taxon_pager->records[$k]);
+    }
+  }
-            e3001c8d
+  // Show the taxa list or go to the singular taxon.
-            6657531f
+  if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
     $singleTaxon = array_pop($taxon_pager->records);
     if ($singleTaxon->class != "Taxon") {
-            e3001c8d
+      // It is a Synonym -> look for the accepted.
       $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_taxonomictree_uuid_selected()));
-            6657531f
+      if (!empty($highlite_synonym_uuid)) {
         drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
+      }
       else {
         drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
+      }
+    }
-            e3001c8d
+    else {
       // It is an accepted taxon.
-            6657531f
+      if (!empty($highlite_synonym_uuid)) {
         drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
+      }
       else {
         drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
+      }
+    }
+  }
-f225a0f
+  else {// More than one taxa case.
-            6657531f
+    $taxon_name_page = new stdClass();
     $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
     if ($taxon_pager->records) {
       $taxon_name_page->content = theme_cdm_list_of_taxa($taxon_pager->records, FALSE);
+    }
     else {
       $taxon_name_page->content = 'This name has no taxa';
+    }
     return $taxon_name_page;
+  }
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_dataportal_view_search_advanced() {
   drupal_set_title(t('Advanced search'), PASS_THROUGH);
   $form = array();
   $form_state = array();
   $searchForm = cdm_dataportal_search_taxon_form($form, $form_state, TRUE);
   return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_dataportal_view_search_taxon_by_description() {
   drupal_set_title(t('Search by description full text'), PASS_THROUGH);
   // $form_state = false;
   // $searchForm = cdm_dataportal_search_taxon_by_description_form($form_state);
   $searchForm = cdm_dataportal_search_taxon_by_description_form();
   return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
+}
 /**
  * Executes the search and generates the result list of taxa.
  */
 function cdm_dataportal_view_search_results_taxon() {
-e178e2
+  $taxonPager = cdm_dataportal_search_execute();
   $showThumbnails = do_showThumbnails();
   $setSessionUri = url('cdm_api/setvalue/session', array(
       'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
   ));
   drupal_add_js('jQuery(document).ready(function() {
       // init
       if(' . $showThumbnails . ' == 1){
       jQuery(\'.media_gallery\').show(20);
   } else {
       jQuery(\'.media_gallery\').hide(20);
+  }
       // add change hander
       jQuery(\'#showThumbnails\').change(
       function(event){
       var state = 0;
       if(jQuery(this).is(\':checked\')){
       jQuery(\'.media_gallery\').show(20);
       state = 1;
   } else {
       jQuery(\'.media_gallery\').hide(20);
+  }
       // store state in session variable
       var uri = \'' . $setSessionUri . '\' + state;
       jQuery.get(uri);
   });
   });',
   array('type' => "inline", 'scope' => JS_DEFAULT));
-            6657531f
+  drupal_set_title(t('Search results'), PASS_THROUGH);
   return theme('cdm_search_results', array(
     'pager' => $taxonPager,
     'path' => 'cdm_dataportal/search/results/taxon',
     ));
-ff9
+            Andreas Kohlbecker
 /**
  * Provides the standart image wich indicated a loading process
+ *
  * @return string
  *  The img html tag
  */
 function loading_image_html() {
   return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
     . '/images/loading_circle_grey_16.gif" style="display:none;">';
-e178e2
+            Andreas Kohlbecker
 /**
  * Returns the state of the the showThumbnails flag set in the
  * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
+ *
  * @return Ambigous <boolean, number>
  *    returns 1 if the flag is set
  */
 function do_showThumbnails() {
   static $showThumbnails = null;
   if($showThumbnails == null) {
     $showThumbnails = FALSE;
     if (isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
       $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
+    }
     if (!is_numeric($showThumbnails)) {
       $showThumbnails = 1;
+    }
+  }
   return $showThumbnails;
-            6657531f
+            Andreas Kohlbecker
 /**
  * View which transforms XML output from a given webservice endpoint into JSON.
  */
 /*
  function cdm_view_xml2json(){
  $file = arg(2);
  $datastr = file_get_contents(variable_get('cdm_webservice_url', '').$file);
  return  xml2json::transformXmlStringToJson($datastr);
+ }
  */
 /* ====================== other functions ====================== */
 /**
  * Creates a URL to the taxon page specified by the $uuid parameter.
+ *
  * The URL will be prepended with a path element to a specific taxon page tab.
+ *
  * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
  * be set globally in the administrative settings or individually in the user
  * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
  * the last portal will stay on this last tab.
+ *
  * A third option is offerered by the $page_tab parameter which allows overwriting this
  * internal mechanism by a specific value.
+ *
  * @param string $uuid
  *   The UUID of the taxon.
  * @param string $page_tab
  *   Overwriting the preset mechanism by defining specific value for the
  *   taxon page tab.
+ *
  * @return string
  *   The created URL.
  */
 function path_to_taxon($uuid, $page_tab = FALSE) {
   $tab = get_default_taxon_tab();
   $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
   if (!$uuid) {
     return FALSE;
+  }
   if ($page_tab) {
     return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
+  }
   elseif (!$tab || strtolower($tab) == 'general') {
     return 'cdm_dataportal/taxon/' . $uuid;
+  }
   elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
     return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
+  }
   else {
     return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
+  }
+}
-c7044
+            Andreas Kohlbecker
 /**
  * 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 $acceptedUuid
  *    The uuid of the according accepted taxon
-            6657531f
+ * @return string
  *    The URL to show a synonmy in the according taxon page
  */
-            d071bed7
+function uri_to_synonym($synonymUuid, $acceptedUuid) {
   $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
   return url($acceptedPath, array(
       'query' => array(
         // highlite the synony in the synonymy
         'highlite' => $synonymUuid,
         // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
-c7044
+        // see theme_taxon_page_title()
         'acceptedFor' => $synonymUuid
-            d071bed7
+      ),
       'fragment' => $synonymUuid
-            6657531f
+  ));
+}
-            b8bfa4bd
+            Andreas Kohlbecker
 /**
  * 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
  *      - ...
-            6657531f
+ * @param UUID $keyUuid
  *   The UUID of the key
  */
 function path_to_key($keyType, $keyUuid) {
   if (!$keyUuid || !$keyType) {
     return FALSE;
+  }
   $keyType{0} = strtolower($keyType{0});
   return "cdm_dataportal/" . $keyType . "/$keyUuid";
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function path_to_reference($uuid) {
   if (!$uuid) {
     return FALSE;
+  }
   return 'cdm_dataportal/reference/' . $uuid;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function path_to_name($name_uuid) {
   $res = FALSE;
   if ($name_uuid) {
     $res = 'cdm_dataportal/name/' . $name_uuid;
+  }
   return $res;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
   if (!$uuid) {
     return FALSE;
+  }
   $out = 'cdm_dataportal/media/' . $uuid;
   if ($representaion_uuid) {
     $out .= '/' . $representaion_uuid;
     if ($partId !== FALSE) {
       $out .= '/' . $partId;
+    }
+  }
   return $out;
+}
 /**
  * Compares thisRank with thatRank.
+ *
  * Returns a negative integer, zero, or a positive integer
  * as the of thisRank is higher than, equal to, or lower than thatRank.
  * e.g:
  * <ul>
  * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
  * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
  * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
  * </ul>
  * <p>
  * This compare logic of the underlying webservice is the
  * <b>inverse logic</b> of the the one implemented in
  * java.lang.Comparable#compareTo(java.lang.Object)
+ *
  * @param $thisRankUuid
  * @param $thatRankUuid
+ *
  * @return int
  *   A negative integer, zero, or a positive integer
  *   as the thisRank is lower than, equal to, or higher than thatRank.
  */
 function rank_compare($thisRankUuid, $thatRankUuid) {
   $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
   return $result->Integer;
+}
 /**
  * Composes an HTML element class attribute value composed of
  * the shortname of the cdm class and the uuid of the entity.
  * This class attribute should be used whereever an cdm-entity is rendered.
+ *
  * These according class selectors in css must be escaped, eg:
  *    .cdm\:TextData
+ *
  * @param $cdmEntity
  */
 function html_class_atttibute_ref($cdmEntity) {
   if (is_cdm_entity($cdmEntity)) {
     return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
+  }
+}
-f5f1c12
+            Andreas Kohlbecker
 /**
-            6657531f
+ * Preprocess the taggedName to normalize newly introduced
  * tagtypes like hybridSign, separator, .. more?
+ *
  * @param unknown_type $taggedTextList
  */
 function normalize_TaggedName(&$taggedTextList) {
   if (is_array($taggedTextList)) {
     // First pass: rename.
     for ($i = 0; $i < count($taggedTextList); $i++) {
       if ($taggedTextList[$i]->type == "hybridSign") {
         $taggedTextList[$i]->type = "name";
+      }
+    }
     // Second pass: resolve separators.
     $taggedNameListNew = array();
     for ($i = 0; $i < count($taggedTextList); $i++) {
       if ($i + 1 < count($taggedTextList) && $taggedTextList[$i + 1]->type == "separator") {
         if ($taggedTextList[$i]->type == $taggedTextList[$i + 2]->type) {
           $taggedName = $taggedTextList[$i];
           $taggedName->text = $taggedName->text . $taggedTextList[$i + 1]->text . $taggedTextList[$i + 2]->text;
           $taggedNameListNew[] = $taggedName;
           ++$i;
           ++$i;
+        }
+      }
       else {
         $taggedNameListNew[] = $taggedTextList[$i];
+      }
+    }
     $taggedTextList = $taggedNameListNew;
+  }
+}
 /**
  * Creates a short taxonname.
+ *
  * The short name is created by using the taggename field of
  * NameSTO or NameTO instances.
  * If the taggename if empty the fullname will be returned.
+ *
  * @param unknown_type $name
  *   Name or TreeNode.
+ *
  * @return string
  */
 function cdm_dataportal_shortname_of($name) {
   $nameStr = '';
   normalize_TaggedName($name->taggedTitle);
   // Get all tagged text tokens of the scientific name.
   foreach ($name->taggedTitle as $tagtxt) {
     if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
       $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
+    }
+  }
   $nameStr = trim($nameStr);
   if ($nameStr) {
     // Do not return short names for these.
     if ($name->unplaced || $name->excluded) {
       return $nameStr;
+    }
     /*
 st capture group (^[a-zA-Z]): First letter of uninomial.
     Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
     Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
     but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
     OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
     */
     $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
     if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
       return $matches[1][0] . "." . $matches[3][0];
+    }
     else {
       return $nameStr;
+    }
+  }
   else {
     return $name->titleCache;
+  }
+}
 /**
  * Check if a taxon is accepted by the current taxonomic tree.
+ *
  * @param mixed $taxon
  *   The Taxon obkect to check.
+ *
  * @return bool
  *   Returns TRUE if $taxon is accepted, FALSE otherwise.
  */
 function _cdm_dataportal_acceptedByCurrentView($taxon) {
   $defaultTreeUuid = get_taxonomictree_uuid_selected();
   if (isset($taxon->taxonNodes)) {
     $taxonNodes = $taxon->taxonNodes;
+  }
   else {
     $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
+  }
   if ($taxon->class == "Taxon" && isset($taxonNodes)) {
     foreach ($taxonNodes as $node) {
       if (is_object($node->classification)) {
         if ($node->classification->uuid == $defaultTreeUuid) {
           return TRUE;
+        }
+      }
       else {
         if ($node->classification == $defaultTreeUuid) {
           return TRUE;
+        }
+      }
+    }
+  }
   return FALSE;
+}
 /**
  * Workaround for missing original source type.
+ *
  * idNamespace is always set in these cases.
  * @todo improve documentation of this function.
+ *
  * @param unknown_type $source
+ *
  * @return unknown_type
  */
 function _is_original_source_type($source) {
   return !$source->idNamespace && strlen($source->idNamespace) == 0;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
   return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
+}
 /**
  * Gets the metadata info such as title or artist of a media file.
+ *
  * The function tries at first to get all the info from the file metadata
  * and if it is not avaible look at the media file info stored at the database.
+ *
  * @param mixed $media
  *   The media file object for which to get the metadata.
+ *
  * @return array
  *   The array with the available specified metadata info.
  * TODO rename to read_media_metadata() and move to *.module.
  */
 function cdm_read_media_metadata($media) {
   $metadata_caption = array(
     'title' => '',// Media_metadata and media.
     'artist' => '',// Media_metadata and media.
     'rights',// Media_metadata and media.
     'location',// Media_metadata.
     'filename' => '',// Media.
     'mediacreated' => '',// Media.
     'description' => '',
   );// Media.
   // Getting the media metadata.
-dfc9
+  $media_metadata = cdm_ws_get(CDM_WS_MEDIA_METADATA, array($media->uuid));
-            6657531f
+  $media_metadata_aux = (array) $media_metadata;
   // Filename.
   if (!empty($media->representations[0]->parts[0]->uri)) {
     $fileUri = $media->representations[0]->parts[0]->uri;
     $filename = substr($fileUri, strrpos($fileUri, "/") + 1);
     $metadata_caption['filename'] = $filename;
+  }
   else {
     $metadata_caption['filename'] = '';
+  }
-dfc9
+  // Title.
-            6657531f
+  if (!empty($media_metadata->ObjectName)) {
     $metadata_caption['title'] = $media_metadata->ObjectName;
-dfc9
+            Andreas Kohlbecker
-            6657531f
+  elseif (!empty($media_metadata_aux['Object Name'])) {
     $metadata_caption['title'] = $media_metadata_aux['Object Name'];
-dfc9
+            Andreas Kohlbecker
-            6657531f
+  elseif (!empty($media->title_L10n)) {
     $metadata_caption['title'] = $media->title_L10n;
+  }
   elseif (!empty($media->titleCache)) {
     $metadata_caption['title'] = $media->titleCache;
+  }
   // Append description to title.
   if (!empty($media->description_L10n)) {
-            ffc86672
+    $metadata_caption['title'] .= '<span class="media-description">' . $media->description_L10n . '<span>';
+  }
-            6657531f
+            Andreas Kohlbecker
-dfc9
+  // Artist.
-            6657531f
+  if (!empty($media_metadata->Artist)) {
     $metadata_caption['artist'] = '' . $media_metadata->Artist;
+  }
   elseif (!empty($media->artist->titleCache)) {
     $metadata_caption['artist'] = $media->artist->titleCache;
+  }
   // Copyright.
   $metadata_caption['rights'] = array(
     'copyright' => array('agentNames' => array()),
     'license' => array(
       'agentNames' => array(),
       'types' => array(),
-dfc9
+      'abbreviatedTexts' => array(),
-            6657531f
+      'uris' => array(),
     ),
   );
   if (!empty($media_metadata->Copyright)) {
     $metadata_caption['rights']['copyright']['agentNames'][] = $media_metadata->Copyright;
+  }
   elseif (isset($media->rights) && is_array($media->rights)) {
     foreach ($media->rights as $right) {
       switch ($right->term->uuid) {
         case UUID_RIGHTS_LICENCE:
           $metadata_caption['rights']['license']['agentNames'][] = ($right->agent ? '' . $right->agent->firstname . ' ' . $right->agent->lastname : '');
           $metadata_caption['rights']['license']['types'][] = ($right->representation_L10n ? '' . $right->representation_L10n : '');
           $metadata_caption['rights']['license']['abbreviatedTexts'][] = ($right->abbreviatedText ? '' . $right->abbreviatedText : '');
           $metadata_caption['rights']['license']['uris'][] = ($right->uri ? '' . $right->uri : '');
           break;
         case UUID_RIGHTS_COPYRIGHT:
           $metadata_caption['rights']['copyright']['agentNames'][] = $right->agent->firstname . ' ' . $right->agent->lastname;
           break;
+      }
+    }
+  }
   else {
     $metadata_caption['rights']['agentNames'][] = '';
+  }
   // Filling the description (though there is no description in the db???).
   // $metadata_caption['description'] = $media->description_L10n;
   // Location.
   $metadata_caption['location'] = array();
   $metadata_caption['location']['sublocation'] = !empty($media_metadata->Sublocation) ? $media_metadata->Sublocation : FALSE;
   $metadata_caption['location']['city'] = !empty($media_metadata->City) ? $media_metadata->City : FALSE;
   $metadata_caption['location']['province'] = !empty($media_metadata->Province) ? $media_metadata->Province : FALSE;
   $metadata_caption['location']['country'] = !empty($media_metadata->Country)? $media_metadata->Country : FALSE;
   /*
    // Creation date.
    if($media_metadata["Modify Date"])
    $metadata_caption['mediacreated'] = $media_metadata["Modify Date"];
    else
    $metadata_caption['mediacreated'] = $media->created;
    */
   // Returned value.
   return $metadata_caption;
+}
 /**
  * Collects all the media from a list of description elements.
+ *
  * @param array $descriptionElements
  *   The description elements from which to collect the media.
+ *
  * @return array
  *   The output with all the collected media.
  */
 function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
   $outArrayOfMedia = array();
   // Avoiding a warning box in Drupal for Flora Malesiana.
   if (isset($descriptionElements) && is_array($descriptionElements)) {
     foreach ($descriptionElements as $descriptionElement) {
       if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
         foreach ($descriptionElement->media as $media) {
           if (is_object($media)) {
             $outArrayOfMedia[] = $media;
+          }
+        }
+      }
+    }
+  }
   return $outArrayOfMedia;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
+ *
  * @param array $cdmBase_list
  *   An array of CdmBase instances or a single instance.
  * @param string $footnote_list_key
-e37
+            Andreas Kohlbecker
  * @return unknown
-            6657531f
+ */
-e37
+function cdm_annotations_as_footnotekeys($cdmBase_list, $footnote_list_key = NULL) {
-            6657531f
+            Andreas Kohlbecker
    static $annotations_types_filter = null;
    if(!$annotations_types_filter) {
      $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
+   }
   $footNoteKeys = array();
   // Is argument cdmBase an array?
   if (!is_array($cdmBase_list)) {
     $cdmBase_array = array();
     $cdmBase_array[] = $cdmBase_list;
+  }
   else {
     $cdmBase_array = $cdmBase_list;
+  }
   // Getting the key for the footnotemanager.
   if (isset($footnote_list_key)) {
     $footnoteListKey = $footnote_list_key;
+  }
   else {
     $footnoteListKey = RenderHints::getFootnoteListKey() . '-annotations';
+  }
   // Adding the footnotes keys.
   foreach ($cdmBase_array as $cdmBase_element) {
     $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
     if (is_array($annotations)) {
       foreach ($annotations as $annotation) {
         $footNoteKeys[] = FootnoteManager::addNewFootnote($footnoteListKey, $annotation->text);
+      }
+    }
+  }
   return $footNoteKeys;
+}
-            c1f5d897
+            Andreas Kohlbecker
 // @WA Comment: should this not be a theme function?
-            6657531f
+/**
  *  Creates a CDM Dynabox.
  * @param string $dynabox_id
  *   a uninque name for tha dynabox, using a cdm entity uuid herefore is good pratice
  * @param string $label
  *   The clickable text to show.
  * @param string $content_url
  *   The cdm REST service request url wich will deliver the content to be shown
  *   once the dynabox toggles open.
  * @param string $theme
  *   The theme to be used for rendering the cdm REST service reponse with is
  *   returned from the $content_url.
  * @param string $link_alt_text
-            c1f5d897
+ *   The value for the alt attribute of the dynabox link.
  * @param array $enclosingtags
  *   An array with two elements: $enclosingtags[0] will be used for the dynabox
  *   element itself, $enclosingtags[1] is the tag to be used for the
  *   dynabox_content (optional)
  * @param string $open_callback
  *   optional javascript call back function to be triggered after toggeling the box to
-            6657531f
+ *   the open state.
  * @param string $close_callback
  *   optional javascript call back function to be triggered after toggeling the box to
  *   the closed state.
-c635db9
+            Andreas Kohlbecker
-            6657531f
+ * @return string
-            c1f5d897
+ *   Returns HTML for a dynabox.
  */
 function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text, $enclosingtags = array('li', 'ul'), $open_callback = 'function(){}', $close_callback = 'function(){}') {
   $out = '';
-            b386ae48
+            Andreas Kohlbecker
-            6657531f
+  // check for plain class attribute string
-            c1f5d897
+  $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
-bb8db6
+            Andreas Kohlbecker
   _add_js_domEvent(); // requires domEvent.js
   drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
   drupal_add_js("
   jQuery(document).ready(
       function() {
         dynabox('". $dynabox_id ."',
+          {
             open_callback: " . $open_callback .",
             close_callback: " . $close_callback ."
+          }
         );
+      }
    );",
    array(
-            6657531f
+    'type'=>'inline',
     'scope'=>'footer'
+    )
-            c1f5d897
+  );
-ff9
+            Andreas Kohlbecker
-            6657531f
+  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
   $out .= '<!-- ' . $content_url . ' -->';
   $out .= '<' . $enclosingtags[0] . ' class="dynabox-' . $dynabox_id . '"><a href="#" class="label" alt="' . t($link_alt_text) . '">' . $label . '</a>';
   $out .= '<' . $enclosingtags[1] . ' class="dynabox-' . $dynabox_id . '-content" title="' . $cdm_proxy_url . '"><' . $enclosingtags[0] . '>' . loading_image_html() . '</' . $enclosingtags[0] . '></' . $enclosingtags[1] . '>';
   $out .= '</' . $enclosingtags[0] . '>';
   return $out;
+}
 /**
  * Checks whether a feature has any description elements.
+ *
  * @param mixed $featureNode
  *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
+ *
  * @see _mergeFeatureTreeDescriptions()
+ *
  * @return bool
  *   Returns TRUE if the given $featureNode or any of its subordinate nodes
  *   contains at least one non empty TextData or at least one DescriptionElement
  *   of an other type. A TextData element holding a multilanguageText or a
  *   source reference is considered to be not empty.
  */
-fc94b
+function hasFeatureNodeDescriptionElements($featureNode) {
-            6657531f
+            Andreas Kohlbecker
   if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
     foreach ($featureNode->descriptionElements as $descriptionElement) {
       if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text) && $descriptionElement->multilanguageText_L10n->text != '' || isset($descriptionElement->sources[0]) || isset($descriptionElement->media[0]) ) {
         return TRUE;
+      }
+    }
+  }
   elseif (isset($featureNode->children) && is_array($featureNode->children)) {
     foreach ($featureNode->children as $child) {
       if (hasFeatureNodeDescriptionElements($child)) {
         return TRUE;
+      }
+    }
+  }
   return FALSE;
+}

Project

General

Profile

EDIT

cdm-dataportal/7.x/modules/cdm_dataportal/cdm_dataportal.module @ c8234bdf