/modules/cdm_dataportal/includes/pages.inc - Annotate - EDIT - EDIT Project Management

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cdm-dataportal/modules/cdm_dataportal/includes/pages.inc @ 72d57201

-            c70b93c3
+<?php
-            f19f47fa
+/**
  * @file
  * Page functions.
+ *
  * @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.
-            c70b93c3
+ * @see http://www.mozilla.org/MPL/MPL-1.1.html
+ *
  * @author
-            f19f47fa
+ *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
  */
 /**
  * Creates a render array representing the ocurrences associetad with the $taxon.
+ *
  * The resulting render array contains two elements:
  *  - 'map': A map showing all point locations of the occurences is availabale
  *  - 'specimen_list': the list of occurences prepated as table for theme_table()
+ *
  * @param object $taxon
  *   A cdm Taxon object
  * @return
  *   A render array suitable for drupal_render()
+ *
-            c70b93c3
+ */
-            f19f47fa
+function cdm_dataportal_taxon_page_specimens($taxon) {
-ce9afb7
+    $render_array = array();
     RenderHints::pushToRenderStack('taxon_page_specimens');
-f78c59
+            Andreas Kohlbecker
-            b8afc4bb
+    $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_parameters = array(
         'relationshipsInvers' => implode(',', $relationship_choice['invers']),
         'relationships' => implode(',', $relationship_choice['direct']),
     );
     if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
         $by_associatedtaxon_query_parameters = array_merge($by_associatedtaxon_query_parameters, $_REQUEST['pager']);
+    }
     $by_associatedtaxon_query = http_build_query($by_associatedtaxon_query_parameters);
-f39f6
+            Katja Luther
-            d3f77ada
+    $ws_string = 'specimensOrObservation';
-f39f6
+    if (variable_get('cdm_dataportal_specimen_derivate_tree')){
-            d3f77ada
+        $ws_string .= "DTOs";
     }else{
         $ws_string .= "s";
+    }
-            b8afc4bb
+            Patric Plitzner
-a124e57
+    $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, $ws_string));
     if(!variable_get('cdm_dataportal_specimen_derivate_tree')) {
         $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
             null,
             $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
         );
         $specimensOrObservations = array();
         if (isset($pager->records[0])) {
             $specimensOrObservations = $pager->records;
+        }
-fc6
+            Katja Luther
-            c10f70e4
+     // cdm_ws_get(CDM_WS_OCCURRENCE_FIELDUNIT_DTO_BY_ASSOCIATEDTAXON,
      // null,
      // $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
     // );
    // $specimensOrObservations = array();
    // if(isset($pager->records[0])){
     //    $specimensOrObservations =  $pager->records;
    // }
-            b8afc4bb
+            Patric Plitzner
     // order occurrences by date but types should be on top of the list
     $type_specimens = array();
     $other_occurrences = array();
-d29
+    foreach ($specimensOrObservations as $occurrence) {
-eaec849
+       $typeDesignationsPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $occurrence->uuid);
-            b8afc4bb
+        if (isset($typeDesignationsPager->count) && $typeDesignationsPager->count > 0) {
             $type_specimens[] = $occurrence;
-eaec849
+       } else {
            $other_occurrences[] = $occurrence;
-            b8afc4bb
+            Patric Plitzner
+    }
     $specimensOrObservations = array_merge($type_specimens, $other_occurrences);
     // Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field
-            a2acff0a
+    if (!variable_get('cdm_dataportal_specimen_derivate_tree')) {
         foreach ($specimensOrObservations as &$occurrence) {
             $occurrence->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
                 $occurrence->uuid,
                 'fieldObjectMediaDTO',
             ));
             $occurrence->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
                 $occurrence->uuid,
                 'derivedUnitMedia',
             ));
+        }
-ef92
+            Katja Luther
-            b8afc4bb
+            Patric Plitzner
-            b5c89485
+    // --- get map service HTTP query parameters
-            c10f70e4
+            Katja Luther
-            b8afc4bb
+    if (count($specimensOrObservations) > 0) {
-e1cf9
+            Katja Luther
         $occurrence_queryDto = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid, $by_associatedtaxon_query);
         $map_visibility = variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT);
         if ($map_visibility == 'always' ||
             variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT) == 'automatic' &&
             (isset($occurrence_queryDto->fieldUnitPoints[0]) || isset($occurrence_queryDto->derivedUnitPoints[0]))) {
             $occurrence_query = $occurrence_queryDto->occurrenceQuery;
             $legend_format_query = null;
             $distribution_query = NULL;
             $render_array['map'] = compose_map('specimens', $occurrence_query, $distribution_query, $legend_format_query, array());
-            c10f70e4
+            Katja Luther
-            b8afc4bb
+            Patric Plitzner
-            db725031
+            Andreas Kohlbecker
     // -------------------------------------------------------
-e1cf9
+            Katja Luther
-            d3f77ada
+            Katja Luther
-ce9afb7
+    if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){
         //COMPRESSED SPECIMEN DERIVATE TABLE
-cb163f8
+        $associatedFieldUnitsQuery_parameters = array();
         if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
             $associatedFieldUnitsQuery_parameters = array_merge($associatedFieldUnitsQuery_parameters, $_REQUEST['pager']);
+        }
         $by_associatedtaxon_query = http_build_query($associatedFieldUnitsQuery_parameters);
-f028e2
+        $pager_field_units = cdm_ws_get(CDM_WS_PORTAL_TAXON,
-e82a602
+            array($taxon->uuid, 'associatedFieldUnits'),
             $by_associatedtaxon_query . '&pageSize=' . variable_get('cdm_dataportal_compressed_specimen_derivate_table_page_size')
         );
-e87f89f
+            Andreas Kohlbecker
-f028e2
+        if (isset($pager_field_units->records[0])) {
           $field_unit_uuids = array();
           foreach ($pager_field_units->records as $field_unit) {
             $field_unit_uuids[] = $field_unit->uuid;
+          }
-f3768c
+          $render_array['derivate_hierarchy_table'] = compose_specimen_table($field_unit_uuids);
+        }
-            f19f47fa
+            Andreas Kohlbecker
-e87f89f
+        $render_array['pager'] = markup_to_render_array(
             theme('cdm_pager', array(
                 'pager' => $pager_field_units,
                 'path' => $_REQUEST['q'],
                 'parameters' => $_REQUEST
             )),
 // weight
         );
-            f19f47fa
+            Andreas Kohlbecker
-f39f6
+    else if(variable_get('cdm_dataportal_specimen_derivate_tree')){
-d57201
+            Katja Luther
         $expand_icon = font_awesome_icon_markup(
             'fa-plus-square-o',
             array(
                 'alt' => 'Show details',
                 'class' => array('expand_icon')
+            )
         );
         $collapse_icon = font_awesome_icon_markup(
             'fa-minus-square-o',
             array(
                 'alt' => 'Show details',
                 'class' => array('collapse_icon')
+            )
         );
         $tableId = "specimen_tree_table";
-ef92
+        $specimen_table = array(
             '#theme' => 'table',
             '#weight' => 2,
             // prefix attributes and rows with '#' to let it pass toF the theme function,
             // otherwise it is handled as child render array
-d57201
+            '#attributes' => array('class' => 'specimens',
                                     'id' => $tableId),
-ef92
+            '#rows' => array(),
         );
-e1cf9
+        $specimen_array = compose_specimen_array($specimensOrObservations);
-d57201
+        $rowcount = 0;
-ef92
+        foreach($specimen_array as $value){
             $renderArray = array(
                 '#theme' => 'item_list',
-d57201
+                '#items' => $value['children'],
-ef92
+                '#type' => 'ul');
             $output = drupal_render($renderArray);
-d57201
+            Katja Luther
-ef92
+            $specimen_table['#rows'][] = array(
-d57201
+                'data' =>array(
                     array(
                         'data' => $expand_icon . $collapse_icon,
                         'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
                     ),
                     $value['data']),
                 'id' => 'label' . $rowcount, // summary row id
                 'class' => array('summary_row'),
-ef92
+            );
-d57201
+            $specimen_table['#rows'][] = array(
                 'data' =>  array(
                         array(
                             'data' => "", //empty first column
                             'class' => array('expand_column')
                         ),
                         array(
                         'data' => $output
+                        )
                     ),
                     'class' =>  array('detail_row')
 //                'class' =>  array(
 //                    'descriptionElement',
 //                    'descriptionElement_IndividualsAssociation'
  //               ),
             );
             $rowcount++;
-f57468
+            Katja Luther
-ef92
+            Katja Luther
-d57201
+        drupal_add_js_rowToggle("#".$tableId);
-ef92
+            Katja Luther
         $render_array['specimen_list'] = $specimen_table;
-f57468
+            Katja Luther
-da0d1
+            Katja Luther
+    }
-ce9afb7
+    else{
         //BOTTOM-UP-SPECIMEN-TABLE
         // --- generate the specimen list as table
         $specimen_table = array(
             '#theme' => 'table',
             '#weight' => 2,
-e87f89f
+            // prefix attributes and rows with '#' to let it pass toF the theme function,
-ce9afb7
+            // otherwise it is handled as child render array
             '#attributes' => array('class' => 'specimens'),
             '#rows' => array(),
         );
-            f19f47fa
+            Andreas Kohlbecker
-ce9afb7
+        if ($specimensOrObservations) {
             foreach ($specimensOrObservations as $specimenOrObservation) {
                 $mediaList = array();
-fc6
+                if (is_array($specimenOrObservation->_fieldObjectMedia)) {
                     $mediaList = array_merge($mediaList, $specimenOrObservation->_fieldObjectMedia);
-ce9afb7
+            Patric Plitzner
-fc6
+                if (is_array($specimenOrObservation->_derivedUnitMedia)) {
-ce9afb7
+                    $mediaList = array_merge($mediaList, $specimenOrObservation->_derivedUnitMedia);
+                }
-fc6
+            Katja Luther
-ce9afb7
+                // typelabel will contain the typeStatus
                 $type_label = '';
                 $typeDesignationPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $specimenOrObservation->uuid);
-e533708
+                if (isset($typeDesignationPager) and isset($typeDesignationPager->records)) {
-ce9afb7
+                    $type_status = array();
                     foreach ($typeDesignationPager->records as $typeDesignation) {
                         if (isset($typeDesignation->typeStatus->representation_L10n)){
                             $type_status[] = $typeDesignation->typeStatus->representation_L10n;
+                        }
+                    }
                     $type_label = implode(', ', $type_status);
                     if($type_label){
                         $type_label .= ': ' ;
+                    }
+                }
                 // --- Specimen entry as dynamic label:
                 //     -> Dynabox for the specimenOrObservation
                 $gallery_name = $specimenOrObservation->uuid;
-            c02da888
+                $derived_unit_ws_request = cdm_compose_url(CDM_WS_OCCURRENCE, array( $specimenOrObservation->uuid));
-da0d1
+                // --- Render associated media.
                 $gallery_html = '';
                 if (count($mediaList) > 0) {
                     $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
                     $captionElements = array(
                         '#uri' => t('open media'),
                     );
                     $gallery_html = compose_cdm_media_gallerie(array(
                         'mediaList' => $mediaList,
                         'galleryName' => $gallery_name,
                         'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
                         'cols' => $gallery_settings['cdm_dataportal_media_cols'],
                         'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
                         'captionElements' => $captionElements,
                         'mediaLinkType' => 'LIGHTBOX',
                         'alternativeMediaUri' => NULL,
                         'galleryLinkUri' => NULL,
                     ));
+                }
-            c10f70e4
+                //here we should use the data we already have
-ce9afb7
+                $label_html = cdm_dynabox(
-            cea412e7
+                  $specimenOrObservation->uuid,
                   $type_label . $specimenOrObservation->titleCache,
                   $derived_unit_ws_request,
-            bd814ea2
+                  'cdm_specimen_or_observation',
-            cea412e7
+                  'Click for details',
                   array('div', 'div'),
                   array(),
                   null, // $content_element_selector
                   'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback
                   'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback
-ce9afb7
+                );
                 // --- Render associated media.
                 $gallery_html = '';
                 if (count($mediaList) > 0) {
                     $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
                     $captionElements = array(
                         '#uri' => t('open media'),
                     );
-            a9815578
+                    $gallery_html = compose_cdm_media_gallerie(array(
-ce9afb7
+                        'mediaList' => $mediaList,
                         'galleryName' => $gallery_name,
                         'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
                         'cols' => $gallery_settings['cdm_dataportal_media_cols'],
                         'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
                         'captionElements' => $captionElements,
                         'mediaLinkType' => 'LIGHTBOX',
                         'alternativeMediaUri' => NULL,
                         'galleryLinkUri' => NULL,
                     ));
+                }
                 $specimen_table['#rows'][] = array(
                     // An array of table rows. Every row is an array of cells, or an associative array
                     'data' => array(
                         // Each cell can be either a string or an associative array
                         $label_html . $gallery_html
                     ),
                     'class' =>  array(
                         'descriptionElement',
                         'descriptionElement_IndividualsAssociation'
                     ),
                 );
+            }
+        }
-            f19f47fa
+            Andreas Kohlbecker
-ce9afb7
+        $render_array['specimen_list'] = $specimen_table;
         $render_array['pager'] = markup_to_render_array(
             theme('cdm_pager', array(
                 'pager' => $pager,
                 'path' => $_REQUEST['q'],
                 'parameters' => $_REQUEST,
             )),
 // weight
         );
+    }
-e1cf9
+            Katja Luther
-ce9afb7
+    RenderHints::popFromRenderStack();
     return $render_array;
-f259ca3
+            Andreas Kohlbecker
-e87f89f
+            Andreas Kohlbecker
 /**
-f32f09
+ * Creates the drupal render array for the table showing all derivated which are
  * derive from a common gathering event.
-e87f89f
+            Andreas Kohlbecker
  * @param $field_unit_uuids array
  *  An array of uuids for cdm FieldUnit entities.
+ *
  * @return array
  *  A drupal render array for a table
+ *
  * @ingroup compose
  */
-f32f09
+function compose_specimen_table($field_unit_uuids)
-e87f89f
+            Andreas Kohlbecker
 // get icon images
   $expand_icon = font_awesome_icon_markup(
     'fa-plus-square-o',
     array(
       'alt' => 'Show details',
       'class' => array('expand_icon')
+    )
   );
   $collapse_icon = font_awesome_icon_markup(
     'fa-minus-square-o',
     array(
       'alt' => 'Show details',
       'class' => array('collapse_icon')
+    )
   );
   $detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
   $checked_box_icon = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/step_done.gif' . '"/>';
   $sequence_icon = '<img title="Molecular Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/sequence_derivate-16x16-32.png' . '"/>';
   $character_data_icon = '<img title="Character Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/character_data_derivate-16x16-32.png' . '"/>';
   $rowcount = 0;
   $rows = array();
   foreach ($field_unit_uuids as $field_unit_uuid) {
     //get derivate hierarchy for the FieldUnit
     $derivateHierarchy = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($field_unit_uuid, 'derivateHierarchy'));
     if ($derivateHierarchy) {
       //summary row
       $rows[] = array(
         'data' => array(
           array(
             'data' => $expand_icon . $collapse_icon,
             'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
           ),
           array(
             'data' => $derivateHierarchy->country,
             'class' => array('summary_row_cell')
           ),
           array(
             'data' => $derivateHierarchy->date,
             'class' => array('summary_row_cell')
           ),
           array(
-eaec849
+            'data' => $derivateHierarchy->collectingString,
-e87f89f
+            'class' => array('summary_row_cell')
           ),
-f047
+          @array(
-            ae7ade6d
+            'data' => $derivateHierarchy->collection,
-e87f89f
+            'class' => array('summary_row_cell')
           ),
           array(
             'data' => $derivateHierarchy->hasType ? $checked_box_icon : "",
             'class' => array('summary_row_cell', 'summary_row_icon')
           ),
           array(
             'data' => $derivateHierarchy->hasSpecimenScan ? $checked_box_icon : "",
             'class' => array('summary_row_cell', 'summary_row_icon')
           ),
           array(
             'data' => ($derivateHierarchy->hasDna ? $sequence_icon : "") . " "
               . ($derivateHierarchy->hasDetailImage ? $detail_image_icon : "") . " "
               . ($derivateHierarchy->hasCharacterData ? $character_data_icon : ""),
             'class' => array('summary_row_cell', 'summary_row_icon')
+          )
         ),
-cba0a5f
+        'id' => 'derivate_summary' . $rowcount, // summary row id
-e87f89f
+        'class' => array('summary_row'),
       );
       //assemble field unit details
       $detail_html = "";
       // - citation
       if ($derivateHierarchy->citation) {
         $detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";
+      }
       //assemble specimen details
-            d68a30b0
+      if ($derivateHierarchy->derivates) {
         foreach ($derivateHierarchy->derivates as $preservedSpecimenDTO) {
-e87f89f
+          $detail_html .= "<br>";
-cba0a5f
+          $detail_html .= render_cdm_specimenDTO_page($preservedSpecimenDTO);
-            a2acff0a
+            Katja Luther
-e87f89f
+            Andreas Kohlbecker
       $detail_html .= "<br>";
       //detail row resp. one BIG detail cell
       $rows[] = array(
         'data' => array(
           array(
             'data' => "", //empty first column
             'class' => array('expand_column')
           ),
           array(
             'data' => $detail_html,
             'colspan' => 7,
           ),
         ),
-cba0a5f
+        'id' => 'derivate_details' . $rowcount,//details row ID
-e87f89f
+        'class' => array('detail_row'),
       );
       $rowcount++;
+    }
+  }
   $tableId = "derivate_hierarchy_table";
   $derivateHierarchyTable = array(
     "#theme" => "table",
     "#weight" => 2,
     "#header" => array(
       array(
         'data' => "",
         'class' => array('expand_column')
       ),
       "Country", "Date", "Collector + collecting number", "Herbaria", "Type", "Scan", "Derivatives"),
     "#rows" => $rows,
     "#attributes" => array(
       "id" => $tableId,
       "border" => 2
+    )
   );
   //add toggle functionality to derivate hierarchy table
   drupal_add_js_rowToggle("#" . $tableId);
   return $derivateHierarchyTable;
+}
-a4de51
+function create_html_link($link, $openInExternalWindow=false){
-d8ef9fa
+    $html = "";
-a4de51
+    if($link->uri && $link->uri!=""){
         $html .= '<a  href="' . $link->uri . '"';
         if($openInExternalWindow){
             $html .= ' target="_blank"';
+        }
         $html .= '>' . $link->linkText . '</a>';
-d8ef9fa
+            Patric Plitzner
     else{
         $html .= $link->linkText;
+    }
     return $html;
+}
 /**
-a4de51
+ * Creates HTML links from the given link list concatenated by default by a comma.
-d8ef9fa
+ * @param $linkList the list with Link objects having "uri" and "linkText" as members
  * @return string the assembled HTML string containing the links
  */
-a4de51
+function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
-d8ef9fa
+            Patric Plitzner
     $html = "";
     if ($linkList) {
         foreach ($linkList as $link) {
-a4de51
+            $html .= create_html_link($link, $openInExternalWindow).$separator;
-d8ef9fa
+            Patric Plitzner
-a4de51
+        $html = rtrim($html, $separator);
-d8ef9fa
+            Patric Plitzner
     return $html;
+}
-a8e4b6
+/**
  * Composes a taxon page which can consist of multiple parts like
  * 'General', 'Synonymy', 'Images', 'Keys'. These parts can be displayed
  * as tabs or as sections of a single page.
+ *
  * It is headed by the name of the accepted taxon without author and reference.
+ *
  * @param $taxon
  *   The CDM Taxon Instance to compose the page for.
  * @param $page_part
  *   Name of the part to display, valid values are:
  *    - 'description' -  for the general part
  *    - 'images'
  *    - 'synonymy'
  *    - 'keys'
  *    - 'all'
+ *
  * @return array
  *   A drupal render array
+ *
  * @ingroup compose
  */
 function compose_cdm_taxon_page($taxon, $page_part = 'description') {
-ae57522
+  // we better cache here since drupal_get_query_parameters has no internal static cache variable
   $http_request_params = drupal_get_query_parameters();
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // add all mandatory js sources
   _add_js_footnotes();
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  $render_array = array();
   $weight = 0; // the weight for the render array elements
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  $tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  $page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
-a8e4b6
+            Andreas Kohlbecker
-f95
+  $synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;
   if(!$synonymy_as_tab){
     unset($tabsToDisplay["Synonymy"]);
-e6dfbb3
+    // the synonymy is located in the general part in this case
     if($page_part == 'synonymy'){
       $page_part = 'description';
+    }
-f95
+            Andreas Kohlbecker
-ae57522
+  $media = _load_media_for_taxon($taxon);
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
-a6d7e8
+    taxon_page_tabs_hidden_add('images');
-ae57522
+            Patric Plitzner
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // --- GET specimensOrObservations --- //
-            c10f70e4
+  $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservationsCount'));
-a8e4b6
+            Andreas Kohlbecker
-            c10f70e4
+  $specimensOrObservationsCount = $specimensOrObservations != null ? $specimensOrObservations->result : 0;
-ae57522
+  if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
-a6d7e8
+    taxon_page_tabs_hidden_add('specimens');
-ae57522
+            Patric Plitzner
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // --- GET polytomousKeys --- //
   $polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
   $identificationKeyCount = 0;
   if ($polytomousKeysPager) {
     $identificationKeyCount += $polytomousKeysPager->count;
+  }
   if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
-a6d7e8
+    taxon_page_tabs_hidden_add('keys');
-ae57522
+            Patric Plitzner
-e1
+            Andreas Kohlbecker
-f95
+  // --- GET TaxonNodeAgentRelations --- //
   $current_classification_uuid = get_current_classification_uuid();
   $taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
       array(
           $taxon->uuid,
           $current_classification_uuid,
       ),
       "pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
   );
   if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
-a6d7e8
+      taxon_page_tabs_hidden_add('experts');
-f95
+            Andreas Kohlbecker
-cd0b
+            Andreas Kohlbecker
-f95
+  if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {
-a6d7e8
+    taxon_page_tabs_hidden_add('synonymy');
-ae57522
+            Patric Plitzner
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // -------------------------------------------- //
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
-d19c
+    $render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
-ae57522
+            Patric Plitzner
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // --- PAGE PART: DESCRIPTION --- //
-a6d7e8
+  if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+    $merged_tree = merged_taxon_feature_tree($taxon);
-a8e4b6
+            Andreas Kohlbecker
-d8ef9fa
+            Patric Plitzner
-f95
+    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
-ae57522
+    $render_array['general']['#weight'] = $weight++;
     $render_array['general']['#prefix'] = '<div id="general" class="page-part">';
     $render_array['general']['#suffix'] = '</div>';
+  }
-d8ef9fa
+            Patric Plitzner
-ae57522
+  // --- PAGE PART: IMAGES --- //
-a6d7e8
+  if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {
-ae57522
+    $images_html = '<div id="images" class="page-part">';
     if ($page_part == 'all') {
-feeabc7
+      $images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
-d8ef9fa
+            Patric Plitzner
-ae57522
+    // Get the image gallery as configured by the admin.
-f4eb9ce
+    $default_image_gallery = 'default';
     $configured_image_gallery_viewer = variable_get('image_gallery_viewer', 'default');
-feeabc7
+    $taxon_image_gallery = '<div class="error">No image gallery viewer configured</div>';
-f4eb9ce
+    if($configured_image_gallery_viewer == $default_image_gallery || $configured_image_gallery_viewer == 'fsi'){
       // the fsi_gallery requires a flash plugin, in case the client browser is not supporting
       // flash we also need to provide an the default gallery as alternative
       $taxon_image_gallery = '<div id="default-gallery-viewer">' .
         call_user_func_array('taxon_image_gallery_' . $default_image_gallery, array(
           $taxon,
           $media,
         ))
         . '</div>';
+    }
     if($configured_image_gallery_viewer == 'fsi'){
       $taxon_image_gallery .= '<div id="'. $configured_image_gallery_viewer .'-gallery-viewer">' .
         call_user_func_array('taxon_image_gallery_' . $configured_image_gallery_viewer, array(
           $taxon,
           $media,
         ))
        . '</div>';
+    }
-ae57522
+    $images_html .= $taxon_image_gallery;
     $images_html .= '</div>';
     $render_array['images'] = markup_to_render_array($images_html, $weight++);
+  }
-d8ef9fa
+            Patric Plitzner
-ae57522
+  // --- PAGE PART: SYNONYMY --- //
-a6d7e8
+  if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
-ae57522
+    $synonymy_html = '<div id="synonymy" class="page-part">';
     if ($page_part == 'all') {
-feeabc7
+      $synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+    $addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);
-b4bfc9
+            Andreas Kohlbecker
-cda248c
+    $synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);
     $synonymy_html .= drupal_render($synonym_a);
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+    $synonymy_html .= '</div>';
     $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+            Patric Plitzner
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // --- PAGE PART: SPECIMENS --- //
-a6d7e8
+  if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {
-ae57522
+    $render_array['specimens'] = array(
-feeabc7
+        '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
-ae57522
+        'content' => cdm_dataportal_taxon_page_specimens($taxon), // returns render array
         '#suffix' => '</div>',
     );
+  }
   // --- PAGE PART: KEYS --- //
-a6d7e8
+  if(!taxon_page_tabs_hidden_check('keys')){
     if ($identificationKeyCount == 1 && $page_part == 'keys'){
       drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
+    }
     else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
       $keys_html = '<div id="keys" class="page-part">';
       if ($page_part == 'all') {
         $keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
+      }
       $keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
       $keys_html .= '</div>';
       $render_array['keys'] = markup_to_render_array($keys_html, $weight++);
-ae57522
+            Patric Plitzner
+  }
-cd0b
+  // --- PAGE PART: EXPERTS --- //
-a6d7e8
+  if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {
-cd0b
+    $render_array['experts'] = array(
-feeabc7
+        '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
-cd0b
+        'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
         '#suffix' => '</div>',
     );
+  }
   // ------------------ END OF PARTS -------------- //
-ae57522
+            Patric Plitzner
   // adjust weights of page and toc elements according to the settings
-feeabc7
+  $taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
-ae57522
+  foreach($taxontabs_weights as $tab_key => $weight){
     if(isset($render_array[$tab_key])){
       $render_array[$tab_key]['#weight'] = $weight;
+    }
+  }
   // set up the TOC for the pages which contain all pageparts
   if($page_part == 'all') {
     asort($taxontabs_weights);
     foreach(array_keys($taxontabs_weights) as $tab_key){
       if(isset($render_array[$tab_key])){
         if($tab_key != 'general'){
           // add entry for page part
           $toc_elements[] = array(
-feeabc7
+              'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
-ae57522
+              'class' => array('page-part-toc-item-' . $tab_key)
           );
         } else {
           // add content of profile part instead
           if(isset($render_array['general'])) {
             // in case all tabs are shown at once the feature tocs
             // should be integrated into the tabs toc as sub list
             // and the profile image should be on top of the page
             if(isset($render_array['general']['taxon_description_feature_toc'])){;
             foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
               $toc_elements[] = $profile_toc_item;
-d8ef9fa
+            Patric Plitzner
-ae57522
+            unset($render_array['general']['taxon_description_feature_toc']);
+            }
+          }
-d8ef9fa
+            Patric Plitzner
-ae57522
+            Patric Plitzner
+    }
-d8ef9fa
+            Patric Plitzner
-ae57522
+    // move profile image in page structure
     if(isset($render_array['general']['taxon_profile_image'])){
       $render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
       $render_array['profile_image']['#weight'] = -100;
       unset($render_array['general']['taxon_profile_image']);
-d8ef9fa
+            Patric Plitzner
-ae57522
+    // finally add the table of contents to the render array
     $render_array['toc'] = array(
         '#theme' => 'item_list',
         '#items' => $toc_elements,
         '#title' => t('Content'),
         '#weight' => -101,
         '#suffix' => '</div>',
         '#prefix'=> '<div id="page-toc">'
     );
+  }
-d8ef9fa
+            Patric Plitzner
-ae57522
+  return $render_array;
-a8e4b6
+            Andreas Kohlbecker
-ce9afb7
+/**
-f5e82d
+ * TODO should this function really be a compose function?
  *     For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
-            bf97c2e8
+            Andreas Kohlbecker
  * composes and returns an render array containing the components of the taxon profile tab:
  *  - 'taxon_profile_image'
  *  - 'taxon_description_feature_toc'
  *  - 'taxon_description_features'
+ *
+ *
-a1b451e
+ * @param object taxon
  * @param object $merged_tree
  * @param object media
  * @param bool $add_synonymy
-            bf97c2e8
+            Andreas Kohlbecker
  * @return array
-            f78fda81
+ *   A Drupal render array with the following elements:
-            bf97c2e8
+ *     - 'taxon_profile_image'
  *     - 'taxon_description_feature_toc'
  *     - 'taxon_description_features'
+ *
-a1b451e
+ * @throws Exception
+ *
-            bf97c2e8
+ * @ingroup compose
  */
-f95
+function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {
-            bf97c2e8
+            Andreas Kohlbecker
-ae57522
+  $render_array = array();
   $taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
   $hide_taxon_profile_image = FALSE;
   if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
     $rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
     $hide_taxon_profile_image = ($rankCompare > -1);
+  }
   if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
     $representationPart = new stdClass();
     $attributes = array();
-faa087
+    if (isset($media[0])) {
       // due to a bug the portal/taxon/{uuid}/media service only delivers a filtered media object
       // which only contains the thumbnail representation even if the height and width filters are not set.
-dd
+      // -->
-faa087
+      $preferred_media = cdm_ws_get(CDM_WS_MEDIA, $media[0]->uuid);
       $preferred_representations = cdm_preferred_media_representations($preferred_media, array(
         'image/jpg',
         'image/jpeg',
         'image/png',
         'image/gif',
       ),
         $taxon_profile_image_settings['maxextend'],
         $taxon_profile_image_settings['maxextend']
       );
       if(count($preferred_representations) > 0){
         $representation = array_shift($preferred_representations);
         $representationPart = $representation->parts[0];
         $attributes['alt'] = $representationPart->uri;
         if (!empty($taxon_profile_image_settings['media_uri_query'])) {
           $representationPart->uri = $representationPart->uri
             . (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
             . $taxon_profile_image_settings['media_uri_query'];
+        }
-ae57522
+            Patric Plitzner
+    }
     else {
-fd1f
+      if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
-            ca47ea76
+        // show placeholder image instead
         if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
           // use the user provided image
           $profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
           $url = file_create_url($profile_image_file->uri);
           $image_info = image_get_info($profile_image_file->uri);
           $representationPart->width = $image_info['width'];
           $representationPart->height = $image_info['height'];
           $representationPart->uri = $url;
+        }
         else {
           // use the hard coded default
           $representationPart->width = 184;
           $representationPart->height = 144;
           $representationPart->uri = base_path() . drupal_get_path('module',
               'cdm_dataportal') . '/images/no_picture.png';
+        }
         $attributes['alt'] = "no image available";
-ae57522
+            Patric Plitzner
+    }
-            ca47ea76
+    if (isset($representationPart->uri)) {
-            a9815578
+      $profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);
-            ca47ea76
+      // NOTE: style="width:${maxextend}px' is needed for IE8 !!!
       $render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $taxon_profile_image_settings['maxextend'] . 'px">' . $profile_image . '</div>',
         -101);
+    }
-ae57522
+            Patric Plitzner
-f95
+  if($add_synonymy){
-cda248c
+    $synonymy_a = compose_cdm_taxon_page_synonymy($taxon, true);
     $synonymy_a['#weight'] = -102;
     $render_array['synonymy'] = $synonymy_a;
-f95
+            Andreas Kohlbecker
-b756c5f
+  $pseudo_feature_blocks = array();
   $pseudo_feature_block_toc_items = array();
-ae57522
+            Patric Plitzner
-b756c5f
+  // Render the sections for each real feature
   $feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
   // Bibliography
-ae57522
+  $bibliography_settings = get_bibliography_settings();
   if($bibliography_settings['enabled'] == 1){
-a7
+    $bibliography_markup = FootnoteManager::renderFootnoteList('BIBLIOGRAPHY', '');
     if($bibliography_markup) {
       $feature_bibliography = make_pseudo_feature('Bibliography', 'BIBLIOGRAPHY');
       $bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
       $bibliography_item = markup_to_render_array($bibliography_markup);
       $bibliography_block->content[] = compose_feature_block_wrap_elements(array($bibliography_item), $feature_bibliography);
-ae57522
+            Patric Plitzner
-b756c5f
+      $pseudo_feature_block_toc_items['Bibliography']= 'bibliography';
       $pseudo_feature_blocks[] = $bibliography_block;
-ae57522
+            Patric Plitzner
-b756c5f
+            Andreas Kohlbecker
   $render_array['taxon_description_features'] = _block_get_renderable_array(
     array_merge($feature_block_list, $pseudo_feature_blocks)
   );
-ae57522
+            Patric Plitzner
-b756c5f
+  if($pseudo_feature_block_toc_items){
     foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
       cdm_toc_list_add_item($label, $fragment);
+    }
-ae57522
+            Patric Plitzner
   // create the table of content
   $toc = array(
       '#theme' => 'item_list',
     '#items' => cdm_toc_list(),
       '#title' => t('Content'),
     '#weight' => -100,                  // move to the top
       '#suffix' => '</div>',
       '#prefix'=> '<div id="page-toc">'
   );
   $render_array['taxon_description_feature_toc'] = $toc;
   return $render_array;
-            bf97c2e8
+            Andreas Kohlbecker
-dabcba
+            Andreas Kohlbecker
 /**
  * Returns HTML containing the synonymy for the accepted taxon.
+ *
  * Shows the whole synonymy for the accepted taxon.
  * The synonymy list is headed by the complete scientific name
  * of the accepted taxon with nomenclatural reference.
+ *
  * @param object $taxon
  * @param boolean $add_accepted_taxon
+ *
  * @return array
  *  Drupal render array for the synonymy
+ *
  * @throws Exception
+ *
  * @ingroup compose
  */
 function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {
   RenderHints::pushToRenderStack('taxon_page_synonymy');
   // footnote key for the homotypic group and accepted taxon,
   // both should have the same footnote key
   RenderHints::setFootnoteListKey(RenderHints::getRenderPath());
   $synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));
   $out = '';
   // Render accepted taxon.
   //
   // foonotes of the accepted taxon will be rendered in the homotypic group section
   // even if there are not synonyms in the homotypic group
   // homotypic group and accepted taxon should have the same footnote key
   $referenceUri = '';
   if ($add_accepted_taxon) {
     // remember the last part of the render path
     $synonymy_render_path = RenderHints::getRenderPath();
     // set new render path for the accepted taxon so
     // it can be styled differently via the name render part definitions
     RenderHints::pushToRenderStack('accepted_taxon');
     $accepted_name = '';
     if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {
       $label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);
       $accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';
+    }
     if (isset($taxon->name->nomenclaturalReference)) {
       $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
+    }
     $accepted_name .= '<div class="accepted-name">';
     $accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);
     $name_relations = cdm_name_relationships_for_taxon($taxon);
     $name_relationships = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
     // Render relationships of accepted name.
     if(isset($name_relationships['list']['items'][0])){
       $accepted_name .= ' ' . drupal_render($name_relationships);
+    }
     // handle annotations of the name and taxon
     $special_annotations_array = array();
     $special_annotations_array[] = $taxon->name;
     $special_annotations_array[] = $taxon;
     $accepted_name .= theme('cdm_annotations_as_footnotekeys', array(
         'cdmBase_list' => $special_annotations_array,
         'footnote_list_key' => $synonymy_render_path . '-annotations')
     );
     $accepted_name .= '</div>';
     RenderHints::popFromRenderStack();
+  }
   // --- Render homotypic synonymy group
   if (!empty($accepted_name)) {
     $out .= $accepted_name;
+  }
   // Render the homotypicSynonymyGroup including the type information.
   $out .= theme(
     'cdm_homotypicSynonymyGroup',
     array(
       'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,
       'accepted_taxon_name_uuid' => $taxon->name->uuid
+    )
   );
   // Render accepted taxon heterotypic synonymy groups.
   if ($synomymie->heterotypicSynonymyGroups) {
     foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {
       $out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));
+    }
+  }
   // Render taxon relationships.
   if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {
     $taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);
     $out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);
+  }
   RenderHints::popFromRenderStack();
   return markup_to_render_array($out);
+}
-            f9a3d0f6
+/**
  * composes and returns an render array for the experts associated with the given taxon
+ *
-a1b451e
+ * @param object taxon
-            f9a3d0f6
+            Andreas Kohlbecker
  * @return array
  *   A Drupal render array for a table with the experts
+ *
  * @ingroup compose
  */
-cd0b
+function compose_cdm_taxon_page_experts($taxon){
   $render_array = array();
   if(!isset($taxon->uuid)){
     return $render_array;
+  }
   $current_classification_uuid = get_current_classification_uuid();
   // TODO use cdm_ws_fetchall below but this failes! needs fix!
   $taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
     array(
       $taxon->uuid,
       $current_classification_uuid
+    )
   );
   $header = array(
     array('data' => t('Expert')),
     array('data' => t('Role'))
   );
   $rows = array();
   foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
-            d9763fd3
+            Andreas Kohlbecker
     $expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
     $expert_details_container_id = 'expert_details_' . $expert_role_id;
     $agent_label_markup = cdm_dynabox(
       'expert_' . $expert_role_id,
       $taxon_node_agent_relation->agent->titleCache,
       // specifying both ends of the relationship will return only one record in the pager
       cdm_compose_url(CDM_WS_PORTAL_AGENT,
          array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
         'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
       'cdm_taxon_expert',
       'Click for details',
       array('div', 'div'),
       array(), // attributes
-            cea412e7
+      '#' . $expert_details_container_id // $content_element_selector
-            d9763fd3
+    );
     // Expert and Role
     $rows[] = array(
       'data' => array(
         array(
           'data' => $agent_label_markup,
           'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
-cd0b
+        ),
-            d9763fd3
+        array(
           'data' => $taxon_node_agent_relation->type->representation_L10n,
           'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
+        )
+      )
     );
     // Agent details
     $rows[] = array(
       'data' => array(
         array(
           'data' => '<!-- expert_details_container -->',
           'id' => $expert_details_container_id,
           'colspan' => 2
+        )
+      )
-cd0b
+    );
-            d9763fd3
+            Andreas Kohlbecker
-cd0b
+            Andreas Kohlbecker
   $render_array['experts_table'] = array(
     '#theme' => 'table',
     '#header' => $header,
     '#rows' => $rows,
   );
   return $render_array;
+}
-            bf97c2e8
+            Andreas Kohlbecker
-f259ca3
+/**
-cd0b
+ * Manages the tabs to be hidden in the taxon page.
-f259ca3
+            Andreas Kohlbecker
  * The tabs are identified by their last menu link path element:
  *  - description
  *  - synonymy
  *  - images
  *  - specimens
  *  - key
+ *
  * Internally the tabs are stored in a static variable which is
  * managed by drupal_static().
+ *
  * @param string $add_tab
-cd0b
+ *   Optional parameter. The given string will be added to the array of tabs
-f259ca3
+            Andreas Kohlbecker
  * @return
  *   The array of tabs
  */
-a6d7e8
+function taxon_page_tabs_hidden_add($add_tab = NULL) {
   $tabs = &drupal_static('taxon_page_tabs_hidden');
-f259ca3
+            Andreas Kohlbecker
-ae57522
+  if(!isset($tabs)){
     $tabs = array();
+  }
-f259ca3
+            Andreas Kohlbecker
-ae57522
+  if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
     $tabs[] = $add_tab;
+  }
-f259ca3
+            Andreas Kohlbecker
-ae57522
+  return $tabs;
-f259ca3
+            Andreas Kohlbecker
-a6d7e8
+/**
  * Manages the tabs to be hidden in the taxon page.
+ *
  * The tabs names are identified by their last menu link path element:
  *  - description
  *  - synonymy
  *  - images
  *  - specimens
  *  - key
+ *
  * Internally the tabs are stored in a static variable which is
  * managed by drupal_static().
+ *
  * @param string $tabname
  *   The name of the tab to check
+ *
  * @return boolean
  *   True if the tab or section is to be hidden
  */
 function taxon_page_tabs_hidden_check($tabname) {
   $tabs = &drupal_static('taxon_page_tabs_hidden');
   if(!isset($tabs)){
     $tabs = array();
+  }
   return array_search($tabname, $tabs) !== FALSE;
+}
-f259ca3
+/**
  * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
+ *
-a6d7e8
+ *  - Removes the tabs to be hidden, @see taxon_page_tabs_hidden_add()
-ad3a
+ *  - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
-f259ca3
+            Andreas Kohlbecker
  * @param array $variables
  *   The variables array
  */
 function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
-a6d7e8
+  $hidden_tabs = taxon_page_tabs_hidden_add();
-f259ca3
+            Andreas Kohlbecker
-be375
+  if (!variable_get(CDM_SEARCH_BLAST_ENABLED)) {
-f6f79f6
+      if (is_array($variables['primary'])) {
           foreach ($variables['primary'] as $key => &$element) {
               if ($element['#link']['path'] == 'cdm_dataportal/search/blast') {
                   // remove the tab
                   unset($variables['primary'][$key]);
+              }
-be375
+            Katja Luther
-f6f79f6
+            Katja Luther
-be375
+            Katja Luther
+  }
-ae57522
+  if (is_array($variables['primary'])) {
     foreach ($variables['primary'] as $key => &$element) {
-f1a217c
+            Andreas Kohlbecker
-ae57522
+      // 1. Remove the tabs to be hidden
       foreach ($hidden_tabs as $tab) {
         if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
           // remove the tab
           unset($variables['primary'][$key]);
-ad3a
+            Andreas Kohlbecker
-ae57522
+            Patric Plitzner
-f259ca3
+            Andreas Kohlbecker
-ae57522
+            Patric Plitzner
-f1a217c
+            Andreas Kohlbecker
 /**
  * Implements the hook_preprocess_HOOK() for theme_menu_local_task()
+ *
+ *
  * @param array $variables
  *   An associative array containing:
  *     - element: A render element containing:
  *          #link: A menu link array with 'title', 'href', and 'localized_options' keys.
  *          #active: A boolean indicating whether the local task is active.
+ *
  */
 function cdm_dataportal_preprocess_menu_local_task(&$variables) {
-ae57522
+  $link = $variables['element']['#link'];
   if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
     $link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
     $link['localized_options']['html'] = TRUE;
-f1a217c
+            Andreas Kohlbecker
-ae57522
+    $variables['element']['#link'] = $link;
+  }
-            f19f47fa
+            Andreas Kohlbecker
-            f9a3d0f6
+            Andreas Kohlbecker
 /* =================== block composition ===================== */
 /**
-ad16a1
+ * Composes and returns an render array for the classification breadcrumbs of the given taxon.
-            f9a3d0f6
+            Andreas Kohlbecker
  * @param taxon
+ *
  * @return array
  *   A Drupal render array for a table with the experts
+ *
  * @ingroup compose
  */
 function compose_classification_breadcrumbs($taxon_uuid) {
-            b0adfd32
+  _add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
-            d0d23caa
+            Andreas Kohlbecker
-            f9a3d0f6
+  $render_array = array();
   $render_array['#theme'] = 'item_list';
   $render_array['#type'] = 'ul';
   $render_array['#attributes'] = array(
     'id' => 'classification-breadcrumbs',
     'class' => 'breadcrumbs inline',
   );
   $items = array();
-da4e54
+  $parent_taxon_nodes = null;
   if($taxon_uuid){
     $parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
+  }
-            f9a3d0f6
+            Andreas Kohlbecker
-da4e54
+  $classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
   // find current classification in list
   $classification = null;
   $current_classification_uuid = get_current_classification_uuid();
   foreach ($classifications as $classification){
     if($classification->uuid == $current_classification_uuid){
       break;
-            b0adfd32
+            Andreas Kohlbecker
-da4e54
+            Andreas Kohlbecker
-            b0adfd32
+            Andreas Kohlbecker
-da4e54
+  $node_name = '';
   if(count($classifications) > 1 ){
     // need to add the current classification as first label
-af3ce28
+            Andreas Kohlbecker
     $label = $classification->titleCache;
     if(strlen($label) > 20){
       $label = substr($label, 0, strpos($label, ' ', 15)) . '...';
+    }
     $node_name = font_awesome_icon_markup('fa-th-list')  . ' ' . l($label, '#', array(
       'attributes' => array(
         'class' => 'taxonomic-children-button classification-chooser',
         'data-destination-uri' => drupal_get_destination(),
         'data-cdm-align-with' => array('prev')
       ),
       'html' => true
     ));
-            f9a3d0f6
+            Andreas Kohlbecker
-            b0adfd32
+            Andreas Kohlbecker
-da4e54
+  $rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
-af3ce28
+            Andreas Kohlbecker
   $rank_separator = '<span> '
-da4e54
+    . font_awesome_icon_markup('fa-chevron-right')
     . ' </span>';
-af3ce28
+  $more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
-fb3dbb
+  $more_children_label = '...';
-da4e54
+            Andreas Kohlbecker
-af3ce28
+  $items[] = $node_name;
-da4e54
+            Andreas Kohlbecker
-af3ce28
+  $more_children_for = null;
-            e3235962
+  if($parent_taxon_nodes){
-af3ce28
+    foreach ($parent_taxon_nodes as $node) {
-da4e54
+            Andreas Kohlbecker
       $is_first_item = count($items) == 0;
-af3ce28
+      $is_last_item = count($items) == count($parent_taxon_nodes);
-da4e54
+      $node_name = cdm_dataportal_shortname_of($node);
       $path = path_to_taxon($node->taxonUuid);
-af3ce28
+      if($node->taxonomicChildrenCount > 0) {
         $more_children_for = $node->taxonUuid;
       } else {
         $more_children_for = null;
-da4e54
+            Andreas Kohlbecker
-af3ce28
+      // 'fa-sitemap'
-da4e54
+      $items[] =
-af3ce28
+        ($is_first_item ? '' : ' ')
         . $rank_separator
         . l(
-b3be949
+          '<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
-af3ce28
+          $path,
           array(
             'attributes' => array(
               'class' => array('taxonomic-children-button'),
               'data-cdm-taxon-uuid' => array($node->taxonUuid),
               'data-cdm-classification-mode' => array('siblings'),
               'data-cdm-align-with' => array('prev')
-b3be949
+            ),
             'html' => true
-af3ce28
+            Andreas Kohlbecker
         );
+      }
-da4e54
+            Andreas Kohlbecker
-af3ce28
+            Andreas Kohlbecker
   // add more button to the end
   if(!$parent_taxon_nodes) {
     // not taxon focused yet, adding button to make  the root nodes available
-fb3dbb
+    $items[] = '<span>'
       . $more_children_icon . '&nbsp;' .
       '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
-c705d4
+      . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
-fb3dbb
+      . '</span>';
-af3ce28
+  } else if($more_children_for){
     // last parent item has child taxon nodes
-fb3dbb
+    $items[] = ' <span>'
       . $more_children_icon . '&nbsp;' .
       '<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
-c705d4
+      . '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
-fb3dbb
+      . '</span>';
-af3ce28
+            Andreas Kohlbecker
-            e3235962
+            Andreas Kohlbecker
-            b0adfd32
+            Andreas Kohlbecker
-bda
+  $render_array['#items'] = $items;
-af3ce28
+            Andreas Kohlbecker
-bda
+  return $render_array;
+}
-af3ce28
+            Andreas Kohlbecker
-fb3dbb
+            Andreas Kohlbecker
-bda
+/**
  * @param $specimen_uuid
  * @return array
  *    The drupal render array for the page
+ *
  * @ingroup compose
  */
-            e89c1115
+function compose_cdm_specimen_page($specimen_uuid)
-bda
+            Andreas Kohlbecker
   drupal_set_title("Specimen Details");
   $render_array = array();
   RenderHints::pushToRenderStack('specimen_page');
-            f9a3d0f6
+            Andreas Kohlbecker
-a42a9b
+  $specimen_table = array(
       '#theme' => 'table',
       '#weight' => 2,
       // prefix attributes and rows with '#' to let it pass toF the theme function,
       // otherwise it is handled as child render array
-f7610
+            Katja Luther
     '#attributes' => array('class' => 'specimens'),
-a42a9b
+      '#rows' => array(),
-fb962c
+      '#prefix' => '<div id="specimens">',
       '#suffix' => '</div>',
-f7610
+            Katja Luther
-a42a9b
+  );
   $specimen = compose_cdm_specimen_or_observation($specimen_uuid, true);
   $renderArray = array(
           '#theme' => 'item_list',
           '#items' => array($specimen),
           '#type' => 'ul');
   $output = drupal_render($renderArray);
   $specimen_table['#rows'][] = array(
           // An array of table rows. Every row is an array of cells, or an associative array
           'data' => array($output),
           'class' =>  array(
               'descriptionElement',
               'descriptionElement_IndividualsAssociation'
           ),
-f7610
+            Katja Luther
-a42a9b
+  );
-            e89c1115
+            Katja Luther
-a42a9b
+ // $detail_html = compose_cdm_specimen_or_observation($specimen_uuid, true);
-fb962c
+//    $render_array['markup'] = array(
 //        '#prefix' => '<div id="specimens" class="page">',
 //        'content' => $specimen_table,
 //        '#suffix' => '</div>',
 //    );
     $render_array['markup'] =  $specimen_table;
-            e89c1115
+            Katja Luther
-bda
+  RenderHints::popFromRenderStack();
-            f9a3d0f6
+  return $render_array;
-bda
+            Andreas Kohlbecker
-            f9a3d0f6
+            Andreas Kohlbecker
-bda
+/**
  * @param $named_area_uuid
  * @return array
  *    The drupal render array for the page
+ *
  * @ingroup compose
  */
 function compose_cdm_named_area_page($named_area_uuid)
+{
   $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
   $render_array = array();
   RenderHints::pushToRenderStack('named_area_page');
   $groups = array();
   @_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
   @_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
   if(isset($named_area->level)) {
     @_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
+  }
   $name_area_details_elements = array(
    // '#title' => $title,
     '#theme' => 'description_list',
     '#groups' => $groups,
     '#attributes' => array('class' => html_class_attribute_ref($named_area)),
   );
   $render_array[] = $name_area_details_elements;
   RenderHints::popFromRenderStack();
   return $render_array;
-            f9a3d0f6
+            Andreas Kohlbecker
-feeabc7
+            Andreas Kohlbecker
-dabcba
+            Andreas Kohlbecker
 /**
  * Returns a drupal render array for a single reference page.
+ *
  * Composes a page with all data on a single reference.
+ *
  * @param string $uuid
  *   An uuid for a cdm reference.
+ *
  * @return array
  *  A drupal render array
+ *
  * @throws Exception
+ *
  * @ingroup compose
  */
 function compose_cdm_reference_page($uuid) {
   $pathelement = "reference_page";
   RenderHints::pushToRenderStack($pathelement);
   $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
   if (isset($reference->titleCache)) {
     drupal_set_title($reference->titleCache, PASS_THROUGH);
+  }
   $field_order = array(
     "title",
     "abbrevTitle",
     // "titleCache" abbrevTitleCache
     // "citation",
     "authorship",
     "editor",
     "publisher",
     "placePublished",
     "datePublished",
     "year",
     "edition",// Class Book.
     "volume",// Class Article.
     "seriesPart",
     "inReference",
     "nomRefBase", // Class BookSection, Book, Article.
     "pages",// Class Article.
     "series",// Class Article, PrintSeries.
     "school",// Class Thesis.
     "institution",// Class Report.
     "organization",// Class Proceedings.
     "nextVersion",
     "previousVersion",
     "isbn",// Class Book.
     "issn",// Class Journal.
     "doi",
     "uri"
   );
   $table_rows = array();
   if (!isset($reference->authorship)) {
     $authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);
     $reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';
+  }
   if (!isset($reference->inReference)) {
     $reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(
       $reference->uuid,
       "inReference",
     ));
+  }
   foreach ($field_order as $fieldname) {
     if (isset($reference->$fieldname)) {
       if ($fieldname == "datePublished") {
         $period = $reference->$fieldname;
         $datePublished = timePeriodToString($period);
         if (isset($datePublished) && $datePublished != '') {
           $table_rows[] = array(
             t("Date published"),
             $datePublished,
           );
+        }
+      }
       elseif ($fieldname == "doi" && is_object($reference->doi)) {
         $table_rows[] = array(
           t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
           cdm_doi($reference->doi, false)
         );
+      }
       elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {
         $table_rows[] = array(
           t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
           cdm_external_uri($reference->uri, false)
         );
+      }
       elseif (is_object($reference->$fieldname)) {
         if ($fieldname == "authorship") {
           $dump = $reference->$fieldname;
           $teammembers = "teamMembers";
           $team = $dump->$teammembers;
           $nameArray = array();
           foreach ($team as $member) {
             if (strlen($member->lastname) > 0) {
               $nname = $member->lastname;
               $name = $nname;
               if (strlen($member->firstname) > 0) {
                 $vname = $member->firstname;
                 $name = $vname . " " . $nname;
+              }
               $nameArray[] = $name;
+            }
             else {
               if (strlen($member->titleCache) > 0) {
                 $nameArray[] = $member->titleCache;
+              }
+            }
+          }
           $value = join($nameArray, ", ");
+        }
         elseif ($fieldname == "inReference") {
           $type = $reference->$fieldname->type;
           $value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));
           switch ($type) {
             case "Book":
               $fieldname = "in book";
               break;
             case "Journal":
               $fieldname = "in journal";
               break;
             case "Proceedings":
               $fieldname = "in proceedings";
               break;
+          }
+        }
         else {
           $value = $reference->$fieldname->titleCache;
+        }
         if (isset($value) && $value != '') {
           $table_rows[] = array(
             t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
             $value,
           );
+        }
+      }
       else {
         if (isset($reference->$fieldname) && $reference->$fieldname != '') {
           $table_rows[] = array(
             t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
             $reference->$fieldname,
           );
+        }
+      }
+    }
+  }
   $out = theme_table(array(
     'header' => array(),
     'rows' => $table_rows,
     'attributes' => array(
       'class' => html_class_attribute_ref($reference)
     ),
     'caption' => NULL,
     'colgroups' => NULL,
     'sticky' => NULL,
     'empty' => NULL,
   ));
   if(isset($reference->referenceAbstract)){
     $out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';
+  }
   // Annotations below the table
   $annotations = cdm_fetch_visible_annotations($reference);
   $out .= theme("cdm_annotations", array('annotations' => $annotations));
   $registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));
   if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){
     $out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list registration-item-list\">";
     foreach($registration_working_set->registrationDTOs as $registration_dto){
       if($registration_dto->status == "PUBLISHED"){
         $registration_render_a = compose_registration_dto_compact($registration_dto, 'citation');
         $registration_render_a["#prefix"] = "<div class=\"item item-registration\">";
         $registration_render_a["#suffix"] = "</div>";
         $out .= drupal_render($registration_render_a);
+      }
+    }
     $out .= "</div>";
+  }
   RenderHints::popFromRenderStack();
   return markup_to_render_array($out);
+}
-feeabc7
+/**
  * Provides the the label string for taxon page tabs.
+ *
  * The $tabname as passed to the method will be returned if no override
  * label is configured in the settings.
  */
 function cdm_taxonpage_tab_label($tabname) {
   static $taxon_tabs_labels = null;
   if($taxon_tabs_labels == null){
     $taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
+  }
   $tabname_key = strtolower($tabname);
   if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
     return $taxon_tabs_labels[$tabname_key];
+  }
   return $tabname;
+}