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

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cdm-dataportal/modules/cdm_dataportal/includes/pages.inc @ beb914ef

-            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);
     $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;
+    }
     // order occurrences by date but types should be on top of the list
     $type_specimens = array();
     $other_occurrences = array();
     foreach ($specimensOrObservations as &$occurrence) {
         $typeDesignationsPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $occurrence->uuid);
         if (isset($typeDesignationsPager->count) && $typeDesignationsPager->count > 0) {
             $type_specimens[] = $occurrence;
         } else {
             $other_occurrences[] = $occurrence;
+        }
+    }
     $specimensOrObservations = array_merge($type_specimens, $other_occurrences);
     // Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field
     // $occurrence->_fieldObjectMedia
     foreach ($specimensOrObservations as &$occurrence) {
         $occurrence->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
             $occurrence->uuid,
             'fieldObjectMedia',
         ));
         $occurrence->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
             $occurrence->uuid,
             'derivedUnitMedia',
         ));
+    }
-            b5c89485
+    // --- get map service HTTP query parameters
-            b8afc4bb
+    if (count($specimensOrObservations) > 0) {
-cd8253
+        $occurrence_queryDto = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid,  $by_associatedtaxon_query);
-            b8afc4bb
+            Patric Plitzner
-cd8253
+        if( isset($occurrence_queryDto->occurrenceQuery) ) {
             $occurrence_query = $occurrence_queryDto->occurrenceQuery;
-            b8afc4bb
+            $legend_format_query = null;
             $distribution_query = NULL;
-dc04
+            $render_array['map'] = compose_map($occurrence_query, $distribution_query, $legend_format_query, array());
-            b8afc4bb
+            Patric Plitzner
+    }
-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);
         $pagerFieldUnits = cdm_ws_get(CDM_WS_PORTAL_TAXON, array($taxon->uuid, 'associatedFieldUnits'), $by_associatedtaxon_query);
-d8ef9fa
+        // get icon images
-cf53dd8
+        $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')
+            )
         );
-ce9afb7
+        $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' . '"/>';
-            d7e61010
+        $character_data_icon = '<img title="Character Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/character_data_derivate-16x16-32.png' . '"/>';
-cb163f8
+        if (isset($pagerFieldUnits->records[0])) {
-ce9afb7
+            $rowcount = 0;
-cb163f8
+            foreach ($pagerFieldUnits->records as $fieldUnit) {
-ce9afb7
+                //get derivate hierarchy for the FieldUnit
                 $derivateHierarchy = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($fieldUnit->uuid, 'derivateHierarchy'), 'taxonUuid=' . $taxon->uuid);
                 if($derivateHierarchy){
                     //summary row
                     $rows[] = array(
                         'data' => array(
-            b8783a48
+                            array(
-eebb6f
+                                'data' => $expand_icon . $collapse_icon,
                                 'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
-            b8783a48
+                            ),
                             array(
                                 'data' => $derivateHierarchy->country,
                                 'class' => array('summary_row_cell')
                             ),
                             array(
                                 'data' => $derivateHierarchy->date,
                                 'class' => array('summary_row_cell')
                             ),
                             array(
                                 'data' => $derivateHierarchy->collection,
                                 'class' => array('summary_row_cell')
                             ),
                             array(
                                 'data' => $derivateHierarchy->herbarium,
                                 'class' => array('summary_row_cell')
                             ),
-ce9afb7
+                            array(
                                 'data' => $derivateHierarchy->hasType? $checked_box_icon:"",
-            b8783a48
+                                'class' => array('summary_row_cell', 'summary_row_icon')
-ce9afb7
+                            ),
                             array(
                                 'data' => $derivateHierarchy->hasSpecimenScan? $checked_box_icon:"",
-            b8783a48
+                                'class' => array('summary_row_cell', 'summary_row_icon')
-ce9afb7
+                            ),
-            b8783a48
+                            array(
                                 'data' => ($derivateHierarchy->hasDna? $sequence_icon :"")." "
                                     .($derivateHierarchy->hasDetailImage?$detail_image_icon:"")." "
                                     .($derivateHierarchy->hasCharacterData?$character_data_icon:""),
                                 'class' => array('summary_row_cell', 'summary_row_icon')
+                            )
-ce9afb7
+                        ),
                         'id' => ('derivate_summary' . $rowcount), // summary row id
                         'class' => array('summary_row'),
                     );
-            e3d43134
+                    //assemble field unit details
                     $detail_html = "";
-d8ef9fa
+                    // - taxon name
-            e3d43134
+                    if (variable_get('cdm_dataportal_compressed_specimen_derivate_table_show_determined_as') && $derivateHierarchy->taxonName) {
-ee2b205
+                        $detail_html .= create_label("Associated with") . $derivateHierarchy->taxonName . "<br>";
-            db390e35
+            Patric Plitzner
-d8ef9fa
+                    // - prtologue
-            e3d43134
+                    if ($derivateHierarchy->protologue) {
                         //$detail_html .= "<strong>Protologue:</strong> " . $derivateHierarchy->protologue . "<br>"
+                    }
-d8ef9fa
+                    // - citation
-            e3d43134
+                    if ($derivateHierarchy->citation) {
-dd58832
+                        $detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";
-ce9afb7
+            Patric Plitzner
-            e3d43134
+                    //assemble specimen details
-af9c5b3
+                    if($derivateHierarchy->preservedSpecimenDTOs){
                         foreach($derivateHierarchy->preservedSpecimenDTOs as $preservedSpecimenDTO) {
-dd58832
+                            $detail_html .= "<br>";
-af9c5b3
+                            $detail_html .= compose_cdm_specimen_page_html($preservedSpecimenDTO);
+                        }
-            e3d43134
+            Patric Plitzner
-dd58832
+                    $detail_html .= "<br>";
-ce9afb7
+                    //detail row resp. one BIG detail cell
                     $rows[] = array(
                         'data' => array(
-            b8783a48
+                            array(
                                 'data' => "", //empty first column
-eebb6f
+                                'class' => array('expand_column')
-            b8783a48
+                            ),
-ce9afb7
+                            array(
                                 'data' => $detail_html,
-            b8783a48
+                                'colspan' => 7,
-ce9afb7
+                            ),
                         ),
                         'id' => ('derivate_details' . $rowcount),//details row ID
                         'class' => array('detail_row'),
                     );
                     $rowcount++;
+                }
+            }
+        }
-            f19f47fa
+            Andreas Kohlbecker
-ce9afb7
+        $tableId = "derivate_hierarchy_table";
         $derivateHierarchyTable = array(
             "#theme" => "table",
             "#weight" => 2,
-eebb6f
+            "#header" => array(
                 array(
                     'data' => "",
                     'class' => array('expand_column')
                 ),
-            f097a7d6
+                "Country", "Date", "Collector + collecting number", "Herbaria", "Type", "Scan", "Derivatives"),
-ce9afb7
+            "#rows" => $rows,
             "#attributes" => array(
                 "id" => $tableId,
                 "border" => 2
+            )
-            f19f47fa
+        );
-ce9afb7
+        //add toggle functionality to derivate hierarchy table
         drupal_add_js_rowToggle("#".$tableId);
-            f19f47fa
+            Andreas Kohlbecker
-ce9afb7
+        $render_array['derivate_hierarchy_table'] = $derivateHierarchyTable;
-cb163f8
+        $render_array['pager'] = markup_to_render_array(
             theme('cdm_pager', array(
                 'pager' => $pagerFieldUnits,
                 'path' => $_REQUEST['q'],
                 'parameters' => $_REQUEST
             )),
 // weight
         );
-            f19f47fa
+            Andreas Kohlbecker
-ce9afb7
+    else{
         //BOTTOM-UP-SPECIMEN-TABLE
         // --- generate the specimen list as table
         $specimen_table = array(
             '#theme' => 'table',
             '#weight' => 2,
             // prefix attributes and rows with '#' to let it pass to the theme function,
             // otherwise it is handled as child render array
             '#attributes' => array('class' => 'specimens'),
             '#rows' => array(),
         );
-            f19f47fa
+            Andreas Kohlbecker
-ce9afb7
+        if ($specimensOrObservations) {
             foreach ($specimensOrObservations as $specimenOrObservation) {
                 $mediaList = array();
                 if (is_array($specimenOrObservation->_fieldObjectMedia)) {
                     $mediaList = array_merge($mediaList, $specimenOrObservation->_fieldObjectMedia);
+                }
                 if (is_array($specimenOrObservation->_derivedUnitMedia)) {
                     $mediaList = array_merge($mediaList, $specimenOrObservation->_derivedUnitMedia);
+                }
                 // 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;
                 $derived_unit_ws_request = cdm_compose_url(CDM_WS_OCCURRENCE, array( $specimenOrObservation->uuid));
                 $label_html = cdm_dynabox(
-            cea412e7
+                  $specimenOrObservation->uuid,
                   $type_label . $specimenOrObservation->titleCache,
                   $derived_unit_ws_request,
                   'cdm_specimenOrObservation',
                   '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'),
                     );
                     $gallery_html = theme('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,
                     ));
+                }
                 $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
         );
+    }
     RenderHints::popFromRenderStack();
     return $render_array;
-f259ca3
+            Andreas Kohlbecker
-            db390e35
+            Patric Plitzner
-a4de51
+function create_html_link($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
-ae57522
+  $media = _load_media_for_taxon($taxon);
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
     taxon_page_tabs_hidden('images');
+  }
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // --- GET specimensOrObservations --- //
   $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservations'));
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  $specimensOrObservationsCount = is_array($specimensOrObservations) ? count($specimensOrObservations) : 0;
   if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
     taxon_page_tabs_hidden('specimens');
+  }
-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')) {
     taxon_page_tabs_hidden('keys');
+  }
-e1
+            Andreas Kohlbecker
-cd0b
+    // --- 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 || $taxon_node_agent_relations_pager->count == 0){
         taxon_page_tabs_hidden('experts');
+    }
     if ($tabsToDisplay["Synonymy"] == '0') {
-ae57522
+    taxon_page_tabs_hidden('synonymy');
+  }
-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']), $weight++);
-ae57522
+            Patric Plitzner
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // --- PAGE PART: DESCRIPTION --- //
   if ($page_part == 'description' || $page_part == 'all') {
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+    $merged_tree = merged_taxon_feature_tree($taxon);
-a8e4b6
+            Andreas Kohlbecker
-d8ef9fa
+            Patric Plitzner
-ae57522
+    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media);
     $render_array['general']['#weight'] = $weight++;
     $render_array['general']['#prefix'] = '<div id="general" class="page-part">';
     $render_array['general']['#suffix'] = '</div>';
+  }
-d8ef9fa
+            Patric Plitzner
-ae57522
+  // --- PAGE PART: IMAGES --- //
   if (array_search('images', taxon_page_tabs_hidden()) === FALSE && ($page_part == 'images' || $page_part == 'all')) {
     $images_html = '<div id="images" class="page-part">';
     if ($page_part == 'all') {
       $images_html .= '<h2>' . t('Images') . '</h2>';
-d8ef9fa
+            Patric Plitzner
-ae57522
+    // Get the image gallery as configured by the admin.
-f4eb9ce
+    $default_image_gallery = 'default';
     $configured_image_gallery_viewer = variable_get('image_gallery_viewer', 'default');
     if($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, $weight++);
+  }
-d8ef9fa
+            Patric Plitzner
-ae57522
+  // --- PAGE PART: SYNONYMY --- //
   if (($page_part == 'synonymy' || $page_part == 'all')) {
     $synonymy_html = '<div id="synonymy" class="page-part">';
     if ($page_part == 'all') {
       $synonymy_html .= '<h2>' . t('Synonymy') . '</h2>';
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+    $addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);
-b4bfc9
+            Andreas Kohlbecker
-ae57522
+    $synonymy_html .= theme('cdm_taxon_page_synonymy', array('taxon' => $taxon, 'addAcceptedTaxon' => $addAcceptedTaxon));
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+    $synonymy_html .= '</div>';
     $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+            Patric Plitzner
-a8e4b6
+            Andreas Kohlbecker
-ae57522
+  // --- PAGE PART: SPECIMENS --- //
   if ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all')) {
     $render_array['specimens'] = array(
         '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t('Specimens') . '</h2>' : ''),
         'content' => cdm_dataportal_taxon_page_specimens($taxon), // returns render array
         '#suffix' => '</div>',
     );
+  }
   // --- PAGE PART: KEYS --- //
   if ($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('Keys') . '</h2>';
+    }
     $keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
     $keys_html .= '</div>';
     $render_array['keys'] = markup_to_render_array($keys_html, $weight++);
+  }
-cd0b
+  // --- PAGE PART: EXPERTS --- //
   if (array_search('experts', taxon_page_tabs_hidden()) === FALSE && ($page_part == 'experts' || $page_part == 'all')) {
     $render_array['experts'] = array(
         '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t('Experts') . '</h2>' : ''),
         '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
   $taxontabs_weights = get_array_variable_merged('cdm_taxonpage_tabs_weight', CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
   foreach($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
           $toc_elements[] = array(
-cc085da
+              'data' => l(t('@tab-name', array('@tab-name' => ucfirst($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 $render_array;
-a8e4b6
+            Andreas Kohlbecker
-ce9afb7
+/**
-f5e82d
+ * TODO should this function really be a compose function?
  *     For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
-            bf97c2e8
+            Andreas Kohlbecker
  * composes and returns an render array containing the components of the taxon profile tab:
  *  - 'taxon_profile_image'
  *  - 'taxon_description_feature_toc'
  *  - 'taxon_description_features'
+ *
+ *
-            f78fda81
+ * @param taxon
  * @param mergedTrees
  * @param media
-            bf97c2e8
+            Andreas Kohlbecker
  * @return array
-            f78fda81
+ *   A Drupal render array with the following elements:
-            bf97c2e8
+ *     - 'taxon_profile_image'
  *     - 'taxon_description_feature_toc'
  *     - 'taxon_description_features'
+ *
  * @ingroup compose
  */
 function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media) {
-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();
     $attributes = array();
     if (isset($media[0]->representations[0]->parts[0])) {
       $representationPart = $media[0]->representations[0]->parts[0];
       $attributes['alt'] = $representationPart->uri;
-            ca47ea76
+      if (!empty($taxon_profile_image_settings['media_uri_query'])) {
-ae57522
+        $representationPart->uri = $representationPart->uri
-            ca47ea76
+          . (strpos($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)) {
       $profile_image = theme('cdm_media_gallerie_image', array(
-ae57522
+        'mediaRepresentationPart' => $representationPart,
         'maxExtend' => $taxon_profile_image_settings['maxextend'],
         'addPassePartout' => FALSE,
         'attributes' => $attributes,
-            ca47ea76
+      ));
       // NOTE: style="width:${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
   // Render the sections for each feature
-            aa26f9f0
+  $render_array['taxon_description_features'] = compose_feature_blocks($merged_tree->root->childNodes, $taxon);
-ae57522
+            Patric Plitzner
   $bibliography_settings = get_bibliography_settings();
   if($bibliography_settings['enabled'] == 1){
     $bibliography_block = feature_block(t('Bibliography'));
     $bibliography_block->content = FootnoteManager::renderFootnoteList('BIBLIOGRAPHY', '');
     if(!empty($bibliography_block->content)){
       $render_array['taxon_description_bibliography'] =  markup_to_render_array(
         theme('block',
           array(
             'elements' => array(
               '#block' => $bibliography_block,
               '#children' => $bibliography_block->content,
+            )
+          )
         ),
 // weight
       );
       cdm_toc_list_add_item('Bibliography', 'bibliography');
+    }
+  }
   // 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 $render_array;
-            bf97c2e8
+            Andreas Kohlbecker
-            f9a3d0f6
+/**
  * composes and returns an render array for the experts associated with the given taxon
+ *
  * @param taxon
+ *
  * @return array
  *   A Drupal render array for a table with the experts
+ *
  * @ingroup compose
  */
-cd0b
+function compose_cdm_taxon_page_experts($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 $add_tab
-cd0b
+ *   Optional parameter. The given string will be added to the array of tabs
-f259ca3
+            Andreas Kohlbecker
  * @return
  *   The array of tabs
  */
 function taxon_page_tabs_hidden($add_tab = NULL) {
-ae57522
+  $tabs = &drupal_static(__FUNCTION__);
-f259ca3
+            Andreas Kohlbecker
-ae57522
+  if(!isset($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
 /**
  * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
+ *
-ad3a
+ *  - Removes the tabs to be hidden, @see taxon_page_tabs_hidden()
  *  - 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) {
-ae57522
+  $hidden_tabs = taxon_page_tabs_hidden();
-f259ca3
+            Andreas Kohlbecker
-ae57522
+  if (is_array($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');
-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(
           $node_name,
           $path,
           array(
             'attributes' => array(
               'class' => array('taxonomic-children-button'),
               'data-cdm-taxon-uuid' => array($node->taxonUuid),
               'data-cdm-classification-mode' => array('siblings'),
               'data-cdm-align-with' => array('prev')
+            )
+          )
         );
+      }
-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
     $items[] = '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
       . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" > '
       . $more_children_icon
       . '&nbsp;</span>';
   } else if($more_children_for){
     // last parent item has child taxon nodes
     $items[] = ' <span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
       . '" data-cdm-classification-mode="children" >'
       . $more_children_icon
       . '&nbsp;</span>';
-            e3235962
+            Andreas Kohlbecker
-            b0adfd32
+            Andreas Kohlbecker
-af3ce28
+            Andreas Kohlbecker
-            f9a3d0f6
+  $render_array['#items'] = $items;
   return $render_array;
+}