EDIT

<?php

/**

 * @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.

 * @see http://www.mozilla.org/MPL/MPL-1.1.html

 *

 * @author

 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>

 */

/**

 * Composes 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()

 *

 * @ingroup Compose

 *

 */

function compose_cdm_taxon_page_specimens($taxon) {

    $render_array = array();

    RenderHints::pushToRenderStack('taxon_page_specimens');

    $fieldUnitDTOs = null;

    $specimensOrObservations = null;

    if (variable_get('cdm_dataportal_specimen_derivate_tree')){

      // get fieldUnitDTOs

      $fieldUnitDTOs = cdm_ws_get(CDM_WS_TAXON_FIELDUNIT_DTOS, array( $taxon->uuid));

      $fieldUnitDTOs = order_fieldUnitDtos_by_date_and_type($fieldUnitDTOs);

    } else {

      // $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservations'));

      // extend by associated taxas occurrences

      $relationship_filter_query_parameters = relationship_filter_query_parameters();

      if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {

        $relationship_filter_query_parameters = array_merge($relationship_filter_query_parameters, $_REQUEST['pager']);

      }

      $by_associatedtaxon_query = http_build_query($relationship_filter_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;

      }

      // 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;

      // }

      // Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field

      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',

        ));

      }

      $specimensOrObservations = order_specimens_or_observations_by_date_and_type($specimensOrObservations);

    }

    // --- get map service HTTP query parameters

    if (count($specimensOrObservations) > 0 || $fieldUnitDTOs > 0) {

        $render_array['map'] = occurrence_map_query_parameters($taxon);

    }

    // -------------------------------------------------------

    if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){

        //COMPRESSED SPECIMEN DERIVATE TABLE

        $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);

        $pager_field_units = cdm_ws_get(CDM_WS_PORTAL_TAXON,

            array($taxon->uuid, 'associatedFieldUnits'),

            $by_associatedtaxon_query . '&pageSize=' . variable_get('cdm_dataportal_compressed_specimen_derivate_table_page_size')

        );

        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;

          }

          $render_array['derivate_hierarchy_table'] = compose_compressed_specimen_derivate_table($field_unit_uuids);

        }

        $render_array['pager'] = markup_to_render_array(

            theme('cdm_pager', array(

                'pager' => $pager_field_units,

                'path' => $_REQUEST['q'],

                'parameters' => $_REQUEST

            )),

            10 // weight

        );

    }

    else if(variable_get('cdm_dataportal_specimen_derivate_tree')){

      $render_array['specimen_list'] = compose_specimen_table_top_down($fieldUnitDTOs);

      $render_array['specimen_list']['#weight'] = 2;

    } else {

      $specimen_table = compose_specimens_table_bottom_up($specimensOrObservations);

      $render_array['specimen_list'] = $specimen_table;

      $render_array['pager'] = markup_to_render_array(

        theme('cdm_pager', array(

          'pager' => $pager,

          'path' => $_REQUEST['q'],

          'parameters' => $_REQUEST,

        )),

        10 // weight

      );

    }

    RenderHints::popFromRenderStack();

    return $render_array;

}

/**

 * @return array

 *

 * TODO move to cdm_dataportal.module or api.module?

 */

function relationship_filter_query_parameters()

{

  $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']),

  );

  return $by_associatedtaxon_query_parameters;

}

function create_html_link($link, $openInExternalWindow=false){

    $html = "";

    if($link->uri && $link->uri!=""){

        $html .= '<a  href="' . $link->uri . '"';

        if($openInExternalWindow){

            $html .= ' target="_blank"';

        }

        $html .= '>' . $link->linkText . '</a>';

    }

    else{

        $html .= $link->linkText;

    }

    return $html;

}

/**

 * Creates HTML links from the given link list concatenated by default by a comma.

 * @param $linkList the list with Link objects having "uri" and "linkText" as members

 * @return string the assembled HTML string containing the links

 */

function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")

{

    $html = "";

    if ($linkList) {

        foreach ($linkList as $link) {

            $html .= create_html_link($link, $openInExternalWindow).$separator;

        }

        $html = rtrim($html, $separator);

    }

    return $html;

}

/**

 * 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') {

  // we better cache here since drupal_get_query_parameters has no internal static cache variable

  $http_request_params = drupal_get_query_parameters();

  // add all mandatory js sources

  _add_js_footnotes();

  $render_array = array();

  $weight = 0; // the weight for the render array elements

  $tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));

  $page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';

  $synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;

  if(!$synonymy_as_tab){

    unset($tabsToDisplay["Synonymy"]);

    // the synonymy is located in the general part in this case

    if($page_part == 'synonymy'){

      $page_part = 'description';

    }

  }

  $media = _load_media_for_taxon($taxon);

  if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {

    taxon_page_tabs_hidden_add('images');

  }

  // --- GET specimensOrObservations --- //

  $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservationsCount'));

  $specimensOrObservationsCount = $specimensOrObservations != null ? $specimensOrObservations->result : 0;

  if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {

    taxon_page_tabs_hidden_add('specimens');

  }

  // --- 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_add('keys');

  }

  // --- 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_add('experts');

  }

  if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {

    taxon_page_tabs_hidden_add('synonymy');

  }

  // -------------------------------------------- //

  if(variable_get(CDM_TAXONPAGE_TAXON_NODE_SHOW_STATES, 1) && ( $page_part == 'description' || $page_part == 'synonymy' || $page_part == 'all')){

    $taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, array($taxon->uuid));

    $render_array['taxon_node_status'] = compose_taxon_node_status($taxon_nodes);

    $render_array['taxon_node_status']['#weight'] = -100;

  }

  if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {

    $render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);

  }

  // --- PAGE PART: DESCRIPTION --- //

  if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {

    $merged_tree = merged_taxon_feature_tree($taxon);

    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);

    $render_array['general']['#weight'] = $weight++;

    $render_array['general']['#prefix'] = '<div id="general" class="page-part">';

    $render_array['general']['#suffix'] = '</div>';

  }

  // --- PAGE PART: IMAGES --- //

  if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {

    $images_html = '<div id="images" class="page-part">';

    if ($page_part == 'all') {

      $images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';

    }

    // Get the image gallery as configured by the admin.

    $configured_image_gallery_viewer = variable_get(CDM_MEDIA_GALLERY_VIEWER, CDM_MEDIA_GALLERY_VIEWER_DEFAULT);

    if($configured_image_gallery_viewer != 'fsi'){

      $images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);

    } else {

      // 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

      $images_html .= render_taxon_media_gallery($taxon, CDM_MEDIA_GALLERY_VIEWER_DEFAULT, $media);

      $images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);

    }

    $images_html .= '</div>'; // END of <div id="images">

    $render_array['images'] = markup_to_render_array($images_html, $weight++);

  }

  // --- PAGE PART: SYNONYMY --- //

  if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {

    $synonymy_html = '<div id="synonymy" class="page-part">';

    if ($page_part == 'all') {

      $synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';

    }

    $addAcceptedTaxon = variable_get(CDM_DATAPORTAL_NOMREF_IN_TITLE, CDM_DATAPORTAL_NOMREF_IN_TITLE_DEFAULT);

    $synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);

    $synonymy_html .= drupal_render($synonym_a);

    $synonymy_html .= '</div>';

    $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);

  }

  // --- PAGE PART: SPECIMENS --- //

  if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {

    $render_array['specimens'] = array(

        '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),

        'content' => compose_cdm_taxon_page_specimens($taxon), // returns render array

        '#suffix' => '</div>',

    );

  }

  // --- PAGE PART: KEYS --- //

  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++);

    }

  }

  // --- PAGE PART: EXPERTS --- //

  if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {

    $render_array['experts'] = array(

        '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),

        'content' => compose_cdm_taxon_page_experts($taxon), // returns render array

        '#suffix' => '</div>',

    );

  }

  // ------------------ END OF PARTS -------------- //

  // adjust weights of page and toc elements according to the settings

  $taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_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 and pseudo feature blocks for the pages which contain all page parts

  if($page_part == 'all' && (!isset( $render_array['general']) || count($render_array['general']) == 0 )) {

    $bibliography_block = make_bibliography_feature_block();

    if($bibliography_block){

      $render_array['bibliography_block'] = _block_get_renderable_array([$bibliography_block]);

      $render_array['bibliography_block']['#weight'] = 100;

      cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $render_array['bibliography_block']['#weight']);

    }

    $toc_elements = [];

    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(

              'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),

              '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;

            }

            unset($render_array['general']['taxon_description_feature_toc']);

            }

          }

        }

      }

    }

    // 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']);

    }

    // 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">'

    );

  }

  return $render_array;

}

/**

 * 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)

 *

 * composes and returns an render array containing the components of the taxon profile tab:

 *  - 'taxon_profile_image'

 *  - 'taxon_description_feature_toc'

 *  - 'taxon_description_features'

 *

 *

 * @param object taxon

 * @param object $merged_tree

 * @param object media

 * @param bool $add_synonymy

 *

 * @return array

 *   A Drupal render array with the following elements:

 *     - 'taxon_profile_image'

 *     - 'taxon_description_feature_toc'

 *     - 'taxon_description_features'

 *

 * @throws Exception

 *

 * @ingroup compose

 */

function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {

  $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])) {

      // 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.

      // -->

      $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'];

        }

      }

    }

    else {

      if ($taxon_profile_image_settings['custom_placeholder_enabled']) {

        // 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";

      }

    }

    if (isset($representationPart->uri)) {

      $profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);

      // NOTE: style="width:${maxextend}px' is needed for IE8 !!!

      $max_extend_with = $taxon_profile_image_settings['maxextend'] . 'px';

      $render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $max_extend_with . '">' . $profile_image . '</div>',

        -101);

    }

  }

  if($add_synonymy){

    $synonymy_a = compose_cdm_taxon_page_synonymy($taxon, true);

    $synonymy_a['#weight'] = -102;

    $synonymy_a['#prefix'] = '<div id="synonymy">';

    $synonymy_a['#suffix'] = '</div>';

    $render_array['synonymy'] = $synonymy_a;

  }

  //  $pseudo_feature_block_toc_items = array();

  // Render the sections for each real feature

  $feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);

  // >>>>>>>>>>>>>>>>>>> PSEUDO FEATURES >>>>>>>>>>>>>>>>>>>

  $pseudo_feature_weights = get_array_variable_merged(CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS, CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS_DEFAULT);

  // Bibliography

  $bibliography_block = make_bibliography_feature_block();

  if($bibliography_block){

    $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]] = $bibliography_block;

    cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]);

  }

  // Descriptions (aggregated)

  $descriptionTypes = array();

  $descriptionTypes['descriptionTypes'] = ("AGGREGATED_STRUC_DESC");

  $aggregatedDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon->uuid . '/descriptions', $descriptionTypes);

  if (isset($aggregatedDescriptions) and !empty($aggregatedDescriptions)) {

      // if($feature_block_list) ....TODO

      $feature_description = make_pseudo_feature('Descriptions (aggregated)', PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS);

      $description_item = '';

      foreach ($aggregatedDescriptions as $description) {

        $description_item = '<div class="' . html_class_attribute_ref($description) . '">';

        $description_item .= render_description_string(get_root_nodes_for_dataset($description));

        $description_item .= ' ' . icon_link(path_to_description($description->uuid));

        $description_item .= '<div class="content-caption">'. statistical_values_explanation() . '</div>';

        $description_item .= '</div>';

      }

      $description_block = feature_block(t('Descriptions (aggregated)'), $feature_description);

      $description_block->content = [];

      $description_block->content[] = compose_feature_block_wrap_elements([$description_item], $feature_description);

      $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]] = $description_block;

      cdm_toc_list_add_item('Descriptions (aggregated)', 'aggregation_descriptions', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]);

  }

  // sort by weight

  ksort($feature_block_list);

  $render_array['taxon_description_features'] = _block_get_renderable_array($feature_block_list);

/*  // update TOC

  if ($pseudo_feature_block_toc_items){

    foreach ($pseudo_feature_block_toc_items as $label=>$fragment){

      cdm_toc_list_add_item($label, $fragment);

    }

  }

*/

  // <<<<<<<<<<<<<<<<<<< PSEUDO FEATURES <<<<<<<<<<<<<<<<<<<

  // 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;

}

/**

 * @return object|\stdclass

 */

function make_bibliography_feature_block() {

  $bibliography_block = null;

  $bibliography_settings = get_bibliography_settings();

  if ($bibliography_settings['enabled'] == 1) {

    $bibliography_markup = FootnoteManager::renderFootnoteList(PSEUDO_FEATURE_BIBLIOGRAPHY, '');

    if ($bibliography_markup) {

      $feature_bibliography = make_pseudo_feature('Bibliography', PSEUDO_FEATURE_BIBLIOGRAPHY);

      $bibliography_item = markup_to_render_array($bibliography_markup);

      $bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);

      $bibliography_block->content = [];

      $bibliography_block->content[] = compose_feature_block_wrap_elements([$bibliography_item], $feature_bibliography);

    }

  }

  return $bibliography_block;

}

/**

 * Renders the link which will lead to the specimen detail page

 * @param object $specimen

 *    the cdm specimen entity which will be linked to

 *

 * @return string

 *     the markup for the link

 */

function render_cdm_specimen_link($specimen) {

  $path = path_to_specimen($specimen->uuid);

  $attributes['class'][] = html_class_attribute_ref($specimen);

  return $specimen->titleCache.icon_link($path);

}

/**

 * 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) {

    // 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);

    }

    $accepted_name .= render_taxon_and_name_footnotes($taxon);

    $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);

}

/**

 * Provides the default configuration for handle_annotations_and_sources() in the

 * synonymy.

 *

 * @return bool[]

 */

function synonymy_annotations_and_source_config() {

  static $annotations_and_sources_config = null;

  if(!$annotations_and_sources_config){

    $bibliography_settings = get_bibliography_settings();

    $annotations_and_sources_config = [

      'sources_as_content' => FALSE,

      'link_to_name_used_in_source' => TRUE,

      'link_to_reference' => TRUE,

      'add_footnote_keys' => TRUE,

      'bibliography_aware' => $bibliography_settings['enabled'] == 1

    ];

  }

  return $annotations_and_sources_config;

}

/**

 * composes and returns an render array for the experts associated with the given taxon

 *

 * @param object taxon

 *

 * @return array

 *   A Drupal render array for a table with the experts

 *

 * @ingroup compose

 */

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){

    $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

      '#' . $expert_details_container_id // $content_element_selector

    );

    // Expert and Role

    $rows[] = array(

      'data' => array(

        array(

          'data' => $agent_label_markup,

          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))

        ),

        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

        )

      )

    );

  }

  $render_array['experts_table'] = array(

    '#theme' => 'table',