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>

 */

/**

 * 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()

 *

 */

function cdm_dataportal_taxon_page_specimens($taxon) {

    $render_array = array();

    RenderHints::pushToRenderStack('taxon_page_specimens');

    $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',

        ));

    }

    // --- get map service HTTP query paramaters

    if (count($specimensOrObservations) > 0) {

        $occurrence_query = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid,  $by_associatedtaxon_query);

        if( isset($occurrence_query->String) ) {

            $occurrence_query = $occurrence_query->String;

            $legend_format_query = null;

            $distribution_query = NULL;

            $render_array['map'] = compose_map($occurrence_query, $distribution_query, $legend_format_query);

        }

    }

    if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){

        //COMPRESSED SPECIMEN DERIVATE TABLE

        $fieldUnits = cdm_ws_get(CDM_WS_PORTAL_TAXON, array($taxon->uuid, 'associatedFieldUnits'));

        $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' . '"/>';

        if ($fieldUnits) {

            $rowcount = 0;

            foreach ($fieldUnits as $fieldUnit) {

                //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(

                            $derivateHierarchy->country,

                            $derivateHierarchy->date,

                            $derivateHierarchy->collection,

                            $derivateHierarchy->herbarium,

                            array(

                                'data' => $derivateHierarchy->hasType? $checked_box_icon:"",

                                'class' => array('checkBoxCell')

                            ),

                            array(

                                'data' => $derivateHierarchy->hasSpecimenScan? $checked_box_icon:"",

                                'class' => array('checkBoxCell')

                            ),

                            ($derivateHierarchy->hasDna? $sequence_icon :"") . ($derivateHierarchy->hasDetailImage?$detail_image_icon:"")

                        ),

                        'id' => ('derivate_summary' . $rowcount), // summary row id

                        'class' => array('summary_row'),

                    );

                    //assemble detail html

                    $taxonName = $derivateHierarchy->taxonName;

                    $protologue = $derivateHierarchy->protologue;

                    $citation = $derivateHierarchy->citation;

                    $types = "";

                    foreach($derivateHierarchy->types as $typeStatus => $accessionList){

                        $types .= $typeStatus;

                        foreach($accessionList as $accessionNumber){

                            $types .= " (" . $accessionNumber . ") ";

                        }

                    }

                    $specimenScans = createLinks($derivateHierarchy->specimenScans);

                    $molecularData = createLinks($derivateHierarchy->molecularData);

                    $detailImages = createLinks($derivateHierarchy->detailImages);

                    $detail_html = "";

                    if($taxonName){

                        $detail_html .= "<b>Name:</b> " . $taxonName . "<br>";

                    }

                    if($protologue){

                        //$detail_html .= "<b>Protologue:</b> " . $protologue . "<br>"

                    }

                    if($citation){

                        $detail_html .= "<b>Citation:</b> " . $citation . "<br>";

                    }

                    if($types){

                        $detail_html .= "<b>Types:</b> " . $types . "<br>";

                    }

                    if($specimenScans){

                        $detail_html .= "<b>Specimen Scans:</b> " . $specimenScans . "<br>";

                    }

                    if($molecularData){

                        $detail_html .= "<b>Molecular Data:</b> " . $molecularData . "<br>";

                    }

                    if($detailImages){

                        $detail_html .=  "<b>Detail Images:</b> " . $detailImages . "<br>";;

                    }

                    //detail row resp. one BIG detail cell

                    $rows[] = array(

                        'data' => array(

                            array(

                                'data' => $detail_html,

                                'colspan' => 8,

                            ),

                        ),

                        'id' => ('derivate_details' . $rowcount),//details row ID

                        'class' => array('detail_row'),

                    );

                    $rowcount++;

                }

            }

        }

        $tableId = "derivate_hierarchy_table";

        $derivateHierarchyTable = array(

            "#theme" => "table",

            "#weight" => 2,

            "#header" => array("Country", "Date", "Collection", "Herbaria", "Type", "Image", "Derivates"),

            "#rows" => $rows,

            "#attributes" => array(

                "id" => $tableId,

                "border" => 2

            )

        );

        //add toggle functionality to derivate hierarchy table

        drupal_add_js_rowToggle("#".$tableId);

        $render_array['derivate_hierarchy_table'] = $derivateHierarchyTable;

    }

    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(),

        );

        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);

                if (isset($typeDesignationPager)) {

                    $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(

                    $specimenOrObservation->uuid,

                    $type_label . $specimenOrObservation->titleCache,

                    $derived_unit_ws_request,

                    'cdm_specimenOrObservation', // the theme or compose function to use

                    'Click for details',

                    array('div','div'),

                    array(),

                    'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback

                    'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback

                );

                // --- 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'

                    ),

                );

            }

        }

        $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;

}

/**

 * Creates HTML links from the given pair list concatenated by a white space.

 * @param $linkTextPairList the list with pairs which hold the uri as "first" and uriText as "second"

 * @return string the assembled HTML string containing the links

 */

function createLinks($linkTextPairList)

{

    $html = "";

    if ($linkTextPairList) {

        foreach ($linkTextPairList as $linkTextPair) {

            $html .= '<a href="' . $linkTextPair->first . '">' . $linkTextPair->second . "</a>";

        }

    }

    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') {

  global $theme;

  // 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';

  $media = _load_media_for_taxon($taxon);

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

    taxon_page_tabs_hidden('images');

  }

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

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

  $specimensOrObservationsCount = is_array($specimensOrObservations) ? count($specimensOrObservations) : 0;

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

    taxon_page_tabs_hidden('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('keys');

  }

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

    taxon_page_tabs_hidden('synonymy');

  }

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

  $render_array['back_to_search'] = markup_to_render_array(theme('cdm_back_to_search_result_button'), -103);

  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(theme('cdm_acceptedFor', array('acceptedFor' => $_REQUEST['acceptedFor'])), $weight++);

  }

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

  if ($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);

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

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

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

  }

  // --- 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>';

    }

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

    $taxon_image_gallery = call_user_func_array('taxon_image_gallery_' . variable_get('image_gallery_viewer', 'default'), array(

        $taxon,

        $media,

    ));

    $images_html .= $taxon_image_gallery;

    $images_html .= '</div>';

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

  }

  // --- 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>';

    }

    $addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);

    $synonymy_html .= theme('cdm_taxon_page_synonymy', array('taxon' => $taxon, 'addAcceptedTaxon' => $addAcceptedTaxon));

    $synonymy_html .= '</div>';

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

  }

  // --- 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++);

  }

  // 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(

              'data' => l(t(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 move into description.inc or in cdm_api.module?

   *

   * @param $taxon

   * @param $distribution_node

   * @return array

   */

  function merged_taxon_feature_tree($taxon) {

    // 1. fetch descriptions_by_featuretree but exclude the distribution feature

    $merged_tree = cdm_ws_descriptions_by_featuretree(get_profile_featureTree(), $taxon->uuid, array(UUID_DISTRIBUTION));

    // 2. find the distribution feature node

    $distribution_node =& cdm_feature_tree_find_node($merged_tree->root->childNodes, UUID_DISTRIBUTION);

    if ($distribution_node) {

      // 3. get the distributionInfoDTO

      $query_parameters = cdm_distribution_filter_query();

      $query_parameters['part'] = array('mapUriParams');

      if (variable_get('distribution_sort', 'NO_SORT') != 'NO_SORT') {

        $query_parameters['part'][] = 'tree';

      }

      else {

        $query_parameters['part'][] = 'elements';

      }

      $query_parameters['omitLevels'] = array(UUID_NAMEDAREALEVEL_TDWGLEVEL_2);

      $customStatusColorsJson = variable_get(DISTRIBUTION_STATUS_COLORS, NULL);

      if ($customStatusColorsJson) {

        $query_parameters['statusColors'] = $customStatusColorsJson;

      }

      $distribution_info_dto = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION_DISTRIBUTION_INFO_FOR, $taxon->uuid, queryString($query_parameters));

      // 4. get distribution TextData is there are any

      $distribution_text_data = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,

        array(

          'taxon' => $taxon->uuid,

          'type' => 'TextData',

          'features' => UUID_DISTRIBUTION

        )

      );

      // 5. put all distribution data into the distribution feature node

      if ($distribution_text_data //if text data exists

        || ($distribution_info_dto && isset($distribution_info_dto->tree) && $distribution_info_dto->tree->rootElement->numberOfChildren > 0) // OR if tree element has distribution elements

        || ($distribution_info_dto && !empty($distribution_info_dto->elements))

      ) { // OR if DTO has distribution elements

        $distribution_node->descriptionElements = array('#type' => 'DTO');

        if ($distribution_text_data) {

          $distribution_node->descriptionElements['TextData'] = $distribution_text_data;

        }

        if ($distribution_info_dto) {

          $distribution_node->descriptionElements['DistributionInfoDTO'] = $distribution_info_dto;

        }

      }

    }

    return $merged_tree;

  }

/**

 * 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 array $variables

 *   An associative array containing:

 *   - taxon

 *   - mergedTrees

 *   - media

 *

 * @return array

 *   A Drupal reder array with the following elements:

 *     - 'taxon_profile_image'

 *     - 'taxon_description_feature_toc'

 *     - 'taxon_description_features'

 *

 * @ingroup compose

 */

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

  $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;

      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 {

      // 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";

    }

    $profile_image = theme('cdm_media_gallerie_image', array(

        'mediaRepresentationPart' => $representationPart,

        'maxExtend' => $taxon_profile_image_settings['maxextend'],

        'addPassePartout' => FALSE,

        'attributes' => $attributes,

    ));

    // 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);

  }

  // Render the sections for each feature

  $render_array['taxon_description_features'] = compose_cdm_feature_nodes($merged_tree->root->childNodes, $taxon);

  $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,

            )

          )

        ),

        100 // 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;

}

/**

 * Manages the tab to be hidden in the taxon page.

 *

 * 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

 *   Optinal parameter. The given string will be added to the array of tabs

 *

 * @return

 *   The array of tabs

 */

function taxon_page_tabs_hidden($add_tab = NULL) {

  $tabs = &drupal_static(__FUNCTION__);

  if(!isset($tabs)){

    $tabs = array();

  }

  if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {

    $tabs[] = $add_tab;

  }

  return $tabs;

}

/**

 * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()

 *

 *  - 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 !!!)

 *

 * @param array $variables

 *   The variables array

 */

function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {

  $hidden_tabs = taxon_page_tabs_hidden();

  if (is_array($variables['primary'])) {

    foreach ($variables['primary'] as $key => &$element) {

      // 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]);

        }

      }

    }

  }

}

/**

 * 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) {

  $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;

    $variables['element']['#link'] = $link;

  }

}