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 parameters

    if (count($specimensOrObservations) > 0) {

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

      $map_visibility = variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT);

      if($map_visibility == 'always' ||

        variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT) == 'automatic' &&

          (isset($occurrence_queryDto->fieldUnitPoints[0]) || isset($occurrence_queryDto->derivedUnitPoints[0]))

        )

      {

        $occurrence_query = $occurrence_queryDto->occurrenceQuery;

        $legend_format_query = null;

        $distribution_query = NULL;

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

      }

    }

    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);

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

        // get icon images

        $expand_icon = font_awesome_icon_markup(

            'fa-plus-square-o',

            array(

                'alt'=>'Show details',

                'class' => array('expand_icon')

            )

        );

        $collapse_icon = font_awesome_icon_markup(

            'fa-minus-square-o',

            array(

                'alt'=>'Show details',

                'class' => array('collapse_icon')

            )

        );

        $detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';

        $checked_box_icon = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/step_done.gif' . '"/>';

        $sequence_icon = '<img title="Molecular Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/sequence_derivate-16x16-32.png' . '"/>';

        $character_data_icon = '<img title="Character Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/character_data_derivate-16x16-32.png' . '"/>';

        if (isset($pagerFieldUnits->records[0])) {

            $rowcount = 0;

            foreach ($pagerFieldUnits->records 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(

                            array(

                                'data' => $expand_icon . $collapse_icon,

                                'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')

                            ),

                            array(

                                'data' => $derivateHierarchy->country,

                                'class' => array('summary_row_cell')

                            ),

                            array(

                                'data' => $derivateHierarchy->date,

                                'class' => array('summary_row_cell')

                            ),

                            array(

                                'data' => $derivateHierarchy->collection,

                                'class' => array('summary_row_cell')

                            ),

                            array(

                                'data' => $derivateHierarchy->herbarium,

                                'class' => array('summary_row_cell')

                            ),

                            array(

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

                                'class' => array('summary_row_cell', 'summary_row_icon')

                            ),

                            array(

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

                                'class' => array('summary_row_cell', 'summary_row_icon')

                            ),

                            array(

                                'data' => ($derivateHierarchy->hasDna? $sequence_icon :"")." "

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

                                    .($derivateHierarchy->hasCharacterData?$character_data_icon:""),

                                'class' => array('summary_row_cell', 'summary_row_icon')

                            )

                        ),

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

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

                    );

                    //assemble field unit details

                    $detail_html = "";

                    // - taxon name

                    if (variable_get('cdm_dataportal_compressed_specimen_derivate_table_show_determined_as') && $derivateHierarchy->taxonName) {

                        $detail_html .= create_label("Associated with") . $derivateHierarchy->taxonName . "<br>";

                    }

                    // - protologue

                    if ($derivateHierarchy->protologue) {

                        //$detail_html .= "<strong>Protologue:</strong> " . $derivateHierarchy->protologue . "<br>"

                    }

                    // - citation

                    if ($derivateHierarchy->citation) {

                        $detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";

                    }

                    //assemble specimen details

                    if($derivateHierarchy->preservedSpecimenDTOs){

                        foreach($derivateHierarchy->preservedSpecimenDTOs as $preservedSpecimenDTO) {

                            $detail_html .= "<br>";

                            $detail_html .= render_cdm_specimen_page($preservedSpecimenDTO);

                        }

                    }

                    $detail_html .= "<br>";

                    //detail row resp. one BIG detail cell

                    $rows[] = array(

                        'data' => array(

                            array(

                                'data' => "", //empty first column

                                'class' => array('expand_column')

                            ),

                            array(

                                'data' => $detail_html,

                                'colspan' => 7,

                            ),

                        ),

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

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

                    );

                    $rowcount++;

                }

            }

        }

        $tableId = "derivate_hierarchy_table";

        $derivateHierarchyTable = array(

            "#theme" => "table",

            "#weight" => 2,

            "#header" => array(

                array(

                    'data' => "",

                    'class' => array('expand_column')

                ),

                "Country", "Date", "Collector + collecting number", "Herbaria", "Type", "Scan", "Derivatives"),

            "#rows" => $rows,

            "#attributes" => array(

                "id" => $tableId,

                "border" => 2

            )

        );

        //add toggle functionality to derivate hierarchy table

        drupal_add_js_rowToggle("#".$tableId);

        $render_array['derivate_hierarchy_table'] = $derivateHierarchyTable;

        $render_array['pager'] = markup_to_render_array(

            theme('cdm_pager', array(

                'pager' => $pagerFieldUnits,

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

                'parameters' => $_REQUEST

            )),

            10 // weight

        );

    }

    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($typeDesignationPager) and isset($typeDesignationPager->records)) {

                    $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',

                  '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

                );

                // --- 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;

}

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';

  $media = _load_media_for_taxon($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');

  }

    // --- 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') {

    taxon_page_tabs_hidden('synonymy');

  }

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

  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 ($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.

    $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>';

    }

    $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++);

  }

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

  // 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('@tab-name', array('@tab-name' => 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 taxon

 * @param mergedTrees

 * @param media

 *

 * @return array

 *   A Drupal render 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 {

      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 = 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

  $render_array['taxon_description_features'] = compose_feature_blocks($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;

}

/**

 * 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

 */

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',

    '#header' => $header,

    '#rows' => $rows,

  );

  return $render_array;

}

/**

 * Manages the tabs 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

 *   Optional 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;

  }

}

/* =================== block composition ===================== */

/**

 * Composes and returns an render array for the classification breadcrumbs of the given taxon.

 *

 * @param taxon

 *

 * @return array

 *   A Drupal render array for a table with the experts

 *

 * @ingroup compose

 */

function compose_classification_breadcrumbs($taxon_uuid) {

  _add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');

  $render_array = array();

  $render_array['#theme'] = 'item_list';

  $render_array['#type'] = 'ul';

  $render_array['#attributes'] = array(

    'id' => 'classification-breadcrumbs',

    'class' => 'breadcrumbs inline',

  );

  $items = array();

  $parent_taxon_nodes = null;

  if($taxon_uuid){

    $parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);

  }

  $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;

    }

  }

  $node_name = '';

  if(count($classifications) > 1 ){

    // need to add the current classification as first label

    $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

    ));

  }

  $rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);

  $rank_separator = '<span> '

    . font_awesome_icon_markup('fa-chevron-right')

    . ' </span>';

  $more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');

  $more_children_label = '...';

  $items[] = $node_name;

  $more_children_for = null;

  if($parent_taxon_nodes){

    foreach ($parent_taxon_nodes as $node) {

      $is_first_item = count($items) == 0;

      $is_last_item = count($items) == count($parent_taxon_nodes);

      $node_name = cdm_dataportal_shortname_of($node);

      $path = path_to_taxon($node->taxonUuid);

      if($node->taxonomicChildrenCount > 0) {

        $more_children_for = $node->taxonUuid;

      } else {

        $more_children_for = null;

      }

      // 'fa-sitemap'

      $items[] =

        ($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')

            )

          )

        );

      }

    }

  // add more button to the end

  if(!$parent_taxon_nodes) {

    // not taxon focused yet, adding button to make  the root nodes available

    $items[] = '<span>'

      . $more_children_icon . ' ' .

      '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid

      . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'

      . '</span>';

  } else if($more_children_for){

    // last parent item has child taxon nodes

    $items[] = ' <span>'

      . $more_children_icon . ' ' .

      '<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for

      . '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'

      . '</span>';

  }

  $render_array['#items'] = $items;

  return $render_array;

}

/**

 * @param $specimen_uuid

 * @return array

 *    The drupal render array for the page

 *

 * @ingroup compose

 */

function compose_cdm_specimen_page($specimen_uuid)

{

  drupal_set_title("Specimen Details");

  $specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($specimen_uuid, 'specimenDerivates'));

  $render_array = array();

  RenderHints::pushToRenderStack('specimen_page');

  $detail_html = render_cdm_specimen_page($specimen, true);

  $render_array['specimen_html'] = array(

    '#markup' => $detail_html

  );

  RenderHints::popFromRenderStack();

  return $render_array;

}

/**

 * @param $named_area_uuid

 * @return array

 *    The drupal render array for the page

 *

 * @ingroup compose

 */

function compose_cdm_named_area_page($named_area_uuid)

{

  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));

  $render_array = array();

  RenderHints::pushToRenderStack('named_area_page');

  $groups = array();

  @_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);

  @_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);

  if(isset($named_area->level)) {

    @_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);

  }

  $name_area_details_elements = array(

   // '#title' => $title,

    '#theme' => 'description_list',

    '#groups' => $groups,

    '#attributes' => array('class' => html_class_attribute_ref($named_area)),

  );

  $render_array[] = $name_area_details_elements;

  RenderHints::popFromRenderStack();

  return $render_array;

}