EDIT

<?php

const BIBLIOGRAPHY_FOOTNOTE_KEY = PSEUDO_FEATURE_BIBLIOGRAPHY;

 * Returns the localized representations of the modifiers hold by the

 * supplied cdm instance concatenated into one string.

 *

 * @param object $iModifieable

 *   cdm instance of an class implementing the interface IModifieable:

 *   DescriptionElementBase, StateDate, State

 *

 * @return String

 *   localized representations of the modifiers hold by the

 *   supplied cdm instance concatenated into one string

 */

function cdm_modifers_representations($iModifieable, $glue = ', ') {

  $modifiers_strings = array();

  if (isset($iModifieable->modifiers)) {

    foreach ($iModifieable->modifiers as $modifier) {

      $modifiers_strings[] = cdm_term_representation($modifier);

}

 * Filters the given set of description elements and prefers computed elements over others.

 *

 * Computed description elements

 * are identified by the MarkerType.COMPUTED()

 *

 * If the given set contains at least one computed element only

 * the computed elements are returned.

 *

 * @param array $description_elements

 *   An array of CDM DescriptionElementBase instances

 *

 * @return array

 *   only the computed description elements otherwise all others.

 *

 * @deprecated this is replaced by the cdmlib DistributionUtil class!!!

 */

function cdm_description_elements_prefer_computed($description_elements){

  $other_elements = array();

    foreach ($description_elements as $element) {

      if (cdm_entity_has_marker($element, UUID_MARKERTYPE_COMPUTED)) {

        $computed_elements[] = $element;

      }

      else {

        $other_elements[] = $element;

    }

    return $computed_elements;

  }

  else {

    return $other_elements;

 * Creates a query parameter array based on the setting stored in the drupal variable CDM_DISTRIBUTION_FILTER.

 *

 * @return array

 *   An array with distribution filter query parameters

 */

function cdm_distribution_filter_query() {

  $cdm_distribution_filter = get_array_variable_merged(CDM_DISTRIBUTION_FILTER, CDM_DISTRIBUTION_FILTER_DEFAULT);

  $query = array();

  if($feature_block_settings['sort_elements'] == SORT_HIERARCHICAL){

    $query['distributionOrder'] = 'AREA_ORDER';

  }

    $query['statusOrderPreference'] = 1;

  }

  if ($cdm_distribution_filter['filter_rules']['subAreaPreference']) {

    $query['subAreaPreference'] = 1;

  }

    $query['hiddenAreaMarkerType'] = '';

    foreach ($cdm_distribution_filter['hiddenAreaMarkerType'] as $marker_type => $enabled) {

}

 * Merge the fields 'annotations', 'markers', 'sources', 'media' from the source CDM DescriptionElement into  the target.

 *

 * @param object $target

 *   The source CDM DescriptionElement

 * @param object $source

 *   The target CDM DescriptionElement

 */

function cdm_merge_description_elements(&$target, &$source) {

  static $fields_to_merge = array('annotations', 'markers', 'sources', 'media');

  foreach ($fields_to_merge as $field) {

    if (is_array($source->$field)) {

      if (!is_array($target->$field)) {

        $target->$field = $source->$field;

      }

      else {

        $target->$field = array_merge($target->$field, $source->$field);

    }

  }

 * Adds an entry to the end of the table of content items list

 *

 * The  table of content items are crated internally by calling

 * toc_list_item() the resulting item is added to the statically cached

 * list of toc elements

 *

 * @param string $label

 *   The label of toc entry

 * @param $class_attribute_suffix

 *   The suffix to be appended to the class attribute prefix: "feature-toc-item-"

 * @param string $fragment

 *   Optional parameter to define a url fragment different from the $label,

 *   if the $fragment is not defined the $label will be used

 *   Place the new item as fist one. This parameter is ignored when $weight is being set

 * @param integer $weight

 *   Defines the weight for the ordering the item in the toc list.

 *   The item will be placed at the end if weigth is NULL.

    $fragment = $label;

  }

  $fragment = generalizeString($fragment);

    theme(

      'cdm_feature_name',

      array('feature_name' => $label)),

      $fragment

    );

    reset($toc_list_items);

    $weight = key($toc_list_items); // returns null for empty arrays

    $weight = $weight !== null ? $weight - FEATURE_BLOCK_WEIGHT_INCREMENT : 0;

      end($toc_list_items);

      $weight = key($toc_list_items); // returns null for empty arrays

      $weight = $weight !== null ? $weight + FEATURE_BLOCK_WEIGHT_INCREMENT : 0;

  ksort($toc_list_items); // sort so that the last element has always the highest weight

 * Returns the statically cached table of content items as render array.

 *

 * @see cdm_toc_list_add_item()

 *

 * @return array

 *   a render array of table of content items suitable for theme_item_list()

 */

function &cdm_toc_list(){

  $toc_list_items = &drupal_static('toc_list_items', array());

  return $toc_list_items;

}

 * Prepares an empty Drupal block for displaying description elements of a specific CDM Feature.

 *

 * The block can also be used for pseudo Features like a bibliography. Pseudo features are

 * features the $feature can be created using make_pseudo_feature().

 * @param $feature_name

 * @param object $feature

  $block = new stdclass();

    . '</span>';

  $block->module = "cdm_dataportal-feature";

  $block->content = '';

  return $block;

}

 * Returns a list of a specific type of IdentificationKeys.

 *

 * The list can be restricted by a taxon.

 *

 * @param string $type

 *   The simple name of the cdm class implementing the interface

 *   IdentificationKey, valid values are:

 *   PolytomousKey, MediaKey, MultiAccessKey.

 * @param string $taxonUuid

 *   If given this parameter restrict the listed keys to those which have

 *   the taxon identified be this uuid in scope.

 *

 * @return array

 *   List with identification keys.

 */

function _list_IdentificationKeys($type, $taxonUuid = NULL, $pageSize = NULL, $pageNumber = NULL) {

  if (!$type) {

    drupal_set_message(t('Type parameter is missing'), 'error');

    return;

  }

  $cdm_ws_pasepath = NULL;

  switch ($type) {

    case "PolytomousKey":

      $cdm_ws_pasepath = CDM_WS_POLYTOMOUSKEY;

      break;

    case "MediaKey":

      $cdm_ws_pasepath = CDM_WS_MEDIAKEY;

      break;

      $cdm_ws_pasepath = CDM_WS_MULTIACCESSKEY;

      break;

  }

  if (!$cdm_ws_pasepath) {

    drupal_set_message(t('Type parameter is not valid: ') . $type, 'error');

  }

  $queryParameters = '';

  if (is_numeric($pageSize)) {

    $queryParameters = "pageSize=" . $pageSize;

  }

  else {

    $queryParameters = "pageSize=0";

  }

  if (is_numeric($pageNumber)) {

    $queryParameters = "pageNumber=" . $pageNumber;

  }

  else {

    $queryParameters = "pageNumber=0";

  }

  $queryParameters = NULL;

  if ($taxonUuid) {

    $queryParameters = "findByTaxonomicScope=$taxonUuid";

  }

  $pager = cdm_ws_get($cdm_ws_pasepath, NULL, $queryParameters);

  if (!$pager || $pager->count == 0) {

    return array();

  }

  return $pager->records;

}

/**

 * Creates a list item for a table of content, suitable as data element for a themed list

 *

 * @see theme_list()

 *

 * @param $label

 * @param $http_request_params

 * @param $attributes

 * @return array

 */

function toc_list_item($label, $attributes = array(), $fragment = null) {

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

  $http_request_params = drupal_static('http_request_params', drupal_get_query_parameters());

  $item =  array(

    'data' => l(

      $label,

      $_GET['q'],

      array(

        'attributes' => array('class' => array('toc')),

        'fragment' => generalizeString($label),

        'query' => $http_request_params,

  );

  $item['attributes'] = $attributes;

  return $item;

}

 * Creates the footnotes for the given CDM instance.

 *

 * parameters $footnote_list_key_suggestion and $is_bibliography_aware, see parameter $footnote_list_key_suggestion

 * for more details.

 *

 * possible keys for

 *     - annotation footnotes:

 *       - $footnote_list_key_suggestion

 *       - RenderHints::getFootnoteListKey().'-annotations'

 *     - original source footnotes

 *       - "BIBLIOGRAPHY" (when !$is_bibliography_aware && bibliography_settings['enabled'] == 1 )

 *       - "BIBLIOGRAPHY-$footnote_list_key_suggestion" (when !$is_bibliography_aware && bibliography_settings['enabled'] == 0 )

 *       - $footnote_list_key_suggestion (when $is_bibliography_aware)

 * @param $descriptionElement

 *   A CDM DescriptionElement instance

 * @param $separator

 *   Optional parameter. The separator string to concatenate the footnote ids, default is ','

 *    Optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined by the nested

 *    method calls by calling RenderHints::getFootnoteListKey(). NOTE: the footnote key for annotations will be set to

 *    RenderHints::getFootnoteListKey().'-annotations'. @see cdm_annotations_as_footnotekeys()

 *    For original sources the $footnote_list_key_suggestion will be overwritten by original_source_footnote_list_key() when

 *    $is_bibliography_aware is set TRUE.

 *    null will cause original_source_footnote_list_key to use the default

 *

 * @return String

 *   The foot note keys

 */

function cdm_create_footnotes(

    $description_element,

    $separator = ',',

    $do_link_to_name_used_in_source = FALSE,

  // Annotations as footnotes.

  // Source references as footnotes.

  if($is_bibliography_aware){

    $bibliography_settings = get_bibliography_settings();

    $sources_footnote_list_key = original_source_footnote_list_key($footnote_list_key_suggestion);

    $original_source_footnote_tag = $bibliography_settings['enabled'] == 1 ? 'div' : null; // null will cause original_source_footnote_list_key to use the default

  } else {

    $sources_footnote_list_key = $footnote_list_key_suggestion;

    $original_source_footnote_tag = NULL;

  }

    if (_is_original_source_type($source)) {

      $fn_key = FootnoteManager::addNewFootnote(

          $source,

          $do_link_to_name_used_in_source

        ),

      );

      // Ensure uniqueness of the footnote keys.

  }

  // Sort and render footnote keys.

  $footnoteKeyListStr = '';

  asort($footNoteKeys);

  foreach ($footNoteKeys as $footNoteKey) {

      $footnoteKeyListStr .= theme('cdm_footnote_key',

        array(

          'footnoteKey' => $footNoteKey,

          'separator' => ($footnoteKeyListStr ? $separator : '')));

    } catch (Exception $e) {

      drupal_set_message("Exception: " . $e->getMessage(),  'error');

    }

}

 * Compare callback to be used in usort() to sort render arrays produced by compose_description_element().

 *

 * @param $a

 * @param $b

 */

function compare_description_element_render_arrays($a, $b){

  if ($a['#value'].$a['#value-suffix'] == $b['#value'].$b['#value-suffix']) {

    return 0;

  }

  return ($a['#value'].$a['#value-suffix'] < $b['#value'].$b['#value-suffix']) ? -1 : 1;

}

/**

 * @param $render_array

 * @param $element

 * @param $feature_block_settings

 * @param $element_markup

 * @param $footnote_list_key_suggestion

 */

  $render_array = array(

    '#type' => 'html_tag',

    '#tag' => cdm_feature_block_element_tag_name($feature_block_settings),

    '#attributes' => array(

        'DescriptionElement',

        'DescriptionElement-' . $element->class,

        html_class_attribute_ref($element)

      )

    '#value' => '',

    '#value_suffix' => NULL

  );

    $element,

    handle_annotations_and_sources_config($feature_block_settings),

    $element_markup,

    $footnote_list_key_suggestion

  );

  if(isset($element->timeperiod)){

  // used in source information without any text stored in it.

  if (!empty($annotations_and_sources['names_used_in_source']) && empty($element_markup)) {

    $names_used_in_source_markup = join(', ', $annotations_and_sources['names_used_in_source']) . ': ';

    // these are expected to be at the end of the strings

    $pattern = '/ <span class="nameUsedInSource">.*$/';

    foreach( $annotations_and_sources['source_references'] as &$source_reference){

      $source_reference = preg_replace($pattern , '', $source_reference);

    }

  $source_references_markup = '';

  if (!empty($annotations_and_sources['source_references'])) {

    $source_references_markup = '<span class="sources">' . join(' ', $annotations_and_sources['source_references']) . '<span>';

  }

  if ($prepend_feature_label) {

    $feature_label = '<span class="nested-feature-tree-feature-label">' . $element->feature->representation_L10n . ':</span> ';

  }

    // no textual content? So skip this element completely, even if there could be an footnote key

    return null;

  }

    $render_array['#value'] = $feature_label . $content_markup;

    $render_array['#value_suffix'] = $annotations_and_sources['foot_note_keys'];

 * Creates a handle_annotations_and_sources configuration array from feature_block_settings.

 *

 * The handle_annotations_and_sources configuration array is meant to be used for the

 * method handle_annotations_and_sources().

 *

 * @param $feature_block_settings array

 *

 * @return array

 *   The configuration array for handle_annotations_and_sources()

 */

function handle_annotations_and_sources_config($feature_block_settings){

  $config = $feature_block_settings;

  unset($config['sources_as_content_to_bibliography']);

    $config['add_footnote_keys'] = 1;

  }

  $config['bibliography_aware'] = 1;

  return $config;

}

   * @param $config array

   *   An associative array to configure the display of the annotations and sources.

   *   The array has the following keys

   *   - sources_as_content

   *   - link_to_name_used_in_source

   *   - link_to_reference

   *   - add_footnote_keys

   *   - bibliography_aware

   *   Valid values are 1 or 0.

   * @param $inline_text_prefix

   *   Only used to decide if the source references should be enclosed in brackets or not when displayed inline.

   *   This text will not be included into the response.

   *    optional parameter. If this paramter is left empty (null, 0, "") the footnote key will be determined by the nested

   *    method calls by calling RenderHints::getFootnoteListKey(). NOTE: the footnore key for annotations will be set to

   *    RenderHints::getFootnoteListKey().'-annotations'. @see cdm_annotations_as_footnotekeys()

   *   an associative array with the following elements:

   *   - foot_note_keys: all footnote keys as markup

   *   - source_references: an array of the source references citations

   *   - names used in source: an associative array of the names in source,

   *        the name in source strings are de-duplicated

   *        !!!NOTE!!!!: this field will most probably be removed soon (TODO)

      'foot_note_keys' => NULL,

      'source_references' => array(),

      'names_used_in_source' => array()

    );

      foreach ($entity->sources as $source) {

            $config['link_to_name_used_in_source'] == 1

          if ($reference_citation) {

            if (empty($inline_text_prefix)) {

              $annotations_and_sources['source_references'][] = $reference_citation;

            } else {

              $annotations_and_sources['source_references'][] = ' (' . $reference_citation . ')';

            }

          // still required to be available separately in some contexts.

            $source,

            $config['link_to_name_used_in_source'] == 1

          );

            $annotations_and_sources['names_used_in_source'][$name_in_source_render_array['#_plaintext']] = drupal_render($name_in_source_render_array);

          }

      } // END of loop over sources

    $annotations_and_sources['foot_note_keys'] = theme('cdm_annotations_as_footnotekeys',

      array(

        'cdmBase_list' => $entity,

        'footnote_list_key' => $footnote_list_key_suggestion,

      )

    );

          $footnote_list_key_suggestion,

          $config['link_to_reference'] == 1,

          !empty($config['bibliography_aware'])

    return $annotations_and_sources;

   *

   * The footnote key depends on the value of the 'enabled' value of the bibliography_settings

   *    - enabled == 1 -> "BIBLIOGRAPHY"

   *    - enabled == 0 -> "BIBLIOGRAPHY-$key_suggestion"

   *

   * @param $key_suggestion string

   *    optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be retrieved by

   *    calling RenderHints::getFootnoteListKey().

   * @return string

   *  the footnote_list_key

  function original_source_footnote_list_key($key_suggestion = null) {

    if(!$key_suggestion){

      $key_suggestion = RenderHints::getFootnoteListKey();

    }

    $bibliography_settings = get_bibliography_settings();

   * Provides the according tag name for the description element markup which fits the  $feature_block_settings['as_list'] value

   *

   * @param $feature_block_settings

   *   A feature_block_settings array, for details, please see get_feature_block_settings($feature_uuid = 'DEFAULT')

   */

  function cdm_feature_block_element_tag_name($feature_block_settings){

    switch ($feature_block_settings['as_list']){

      case 'ul':

      case 'ol':

        return 'li';

      case 'div':

          return $feature_block_settings['element_tag'];

        }

      case 'dl':

        return 'dd';

      default:

        return 'div'; // should never happen, throw error instead?

    }

  }

/* ==================== COMPOSE FUNCTIONS =============== */

  /**

   * Returns a set of feature blocks for a taxon profile from the $mergedFeatureNodes of a given $taxon.

   *

   * The taxon profile consists of drupal block elements, one for the description elements

   * of a specific feature. The structure is defined by specific FeatureTree.

   * The chosen FeatureTree is merged with the list of description elements prior to using this method.

   *

   * The merged nodes can be obtained by making use of the

   * function cdm_ws_descriptions_by_featuretree().

   *

   * @see cdm_ws_descriptions_by_featuretree()

   *

   * @param $mergedFeatureNodes

   *

   * @param $taxon

   *

   * @return array

   *  A Drupal render array containing feature blocks and the table of content

   *

   * @ingroup compose

   */

    $block_list = array();

    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME);

    RenderHints::pushToRenderStack('feature_block');

          has_feature_node_description_elements($feature_node)) && $feature_node->term->uuid != UUID_IMAGE) { // skip empty or suppressed features

        $feature_block_settings = get_feature_block_settings($feature_node->term->uuid);

        $block_content_is_empty = TRUE;

        }

         * Content/DISTRIBUTION.

         */

          $block = compose_feature_block_distribution($taxon, $feature_node->descriptionElements, $feature_node->term);

        }

         * Content/COMMON_NAME.

         */

          $common_names_render_array = compose_feature_block_items_feature_common_name($feature_node->descriptionElements, $feature_node->term);

          $block_content_is_empty = FALSE;

        }