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.

 *

 *   DescriptionElementBase, StateDate, State

 *

 * @return String

 *   localized representations of the modifiers hold by the

 *   supplied cdm instance concatenated into one string

 */

    foreach ($is_modifieable->modifiers as $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

 */

  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

 *   "feature-toc-item-"

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

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

 *   being set

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

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

 * @throws \Exception re-throws exception from theme()

    $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(){

  return $toc_list_items;

}

 * specific CDM Feature.

 * features are derived from other data on the fly and so not exist as such in

 * the cdm data. For pseudo features the $feature can be created using

 * make_pseudo_feature().

 * @param $feature_name

 *   representation.

 * @throws \Exception re-throws exception from theme()

  $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;

  }

    case "PolytomousKey":

    case "MediaKey":

  }

  }

  $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";

  }

  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)

 *    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

 *    Create a link to the reference pages for sources when TRUE.

 * @param bool $do_link_to_name_used_in_source

 *    Create a link to the name pages for name in source when TRUE.

 * @param bool $is_bibliography_aware

 *    Put source references into the bibliography when this param is TRUE.

 * @return String

 *

function cdm_create_footnotes(

    $description_element,

    $separator = ',',

    $do_link_to_name_used_in_source = FALSE,

  // Source references as footnotes.

    $bibliography_settings = get_bibliography_settings();

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

    if(!$sources_footnote_list_key) {

      RenderHints::getFootnoteListKey();

    }

  }

      $fn_key = FootnoteManager::addNewFootnote(

          $source,

          $do_link_to_name_used_in_source

        ),

      );

      // Ensure uniqueness of the footnote keys.

  }

  // Sort and render footnote keys.

/**

 * Creates markup for an array of foot note keys

 *

 * @param array $footnote_keys

 * @param string $separator

 *

 * @return string

 */

  $footnotes_markup = '';

  foreach ($footnote_keys as $foot_note_key) {

    try {

      $footnotes_markup .= theme('cdm_footnote_key',

          'separator' => ($footnotes_markup ? $separator : '')

        ));

 * compose_description_element().

 * @param $a

 * @param $b

 * @return int Returns < 0 if $a['#value'].$a['#value-suffix'] from is less than

 * $b['#value'].$b['#value-suffix'], > 0 if it is greater than $b['#value'].$b['#value-suffix'],

 * and 0 if they are equal.

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 $element

 * @param $feature_block_settings

 * @param $element_markup

 * @param $footnote_list_key_suggestion

 *

 * @return array|null

  $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 $entity

 * @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.

 * @param $footnote_list_key_suggestion string

 *    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'. @return

 *   array 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)

 *

 * @throws \Exception

 *

 * @see cdm_entities_annotations_as_footnotekeys()

 */

      'foot_note_keys' => NULL,

      'names_used_in_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'] = footnote_keys_to_markup(

        cdm_entity_annotations_as_footnotekeys($entity, $footnote_list_key_suggestion), ', '

          $footnote_list_key_suggestion,

          $config['link_to_reference'] == 1,

          !empty($config['bibliography_aware'])

    return $annotations_and_sources;

 * Get the source or the sources from a cdm entity and return them ordered by see compare_original_sources()

 * (Some entity types only have single sources)

 * @param $entity

 *

 * @return array

 */

function cdm_entity_sources_sorted($entity) {

  if (isset($entity->source) && is_object($entity->source)) {

    $sources = [$entity->source];

  }

  else if (isset($entity->sources)) {

    $sources = $entity->sources;

  }

  else {

    $sources = [];

  }

  usort($sources, 'compare_original_sources');

  return $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

      $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')

 *

 * @return mixed|string

 */

    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