EDIT

<?php

 * 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();

    $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

 */

function cdm_toc_list_add_item($label, $class_attribute_suffix, $fragment = NULL, $as_first_element = FALSE) {

  $toc_list_items = &cdm_toc_list();

    $fragment = $label;

  }

  $fragment = generalizeString($fragment);

    theme(

      'cdm_feature_name',

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

      $fragment

    );

    array_unshift($toc_list_items, $new_item);

  }

  else {

    $toc_list_items[] = $new_item;

 * 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

 * derived from other data on the fly and so not exist as such in the cdm data. In case

 * of pseudo features the $feature is left empty

 *

 * @param $feature_name

 * @param object $feature

 *   The CDM Feature for which the block is created. (optional)

  $block->module = 'cdm_dataportal';

  $block->delta = generalizeString($feature_name);

    . theme('cdm_feature_name', array('feature_name' => $feature_name))

    . '</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 DescriptionElement instance.

 *

 * Footnotes are created for annotations and original sources,

 * optionally the sources are put into a separate bibliography.

 *

 * @param $descriptionElement

 * @return String

function cdm_create_description_element_footnotes($description_element, $separator = ',',

          $footnote_list_key_suggestion = null, $do_link_to_reference = FALSE,

          $do_link_to_name_used_in_source = FALSE

    ){

  // Annotations as footnotes.

  $footNoteKeys = cdm_annotations_as_footnotekeys($description_element, $footnote_list_key_suggestion);

  // Source references as footnotes.

  $bibliography_settings = get_bibliography_settings();

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

    if (_is_original_source_type($source)) {

      $fn_key = FootnoteManager::addNewFootnote(

        original_source_footnote_list_key($footnote_list_key_suggestion),

        theme('cdm_OriginalSource', array(

          'source' => $source,

          'doLink' => $do_link_to_reference,

          'do_link_to_name_used_in_source' => $do_link_to_name_used_in_source

        )),

        $original_source_footnote_tag

      );

      // Ensure uniqueness of the footnote keys.

      cdm_add_footnote_to_array($footNoteKeys, $fn_key);

    }

  }

  // Sort and render footnote keys.

  $footnoteKeyListStr = '';

  asort($footNoteKeys);

  foreach ($footNoteKeys as $footNoteKey) {

    $footnoteKeyListStr .= theme('cdm_footnote_key',

      array(

        'footnoteKey' => $footNoteKey,

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

}

 * 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

  );

  // 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);

    }

  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> ';

  }

  $render_array['#value'] = $feature_label . $names_used_in_source_markup . $element_markup . $source_references_markup;

  return $render_array;

   * @param $feature_block_settings

   * @param $element_text

   *   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)

   *

    $annotations_and_sources = array(

      'foot_note_keys' => NULL,

      'source_references' => array(),

      'names_used_in_source' => array()

    );

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

          array(

            'do_link_to_name_used_in_source' => $feature_block_settings['link_to_name_used_in_source'] == 1,

          )

        );

        if ($referenceCitation) {

          if (empty($element_text)) {

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

          }

          else {

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

          }

        }

          $source,

          $feature_block_settings['link_to_name_used_in_source'] == 1

        if(!empty($name_in_source_render_array)){

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

        }

      } // END of loop over sources

      // annotations footnotes separate.

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

          'footnote_list_key' => $footnote_list_key_suggestion,

        )

      );

    } // END of references inline

    // put sources into bibliography if requested ...

    if ($feature_block_settings['sources_as_content'] !== 1 || $feature_block_settings['sources_as_content_to_bibliography'] == 1) {

      $annotations_and_sources['foot_note_keys'] = cdm_create_description_element_footnotes(

        $element, ',',

        $footnote_list_key_suggestion,

        $feature_block_settings['link_to_reference'] == 1,

        $feature_block_settings['link_to_name_used_in_source'] == 1

      );

    return $annotations_and_sources;

   *

   * @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();

    RenderHints::pushToRenderStack('feature_nodes');

    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME);

    // Create a drupal block for each feature

    foreach ($mergedFeatureNodes as $node) {

      if ((isset($node->descriptionElements['#type']) ||

        $feature_name = cdm_term_representation($node->feature, 'Unnamed Feature');

        $block = feature_block($feature_name, $node->feature);

        $block->content = array();

        $block_content_is_empty = TRUE;

        /*

         * Content/DISTRIBUTION.

         */

        if ($node->feature->uuid == UUID_DISTRIBUTION) {

          $block = compose_feature_block_distribution($taxon, $node->descriptionElements, $node->feature);

          $block_content_is_empty = FALSE;

        }

        /*

         * Content/COMMON_NAME.

         */

        else if ($node->feature->uuid == UUID_COMMON_NAME) {

          $block_content_is_empty = FALSE;

        }

        else if ($node->feature->uuid == UUID_USE_RECORD) {

          $block_uses_content_html = theme('cdm_block_Uses', array('taxonUuid' => $taxon->uuid));

          $block->content[] = markup_to_render_array($block_uses_content_html);

          $block_content_is_empty = FALSE;

        }

        /*

         * Content/ALL OTHER FEATURES.

         */

        else {

          $media_list = array();

          $child_elements_render_array = null;

          // Content/ALL OTHER FEATURES/Subordinate Features

          // subordinate features are printed inline in one floating text,

          // it is expected hat subordinate features can "contain" TextData,

            $elements_render_array = array_merge($elements_render_array, $child_elements_render_array);

          }

          $block_content_is_empty = $block_content_is_empty && empty($media_list) && empty($elements_render_array);

          if(!$block_content_is_empty){

            $block->content[] = compose_feature_block_wrap_elements($elements_render_array, $node->feature);

            $block->content[] = compose_feature_media_gallery($node, $media_list, $gallery_settings);

            /*

             * Footnotes for the feature block

             */

            $block->content[] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => 'BIBLIOGRAPHY-' . $node->feature->uuid)));

            $block->content[] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => $node->feature->uuid)));

            $block->content[] = markup_to_render_array(theme('cdm_annotation_footnotes', array('footnoteListKey' => $node->feature->uuid)));

        } // END all other features

        drupal_alter('cdm_feature_node_block_content', $block->content, $node->feature, $node->descriptionElements);

          $block_list[] = $block;

          cdm_toc_list_add_item(cdm_term_representation($node->feature), $node->feature->uuid);

        } // END: skip empty block content

    drupal_alter('cdm_feature_node_blocks', $block_list, $taxon);

    RenderHints::popFromRenderStack();

    return _block_get_renderable_array($block_list);

  }

 * Creates a render array of description elements  held by child nodes of the given feature node.

 *

 * This function is called recursively!

 *

 * @param $node

 *   The feature node.

 * @param array $media_list

 *   List of CDM Media entities. All media of subordinate elements should be passed to the main feature.ä

 * @param $feature_block_settings

 *   The feature block settings.

 * @param $main_feature

 *  Only used internally in recursive calls.

 *

 * @return array

 *  A Drupal render array

 *

 * @ingroup compose

 */

function compose_feature_block_items_nested($node, &$media_list, $feature_block_settings, $main_feature = NULL)

{

  if(!$main_feature){

    $main_feature = $node->feature;

  }

  /*

   * TODO should be configurable, options; YES, NO, AUTOMATIC

   * (automatic will only place the label if the first word of the description element text is not the same)

   */

  $prepend_feature_label = false;

  $render_arrays = array();

  foreach ($node->childNodes as $child_node) {

    if (isset($child_node->descriptionElements[0])) {

      foreach ($child_node->descriptionElements as $element) {

        if (isset($element->media[0])) {

          // Append media of subordinate elements to list of main

          // feature.

          $media_list = array_merge($media_list, $element->media);

        }

        $child_node_element = null;

        switch ($element->class) {

          case 'TextData':

            $child_node_element = compose_description_element_text_data($element, $element->feature->uuid, $feature_block_settings, $prepend_feature_label);

            break;

          case 'CategoricalData':

            $child_node_element = compose_description_element_categorical_data($element, $feature_block_settings, $prepend_feature_label);

            break;

          case 'QuantitativeData':

            $child_node_element = compose_description_element_quantitative_data($element, $feature_block_settings, $prepend_feature_label);

        }

        if (is_array($child_node_element)) {

          $render_arrays[] = $child_node_element;

        }

      }

    }

    if(isset($child_node->childNodes[0])){

      $render_arrays = array_merge($render_arrays, compose_feature_block_items_nested($child_node, $media_list, $feature_block_settings, $main_feature ));

    }

  }

  return $render_arrays;

}