Edit

<?php

/**

 * @file

 * Functions for dealing with CDM entities from the package model.name

 *

 * @copyright

 *   (C) 2007-2015 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>

 */

/**

 * @defgroup compose Compose functions

 * @{

 * Functions which are composing Drupal render arays

 *

 * The cdm_dataportal module needs to compose rather complex render arrays from

 * the data returned by the CDM REST service. The compose functions are

 * responsible for creating the render arrays.

 *

 * All these functions are also implementations of the compose_hook()

 * which is used in the proxy_content() function.

 * @}

 */

/**

 * Provides the name render template to be used within the page elements identified the the $renderPath.

 *

 * The render templates arrays contains one or more name render templates to be used within the page elements identified the the

 * renderPath. The renderPath is the key of the subelements whereas the value is the name render template.

 *

 * The render paths used for a cdm_dataportal page can be visualized by supplying the HTTP query parameter RENDER_PATH=1.

 *

 * It will be tried to find  the best matching default RenderTemplate by stripping the dot separated render path

 * element by element. If no matching template is found the DEFAULT will be used:

 *

 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy

 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy

 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy

 *

 * A single render template can be used for multiple render paths. In this case the according key of the render templates

 * array element should be the list of these render paths concatenated by ONLY a comma character without any whitespace.

 *

 * A render template is an associative array. The keys of this array are referring to the keys as defined in the part

 * definitions array.

 * @see get_partDefinition($taxonNameType) for more information

 *

 * The value of the render template element must be set to TRUE in order to let this part being rendered.

 * The namePart, nameAuthorPart and referencePart can also hold an associative array with a single

 * element: array('#uri' => TRUE). The value of the #uri element will be replaced by the according

 * links if the parameters $nameLink or $refenceLink are set.

 *

 * @param string $render_path

 *   The render path can consist of multiple dot separated elements

 *   @see RenderHints::getRenderPath()

 * @param string $nameLink

 *   The link path or URL to be used for name parts if a link is forseen in the template

 *   matching the given $renderPath.

 * @param string $referenceLink

 *   The link path ot URL to be used for nomenclatural reference parts if a link is forseen

 *   in the template matching the given $renderPath.

 * @return array

 *   An associative array, the render template

 */

function get_nameRenderTemplate($render_path, $nameLink = NULL, $referenceLink = NULL) {

  static $default_render_templates = NULL;

  static $split_render_templates = NULL;

  if (!isset($default_render_templates)) {

    $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);

  }

  if($split_render_templates == NULL) {

    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);

    // needs to be converted to an array

    $render_templates = (object_to_array($render_templates));

    // separate render templates which are combined with a comma

    $split_render_templates = array();

    foreach($render_templates as $key => $template){

      if(strpos($key, ',')){

        foreach(explode(',', $key) as $path){

          $split_render_templates[$path] = $template;

        }

      } else {

        $split_render_templates[$key] = $template;

      }

    }

  }

  // get the base element of the renderPath

  if (($separatorPos = strpos($render_path, '.')) > 0) {

    $renderPath_base = substr($render_path, 0, $separatorPos);

  } else {

    $renderPath_base = $render_path;

  }

  $template = NULL;

  // 1. try to find a template using the render path base element

  if(array_key_exists($renderPath_base, $split_render_templates)){

    $template = (array)$split_render_templates[$renderPath_base];

  }

  // 2. Find best matching default RenderTemplate

  // by stripping the dot separated render path element by element

  // if no matching template is found the DEFAULT will be used.

  while (!is_array($template) && strlen($render_path) > 0) {

    foreach ($split_render_templates as $path => $t) {

      if ($path == $render_path) {

        $template = $t;

        break;

      }

    }

    // shorten by one element

    $render_path = substr($render_path, strrpos($render_path, '.') + 1, strlen($render_path));

  }

  // 3. Otherwise get default RenderTemplate from theme.

  if (!is_array($template)) {

    $template = $split_render_templates['#DEFAULT'];

  }

  // --- set the link uris to the according template fields if they exist

  if(isset($template['nameAuthorPart']) && isset($template['nameAuthorPart']['#uri'])) {

    if ($nameLink) {

      $template['nameAuthorPart']['#uri'] = $nameLink;

    }

    else {

      unset($template['nameAuthorPart']['#uri']);

    }

  }

  if ($nameLink && isset($template['namePart']['#uri'])) {

    $template['namePart']['#uri'] = $nameLink;

  }

  else {

    unset($template['namePart']['#uri']);

  }

  if ($referenceLink && isset($template['referencePart']['#uri'])) {

    $template['referencePart']['#uri'] = $referenceLink;

  }

  else {

    unset($template['referencePart']['#uri']);

  }

  return $template;

}

/**

 * The part definitions define the specific parts of which a rendered taxon name plus additional information will consist.

 *

 * A full taxon name plus additional information can consist of the following elements:

 *

 *   - name: the taxon name inclugin rank nbut without author

 *   - authorTeam:  The authors of a reference, also used in taxon names

 *   - authors:  The authors of a reference, also used in taxon names

 *   - reference: the nomenclatural reference,

 *   - microreference:  Volume, page number etc.

 *   - status:  The nomenclatural status of a name

 *   - description: name descriptions like protologues etc ...

 *

 * These elements are combined in the part definitions array to from the specific parts to be rendered.

 * Usually the following parts are formed:

 *

 * The name "Lapsana communis L., Sp. Pl.: 811. 1753" shall be an example here:

 *  - namePart: the name and rank (in example: "Lapsana communis")

 *  - authorshipPart: the author (in example: "L.")

 *  - nameAuthorPart: the combination of name and author part (in example: "Lapsana communis L.").

 *     This is useful for zoological names where the authorshipPart belongs to the name and both should

 *     be combined when a link to the taxon is rendered.

 *  - referencePart: the nomencaltural reference (in example: "Sp. Pl. 1753")

 *  - microreferencePart: usually the page number (in example ": 811.")

 *  - statusPart: the nomenclatorical status

 *  - descriptionPart:

 *

 * Each set of parts is dedicated to render a specific TaxonName type, the type names are used as keys for the

 * specific parts part definitions:

 *

 *  - BotanicalName

 *  - ZoologicalName

 *  - #DEFAULT:  covers ViralNames and general NonViralNames

 *

 * An example:

 * @code

 * array(

 *    'ZoologicalName' => array(

 *        'namePart' => array('name' => TRUE),

 *        'referencePart' => array('authorTeam' => TRUE),

 *        'microreferencePart' => array('microreference' => TRUE),

 *        'statusPart' => array('status' => TRUE),

 *        'descriptionPart' => array('description' => TRUE),

 *    ),

 *    'BotanicalName' => array(

 *        'namePart' => array(

 *            'name' => TRUE,

 *            'authors' => TRUE,

 *        ),

 *        'referencePart' => array(

 *            'reference' => TRUE,

 *            'microreference' => TRUE,

 *        ),

 *        'statusPart' => array('status' => TRUE),

 *        'descriptionPart' => array('description' => TRUE),

 *    ),

 *  );

 * @endcode

 *

 * @param object $taxonNameType

 *    A cdm TaxonNameType entity

 *

 */

function get_partDefinition($taxonNameType) {

  static $default_part_definitions = null;

  if (!isset($default_part_definitions)) {

    $default_part_definitions= unserialize(CDM_PART_DEFINITIONS_DEFAULT);

  }

  static $part_definitions = null;

  if (!isset($part_definitions)) {

    $part_definitions = object_to_array(variable_get(CDM_PART_DEFINITIONS, $default_part_definitions));

  }

  $dtype = nameTypeToDTYPE($taxonNameType);

  if (array_key_exists($taxonNameType, $part_definitions)) {

    return $part_definitions[$taxonNameType];

  } else if (array_key_exists($dtype, $part_definitions)) {

    return $part_definitions[$dtype];

  } else {

    return $part_definitions['#DEFAULT']; // covers ViralNames and general NonViralNames

  }

}

/**

 * Renders the markup for a CDM TaxonName instance.

 *

 * The layout of the name representation is configured by the

 * part_definitions and render_templates (see get_partDefinition() and

 * get_nameRenderTemplate())

 *

 * @param $taxonName

 *    cdm TaxonName instance

 * @param $name_link

 *    URI to the taxon, @see path_to_taxon(), must be processed by url() before passing to this method

 * @param $reference_link

 *    URI to the reference, @see path_to_reference(), must be processed by url() before passing to this method

 * @param $show_annotations

 *    turns the display of annotations on

 * @param $is_type_designation

 *    To indicate that the supplied taxon name is a name type designation.

 * @param $skiptags

 *    an array of name elements tags like 'name', 'rank' to skip. The name part

 *          'authors' will not ber affected by this filter. This part is managed though the render template

 *          mechanism.

 * @param $is_invalid

 *   Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.

 *   This is useful when rendering taxon relation ships.

 *

 * @return string

 *  The markup for a taxon name.

 *

 */

function render_taxon_or_name($taxon_name_or_taxon_base, $name_link = NULL, $reference_link = NULL,

  $show_annotations = true, $is_type_designation = false, $skiptags = array(), $is_invalid = false) {

  $is_doubtful = false;

  if($taxon_name_or_taxon_base->class == 'Taxon' || $taxon_name_or_taxon_base->class == 'Synonym'){

    if(isset($taxon_name_or_taxon_base->name)){

      $taxonName = $taxon_name_or_taxon_base->name;

    } else {

      $taxonName = cdm_ws_get(CDM_WS_TAXON . '/$0/name', array($taxon_name_or_taxon_base->uuid));

    }

    $is_doubtful = $taxon_name_or_taxon_base->doubtful;

    // use the TaxonBase.tagged_title so we have the secRef

    $tagged_title = $taxon_name_or_taxon_base->taggedTitle;

  } else {

    // assuming this is a TaxonName

    $taxonName = $taxon_name_or_taxon_base;

    if(isset($taxonName->taggedFullTitle)){

      $tagged_title = $taxon_name_or_taxon_base->taggedFullTitle;

    } else {

      $tagged_title = $taxon_name_or_taxon_base->taggedName;

    }

  }

  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $name_link, $reference_link);

  $partDefinition = get_partDefinition($taxonName->nameType);

  // Apply definitions to template.

  foreach ($renderTemplate as $part => $uri) {

    if (isset($partDefinition[$part])) {

      $renderTemplate[$part] = $partDefinition[$part];

    }

    if (is_array($uri) && isset($uri['#uri'])) {

      $renderTemplate[$part]['#uri'] = $uri['#uri'];

    }

  }

  $secref_tagged_text = tagged_text_extract_reference_and_detail($tagged_title);

  // taxon names will have the nomenclatural reference in the tagged full title:

  $nomref_tagged_text = tagged_text_extract_reference($tagged_title);

  $nom_status_tagged_text = tagged_text_extract_nomstatus($tagged_title);

  $appended_phrase_tagged_text = array(); // this is filled later

  normalize_tagged_text($tagged_title);

  $is_valid_tagged_title =

    isset($tagged_title)

    && is_array($tagged_title)

    && isset($tagged_title[0]->text)

    && is_string($tagged_title[0]->text)

    && $tagged_title[0]->text != ''

    && isset($tagged_title[0]->type);

  $lastAuthorElementString = FALSE;

  $name_encasement = $is_invalid ? '"' : '';

  $doubtful_marker = $is_doubtful ? '? ' : ''; // 	  =  NARROW NO-BREAK SPACE

  $doubtful_marker_markup = '';

  if($doubtful_marker){

    $doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';

    if($tagged_title[0]->text == '?' ){

      // remove the first tagged text element

      unset($tagged_title[0]);

    }

  }

  // split off all appendedPhrase item  from the end of the array (usually there only should  be one)

  while($tagged_title[count($tagged_title)-1]->type == "appendedPhrase"){

    $appended_phrase_tagged_text[] = array_pop($tagged_title);

  }

  // Got to use second entry as first one, see ToDo comment below ...

  if ($is_valid_tagged_title) {

    $taggedName = $tagged_title;

    $hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);

    $hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);

    if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {

      // Find author and split off from name.

      // TODO expecting to find the author as the last element.

      /*

      if($taggedName[count($taggedName)- 1]->type == 'authors'){

        $authorTeam = $taggedName[count($taggedName)- 1]->text;

        unset($taggedName[count($taggedName)- 1]);

      }

      */

      // Remove all authors.

      $taggedNameNew = array();

      foreach ($taggedName as $element) {

        if ($element->type != 'authors') {

          $taggedNameNew[] = $element;

        }

        else {

          $lastAuthorElementString = $element->text;

        }

      }

      $taggedName = $taggedNameNew;

      unset($taggedNameNew);

    }

    $name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';

  }

  else {

    // use titleCache instead

    $name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';

  }

  if(isset($appended_phrase_tagged_text[0])){

    $name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';

  }

  // Fill name into $renderTemplate.

  array_setr('name', $name , $renderTemplate);

  // Fill with authorTeam.

  /*

  if($authorTeam){

    $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';

    array_setr('authorTeam', $authorTeamHtml, $renderTemplate);

  }

  */

  // Fill with reference.

  if (isset($renderTemplate['referencePart']) && !$is_type_designation) {

    $registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));

    $registration_markup = render_registrations($registrations);

    // default separator

    $separator = '';

    // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,

    // Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."

    if (isset($renderTemplate['referencePart']['reference'])) {

      $microreference = NULL;

      if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {

        $microreference = $taxonName->nomenclaturalMicroReference;

      }

      if(count($nomref_tagged_text) == 0 && isset($taxonName->nomenclaturalReference)){

        // TODO is this case still relevant? The tagged text should already contain all information!

        $citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);

        // Find preceding element of the reference.

        $precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);

        if (str_beginsWith($citation, ", in")) {

          $citation = substr($citation, 2);

          $separator = ' ';

        }

        elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {

          $separator = ', ';

        } else {

          $separator = ' ';

        }

        $referenceArray['#separator'] = $separator;

        $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;

      } else {

        // this ist the case for taxon names

        $referenceArray['#html'] = cdm_tagged_text_to_markup($nomref_tagged_text);

      }

      array_setr('reference', $referenceArray, $renderTemplate);

    }

    // If authors have been removed from the name part the last named authorteam

    // should be added to the reference citation, otherwise, keep the separator

    // out of the reference.

    if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {

      // If the nomenclaturalReference citation is not included in the

      // reference part but display of the microreference

      // is wanted, append the microreference to the authorTeam.

      $citation = '';

      if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {

        $separator = ": ";

        $citation = $taxonName->nomenclaturalMicroReference;

      }

      $referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';

      array_setr('authors', $referenceArray, $renderTemplate);

    }

  }

  $is_reference_year = false;

  if (isset($renderTemplate['referenceYearPart']['reference.year'])) {

    if(isset($taxonName->nomenclaturalReference->datePublished)){

      $referenceArray['#html'] = ' <span class="reference">' . timePeriodToString($taxonName->nomenclaturalReference->datePublished) . '</span>';

      array_setr('reference.year', $referenceArray, $renderTemplate);

      $is_reference_year = true;

    }

  }

  // Fill with status.

  if(isset($renderTemplate['statusPart']['status'])){

    if (isset($nom_status_tagged_text[0])) {

        $tt_to_markup_options = array('html' => false);

        foreach ($nom_status_tagged_text as &$tt){

         if($tt->type == 'nomStatus'&& isset($tt->entityReference)) {

           $nom_status = cdm_ws_get(CDM_WS_NOMENCLATURALSTATUS, array($tt->entityReference->uuid));

           $nom_status_fkey = nomenclatural_status_footnote_markup($nom_status);

           $tt->text .= $nom_status_fkey;

           $tt_to_markup_options['html'] = true;

         }

        }

        array_setr(

          'status',

          '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator'), 'span', $tt_to_markup_options) . '</span>',

          $renderTemplate);

    }

  }

  if (isset($renderTemplate['secReferencePart'])){

    if(isset($secref_tagged_text[1])){

      $post_separator_markup = $is_reference_year ? '.': '';

      if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type ==  'postSeparator')){

        $post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));

      };

      array_setr('secReference',

        $post_separator_markup

          . ' <span class="sec_reference">'

          . join('', cdm_tagged_text_values($secref_tagged_text))

          . '</span>', $renderTemplate);

    }

  }

  // Fill with protologues etc...

  $descriptionHtml = '';

  if (array_setr('description', TRUE, $renderTemplate)) {

    $descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);

    if($descriptions){

      foreach ($descriptions as $description) {

        if (!empty($description)) {

          foreach ($description->elements as $description_element) {

            $second_citation = '';

            if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {

              if(isset($description_element->feature) && $description_element->feature->uuid == UUID_ADDITIONAL_PUBLICATION){

                $prefix =  '& ';

              } else {

                $prefix = '';

              }

              $second_citation = ' [' . $prefix . $description_element->multilanguageText_L10n->text . '].';

            }

            $descriptionHtml .= $second_citation;

            $descriptionHtml .= cdm_description_element_media(

                $description_element,

                array(

                  'application/pdf',

                  'image/png',

                  'image/jpeg',

                  'image/gif',

                  'text/html',

                )

            );

          }

        }

      }

    }

    array_setr('description', $descriptionHtml, $renderTemplate);

  }

  // Render.

  $out = '';

  if(isset($_REQUEST['RENDER_PATH'])){

    // developer option to show the render path with each taxon name

    $out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';

  }

  $out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)

    . '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';

  foreach ($renderTemplate as $partName => $part) {

    $separator = '';

    $partHtml = '';

    $uri = FALSE;

    if (!is_array($part)) {

      continue;

    }

    if (isset($part['#uri']) && is_string($part['#uri'])) {

      $uri = $part['#uri'];

      unset($part['#uri']);

    }

    foreach ($part as $key => $content) {

      $html = '';

      if (is_array($content)) {

        $html = $content['#html'];

        if(isset($content['#separator'])) {

          $separator = $content['#separator'];

        }

      }

      elseif (is_string($content)) {

        $html = $content;

      }

      $partHtml .= '<span class="' . $key . '">' . $html . '</span>';

    }

    if ($uri) {

      // cannot use l() here since the #uri aleady should have been processed through uri() at this point

      $out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';

    }

    else {

      $out .= $separator . $partHtml;

    }

  }

  $out .= '</span>';

  if ($show_annotations) {

    // $out .= theme('cdm_entities_annotations_as_footnotekeys', $taxonName);

  }

  return $out;

}

/**

 * Composes information for a registration from a dto object.

 *

 * Registrations which are not yet published are suppressed.

 *

 * @param $registration_dto

 * @param $with_citation

 *   Whether to show the citation.

 *

 * @return array

 *    A drupal render array with the elements:

 *    - 'name'

 *    - 'name-relations'

 *    - 'specimen_type_designations'

 *    - 'name_type_designations'

 *    - 'citation'

 *    - 'registration_date_and_institute'

 * @ingroup compose

 */

function compose_registration_dto_full($registration_dto, $with_citation = true)

{

  $render_array = array(

    '#prefix' => '<div class="registration">',

    '#suffix' => '</div>'

  );

  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){

    return $render_array;

  }

  $render_array['sub_headline'] = markup_to_render_array(join(", ", registration_types($registration_dto)),-10, '<h3 class="registration_type">' . t('Event: '), '</h3>' );

  $render_array['nomenclatural_act'] = array(

    '#weight' => 0,

    '#prefix' => '<div class="nomenclatural_act">',

    '#suffix' => '</div>'

  );

  // name

  $name_relations = null;

  if($registration_dto->nameRef){

    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);

    cdm_load_tagged_full_title($name);

    $render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);

    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));

    // need to create the name relationships later, so that the foot notes are in correct order, see section // name relations

  } else {

    // in this case the registration must have a

    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);

    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);

  }

  // typedesignation in detail

  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {

    $field_unit_uuids = array();

    $specimen_type_designation_refs = array();

    $name_type_designation_refs = array();

    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {

      $tokens = explode("#", $workingset_ref);

      $types_in_fieldunit = get_object_vars($obj); // convert into associative array

      if ($tokens[0] == 'NameTypeDesignation') {

        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {

          if(!isset($name_type_designation_refs[$type_status])){

            $name_type_designation_refs[$type_status]  = $entity_reference_list;

          } else {

            array_push($name_type_designation_refs[$type_status] ,$entity_reference_list);

          }

        }

      } else if ($tokens[0] == 'FieldUnit'){

        $field_unit_uuids[] = $tokens[1];

        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {

          if(!isset($specimen_type_designation_refs[$type_status])){

            $specimen_type_designation_refs[$type_status] =  $entity_reference_list;

          } else {

            array_push($specimen_type_designation_refs[$type_status], $entity_reference_list);

          }

        }

      } else {

        drupal_set_message("Unimplemented type: " . $tokens[0], 'error');

      }

    }

    // type designations which are in this nomenclatural act.

    if (count($name_type_designation_refs) > 0) {

      $render_array['nomenclatural_act']['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);

      $render_array['nomenclatural_act']['name_type_designations']['#prefix'] = '<p class="name_type_designations">';

      $render_array['nomenclatural_act']['name_type_designations']['#suffix'] = '</p>';

      $render_array['nomenclatural_act']['name_type_designations']['#weight'] = 20;

    }

    if (count($field_unit_uuids) > 0) {

      $specimen_type_designations_array = compose_specimen_type_designations($specimen_type_designation_refs, true);

      $render_array['nomenclatural_act']['specimen_type_designations'] = $specimen_type_designations_array['type_designations'];

      $render_array['map'] = $specimen_type_designations_array['map'];

      $render_array['map']['#weight'] = $render_array['nomenclatural_act']['#weight'] + 20;

    }

  }

  // name relations

  if($name_relations){

    $render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);

    $render_array['nomenclatural_act']['name_relations']['#weight'] = 10;

  }

  // citation

  if ($with_citation) {

    $render_array['citation'] = markup_to_render_array(

      "<div class=\"citation nomenclatural_act_citation" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"

      . "<span class=\"label\">published in: </span>"

      . $registration_dto->bibliographicInRefCitationString

      . l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($registration_dto->citationUuid), array('html' => true))

      . "</div>",

      $render_array['nomenclatural_act']['#weight'] + 10 );

  }

  $render_array['nomenclatural_act']['footnotes'] = markup_to_render_array(render_cdm_footnotes(),

    100

  );

  // registration date and office

  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);

  if($registration_date_insitute_markup){

    $render_array['registration_date_and_institute'] = markup_to_render_array(

      $registration_date_insitute_markup . '</p>',

      100);

  }

  return $render_array;

}

/**

 * Composes a compact representation for a registrationDTO object

 *

 * Registrations which are not yet published are suppressed.

 *

 * @param $registration_dto

 * @param $style string

 *   The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary

 *   - 'citation': Similar to the arrearance of nomenclatural acts in print media

 *   - 'list-item' : style suitable for result lists etc

 *

 * @return array

 *    A drupal render array with the elements:

 *    - 'registration-metadata' when $style == 'list-item'

 *    - 'summary'

 * @ingroup compose

 */

function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')

{

  $render_array = array();

  $media_link_map = array();

  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){

    return $render_array;

  }

  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');

  $itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));

  $tagged_text_options = array();

  if(isset($registration_dto->nameRef)){

    $tagged_text_options[] = array(

      'filter-type' => 'name',

      'prefix' => '<span class="registered_name">',

      'suffix' => '</span>',

    );

  } else {

    $tagged_text_options[] = array(

      'filter-type' => 'name',

      'prefix' => '<span class="referenced_typified_name">',

      'suffix' => '</span>',

    );

  }

  cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);

  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);

  foreach ($taggged_text_expanded  as $tagged_text){

    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {

      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));

      if(isset($mediaDTOs[0]->uri)){

        $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';

        $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);

        $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);

      }

    }

  }

  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);

  foreach($media_link_map as $media_url_key => $link){

    $registation_markup = str_replace($media_url_key, $link, $registation_markup);

  }

  if($style == 'citation') {

    $registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;

  } else {

    $render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);

  }

  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);

  return $render_array;

}

/**

 * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.

 *

 * @param $registration_dto

 * @return string

 *    The markup or an empty string

 */

function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {

  $registration_date_institute_markup = '';

  if ($registration_dto->registrationDate) {

    $date_string = format_datetime($registration_dto->registrationDate);

    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {

      $registration_date_institute_markup =

        t("Registration on @date in @institution", array(

          '@date' => $date_string,

          '@institution' => $registration_dto->institutionTitleCache,

        ));

    } else {

      $registration_date_institute_markup =

        t("Registration on @date", array(

          '@date' => $date_string

        ));

    }

    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';

  }

  return $registration_date_institute_markup;

}

/**

 * @param $registrations

 * @return string

 */

function render_registrations($registrations)

{

  $registration_markup = '';

  $registration_markup_array = array();

  if ($registrations) {

    foreach ($registrations as $reg) {

      $registration_markup_array[] = render_registration($reg);

    }

    $registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')

      . join(', ', $registration_markup_array);

  }

  return $registration_markup;

}

/**

 * Renders a registration

 *

 * TODO replace by compose_registration_dto_compact

 * @param $registration

 */

function render_registration($registration){

  $markup = '';

  if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){

    $office_class_attribute = '';

    if(isset($registration->institution->titleCache)){

      $office_class_attribute = registration_intitute_class_attribute($registration);

    }

    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '

      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)

      . '</span>';

  }

  return $markup;

}

/**

 * @param $registration

 * @return string

 */

function registration_intitute_class_attribute($registration_dto)

{

  if(isset($registration_dto->institutionTitleCache)){

    $institutionTitleCache = $registration_dto->institutionTitleCache;

  } else {

    // fall back option to also support cdm entities

    $institutionTitleCache = @$registration_dto->institution->titleCache;

  }

  return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';

}

/**

 * Renders and array of CDM TypeDesignations

 *

 *  - NameTypeDesignation

 *  - SpecimenTypeDesignation

 *  - TextualTypeDesignation

 *

 * @param object $type_designations an array of cdm TypeDesignation entities

 *  to render

 * @param string $enclosing_tag the tag element type to enclose the whole list

 *  of type designation with. By default this DOM element is <ul>

 * @param string $element_tag the tag element type to be used for each

 *  type designation item.

 * @param bool $link_to_specimen_page whether a specimen in type designation element

 *  should be a link or not.

 *

 * @return string The markup.

 *

 * @InGroup Render

 */

function render_type_designations($type_designations, $enclosing_tag = 'ul', $element_tag =  'li', $link_to_specimen_page = true) {

  // need to add element to render path since type designations

  // need other name render template

  RenderHints::pushToRenderStack('typedesignations');

  $out = '<' . $enclosing_tag .' class="typeDesignations">';

  $specimen_type_designations = array();

  $name_type_designations = array();

  $textual_type_designations = array();

  $separator = ',';

  foreach ($type_designations as $type_designation) {

    switch ($type_designation->class) {

      case 'SpecimenTypeDesignation':

        $specimen_type_designations[] = $type_designation;

        break;

      case 'NameTypeDesignation':

        $name_type_designations[] = $type_designation;

        break;

      case 'TextualTypeDesignation':

        $textual_type_designations[] = $type_designation;

        break;

      default:  throw new Exception('Unknown type designation class: ' . $type_designation->class);

    }

  }

  // NameTypeDesignation ..................................

  if(!empty($name_type_designations)){

    usort($name_type_designations, "compare_type_designations_by_status");

    foreach($name_type_designations as $name_type_designation){

      if ($name_type_designation->notDesignated) {

        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation)  . ': '

          . t('not designated') . '</'. $element_tag .'>';

      }

      elseif (isset($name_type_designation->typeName)) {

        $link_to_name_page = url(path_to_name($name_type_designation->typeName->uuid));

        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation) ;

        if (!empty($name_type_designation->citation)) {

          $out .= type_designation_citation_layout($name_type_designation, $separator); // TODO type_designation_citation_layout() needs most probably to be replaced

        }

        $referenceUri = '';

        if (isset($name_type_designation->typeName->nomenclaturalReference)) {

          $referenceUri = url(path_to_reference($name_type_designation->typeName->nomenclaturalReference->uuid));

        }

        $out .= ': ' . render_taxon_or_name($name_type_designation->typeName, $link_to_name_page, $referenceUri, TRUE, TRUE);

      }

      $annotations_and_sources = handle_annotations_and_sources(

        $name_type_designation,

        typedesignations_annotations_and_sources_config(),

        '',

        RenderHints::getFootnoteListKey());

      $out .= $annotations_and_sources['foot_note_keys'];

    }

  } // END NameTypeDesignation

  // SpecimenTypeDesignation ...................................

  if (!empty($specimen_type_designations)) {

    usort($specimen_type_designations, "compare_specimen_type_designation");

    foreach ($specimen_type_designations as $specimen_type_designation) {

      $type_citation_markup = '';

      if (!empty($specimen_type_designation->citation)) {

        $citation_footnote_str = cdm_reference_markup($specimen_type_designation->citation, null, false, true);

        $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $specimen_type_designation->citation->uuid);

        if (!empty($author_team->titleCache)) {

          $year = @timePeriodToString($specimen_type_designation->citation->datePublished, true, 'YYYY');

          $authorteam_str = $author_team->titleCache . ($year ? ' ' : '') . $year;

          if ($authorteam_str == $specimen_type_designation->citation->titleCache) {

            $citation_footnote_str = '';

          }

        } else {

          $authorteam_str = $citation_footnote_str;

          // no need for a footnote in case in case it is used as replacement for missing author teams

          $citation_footnote_str = '';

        }

        // for being registered a typedesignation MUST HAVE a citation, so it is save to handle the

        // Registration output in if condition checking if the citation is present

        $registration_markup = render_registrations($specimen_type_designation->registrations);

        $citation_footnote_str .= ($citation_footnote_str ? ' ' : '') . $registration_markup;

        $footnote_key_markup = '';

        if ($citation_footnote_str) {

          // footnotes should be rendered in the parent element so we

          // are relying on the FootnoteListKey set there

          $_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $citation_footnote_str);

          $footnote_key_markup = theme('cdm_footnote_key', array(

            'footnoteKey' => $_fkey2,

            'separator' => $separator,

            'highlightable' => TRUE,

            'separator_off' => TRUE,

          ));

        }

        $type_citation_markup .= '&nbsp;(' . t('designated by') . '&nbsp;<span class="typeReference">' . $authorteam_str . '</span>';

        if (!empty($specimen_type_designation->citationMicroReference)) {

          $type_citation_markup .= ': ' . trim($specimen_type_designation->citationMicroReference);

        }

        $type_citation_markup .= $footnote_key_markup . ')';

      }

      $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($specimen_type_designation) . '">';

      $out .= type_designation_status_label_markup($specimen_type_designation) . $type_citation_markup;

      $derivedUnitFacadeInstance = null;

      if (isset($specimen_type_designation->typeSpecimen)) {

        $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $specimen_type_designation->typeSpecimen->uuid);

      }

      if (!empty($derivedUnitFacadeInstance->titleCache)) {

        $specimen_markup = $derivedUnitFacadeInstance->titleCache;

        if($link_to_specimen_page && isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){

          $specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($specimen_type_designation->typeSpecimen->uuid)), $specimen_markup);

        }

        $annotations_and_sources = handle_annotations_and_sources(

          $derivedUnitFacadeInstance,

          typedesignations_annotations_and_sources_config(),

          '',

          RenderHints::getFootnoteListKey()

        );

        $out .= ': <span class="' . html_class_attribute_ref($specimen_type_designation->typeSpecimen) . '">'

          . $specimen_markup

          . '</span>'; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));

        if(!empty($derivedUnitFacadeInstance->preferredStableUri)){

          $out .= ' ' . l($derivedUnitFacadeInstance->preferredStableUri, $derivedUnitFacadeInstance->preferredStableUri, array('absolute' => true));

        }

        $out .= $annotations_and_sources['foot_note_keys'];

      }

      $out .= '</'. $element_tag .'>';

    }

  } // END Specimen type designations

  // TextualTypeDesignation .........................

  usort($textual_type_designations, 'compare_textual_type_designation');

  if(!empty($textual_type_designations)) {

    foreach ($textual_type_designations as $textual_type_designation) {

      $annotations_and_sources = handle_annotations_and_sources(

        $textual_type_designation,

        array(

          'sources_as_content' => false, // as footnotes

          'link_to_name_used_in_source' => false,

          'link_to_reference' => true,

          'add_footnote_keys' => true,

          'bibliography_aware' => false

        ),

        '',

        RenderHints::getFootnoteListKey() // passing a defined key to avoid a separate annotation footnote key see https://dev.e-taxonomy.eu/redmine/issues/8543

      );

      $encasement =  $textual_type_designation->verbatim ? '"' : '';

      $out .= '<' . $element_tag . ' class="' . html_class_attribute_ref($textual_type_designation) . '">' . type_designation_status_label_markup(null)

        . ': ' .  $encasement . trim($textual_type_designation->text_L10n->text) . $encasement .  $annotations_and_sources['foot_note_keys'] .'</' . $element_tag . '>';

//      if(is_array( $annotations_and_sources['source_references'])){

//        $citation_markup = join(', ', $annotations_and_sources['source_references']);

//      }

//      $out .= $citation_markup;

    }

  }

  // Footnotes for citations, collection acronyms.

  // footnotes should be rendered in the parent element so we

  // are relying on the FootnoteListKey set there

  $_fkey = FootnoteManager::addNewFootnote(

    RenderHints::getFootnoteListKey(),

    (isset($derivedUnitFacadeInstance->collection->titleCache) ? $derivedUnitFacadeInstance->collection->titleCache : FALSE)

  );

  $out .= theme('cdm_footnote_key', array('footnoteKey' => $_fkey, 'separator' => $separator));

  $out .= '</' . $enclosing_tag .'>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.

 *

 * @param $taxon_name_uuid

 * @param $show_specimen_details

 * @return array

 *    A drupal render array with the following elements:

 *    - 'type_designations'

 *    - 'map'

 *    - 'specimens'

 *

 * @ingroup compose

 */

function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)

{

  $render_array = array(

    'type_designations' => array(),

    'map' => array(),

    );

  $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);

  if ($type_designations) {

    usort($type_designations, 'compare_specimen_type_designation');

    $render_array['type_designations'] = markup_to_render_array(

      render_type_designations($type_designations, 'div', 'div')

    );

    $render_array['map'] = compose_type_designations_map($type_designations);

  }

  return $render_array;

}

/**

 * Composes the TypedEntityReference to name type designations passed as associatve array.

 *

 * @param $type_entity_refs_by_status array

 *   an associative array of name type type => TypedEntityReference for name type designations as

 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager

 *

 * @ingroup compose

 */

function compose_name_type_designations($type_entity_refs_by_status){

  $render_array = array();

  $preferredStableUri = '';

  foreach($type_entity_refs_by_status as $type_status => $name_type_entityRefs){

    foreach ($name_type_entityRefs as $name_type_entity_ref){

      $type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type_entity_ref->uuid, 'preferredUri'));

      $footnote_keys = '';

      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){

        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;

      }

      // annotations and sources for the $derived_unit_facade_dto

      $annotations_and_sources = handle_annotations_and_sources(

        $name_type_entity_ref,

        typedesignations_annotations_and_sources_config(),

        '',

        RenderHints::getFootnoteListKey()

      );

      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type_entity_ref)  . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "

        . $name_type_entity_ref->label

        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')

        . $annotations_and_sources['foot_note_keys']

        . '</div>');

      }

  }

  return $render_array;

}

/**

 * Composes the specimen type designations with map from the the $type_entity_refs

 *

 * @param $type_entity_refs array

 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as

 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager

 *

 * @param $show_media_specimen

 * @return array

 *    A drupal render array with the following elements:

 *    - 'type_designations'

 *    - 'map'

 *

 * @ingroup compose

 *

 */

function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){

  $render_array = array();

  $type_designation_list = array();

  uksort($type_entity_refs, "compare_type_designation_status_labels");

  foreach($type_entity_refs as $type_status => $type_designation_entity_refs){

    foreach($type_designation_entity_refs as $type_designation_entity_ref){

      $type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($type_designation_entity_ref->uuid));

      $type_designation_list[] = $type_designation; // collect for the map

      $derived_unit_facade_dto = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);

      // the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately

      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));

      $preferredStableUri = '';

      $citation_markup = '';

      $media = '';

      // annotations and sources for the $derived_unit_facade_dto

      $annotations_and_sources = handle_annotations_and_sources(

        $derived_unit_facade_dto,

        typedesignations_annotations_and_sources_config(),

        '',

        RenderHints::getFootnoteListKey()

      );

      $source_citations = $annotations_and_sources['source_references'];

      $foot_note_keys = $annotations_and_sources['foot_note_keys'];

      // preferredStableUri

      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){

        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;

      }

      if($show_media_specimen && $mediaSpecimen){

        // compose output

        // mediaURI

        if(isset($mediaSpecimen->representations[0])) {

          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);

          $captionElements = array(

            '#uri' => t('open media'),

            'elements' => array('-none-'),

            'sources_as_content' => true

          );

          $media = compose_cdm_media_gallerie(array(

            'mediaList' => array($mediaSpecimen),

            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $type_designation_entity_ref->uuid,

            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],

            'cols' => $gallery_settings['cdm_dataportal_media_cols'],

            'captionElements' => $captionElements,

          ));

        }

        // citation and detail for the media specimen

        $annotations_and_sources = handle_annotations_and_sources(

          $mediaSpecimen,

          typedesignations_annotations_and_sources_config(),

          '',

          null

        );

        if(is_array( $annotations_and_sources['source_references'])){

          $source_citations = array_merge($source_citations, $annotations_and_sources['source_references']);

        }

        if($annotations_and_sources['foot_note_keys']){

          $foot_note_keys .= ', ' . $annotations_and_sources['foot_note_keys'];

        }

      }

      $citation_markup = join(', ', $source_citations);

      $specimen_markup = $derived_unit_facade_dto->titleCache;

      if(isset($derived_unit_facade_dto->specimenLabel) && $derived_unit_facade_dto->specimenLabel){

        $specimen_markup = str_replace(

          $derived_unit_facade_dto->specimenLabel,

          l($derived_unit_facade_dto->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup);

      }

      $type_designation_render_array = markup_to_render_array(

        '<div class="type_designation_entity_ref ' . html_class_attribute_ref($type_designation_entity_ref)  . '">

          <span class="type-status">' . ucfirst($type_status) . "</span>: "

        . $specimen_markup . $foot_note_keys

        . ($citation_markup ? ' '. $citation_markup : '')

        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')

        . $media

        . '</div>');

      $render_array['type_designations'][] = $type_designation_render_array;

    }

  }

  if(count($type_designation_list) > 0 ){

    $render_array['map'] = compose_type_designations_map($type_designation_list);

  } else {

    $render_array['map'] = array();

  }

  return $render_array;

}

/**

 * Provides the default configuration for typedesignations which

 * are passed to the handle_annotations_and_sources()

 * function:

 * - 'sources_as_content' => TRUE,

 * - 'link_to_name_used_in_source' => FALSE,

 * - 'link_to_reference' => TRUE,

 * - 'add_footnote_keys' => FALSE,

 * - 'bibliography_aware' => FALSE

 *

 * @return array

 */

function typedesignations_annotations_and_sources_config() {

  static $annotations_and_sources_config = [

    'sources_as_content' => TRUE,

    'link_to_name_used_in_source' => FALSE,

    'link_to_reference' => TRUE,

    'add_footnote_keys' => FALSE,

    'bibliography_aware' => FALSE

  ];

  return $annotations_and_sources_config;

}

/**

 * @param $name_rel

 * @param $current_name_uuid

 * @param $current_taxon_uuid

 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!

 * @param $show_name_cache_only

 *    The nameCache will be shown instead of the titleCache if this parameter is true.

 * @return null|string

 *    The markup or null

 */

function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){

  $relationship_markup = null;

  $current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;

  if($current_name_is_toName){

    $name = $name_rel->fromName;

  } else {

    $name = $name_rel->toName;

  }

  cdm_load_tagged_full_title($name);

  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';

  if(!$show_name_cache_only){

    $relationship_markup = render_taxon_or_name($name,

      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))

    );

  } else {

    $relationship_markup = l(

      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',

      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),

      array('html' => true)

    );

  }

  return $relationship_markup;

}

/**

 * Composes an inline representation of selected name relationships

 *

 * The output of this function will be usually appended to taxon name representations.

 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT

 *

 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as

 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names

 * are ordered alphabetically.

 *

 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'

 *

 * Related issues:

 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"

 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"

 *   - https://dev.e-taxonomy.eu/redmine/issues/5857

 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"

 *

 * @param $name_relations

 *    The list of CDM NameRelationsips

 * @param $current_name_uuid

 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when

 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.

 * @param $suppress_if_current_name_is_source

 *    The display of the relation will be

 *    suppressed is the current name is on the source of the relation edge.

 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is

 *    an inverse relation. For this relation type the toName is taken in to account.

 * @param $current_taxon_uuid

 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()

 * @return array

 *    A drupal render array

 *

 * @ingroup Compose

 */

function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {

  RenderHints::pushToRenderStack('homonym');

  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT

  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));

  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());

  foreach ($selected_name_rel_uuids as $uuid){

    $name_rel_type_filter['direct'][$uuid] = $uuid;

    if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){

      $name_rel_type_filter['inverse'][$uuid] = $uuid;

    }

  }

  $list_prefix = '<span class="name_relationships">[';

  $list_suffix = ']</span>';

  $item_prefix = '<span class="item">';

  $item_suffix = '</span> ';

  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);

  // remove the glue space from the last item element which has been added by the $item_suffix = '</span> '

  $items_ctn = count($render_array['list']['items']);

  if($items_ctn){

    $render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';

  }

  RenderHints::popFromRenderStack();

  return $render_array;

}

/**

 * Composes an list representation of the name relationships.

 *

 * The output of this function will be usually appended to taxon name representations.

 *

 * Related issues:

 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"

 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"

 *   - https://dev.e-taxonomy.eu/redmine/issues/5857

 *

 * @param $name_relations

 *    The list of CDM NameRelationsips

 * @param $current_name_uuid

 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when

 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.

 * @param $current_taxon_uuid

 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()

 * @return array

 *    A drupal render array

 *

 * @ingroup Compose

 */

function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {

  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));

  $key = 'name_relationships';

  RenderHints::pushToRenderStack($key);

  if(!RenderHints::getFootnoteListKey()){

    RenderHints::setFootnoteListKey($key);

  }

  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT

  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));

  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());

  foreach ($selected_name_rel_uuids as $uuid){

    $name_rel_type_filter['direct'][$uuid] = $uuid;

    $name_rel_type_filter['inverse'][$uuid] = $uuid;

  }

  $list_prefix = '<div class="relationships_list name_relationships">';

  $list_suffix = '</div>';

  $item_prefix = '<div class="item">';

  $item_suffix = '</div>';

  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);

  RenderHints::popFromRenderStack();

  if(RenderHints::getFootnoteListKey() == $key) {

    $render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));

    RenderHints::clearFootnoteListKey();

  }

  return $render_array;

}

/**

 * @param $name_relations

 * @param $name_rel_type_filter

 *   Associative array with two keys:

 *   - 'direct': the relationship type uuids for the direct direction of the relation edge to be included

 *   - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included

 * @param $current_name_uuid

 * @param $current_taxon_uuid

 * @param $list_prefix

 * @param $list_suffix

 * @param $item_prefix

 * @param $item_suffix

 * @return array

 *

 * @ingroup Compose

 */

function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,

                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)

{

  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,

    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,

    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,

    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,

    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);

  $render_array = array(

    'list' => array(

      '#prefix' => $list_prefix,

      '#suffix' => $list_suffix,

      'items' => array()

    ),

    'footnotes' => array()

  );

  if ($name_relations) {

    // remove all relations which are not selected in the settings and

    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs

    // for special handling

    $filtered_name_rels = array();

    $non_nec_name_rels = array();

    $orthographic_variants = array();

    foreach ($name_relations as $name_rel) {

      $rel_type_uuid = $name_rel->type->uuid;

      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;

      if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])

        ||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {

        if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (

            $current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR

            || $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR

          )

        ){

          $non_nec_name_rels[] = $name_rel;

        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {

          $orthographic_variants[] = $name_rel;

        } else {

          $filtered_name_rels[] = $name_rel;

        }

      }

    }

    $name_relations = $filtered_name_rels;

    usort($name_relations, 'compare_name_relations_by_term_order_index');

    // compose

    foreach ($name_relations as $name_rel) {

      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;

      $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);

      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);

      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);

      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);

      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';

      $relationship_markup = $symbol_markup . $relationship_markup;

      if ($relationship_markup) {

        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,

          null,

          $item_prefix,

          $item_suffix);

      }

    }

    // name relationships to be displayed as non nec

    if (count($non_nec_name_rels) > 0) {

      $non_nec_markup = '';

      foreach ($non_nec_name_rels as $name_rel) {

        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;

        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);

        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);

        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);

        $symbol = $non_nec_markup ? ' nec ' : 'non';

        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';

        $non_nec_markup .= $symbol_markup . $relationship_markup;

      }

      if ($non_nec_markup) {

        $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,

          null,

          $item_prefix,

          $item_suffix);

      }

    }