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.

 *

 *

 *

 * 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.

 *

 *   @see RenderHints::getRenderPath()

 * @param string $nameLink

 * @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

 */

  if($split_render_templates == NULL) {

    // 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

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

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

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

        break;

      }

    }

    // shorten by one element

  if (!is_array($template)) {

  // --- 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

 *

 *    A cdm TaxonNameType entity

 *

function get_partDefinition($taxonNameType) {

  static $part_definitions = null;

  if (!isset($part_definitions)) {

    return $part_definitions[$taxonNameType];

    return $part_definitions[$dtype];

    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())

 *

 *    A cdm TaxonBase or TaxonName entity

 *    by url() before passing to this method

 * @param $reference_link

 *    URI to the reference, the path provided by path_to_reference() must be

 *    processed by url() before passing to this method

 *    Enable the display of footnotes for annotations on the taxon and name

 *    (default: true)

 * @param array $skip_render_template_parts

 *    The render template elements matching these part names will bes skipped.

 *    This parameter should only be used in rare cases like for suppressing

 *    the sec reference of synonyms. Normally the configuration of the

 *    name appearance should only be done via the render templates themselves. (default: [])

 * @return string

 *  The markup for a taxon name.

 */

    $tagged_title = $taxon_name_or_taxon_base->taggedTitle;

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

    } else {

      $tagged_title = $taxon_name_or_taxon_base->taggedName;

    }

  // 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'];

    }

  }

    unset($renderTemplate[$part]);

  }

  // 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);

    && is_array($tagged_title)

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

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

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

  if($doubtful_marker){

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

      // 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)

    $appended_phrase_tagged_text[] = array_pop($tagged_title);

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

  else {

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

  // Fill name into $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) {

    $separator = '';

      $microreference = $taxon_name->nomenclaturalSource->citationMicroReference;

        // drupal_set_message("reference/$0/nomenclaturalCitation' must no longer be used (type: "

        //  . $taxon_name_or_taxon_base->class . (isset($taxon_name_or_taxon_base->type) ? " - " +$taxon_name_or_taxon_base->type : ""  . ")"), "error");

        $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;

      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

      $citation = '';

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

        $separator = ": ";

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

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

    }

  }

  $is_reference_year = false;

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

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

      $is_reference_year = true;

    }

  }

        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));

         }

        }

        array_setr(

          'status',

          $renderTemplate);

  }

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

    }

  }

  // Fill with protologues etc...

    if($external_links){

      foreach ($external_links as $link) {

        if (!empty($link->uri)) {

      }

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

    $additional_pub_markup = '';

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

      if($descriptions) {

        foreach ($descriptions as $description) {

          if (!empty($description)) {

            $additional_citations = [];

            $additional_data = [];

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

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

                $annotations_and_sources = handle_annotations_and_sources($description_element);

                // synonymy_annotations_and_source_config() has 'sources_as_content' => FALSE, so no need to handle inline sources here

                  $description_element,

                  [

                    'application/pdf',

                    'image/png',

                    'image/jpeg',

                    'image/gif',

                    'text/html',

                  ]

                );

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

              }

            }

            // merge

            $additional_citations = array_merge($additional_citations, $additional_data);

            $additional_pub_markup .= join(',', $additional_citations);

          }

        }

      }

      if($additional_pub_markup){

  // Render.

  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)

  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']);

    }

      if (is_array($content)) {

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

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

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

        }

      }

      elseif (is_string($content)) {

        $html = $content;

      }

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

      }

    if ($uri) {

    }

    else {

      $out .= $separator . $partHtml;

    }

  }

  $out .= '</span>';

  $annotations_and_sources = new AnnotationsAndSources();

  if($nom_status_fkey){

    // the nomenclatural status footnote key refers to the source citation

    $annotations_and_sources->addFootNoteKey($nom_status_fkey);

  }

  if ($show_taxon_name_annotations) {

        null, null, $annotations_and_sources);

      null, null, $annotations_and_sources);

}

/**

 *

 * 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-relations'

 *    - 'specimen_type_designations'

 *    - 'name_type_designations'

 */

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

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

  );

    return $render_array;

  }

    '#weight' => 0,

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

  );

  // Nomenclatural act block element

  $last_footnote_listkey = RenderHints::setFootnoteListKey("nomenclatural_act");

    // in this case the registration must have a

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

    $specimen_type_designation_refs = array();

    $name_type_designation_refs = array();

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

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

            $name_type_designation_refs[$type_status]  = $entity_reference_list;

          } else {