/modules/cdm_dataportal/includes/name.inc - Annotate - EDIT - EDIT Project Management

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cdm-dataportal/modules/cdm_dataportal/includes/name.inc @ 0e617798

-fd6da0b
+<?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 $renderPath.
+ *
-            a565e612
+ * The render templates arrays contains one or more name render templates to be used within the page elements identified the the
-fd6da0b
+ * renderPath. The renderPath is the key of the subelements whereas the value is the name render template.
+ *
-            a565e612
+ * The render paths used for a cdm_dataportal page can be visualized by supplying the HTTP query parameter RENDER_PATH=1.
+ *
  * It will be tried to find  the best matching default RenderTemplate by stripping the dot separated render path
  * element by element. If no matching template is found the DEFAULT will be used:
+ *
  * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
  * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
  * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
-fd6da0b
+            Andreas Kohlbecker
  * A single render template can be used for multiple render paths. In this case the according key of the render templates
  * array element should be the list of these render paths concatenated by ONLY a comma character without any whitespace.
+ *
  * A render template is an associative array. The keys of this array are referring to the keys as defined in the part
  * definitions array.
  * @see get_partDefinition($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.
+ *
-            a565e612
+ * @param string $render_path
-fd6da0b
+ *   The render path can consist of multiple dot separated elements
  *   @see RenderHints::getRenderPath()
  * @param string $nameLink
-aa88d6
+ *   The link path or URL to be used for name parts if a link is forseen in the template
-fd6da0b
+ *   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 $renderPath.
  * @return array
  *   An associative array, the render template
  */
-            a565e612
+function get_nameRenderTemplate($render_path, $nameLink = NULL, $referenceLink = NULL) {
-fd6da0b
+            Andreas Kohlbecker
   static $default_render_templates = NULL;
-f4f6f7
+  static $split_render_templates = NULL;
-fd6da0b
+  if (!isset($default_render_templates)) {
     $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);
+  }
-f4f6f7
+  if($split_render_templates == NULL) {
-fd6da0b
+    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
     // needs to be converted to an array
-            db725031
+    $render_templates = (object_to_array($render_templates));
-f4f6f7
+            Andreas Kohlbecker
     // 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] = $template;
+      }
+    }
-fd6da0b
+            Andreas Kohlbecker
   // get the base element of the renderPath
-            a565e612
+  if (($separatorPos = strpos($render_path, '.')) > 0) {
     $renderPath_base = substr($render_path, 0, $separatorPos);
-fd6da0b
+  } else {
-            a565e612
+    $renderPath_base = $render_path;
-fd6da0b
+            Andreas Kohlbecker
-f4f6f7
+  $template = NULL;
-fd6da0b
+  // 1. try to find a template using the render path base element
-f4f6f7
+  if(array_key_exists($renderPath_base, $split_render_templates)){
     $template = (array)$split_render_templates[$renderPath_base];
-fd6da0b
+            Andreas Kohlbecker
-            a565e612
+  // 2. Find best matching default RenderTemplate
-fd6da0b
+  // by stripping the dot separated render path element by element
-            a565e612
+  // if no matching template is found the DEFAULT will be used.
   while (!is_array($template) && strlen($render_path) > 0) {
-f4f6f7
+    foreach ($split_render_templates as $path => $t) {
-            a565e612
+      if ($path == $render_path) {
-fd6da0b
+        $template = $t;
         break;
+      }
+    }
     // shorten by one element
-            a565e612
+    $render_path = substr($render_path, strrpos($render_path, '.') + 1, strlen($render_path));
-fd6da0b
+            Andreas Kohlbecker
-f4f6f7
+            Andreas Kohlbecker
-fd6da0b
+  // 3. Otherwise get default RenderTemplate from theme.
   if (!is_array($template)) {
-f4f6f7
+    $template = $split_render_templates['#DEFAULT'];
-fd6da0b
+            Andreas Kohlbecker
   // --- set the link uris to the according template fields if they exist
   if(isset($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
+ *
-a0c8c
+ * @param object $taxonNameType
  *    A cdm TaxonNameType entity
+ *
-fd6da0b
+ */
 function get_partDefinition($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)) {
-            db725031
+    $part_definitions = object_to_array(variable_get(CDM_PART_DEFINITIONS, $default_part_definitions));
-fd6da0b
+            Andreas Kohlbecker
-            c2545e1c
+  $dtype = nameTypeToDTYPE($taxonNameType);
-fd6da0b
+  if (array_key_exists($taxonNameType, $part_definitions)) {
     return $part_definitions[$taxonNameType];
-            c2545e1c
+  } else if (array_key_exists($dtype, $part_definitions)) {
     return $part_definitions[$dtype];
-fd6da0b
+  } 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
-f8c26
+ *    cdm TaxonName instance
-bfe15b
+ * @param $name_link
-fd6da0b
+ *    URI to the taxon, @see path_to_taxon(), must be processed by url() before passing to this method
-bfe15b
+ * @param $reference_link
-fd6da0b
+ *    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.
-            c35bab7f
+ * @param $is_invalid
  *   Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.
  *   This is useful when rendering taxon relation ships.
-fd6da0b
+            Andreas Kohlbecker
  * @return string
  *  The markup for a taxon name.
+ *
  */
-bfe15b
+function render_taxon_or_name($taxon_name_or_taxon_base, $name_link = NULL, $reference_link = NULL,
-            c35bab7f
+  $show_annotations = true, $is_type_designation = false, $skiptags = array(), $is_invalid = false) {
-fd6da0b
+            Andreas Kohlbecker
-            ea3933d7
+  $is_doubtful = false;
-fd6da0b
+  if($taxon_name_or_taxon_base->class == 'Taxon' || $taxon_name_or_taxon_base->class == 'Synonym'){
-            e95b14dd
+    if(isset($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));
+    }
-            ea3933d7
+    $is_doubtful = $taxon_name_or_taxon_base->doubtful;
-            de7bcbcc
+    // use the TaxonBase.tagged_title so we have the secRef
     $tagged_title = $taxon_name_or_taxon_base->taggedTitle;
-fd6da0b
+  } else {
-f8c26
+    // assuming this is a TaxonName
-fd6da0b
+    $taxonName = $taxon_name_or_taxon_base;
-            de7bcbcc
+    if(isset($taxonName->taggedFullTitle)){
       $tagged_title = $taxon_name_or_taxon_base->taggedFullTitle;
     } else {
       $tagged_title = $taxon_name_or_taxon_base->taggedName;
+    }
-fd6da0b
+            Andreas Kohlbecker
-bfe15b
+  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $name_link, $reference_link);
-            c2545e1c
+  $partDefinition = get_partDefinition($taxonName->nameType);
-fd6da0b
+            Andreas Kohlbecker
   // 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'];
+    }
+  }
-            de7bcbcc
+  $secref_tagged_text = tagged_text_extract_reference_and_detail($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);
-            c35bab7f
+  $appended_phrase_tagged_text = array(); // this is filled later
-            de7bcbcc
+  normalize_tagged_text($tagged_title);
-fd6da0b
+            Andreas Kohlbecker
-fc6c93
+  $is_valid_tagged_title =
-            de7bcbcc
+    isset($tagged_title)
     && is_array($tagged_title)
     && isset($tagged_title[0]->text)
     && is_string($tagged_title[0]->text)
     && $tagged_title[0]->text != ''
-fc6c93
+    && isset($tagged_title[0]->type);
-fd6da0b
+  $lastAuthorElementString = FALSE;
-            c35bab7f
+  $name_encasement = $is_invalid ? '"' : '';
-a3c136
+  $doubtful_marker = $is_doubtful ? '?&#8239;' : ''; // 	&#8239; =  NARROW NO-BREAK SPACE
-b553
+  $doubtful_marker_markup = '';
   if($doubtful_marker){
     $doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';
-fc6c93
+    if($tagged_title[0]->text == '?' ){
       // remove the first tagged text element
       unset($tagged_title[0]);
+    }
-b553
+            Andreas Kohlbecker
-            c35bab7f
+            Andreas Kohlbecker
   // split off all appendedPhrase item  from the end of the array (usually there only should  be one)
-            de7bcbcc
+  while($tagged_title[count($tagged_title)-1]->type == "appendedPhrase"){
     $appended_phrase_tagged_text[] = array_pop($tagged_title);
-            c35bab7f
+            Andreas Kohlbecker
-fd6da0b
+  // Got to use second entry as first one, see ToDo comment below ...
-fc6c93
+  if ($is_valid_tagged_title) {
-fd6da0b
+            Andreas Kohlbecker
-            de7bcbcc
+    $taggedName = $tagged_title;
-fd6da0b
+    $hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
     $hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
-            c35bab7f
+            Andreas Kohlbecker
-fd6da0b
+    if (!(($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 = $taggedNameNew;
-            e90899ac
+      unset($taggedNameNew);
-fd6da0b
+            Andreas Kohlbecker
-f129a6f
+    $name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';
-fd6da0b
+            Andreas Kohlbecker
   else {
-fc6c93
+    // use titleCache instead
-b553
+    $name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';
-            c35bab7f
+            Andreas Kohlbecker
   if(isset($appended_phrase_tagged_text[0])){
-a3c136
+    $name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';
-fd6da0b
+            Andreas Kohlbecker
   // Fill name into $renderTemplate.
-            c35bab7f
+  array_setr('name', $name , $renderTemplate);
-fd6da0b
+            Andreas Kohlbecker
   // Fill with authorTeam.
   /*
   if($authorTeam){
     $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
     array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
+  }
   */
   // Fill with reference.
   if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
-            eaff53f7
+    $registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));
     $registration_markup = render_registrations($registrations);
-fd6da0b
+    // default separator
     $separator = '';
     // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
     // Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
-            c21cfd4b
+    if (isset($renderTemplate['referencePart']['reference'])) {
-fd6da0b
+      $microreference = NULL;
       if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
         $microreference = $taxonName->nomenclaturalMicroReference;
+      }
-            c21cfd4b
+      if(count($nomref_tagged_text) == 0 && isset($taxonName->nomenclaturalReference)){
         // TODO is this case still relevant? The tagged text should already contain all information!
-            de7bcbcc
+        $citation = cdm_ws_getNomenclaturalReference($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;
-fd6da0b
+      } else {
-            de7bcbcc
+        // this ist the case for taxon names
         $referenceArray['#html'] = cdm_tagged_text_to_markup($nomref_tagged_text);
-fd6da0b
+            Andreas Kohlbecker
       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
-            eaff53f7
+      // reference part but display of the microreference
-fd6da0b
+      // 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);
       $is_reference_year = true;
+    }
+  }
-            e90899ac
+  // Fill with status.
-            dce1dacc
+  if(isset($renderTemplate['statusPart']['status'])){
-d0407b7
+    if (isset($nom_status_tagged_text[0])) {
-c5
+        $tt_to_markup_options = array('html' => false);
         foreach ($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;
            $tt_to_markup_options['html'] = true;
+         }
+        }
         array_setr(
           'status',
-            e9ac7c6f
+          '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator'), 'span', $tt_to_markup_options) . '</span>',
           $renderTemplate);
-            e90899ac
+            Andreas Kohlbecker
+  }
-fd6da0b
+  if (isset($renderTemplate['secReferencePart'])){
     if(isset($secref_tagged_text[1])){
-            e90899ac
+      $post_separator_markup = $is_reference_year ? '.': '';
-aad9da8
+      if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type ==  'postSeparator')){
-a1ab871
+        $post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));
-            e90899ac
+      };
-fd6da0b
+      array_setr('secReference',
-            e90899ac
+        $post_separator_markup
-fd6da0b
+          . ' <span class="sec_reference">'
-bfe18f9
+          . join('', cdm_tagged_text_values($secref_tagged_text))
-fd6da0b
+          . '</span>', $renderTemplate);
+    }
+  }
   // Fill with protologues etc...
   $descriptionHtml = '';
   if (array_setr('description', TRUE, $renderTemplate)) {
     $descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
-bfe15b
+    if($descriptions){
       foreach ($descriptions as $description) {
         if (!empty($description)) {
           foreach ($description->elements as $description_element) {
             $second_citation = '';
             if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
-c7c424f
+              if(isset($description_element->feature) && $description_element->feature->uuid == UUID_ADDITIONAL_PUBLICATION){
                 $prefix =  '& ';
               } else {
                 $prefix = '';
+              }
               $second_citation = ' [' . $prefix . $description_element->multilanguageText_L10n->text . '].';
-bfe15b
+            Andreas Kohlbecker
             $descriptionHtml .= $second_citation;
             $descriptionHtml .= cdm_description_element_media(
                 $description_element,
                 array(
                   'application/pdf',
                   'image/png',
                   'image/jpeg',
                   'image/gif',
                   'text/html',
+                )
             );
-fd6da0b
+            Andreas Kohlbecker
-bfe15b
+            Andreas Kohlbecker
-fd6da0b
+            Andreas Kohlbecker
+      }
+    }
     array_setr('description', $descriptionHtml, $renderTemplate);
+  }
   // Render.
-            f695daf4
+  $out = '';
   if(isset($_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/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
-fd6da0b
+            Andreas Kohlbecker
   foreach ($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) {
-fc5c836
+    // $out .= theme('cdm_entities_annotations_as_footnotekeys', $taxonName);
-fd6da0b
+            Andreas Kohlbecker
   return $out;
+}
-f0bc
+            Andreas Kohlbecker
 /**
-b8a1bc
+ * Composes information for a registration from a dto object.
+ *
  * Registrations which are not yet published are suppressed.
-f0bc
+            Andreas Kohlbecker
  * @param $registration_dto
  * @param $with_citation
  *   Whether to show the citation.
+ *
  * @return array
  *    A drupal render array with the elements:
-b8a1bc
+ *    - 'name'
  *    - 'name-relations'
  *    - 'specimen_type_designations'
  *    - 'name_type_designations'
-f0bc
+ *    - 'citation'
-b8a1bc
+ *    - 'registration_date_and_institute'
-f0bc
+ * @ingroup compose
  */
-b8a1bc
+function compose_registration_dto_full($registration_dto, $with_citation = true)
-f0bc
+            Andreas Kohlbecker
-c10803
+  $render_array = array(
     '#prefix' => '<div class="registration">',
     '#suffix' => '</div>'
   );
-f0bc
+            Andreas Kohlbecker
-b8a1bc
+  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
     return $render_array;
+  }
-            b7e96f18
+  $render_array['sub_headline'] = markup_to_render_array(join(", ", registration_types($registration_dto)),-10, '<h3 class="registration_type">' . t('Event: '), '</h3>' );
-            c5abae79
+  $render_array['nomenclatural_act'] = array(
     '#weight' => 0,
     '#prefix' => '<div class="nomenclatural_act">',
-            b7e96f18
+            Andreas Kohlbecker
-            c5abae79
+    '#suffix' => '</div>'
   );
-            b90ef618
+            Andreas Kohlbecker
-            e69c4103
+  // name
-b8a1bc
+  if($registration_dto->nameRef){
     $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
-            a7560a18
+    cdm_load_tagged_full_title($name);
-            c5abae79
+    $render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);
-b8a1bc
+    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
-            c5abae79
+    $render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
     $render_array['nomenclatural_act']['name_relations']['#weight'] = 10;
-dce3b2a
+  } else {
     // in this case the registration must have a
     $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
-c10803
+    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);
-b8a1bc
+            Andreas Kohlbecker
-            e69c4103
+  // typedesignation in detail
-b8a1bc
+  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
     $field_unit_uuids = array();
     $specimen_type_designation_refs = array();
     $name_type_designation_refs = array();
-f5eac2
+    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
       $tokens = explode("#", $workingset_ref);
       $types_in_fieldunit = get_object_vars($obj); // convert into associative array
-b8a1bc
+      if ($tokens[0] == 'NameTypeDesignation') {
-f5eac2
+        foreach ($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);
+          }
-f0bc
+            Andreas Kohlbecker
-b8a1bc
+      } else if ($tokens[0] == 'FieldUnit'){
         $field_unit_uuids[] = $tokens[1];
-f5eac2
+        foreach ($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);
+          }
+        }
-b8a1bc
+      } else {
         drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
-f0bc
+            Andreas Kohlbecker
+    }
-            a9a04561
+    // type designations wich are in this nomenclatural act.
-b8a1bc
+    if (count($name_type_designation_refs) > 0) {
-            c5abae79
+      $render_array['nomenclatural_act']['name_type_designations'] = compose_name_type_designations($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>';
       $render_array['nomenclatural_act']['name_type_designations']['#weight'] = 20;
-b8a1bc
+            Andreas Kohlbecker
     if (count($field_unit_uuids) > 0) {
-            e69c4103
+      $specimen_type_designations_array = compose_specimen_type_designations($specimen_type_designation_refs, true);
-            c5abae79
+      $render_array['nomenclatural_act']['specimen_type_designations'] = $specimen_type_designations_array['type_designations'];
-a348be
+      $render_array['map'] = $specimen_type_designations_array['map'];
-            c5abae79
+      $render_array['map']['#weight'] = $render_array['nomenclatural_act']['#weight'] + 20;
-b8a1bc
+            Andreas Kohlbecker
-f0bc
+            Andreas Kohlbecker
   // citation
   if ($with_citation) {
     $render_array['citation'] = markup_to_render_array(
-            c5abae79
+      "<div class=\"citation nomenclatural_act_citation" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
       . "<span class=\"label\">published in: </span>"
-ffe4d59
+      . $registration_dto->bibliographicInRefCitationString
       . l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($registration_dto->citationUuid), array('html' => true))
-            c5abae79
+      . "</div>",
       $render_array['nomenclatural_act']['#weight'] + 10 );
-f0bc
+            Andreas Kohlbecker
-e617798
+  $render_array['footnotes'] = markup_to_render_array(
     theme('cdm_annotation_footnotes', ['footnoteListKey' => RenderHints::getFootnoteListKey() ]),
   );
-f0bc
+  // registration date and office
-            12466422
+  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
-b8a1bc
+  if($registration_date_insitute_markup){
     $render_array['registration_date_and_institute'] = markup_to_render_array(
       $registration_date_insitute_markup . '</p>',
 );
+  }
-e617798
+            Andreas Kohlbecker
-b8a1bc
+  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;
+  }
-            12466422
+  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
-bba78
+  $itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));
-b8a1bc
+            Andreas Kohlbecker
-            f461a488
+  $tagged_text_options = array();
   if(isset($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);
-b8a1bc
+  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($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);
+  }
-            f461a488
+  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
-b8a1bc
+            Andreas Kohlbecker
   return $render_array;
+}
 /**
  * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
+ *
  * @param $registration_dto
  * @return string
  *    The markup or an empty string
  */
-            12466422
+function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
   $registration_date_institute_markup = '';
-b8a1bc
+  if ($registration_dto->registrationDate) {
-f0bc
+    $date_string = format_datetime($registration_dto->registrationDate);
-b8a1bc
+    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
-            12466422
+      $registration_date_institute_markup =
-f0bc
+        t("Registration on @date in @institution", array(
           '@date' => $date_string,
           '@institution' => $registration_dto->institutionTitleCache,
         ));
     } else {
-            12466422
+      $registration_date_institute_markup =
-f0bc
+        t("Registration on @date", array(
           '@date' => $date_string
         ));
+    }
-            12466422
+    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
-f0bc
+            Andreas Kohlbecker
-            12466422
+  return $registration_date_institute_markup;
-f0bc
+            Andreas Kohlbecker
-            eaff53f7
+/**
  * @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;
+}
-e3
+            Andreas Kohlbecker
-f0bc
+/**
  * Renders a registration
+ *
-b8a1bc
+ * TODO replace by compose_registration_dto_compact
-f0bc
+ * @param $registration
  */
 function render_registration($registration){
   $markup = '';
   if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
     $office_class_attribute = '';
     if(isset($registration->institution->titleCache)){
-b8a1bc
+      $office_class_attribute = registration_intitute_class_attribute($registration);
-f0bc
+            Andreas Kohlbecker
-bba78
+    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '
-f0bc
+      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
       . '</span>';
+  }
   return $markup;
+}
-b8a1bc
+/**
  * @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)) : '';
+}
-f0bc
+            Andreas Kohlbecker
-            79904336
+/**
  * Renders and array of CDM TypeDesignations
+ *
-e617798
+ *  - NameTypeDesignation
  *  - SpecimenTypeDesignation
  *  - TextualTypeDesignation
+ *
-            79904336
+ * @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)){
-d5812b
+    usort($name_type_designations, "compare_type_designations_by_status");
-            79904336
+    foreach($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, $referenceUri, TRUE, TRUE);
+      }
+    }
   } // END NameTypeDesignation
   // SpecimenTypeDesignation ...................................
   if (!empty($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)) {
-            e7f3789b
+        $citation_footnote_str = cdm_reference_markup($specimen_type_designation->citation, null, false, true);
-            79904336
+        $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);
+        }
         $out .= ': <span class="' . html_class_attribute_ref($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 .= '</'. $element_tag .'>';
+    }
   } // END Specimen type designations
   // TextualTypeDesignation .........................
-d5812b
+  usort($textual_type_designations, 'compare_textual_type_designation');
-            79904336
+  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,
-            a6c4c53c
+          'add_footnote_keys' => true,
           'bibliography_aware' => false
         ),
-            79904336
+        '',
         RenderHints::getFootnoteListKey() // passing a defined key to avoid separate annotation footnote key see https://dev.e-taxonomy.eu/redmine/issues/8543
       );
-            a6c4c53c
+      $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;
-            79904336
+            Andreas Kohlbecker
+  }
   // Footnotes for citations, collection acronym?s.
   // 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;
+}
-            a9a04561
+/**
  * Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.
-a348be
+            Andreas Kohlbecker
-            a9a04561
+ * @param $taxon_name_uuid
-            10858926
+ * @param $show_specimen_details
-            a9a04561
+ * @return array
-            ae177dac
+ *    A drupal render array with the following elements:
-            a9a04561
+ *    - 'type_designations'
  *    - 'map'
-            ae177dac
+ *    - 'specimens'
-            a9a04561
+            Andreas Kohlbecker
  * @ingroup compose
  */
-            10858926
+function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)
-            a9a04561
+            Andreas Kohlbecker
-a348be
+  $render_array = array(
     'type_designations' => array(),
     'map' => array(),
     );
-            a9a04561
+  $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);
   if ($type_designations) {
-            fb939fdc
+    usort($type_designations, 'compare_specimen_type_designation');
-            a9a04561
+    $render_array['type_designations'] = markup_to_render_array(
-c720425
+      render_type_designations($type_designations, 'div', 'div')
-            a9a04561
+    );
     $render_array['map'] = compose_type_designations_map($type_designations);
+  }
   return $render_array;
+}
-e3
+/**
  * Composes the TypedEntityReference to name type designations passed as associatve array.
+ *
-e617798
+ * @param $type_entity_refs array
-e3
+ *   an associative array of name type type => TypedEntityReference for name type designations as
  *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
+ *
  * @ingroup compose
  */
 function compose_name_type_designations($type_entity_refs){
   $render_array = array();
-            e1e2d593
+  $preferredStableUri = '';
-            f5396e17
+  foreach($type_entity_refs as $type_status => $name_types){
     foreach ($name_types as $name_type){
-d95e99f
+      $type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
-            f5396e17
+      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
         $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
+      }
-c12cb7f
+      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type)  . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "
-            f5396e17
+        . $name_type->label
         . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
         . '</div>');
+      }
-            f5e7f68e
+            Andreas Kohlbecker
   return $render_array;
+}
 /**
-a348be
+ * Composes the specimen type designations with map from the the $type_entity_refs
-            f5e7f68e
+            Andreas Kohlbecker
  * @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
+ *
-            e69c4103
+ * @param $show_media_specimen
-a348be
+ * @return array
-abd581c
+ *    A drupal render array with the following elements:
-a348be
+ *    - 'type_designations'
  *    - 'map'
+ *
  * @ingroup compose
+ *
-            f5e7f68e
+ */
-            e69c4103
+function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){
-e8173
+            Andreas Kohlbecker
-            f5e7f68e
+  $render_array = array();
-e8173
+            Andreas Kohlbecker
-e617798
+  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
   ];
-a348be
+  $type_designation_list = array();
-            d8de8d4d
+  uksort($type_entity_refs, "compare_type_designation_status_labels");
-e617798
+  foreach($type_entity_refs as $type_status => $type_designation_entity_refs){
     foreach($type_designation_entity_refs as $type_designation_entity_ref){
-e8173
+            Andreas Kohlbecker
-e617798
+      $type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($type_designation_entity_ref->uuid));
-            e69c4103
+      $type_designation_list[] = $type_designation; // collect for the map
-e617798
+      $derived_unit_facade_dto = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
-            b8a0efb3
+      // 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'));
-e8173
+            Andreas Kohlbecker
-f5eac2
+      $preferredStableUri = '';
       $citation_markup = '';
       $media = '';
-e8173
+            Andreas Kohlbecker
-e617798
+      // annotations and sources for the $derived_unit_facade_dto
       $annotations_and_sources = handle_annotations_and_sources(
         $derived_unit_facade_dto,
         $annotations_and_sources_config,
         '',
         null
       );
       $source_citations = $annotations_and_sources['source_references'];
       $foot_note_keys = $annotations_and_sources['foot_note_keys'];
-f5eac2
+      // preferredStableUri
       if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
         $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
-e8173
+            Andreas Kohlbecker
-f5eac2
+            Andreas Kohlbecker
-            e69c4103
+      if($show_media_specimen && $mediaSpecimen){
-f5eac2
+        // compose output
         // mediaURI
         if(isset($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),
-e617798
+            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $type_designation_entity_ref->uuid,
-f5eac2
+            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
             'cols' => $gallery_settings['cdm_dataportal_media_cols'],
             'captionElements' => $captionElements,
           ));
+        }
-e617798
+        // citation and detail for the media specimen
-f5eac2
+        $annotations_and_sources = handle_annotations_and_sources(
-e617798
+          $mediaSpecimen,
           $annotations_and_sources_config,
           '',
           null
-f5eac2
+        );
         if(is_array( $annotations_and_sources['source_references'])){
-e617798
+          $source_citations = array_merge($source_citations, $annotations_and_sources['source_references']);
+        }
         if($annotations_and_sources['foot_note_keys']){
           $foot_note_keys .= ', ' . $annotations_and_sources['foot_note_keys'];
-f5eac2
+            Andreas Kohlbecker
-e8173
+            Andreas Kohlbecker
-e617798
+      $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);
-            e69c4103
+            Andreas Kohlbecker
-e617798
+      $type_designation_render_array = markup_to_render_array(
         '<div class="type_designation_entity_ref ' . html_class_attribute_ref($type_designation_entity_ref)  . '">
-d631
+          <span class="type-status">' . ucfirst($type_status) . "</span>: "
-e617798
+        . $specimen_markup . $foot_note_keys
-f5eac2
+        . ($citation_markup ? ' '. $citation_markup : '')
         . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
         . $media
         . '</div>');
-            e69c4103
+            Andreas Kohlbecker
       $render_array['type_designations'][] = $type_designation_render_array;
-f5eac2
+            Andreas Kohlbecker
-e3
+            Andreas Kohlbecker
-a348be
+  if(count($type_designation_list) > 0 ){
     $render_array['map'] = compose_type_designations_map($type_designation_list);
   } else {
     $render_array['map'] = array();
+  }
-e3
+  return $render_array;
+}
-fd6da0b
+/**
-            ef686dd8
+ * @param $name_rel
  * @param $current_name_uuid
  * @param $current_taxon_uuid
  * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
  * @param $show_name_cache_only
  *    The nameCache will be shown instead of the titleCache if this parameter is true.
  * @return null|string
  */
-dfe
+function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
-            ef686dd8
+            Andreas Kohlbecker
   $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 = $name_rel->toName;
+  }
-            a7560a18
+  cdm_load_tagged_full_title($name);
-            ef686dd8
+  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
   if(!$show_name_cache_only){
     $relationship_markup = render_taxon_or_name($name,
-f65af04
+      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
-            ef686dd8
+    );
   } else {
     $relationship_markup = l(
       '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
-f65af04
+      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
-            ef686dd8
+      array('html' => true)
     );
+  }
   return $relationship_markup;
+}
 /**
-dfe
+ * Composes an inline representation of selected name relationships
-d77
+            Andreas Kohlbecker
-a017dd
+ * The output of this function will be usually appended to taxon name representations.
-            ef686dd8
+ * 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}'
-a017dd
+            Andreas Kohlbecker
  * 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
-            ef686dd8
+ *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
-b7bbf68
+            Andreas Kohlbecker
-            d4ea0dd9
+ * @param $name_relations
  *    The list of CDM NameRelationsips
  * @param $current_name_uuid
-c088da3
+ *    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.
-            d4ea0dd9
+ * @param $current_taxon_uuid
  *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
-dfe
+ * @return array
  *    A drupal render array
+ *
  * @ingroup Compose
-b7bbf68
+ */
-dfe
+function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
-            f695daf4
+            Andreas Kohlbecker
-b7bbf68
+  RenderHints::pushToRenderStack('homonym');
   // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
-            ef686dd8
+  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
-efd13a9
+  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
   foreach ($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;
+    }
+  }
-            6421984d
+            Andreas Kohlbecker
-cc86
+  $list_prefix = '<span class="name_relationships">[';
   $list_suffix = ']</span>';
-dfe
+  $item_prefix = '<span class="item">';
   $item_suffix = '</span> ';
-            f8d5d6d9
+  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
-efd13a9
+            Andreas Kohlbecker
   // 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>';
+  }
-b7bbf68
+            Andreas Kohlbecker
   RenderHints::popFromRenderStack();
-dfe
+  return $render_array;
-            d4ea0dd9
+            Andreas Kohlbecker
-            ef686dd8
+/**
  * 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 $current_taxon_uuid
  *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
  * @return array
  *    A drupal render array
+ *
  * @ingroup Compose
  */
-dfe
+function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
-            ef686dd8
+            Andreas Kohlbecker
   // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
-c5
+  $key = 'name_relationships';
   RenderHints::pushToRenderStack($key);
   if(!RenderHints::getFootnoteListKey()){
     RenderHints::setFootnoteListKey($key);
+  }
-            ef686dd8
+  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
-a85
+  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));
-efd13a9
+  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
   foreach ($selected_name_rel_uuids as $uuid){
     $name_rel_type_filter['direct'][$uuid] = $uuid;
     $name_rel_type_filter['inverse'][$uuid] = $uuid;
+  }
-            ef686dd8
+            Andreas Kohlbecker
-dfe
+  $list_prefix = '<div class="relationships_list name_relationships">';
   $list_suffix = '</div>';
   $item_prefix = '<div class="item">';
   $item_suffix = '</div>';
-            f8d5d6d9
+  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
-dfe
+            Andreas Kohlbecker
   RenderHints::popFromRenderStack();
   $render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
-c5
+  if(RenderHints::getFootnoteListKey() == $key) {
     RenderHints::clearFootnoteListKey();
+  }
-dfe
+  return $render_array;
+}
 /**
  * @param $name_relations
-efd13a9
+ * @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
-dfe
+ * @param $current_name_uuid
  * @param $current_taxon_uuid
  * @param $list_prefix
  * @param $list_suffix
  * @param $item_prefix
  * @param $item_suffix
  * @return array
+ *
  * @ingroup Compose
  */
-efd13a9
+function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
-            f8d5d6d9
+                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)
-dfe
+            Andreas Kohlbecker
   $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
     UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
-cc86
+    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
-efd13a9
+    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
-dfe
+    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
-            ef686dd8
+  $render_array = array(
     'list' => array(
-dfe
+      '#prefix' => $list_prefix,
       '#suffix' => $list_suffix,
-            ef686dd8
+      'items' => array()
     ),
     'footnotes' => array()
   );
-dfe
+  if ($name_relations) {
-            ef686dd8
+            Andreas Kohlbecker
     // remove all relations which are not selected in the settings and
-dfe
+    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
-            ef686dd8
+    // for special handling
     $filtered_name_rels = array();
     $non_nec_name_rels = array();
     $orthographic_variants = array();
-dfe
+    foreach ($name_relations as $name_rel) {
       $rel_type_uuid = $name_rel->type->uuid;
-efd13a9
+      $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])) {
-dfe
+        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
+          )
         ){
-            ef686dd8
+          $non_nec_name_rels[] = $name_rel;
-dfe
+        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
-            ef686dd8
+          $orthographic_variants[] = $name_rel;
         } else {
-dfe
+            Andreas Kohlbecker
-            ef686dd8
+          $filtered_name_rels[] = $name_rel;
+        }
+      }
+    }
     $name_relations = $filtered_name_rels;
     usort($name_relations, 'compare_name_relations_by_term_order_index');
-efd13a9
+    // compose
-dfe
+    foreach ($name_relations as $name_rel) {
-            ef686dd8
+            Andreas Kohlbecker
-dfe
+      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
-            ef686dd8
+            Andreas Kohlbecker
-            f8d5d6d9
+      $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
-dfe
+      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
-            ef686dd8
+            Andreas Kohlbecker
       $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
       $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
-            f8d5d6d9
+      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
       $relationship_markup = $symbol_markup . $relationship_markup;
-dfe
+      if ($relationship_markup) {
-            ef686dd8
+        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
           null,
-dfe
+          $item_prefix,
           $item_suffix);
-            ef686dd8
+            Andreas Kohlbecker
+    }
     // name relationships to be displayed as non nec
-dfe
+    if (count($non_nec_name_rels) > 0) {
-            ef686dd8
+      $non_nec_markup = '';
-dfe
+      foreach ($non_nec_name_rels as $name_rel) {
         $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
-            f8d5d6d9
+        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
-dfe
+        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
         $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
-            ef686dd8
+        $symbol = $non_nec_markup ? ' nec ' : 'non';
-            f8d5d6d9
+        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
         $non_nec_markup .= $symbol_markup . $relationship_markup;
-dfe
+            Andreas Kohlbecker
       if ($non_nec_markup) {
         $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
           null,
           $item_prefix,
           $item_suffix);
-            ef686dd8
+            Andreas Kohlbecker
+    }
     // orthographic variants
-dfe
+    if (count($orthographic_variants) > 0) {
       foreach ($orthographic_variants as $name_rel) {
         $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
-            f8d5d6d9
+        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
-dfe
+        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
-c5
+        $nomref_footnote_key_markup = nomenclatural_reference_footnote_key_markup($name_rel->toName);
-dfe
+        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
-            ef686dd8
+        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
-            f8d5d6d9
+        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
-c5
+        $relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
-            ef686dd8
+            Andreas Kohlbecker
-dfe
+      if ($relationship_markup) {
-            ef686dd8
+        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
           null,
-dfe
+          $item_prefix,
           $item_suffix);
-            ef686dd8
+            Andreas Kohlbecker
+    }
+  }
   return $render_array;
+}
 /**
  * @param $name_rel
  * @return string
  */
 function name_relationship_footnote_markup($name_rel)
+{
   $footnote_markup = '';
   $footnote_key_markup = '';
-c5
+  if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
-            ef686dd8
+    $footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
+  }
   if (isset($name_rel->citation)) {
-bf76f
+    $footnote_markup .= '<span class="reference">' . $name_rel->citation->titleCache . '</span>';
-            ef686dd8
+            Andreas Kohlbecker
-c5
+  if (isset($name_rel->citationMicroReference) && $name_rel->citationMicroReference) {
-d8d07
+    $footnote_markup .= (isset($name_rel->citation) ? ':' : '') . ' <span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';
-            ef686dd8
+            Andreas Kohlbecker
   if ($footnote_markup) {
     $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
     $footnote_key_markup = theme('cdm_footnote_key', array(
       'footnoteKey' => $fnkey,
       'separator' => ',',
       'highlightable' => TRUE,
       'separator_off' => TRUE,
     ));
+  }
   return $footnote_key_markup;
+}
-c5
+/**
  * @param $nom_status
  * @return string
  */
 function nomenclatural_status_footnote_markup($nom_status)
+{
   // NomenclaturalStatus is a subclass of ReferencedEntityBase
   // and has the same structure as TaxonNameRelationship
   return name_relationship_footnote_markup($nom_status);
+}
-            ef686dd8
+/**
  * @param $name
  * @return string
  */
-c5
+function nomenclatural_reference_footnote_key_markup($name)
-            ef686dd8
+            Andreas Kohlbecker
   $footnote_markup = '';
   $footnote_key_markup = '';
   if (isset($name->nomenclaturalReference) && $name->nomenclaturalReference) {
     $footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';
+  }
   if (isset($name->nomenclaturalMicroReference)) {
     $footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalMicroReference . '</span>';
+  }
   if ($footnote_markup) {
     $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
     $footnote_key_markup = theme('cdm_footnote_key', array(
       'footnoteKey' => $fnkey,
       'separator' => ',',
       'highlightable' => TRUE,
       'separator_off' => TRUE,
     ));
+  }
   return $footnote_key_markup;
+}
-c5
+            Andreas Kohlbecker
-            d4ea0dd9
+/**
  * @param $taxon
  * @return array
  */
 function cdm_name_relationships_for_taxon($taxon)
+{
   $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
   $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
   $name_relations = array_merge($from_name_relations, $to_name_relations);
   return $name_relations;
-b7bbf68
+            Andreas Kohlbecker
-            d4ea0dd9
+/**
-fd6da0b
+ * Recursively searches the array for the $key and sets the given value.
+ *
  * @param mixed $key
  *   Key to search for.
  * @param mixed $value
  *   Value to set.'
  * @param array $array
  *   Array to search in.
+ *
  * @return bool
  *   True if the key has been found.
  */
 function &array_setr($key, $value, array &$array) {
   $res = NULL;
   foreach ($array as $k => &$v) {
     if ($key == $k) {
       $v = $value;
       return $array;
+    }
     elseif (is_array($v)) {
       $innerArray = array_setr($key, $value, $v);
       if ($innerArray) {
         return $array;
+      }
+    }
+  }
   return $res;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
   $res = NULL;
   $precedingElement = NULL;
   foreach ($renderTemplate as &$part) {
     foreach ($part as $key => &$element) {
       if ($key == $contentElementKey) {
         return $precedingElement;
+      }
       $precedingElement = $element;
+    }
+  }
   return $res;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
   $res = NULL;
   $precedingKey = NULL;
   foreach ($renderTemplate as &$part) {
     if (is_array($part)) {
       foreach ($part as $key => &$element) {
         if ($key == $contentElementKey) {
           return $precedingKey;
+        }
         if (!str_beginsWith($key, '#')) {
           $precedingKey = $key;
+        }
+      }
+    }
+  }
   return $res;
+}
-            c2545e1c
+            Andreas Kohlbecker
 function nameTypeToDTYPE($dtype){
   static $nameTypeLabelMap = array(
     "ICNB" => "BacterialName",
     "ICNAFP" => "BotanicalName",
     "ICNCP" => "CultivarPlantName",
     "ICZN" => "ZoologicalName",
     "ICVCN" => "ViralName",
     "Any taxon name" => "TaxonName",
     "NonViral" => "TaxonName",
     "Fungus" => "BotanicalName",
     "Plant" => "BotanicalName",
     "Algae" => "BotanicalName",
   );
   return $nameTypeLabelMap[$dtype];
+}
-            ef686dd8
+            Andreas Kohlbecker
 function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
   return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
+}
-            b90ef618
+            Andreas Kohlbecker
 /**
  * Provides an array with the different registration types covered by the passed registration.
+ *
  * The labels in the returned array are translatable.
+ *
  * See also https://dev.e-taxonomy.eu/redmine/issues/8016
+ *
  * @param $registration_dto
  * @return array
  *    An array of the labels describing the different registration types covered by the passed registration.
  */
 function registration_types($registration_dto){
   $reg_type_labels = array();
   if(isset($registration_dto->nameRef)){
-a02c62f
+    $reg_type_labels["name"] = t("new name");
     $reg_type_labels["taxon"] = t("new taxon");
-            b90ef618
+    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
-a02c62f
+    $is_new_combination = true;
-            b90ef618
+    foreach($name_relations as $name_rel){
       if(isset($name_rel->type->uuid)){
         $name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
         switch($name_rel->type->uuid) {
           case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
             if(!$name_is_from_name){
-a02c62f
+              $reg_type_labels["basionym"] = t("new combination");
               $is_new_combination = true;
-            b90ef618
+            Andreas Kohlbecker
             break;
           case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
             if(!$name_is_from_name) {
-a02c62f
+              $is_new_combination = true;
-            b90ef618
+            Andreas Kohlbecker
             break;
           case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
             if(!$name_is_from_name) {
-a02c62f
+              $reg_type_labels["validation"] = t("validation");
-            b90ef618
+            Andreas Kohlbecker
             break;
           case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
             if(!$name_is_from_name) {
-a02c62f
+              $reg_type_labels["orth_var"] = t("orthographical correction");
-            b90ef618
+            }break;
           default:
             // NOTHING
+        }
+      }
+    }
-a02c62f
+    if($is_new_combination){
       unset($reg_type_labels["taxon"]);
+    }
-            b90ef618
+            Andreas Kohlbecker
   if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
-a02c62f
+    $reg_type_labels[] = t("new nomenclatural type");
-            b90ef618
+            Andreas Kohlbecker
   return $reg_type_labels;
-            b059b449
+            Andreas Kohlbecker
 /**
  * Collects and deduplicates the type designations associated with the passes synonyms.
+ *
  * @param $synonymy_group
  *    An array containing a homotypic or heterotypic group of names.
-f188298
+ * @param $accepted_taxon_name_uuid
-f2d
+ *    The uuid of the accepted taxon name. Optional parameter which is required when composing
  *    the information for the homotypic group. In this case the accepted taxon is not included
  *    in the $synonymy_group and must therefor passed in this second parameter.
+ *
-            b059b449
+ * @return array
  *    The type designations
  */
-            dfbc27b0
+function type_designations_for_synonymy_group($synonymy_group, $accepted_taxon_name_uuid = null)
+{
   if (count($synonymy_group) > 0) {
-f2d
+    $name_uuid = array_pop($synonymy_group)->name->uuid;
   } else {
     $name_uuid = $accepted_taxon_name_uuid;
+  }
   if ($name_uuid) {
    $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS_IN_HOMOTYPICAL_GROUP, $name_uuid);
     if ($type_designations) {
-d14fdcf
+      return $type_designations;
+    }
-            b059b449
+            Andreas Kohlbecker
-f2d
+            Andreas Kohlbecker
-            dfbc27b0
+  return array();
-            fb939fdc
+            Andreas Kohlbecker
 /**
-d5812b
+ * Compares two SpecimenTypeDesignations
-            fb939fdc
+            Andreas Kohlbecker
  * @param object $a
  *   A SpecimenTypeDesignation.
  * @param object $b
  *   SpecimenTypeDesignation.
  */
 function compare_specimen_type_designation($a, $b) {
-d5812b
+  $cmp_by_status = compare_type_designations_by_status($a,$b);
   if($cmp_by_status !== 0){
     return $cmp_by_status;
+  }
-            fb939fdc
+            Andreas Kohlbecker
   $aQuantifier = FALSE;
   $bQuantifier = FALSE;
   if ($aQuantifier == $bQuantifier) {
     // Sort alphabetically.
     $a_text =  isset($a->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $a->typeSpecimen->titleCache) : '';
     $b_text =  isset($b->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $b->typeSpecimen->titleCache) : '';
     return strcasecmp($a_text, $b_text);
+  }
-d5812b
+  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
+}
 /**
  * Compares the status of two TypeDesignations
+ *
  * @param object $a
  *   A TypeDesignation
  * @param object $b
  *   TypeDesignation
  */
 function compare_type_designations_by_status($a, $b) {
-            e5a89a58
+  $status_a = isset($a->typeStatus) ? $a->typeStatus : null;
   $status_b = isset($b->typeStatus) ? $b->typeStatus : null;
   return compare_type_designation_status($status_a, $status_b);
-            fb939fdc
+            Andreas Kohlbecker
 /**
-d5812b
+ * Compares two TypeDesignationStatusBase
-            fb939fdc
+            Andreas Kohlbecker
  * @param object $a
  *   A TypeDesignationStatusBase.
  * @param object $b
  *   TypeDesignationStatusBase.
  */
 function compare_type_designation_status($a, $b) {
   $type_status_order = type_status_order();
   $aQuantifier = FALSE;
   $bQuantifier = FALSE;
   if (isset($a->label) && isset($b->label)) {
     $aQuantifier = array_search($a->label, $type_status_order);
     $bQuantifier = array_search($b->label, $type_status_order);
+  }
-d5812b
+  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
+}
 /**
  * Compares the two TextualTypeDesignations
+ *
  * @param object $a
  *   A TextualTypeDesignations.
  * @param object $b
  *   TextualTypeDesignations.
  */
 function compare_textual_type_designation($a, $b) {
   $cmp_by_status = compare_type_designations_by_status($a,$b);
   if($cmp_by_status !== 0){
     return $cmp_by_status;
+  }
   $aQuantifier = FALSE;
   $bQuantifier = FALSE;
   if ($aQuantifier == $bQuantifier) {
     // Sort alphabetically.
     $a_text =  isset($a->text_L10n->text) ? $a->text_L10n->text : '';
     $b_text =  isset($b->text_L10n->text) ? $b->text_L10n->text : '';
     return strcasecmp($a_text, $b_text);
+  }
   return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
-            fb939fdc
+            Andreas Kohlbecker
-            d8de8d4d
+            Andreas Kohlbecker
 /**
  * Compares two SpecimenTypeDesignation status labels
+ *
  * @param string $a
  *   A TypeDesignationStatus label.
  * @param string $b
  *   A TypeDesignationStatus label.
  */
 function compare_type_designation_status_labels($a, $b) {
   $type_status_order = type_status_order();
   $aQuantifier = FALSE;
   $bQuantifier = FALSE;
   if (isset($a) && isset($b)) {
     $aQuantifier = array_search($a, $type_status_order);
     $bQuantifier = array_search($b, $type_status_order);
+  }
   return ($aQuantifier < $bQuantifier) ? -1 : 1;
+}
-            fb939fdc
+/**
  * @return array
  */
 function type_status_order()
+{
   /*
     This is the desired sort order as of now: Holotype Isotype Lectotype
     Isolectotype Syntype.
     TODO Basically, what we are trying to do is, we define
     an ordered array of TypeDesignation-states and use the index of this array
     for comparison. This array has to be filled with the cdm- TypeDesignation
     states and the order should be parameterisable inside the dataportal.
     */
   // Make that static for now.
   $type_status_order = array(
     'Epitype',
     'Holotype',
     'Isotype',
     'Lectotype',
     'Isolectotype',
     'Syntype',
     'Paratype'
   );
   return $type_status_order;
-eab6eeb
+            Andreas Kohlbecker
 /**
  * Return HTML for the lectotype citation with the correct layout.
+ *
  * This function prints the lectotype citation with the correct layout.
  * Lectotypes are renderized in the synonymy tab of a taxon if they exist.
+ *
  * @param mixed $typeDesignation
  *   Object containing the lectotype citation to print.
+ *
  * @return string
  *   Valid html string.
  */
 function type_designation_citation_layout($typeDesignation, $footnote_separator = ',') {
   $res = '';
   $citation = $typeDesignation->citation;
   $pages = $typeDesignation->citationMicroReference;
   if(isset($typeDesignation->typeStatus->uuid) && isset($typeDesignation->typeStatus->representation_L10n)) {
     if ( $typeDesignation->typeStatus->uuid == UUID_NTD_ORIGINAL_DESIGNATION || $typeDesignation->typeStatus->uuid == UUID_NTD_MONOTYPY) {
       $res = ' (' . $typeDesignation->typeStatus->representation_L10n . ')';
       return $res;
+    }
+  }
   if ($citation) {
     // $type = $typeDesignation_citation->type;
     $year = isset($citation->datePublished->start) ? substr($citation->datePublished->start, 0, 4) : '';
     $author = isset($citation->authorship->titleCache) ? $citation->authorship->titleCache : '';
     $res .= ' (designated by ';
     $res .= $author;
     $res .= ($year ? ' ' . $year : '');
     $res .= ($pages ? ': ' . $pages : '');
     // $res .= ')';
     // footnotes should be rendered in the parent element so we
     // are relying on the FootnoteListKey set there
     $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $typeDesignation->citation->titleCache);
     $res .= theme('cdm_footnote_key', array(
         'footnoteKey' => $fkey_typeDesignation,
         'separator' => $footnote_separator,
         'highlightable' => TRUE,
         'separator_off' => TRUE,
       )) . ')';
+  }
   return $res;
+}
 /**
  * Creates markup for the status of a type designation. In case the status or its representation is missing the label will be set to "Type"
+ *
  * @param $type_designation
  * @return string
  */
 function type_designation_status_label_markup($type_designation)
+{
   return '<span class="type-status">'
     . ((isset($type_designation->typeStatus->representation_L10n)) ? ucfirst($type_designation->typeStatus->representation_L10n) : t('Type')) . '</span>'
+    ;
+}

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