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

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cdm-dataportal/modules/cdm_dataportal/includes/name.inc @ 7212f0bc

-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
  *   The link path ot URL to be used for name parts if a link is forseen in the template
  *   matching the given $renderPath.
  * @param string $referenceLink
  *   The link path ot URL to be used for nomenclatural reference parts if a link is forseen
  *   in the template matching the given $renderPath.
  * @return array
  *   An associative array, the render template
  */
-            a565e612
+function get_nameRenderTemplate($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
-fd6da0b
+ * @param $nameLink
  *    URI to the taxon, @see path_to_taxon(), must be processed by url() before passing to this method
  * @param $refenceLink
  *    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 $is_invalid
  *   Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.
  *   This is useful when rendering taxon relation ships.
-fd6da0b
+            Andreas Kohlbecker
  * @return string
  *  The markup for a taxon name.
+ *
  */
 function render_taxon_or_name($taxon_name_or_taxon_base, $nameLink = NULL, $refenceLink = 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'){
     $taxonName = $taxon_name_or_taxon_base->name;
-            ea3933d7
+    $is_doubtful = $taxon_name_or_taxon_base->doubtful;
-fd6da0b
+    // use the TaxonBase.taggedTitle so we have the secRef
     $taggedTitle = $taxon_name_or_taxon_base->taggedTitle;
   } else {
-f8c26
+    // assuming this is a TaxonName
-fd6da0b
+    $taxonName = $taxon_name_or_taxon_base;
     $taggedTitle = $taxon_name_or_taxon_base->taggedName;
+  }
   $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
-            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'];
+    }
+  }
-dc60b9
+  $secref_tagged_text = tagged_text_extract_secref($taggedTitle);
   $nom_status_tagged_text = tagged_text_extract_nomstatus($taggedTitle);
-            c35bab7f
+  $appended_phrase_tagged_text = array(); // this is filled later
-            e90899ac
+  normalize_tagged_text($taggedTitle);
-fd6da0b
+            Andreas Kohlbecker
   $firstEntryIsValidNamePart =
     isset($taggedTitle)
     && is_array($taggedTitle)
     && isset($taggedTitle[0]->text)
     && is_string($taggedTitle[0]->text)
     && $taggedTitle[0]->text != ''
     && isset($taggedTitle[0]->type)
     && $taggedTitle[0]->type == 'name';
   $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">' . $doubtful_marker . '</span>';
+  }
-            c35bab7f
+            Andreas Kohlbecker
   // split off all appendedPhrase item  from the end of the array (usually there only should  be one)
   while($taggedTitle[count($taggedTitle)-1]->type == "appendedPhrase"){
     $appended_phrase_tagged_text[] = array_pop($taggedTitle);
+  }
-fd6da0b
+  // Got to use second entry as first one, see ToDo comment below ...
   if ($firstEntryIsValidNamePart) {
     $taggedName = $taggedTitle;
     $hasNamePart_with_Authors = isset($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 {
-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
     $separator = '';
     // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
     // Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
     if (isset($renderTemplate['referencePart']['reference']) && isset($taxonName->nomenclaturalReference)) {
       $microreference = NULL;
       if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
         $microreference = $taxonName->nomenclaturalMicroReference;
+      }
       $citation = cdm_ws_getNomenclaturalReference($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;
-            eaff53f7
+      $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
-fd6da0b
+      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($nom_status_tagged_text[0])) {
-f129a6f
+        array_setr('status', '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator')) . '</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, $taxonName->uuid);
     foreach ($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) {
             $second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
+          }
           $descriptionHtml .= $second_citation;
-b2642
+          $descriptionHtml .= cdm_description_element_media(
               $description_element,
               array(
-fd6da0b
+                'application/pdf',
                 'image/png',
                 'image/jpeg',
                 'image/gif',
                 'text/html',
+              )
           );
+        }
+      }
+    }
     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) {
     // $out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
+  }
   return $out;
+}
-f0bc
+            Andreas Kohlbecker
 /**
  * Composes information for a registration from a dto object
+ *
  * @param $registration_dto
  * @param $with_citation
  *   Whether to show the citation.
  * @param $with_identifier
  *   Whether to add the identifier to the summary (in enabled)
  * @param $with_compact_summary
  *   Whether to display the name and type designations as compact summary or in extended form.
+ *
  * @return array
  *    A drupal render array with the elements:
  *    - 'publication_date_and_office'
  *    - 'citation'
  *    - 'summary' OR  'name', 'name-relations', 'name_type_designations', 'specimen_table' (depending on parameter $with_compact_summary)
  * @ingroup compose
  */
 function compose_registration_dto($registration_dto, $with_citation = true, $with_identifier = false, $with_compact_summary = true)
+{
   $render_array = array();
   $media_link_map = array();
   if($with_compact_summary){
     // summary
     $taggged_text_expanded = cdm_tagged_text_expand_entity_references($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, $registation_markup);
+    }
     if($with_identifier){
       $registation_markup .= " " . l ($registration_dto->identifier, $registration_dto->identifier);
+    }
     $render_array['summary'] = markup_to_render_array('<p class="registration-summary">' . $registation_markup . "</p>", 0);
   } else {
     // name and typedesignation in detail
     if($registration_dto->nameRef){
       $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
       $render_array['name'] = markup_to_render_array('<p class="name">' . render_taxon_or_name($name) . '</p>', 0);
       $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
       $render_array['name_relations'] = markup_to_render_array(render_name_relationships_of($name_relations, $registration_dto->nameRef->uuid, null, false));
       $render_array['name_relations']['#weight'] = 10;
+    }
     if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
       $field_unit_uuids = array();
       $specimen_type_designation_refs = array();
       $name_type_designation_refs = array();
       foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $field_unit_ref => $obj) {
         $tokens = explode("#", $field_unit_ref);
         foreach ($obj as $type_status => $entity_reference_list) {
           // NOTE: there is always only one element, since we use the foreach to extract the objects field name and value
           $entity_reference = $entity_reference_list[0];
+        }
         if ($tokens[0] == 'NameTypeDesignation') {
           foreach ($obj as $type_status => $entity_reference_list) {
             $name_type_designation_refs[$type_status] = $entity_reference;
+          }
         } else if ($tokens[0] == 'FieldUnit'){
           $field_unit_uuids[] = $tokens[1];
           $specimen_type_designation_refs[$type_status] = $entity_reference;
         } else {
           drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
+        }
+      }
       if (count($name_type_designation_refs) > 0) {
         $render_array['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
         $render_array['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
         $render_array['name_type_designations']['#suffix'] = '</p>';
         $render_array['name_type_designations']['#weight'] = 20;
+      }
       if (count($field_unit_uuids) > 0) {
         $render_array['specimen_type_designations'] = compose_specimen_type_designations($specimen_type_designation_refs);
         // $render_array['specimen_table'] = compose_specimen_table($field_unit_uuids);
         // below citation (weight=20)
         $render_array['specimen_table']['#weight'] = 21;
+      }
+    }
+  }
   // citation
   if ($with_citation) {
     $render_array['citation'] = markup_to_render_array(
       "<p class=\"citation " . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
       . l($registration_dto->bibliographicInRefCitationString, path_to_reference($registration_dto->citationUuid))
       . "</p>",
 );
+  }
   // registration date and office
   if($registration_dto->registrationDate){
     $date_string = format_datetime($registration_dto->registrationDate);
     if(isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache){
       $registration_date_insitute_markup =
         t("Registration on @date in @institution", array(
           '@date' => $date_string,
           '@institution' => $registration_dto->institutionTitleCache,
         ));
     } else {
       $registration_date_insitute_markup =
         t("Registration on @date", array(
           '@date' => $date_string
         ));
+    }
     $render_array['publication_date_and_office'] = markup_to_render_array(
       '<p class"date-and-institute">'.$registration_date_insitute_markup . '</p>',
 );
+  }
   return $render_array;
+}
-            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
+ *
  * @param $registration
  */
 function render_registration($registration){
   $markup = '';
   if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
     $office_class_attribute = '';
     if(isset($registration->institution->titleCache)){
       $office_class_attribute = 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $registration->institution->titleCache));
+    }
     $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, $registration->identifier) . ', '
       .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
       . '</span>';
+  }
   return $markup;
+}
-e3
+/**
  * Composes the TypedEntityReference to name type designations passed as associatve array.
+ *
-            f5e7f68e
+ * @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){
   $render_array = array();
   foreach($type_entity_refs as $type_status => $name_type){
-            f5e7f68e
+    $type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
     if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
       $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
+    }
     $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type)  . '"><span class="type_status">'. ucfirst($type_status) . "</span>: "
       . $name_type->label
       . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
       . '</div>');
+  }
   return $render_array;
+}
 /**
  * Composes the TypedEntityReference to specimen type designations passed as associatve array.
+ *
  * @param $type_entity_refs array
  *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
  *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
+ *
  * @ingroup compose
  */
 function compose_specimen_type_designations($type_entity_refs){
-e8173
+            Andreas Kohlbecker
-            f5e7f68e
+  $render_array = array();
-e8173
+            Andreas Kohlbecker
-            f5e7f68e
+  foreach($type_entity_refs as $type_status => $specimen_type){
     $type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($specimen_type->uuid));
-e8173
+            Andreas Kohlbecker
-            f5e7f68e
+    $preferredStableUri = '';
-e8173
+    $citation_markup = '';
     $media = '';
     // preferredStableUri
-            f5e7f68e
+    if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
       $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
+    }
-e8173
+            Andreas Kohlbecker
     $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
     if($mediaSpecimen){
       // compose output
       // mediaURI
       if(isset($mediaSpecimen->representations[0])) {
         $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
         $captionElements = array(
           '#uri' => t('open media'),
           'elements' => array('-none-'),
           'sources_as_content' => true
         );
         $media = compose_cdm_media_gallerie(array(
           'mediaList' => array($mediaSpecimen),
           'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
           'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
           'cols' => $gallery_settings['cdm_dataportal_media_cols'],
           'captionElements' => $captionElements,
         ));
+      }
       // citation and detail
       $annotations_and_sources = handle_annotations_and_sources(
           $mediaSpecimen,
           array(
               'sources_as_content' => true,
               'link_to_name_used_in_source' => false,
               'link_to_reference' => true,
               'add_footnote_keys' => false,
               'bibliography_aware' => false),
           '',
           null
       );
       if(is_array( $annotations_and_sources['source_references'])){
         $citation_markup = join(', ', $annotations_and_sources['source_references']);
+      }
+    }
     $render_array[] = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type)  . '">
         <span class="type_status">' . ucfirst($type_status) . "</span>: "
-            f5e7f68e
+      . $specimen_type->label
-e8173
+      . ($citation_markup ? ' '. $citation_markup : '')
-            f5e7f68e
+      . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
-e8173
+      . $media
-            f5e7f68e
+      . '</div>');
-e3
+            Andreas Kohlbecker
   return $render_array;
+}
-fd6da0b
+/**
-            d4ea0dd9
+ * Renders the name relationships.
-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 $current_taxon_uuid
  *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
-b7bbf68
+ * @return String
-            d4ea0dd9
+ *    The markup for the name relationships
-b7bbf68
+ */
-c088da3
+function render_name_relationships_of($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
-            f695daf4
+            Andreas Kohlbecker
-            6421984d
+  static $inverse_name_rels_uuids = array(UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
-b7bbf68
+  RenderHints::pushToRenderStack('homonym');
   // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
-            6421984d
+  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_TYPES, unserialize(CDM_NAME_RELATIONSHIP_TYPES_DEFAULT));
-            d4ea0dd9
+  $relations_array = array();
-b7bbf68
+            Andreas Kohlbecker
   if ($name_relations) {
-            d4ea0dd9
+    foreach ($name_relations as $name_rel) {
-c088da3
+      if (!(isset($selected_name_rel_uuids[$name_rel->type->uuid]) && $selected_name_rel_uuids[$name_rel->type->uuid])) {
-            6421984d
+        // skip if not selected in the settings
         continue;
-b7bbf68
+            Andreas Kohlbecker
-c088da3
+      $is_inverse_relation = array_search($name_rel->type->uuid, $inverse_name_rels_uuids) !== false;
       $is_current_name_to_name = $current_name_uuid == $name_rel->toName->uuid;
       $is_current_name_from_name = $current_name_uuid == $name_rel->fromName->uuid;
-            d4ea0dd9
+      $relationship_markup = null;
-            f1c8d19a
+            Andreas Kohlbecker
-c088da3
+      if($is_current_name_to_name && ($suppress_if_current_name_is_source && $is_inverse_relation || !$suppress_if_current_name_is_source)){
         $highlited_synonym_uuid = isset ($name_rel->fromName->taxonBases[0]->uuid) ? $name_rel->fromName->taxonBases[0]->uuid : '';
         $relationship_markup = render_taxon_or_name($name_rel->fromName,
           url(path_to_name($name_rel->fromName->uuid, $current_taxon_uuid, $highlited_synonym_uuid))
         );
       } else if($is_current_name_from_name && ($suppress_if_current_name_is_source && !$is_inverse_relation || !$suppress_if_current_name_is_source)){
-            d4ea0dd9
+        $highlited_synonym_uuid = isset ($name_rel->toName->taxonBases[0]->uuid) ? $name_rel->toName->taxonBases[0]->uuid : '';
-c088da3
+        $relationship_markup = render_taxon_or_name($name_rel->toName,
           url(path_to_name($name_rel->toName->uuid, $current_taxon_uuid, $highlited_synonym_uuid))
         );
-b7bbf68
+            Andreas Kohlbecker
-c088da3
+            Andreas Kohlbecker
-            d4ea0dd9
+      if($relationship_markup){
         if (count($relations_array)) {
-aa5dc6a
+          // lat: "non nec" == german: "weder noch"
-            d4ea0dd9
+          $relations_array [] = 'nec ' . $relationship_markup;
-aa5dc6a
+        } else {
-            d4ea0dd9
+          $relations_array [] = 'non ' . $relationship_markup;
-aa5dc6a
+            Andreas Kohlbecker
-            6421984d
+            Andreas Kohlbecker
-b7bbf68
+            Andreas Kohlbecker
+  }
   RenderHints::popFromRenderStack();
-            bbeade6a
+  return (count($relations_array) ?'<div class="name-relationships">[' . trim(join(" ", $relations_array)) . ']</div>' : '');
-            d4ea0dd9
+            Andreas Kohlbecker
 /**
  * @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];
+}

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