EDIT

<?php

/**

 * @file

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

 *

 * @copyright

 *   (C) 2007-2015 EDIT

 *   European Distributed Institute of Taxonomy

 *   http://www.e-taxonomy.eu

 *

 *   The contents of this module are subject to the Mozilla

 *   Public License Version 1.1.

 * @see http://www.mozilla.org/MPL/MPL-1.1.html

 *

 * @author

 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>

 */

/**

 * @defgroup compose Compose functions

 * @{

 * Functions which are composing Drupal render arays

 *

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

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

 * responsible for creating the render arrays.

 *

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

 * which is used in the proxy_content() function.

 * @}

 */

/**

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

 *

 *

 *

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

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

 *

 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy

 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy

 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy

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

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

 *

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

 * definitions array.

 * @see get_partDefinition($taxonNameType) for more information

 *

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

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

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

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

 *

 *   @see RenderHints::getRenderPath()

 * @param string $nameLink

 *   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

 */

  static $default_render_templates = NULL;

    $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);

  }

    // needs to be converted to an array

    // separate render templates which are combined with a comma

    $split_render_templates = array();

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

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

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

          $split_render_templates[$path] = $template;

        }

      } else {

        $split_render_templates[$key] = $template;

      }

    }

  // get the base element of the renderPath

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

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

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

        break;

      }

    }

    // shorten by one element

  if (!is_array($template)) {

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

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

    if ($nameLink) {

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

    }

    else {

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

    }

  }

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

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

  }

  else {

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

  }

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

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

  }

  else {

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

  }

  return $template;

}

/**

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

 *

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

 *

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

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

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

 *   - reference: the nomenclatural reference,

 *   - microreference:  Volume, page number etc.

 *   - status:  The nomenclatural status of a name

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

 *

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

 * Usually the following parts are formed:

 *

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

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

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

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

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

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

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

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

 *  - statusPart: the nomenclatorical status

 *  - descriptionPart:

 *

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

 * specific parts part definitions:

 *

 *  - BotanicalName

 *  - ZoologicalName

 *  - #DEFAULT:  covers ViralNames and general NonViralNames

 *

 * An example:

 * @code

 * array(

 *    'ZoologicalName' => array(

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

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

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

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

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

 *    ),

 *    'BotanicalName' => array(

 *        'namePart' => array(

 *            'name' => TRUE,

 *            'authors' => TRUE,

 *        ),

 *        'referencePart' => array(

 *            'reference' => TRUE,

 *            'microreference' => TRUE,

 *        ),

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

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

 *    ),

 *  );

 * @endcode

 *

 *    A cdm TaxonNameType entity

 *

function get_partDefinition($taxonNameType) {

  static $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)) {

    return $part_definitions[$taxonNameType];

    return $part_definitions[$dtype];

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

  }

}

/**

 * Renders the markup for a CDM TaxonName instance.

 *

 * The layout of the name representation is configured by the

 * part_definitions and render_templates (see get_partDefinition() and

 * get_nameRenderTemplate())

 *

 * @param $taxonName

 *    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.

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

 *   This is useful when rendering taxon relation ships.

 * @return string

 *  The markup for a taxon name.

 *

 */

function render_taxon_or_name($taxon_name_or_taxon_base, $nameLink = NULL, $refenceLink = NULL,

    $taxonName = $taxon_name_or_taxon_base->name;

    $taggedTitle = $taxon_name_or_taxon_base->taggedTitle;

  } else {

    $taggedTitle = $taxon_name_or_taxon_base->taggedName;

  }

  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);

  // 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'];

    }

  }

  $nom_status_tagged_text = tagged_text_extract_nomstatus($taggedTitle);

  $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;

  if($doubtful_marker){

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

  }

  // 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);

  }

  if ($firstEntryIsValidNamePart) {

    $taggedName = $taggedTitle;

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

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

      // Find author and split off from name.

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

      /*

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

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

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

      }

      */

      // Remove all authors.

      $taggedNameNew = array();

      foreach ($taggedName as $element) {

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

          $taggedNameNew[] = $element;

        }

        else {

          $lastAuthorElementString = $element->text;

        }

      }

      $taggedName = $taggedNameNew;

  else {

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

  // Fill name into $renderTemplate.

  // Fill with authorTeam.

  /*

  if($authorTeam){

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

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

  }

  */

  // Fill with reference.

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

    $registration_markup = render_registrations($registrations);

    $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;

    }

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

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

    // out of the reference.

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

      // If the nomenclaturalReference citation is not included in the

      $citation = '';

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

        $separator = ": ";

        $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;

    }

  }

  }

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

    }

  }

  // 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;

              $description_element,

              array(

                'image/png',

                'image/jpeg',

                'image/gif',

                'text/html',

              )

          );

        }

      }

    }

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

  }

  // Render.

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

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

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

  }

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

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

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

    $separator = '';

    $partHtml = '';

    $uri = FALSE;

    if (!is_array($part)) {

      continue;

    }

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

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

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

    }

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

      $html = '';

      if (is_array($content)) {

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

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

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

        }

      }

      elseif (is_string($content)) {

        $html = $content;

      }

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

    }

    if ($uri) {

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

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

    }

    else {

      $out .= $separator . $partHtml;

    }

  }

  $out .= '</span>';

  if ($show_annotations) {

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

  }

  return $out;

}

 * @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;

}

/**

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

 *

 *   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){

    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){

    $type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($specimen_type->uuid));

    $media = '';

    // preferredStableUri

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

    }

    $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($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>: "

  return $render_array;

}

 *    The list of CDM NameRelationsips

 * @param $current_name_uuid

 *    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.

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

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

  if ($name_relations) {

        continue;

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

      $is_current_name_from_name = $current_name_uuid == $name_rel->fromName->uuid;

        $highlited_synonym_uuid = isset ($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))