EDIT

<?php

/**

 * @file

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

 *

 * @copyright

 *   (C) 2007-2015 EDIT

 *   European Distributed Institute of Taxonomy

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

 *

 *   The contents of this module are subject to the Mozilla

 *   Public License Version 1.1.

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

 *

 * @author

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

 */

/**

 * @defgroup compose Compose functions

 * @{

 * Functions which are composing Drupal render arays

 *

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

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

 * responsible for creating the render arrays.

 *

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

 * which is used in the proxy_content() function.

 * @}

 */

/**

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

 *

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

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

 * The following keys are curretly recogized:

 *

 *   - list_of_taxa:

 *   - acceptedFor:

 *   - taxon_page_synonymy

 *   - typedesignations

 *   - taxon_page_title

 *   - polytomousKey

 *   - na: name + authorship

 *   - nar:name + authorship + reference

 *   - #DEFAULT

 *

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

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

 *

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

 * definitions array.

 * @see get_partDefinition($taxonNameType) for more information

 *

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

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

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

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

 *

 * @param string $renderPath

 *   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

 */

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

  static $default_render_templates = NULL;

  static $split_render_templates = NULL;

  if (!isset($default_render_templates)) {

    $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);

  }

  if($split_render_templates == NULL) {

    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);

    // needs to be converted to an array

    $render_templates = (convert_to_array($render_templates));

    // separate render templates which are combined with a comma

    $split_render_templates = array();

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

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

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

          $split_render_templates[$path] = $template;

        }

      } else {

        $split_render_templates[$key] = $template;

      }

    }

  }

  // get the base element of the renderPath

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

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

  } else {

    $renderPath_base = $renderPath;

  }

  $template = NULL;

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

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

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

  }

  // 2. Find best matching default RenderTemplate in theme

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

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

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

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

      if ($path == $renderPath) {

        $template = $t;

        break;

      }

    }

    // shorten by one element

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

  }

  // 3. Otherwise get default RenderTemplate from theme.

  if (!is_array($template)) {

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

  }

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

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

    if ($nameLink) {

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

    }

    else {

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

    }

  }

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

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

  }

  else {

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

  }

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

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

  }

  else {

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

  }

  return $template;

}

/**

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

 *

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

 *

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

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

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

 *   - reference: the nomenclatural reference,

 *   - microreference:  Volume, page number etc.

 *   - status:  The nomenclatural status of a name

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

 *

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

 * Usually the following parts are formed:

 *

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

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

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

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

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

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

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

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

 *  - statusPart: the nomenclatorical status

 *  - descriptionPart:

 *

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

 * specific parts part definitions:

 *

 *  - BotanicalName

 *  - ZoologicalName

 *  - #DEFAULT:  covers ViralNames and general NonViralNames

 *

 * An example:

 * @code

 * array(

 *    'ZoologicalName' => array(

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

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

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

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

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

 *    ),

 *    'BotanicalName' => array(

 *        'namePart' => array(

 *            'name' => TRUE,

 *            'authors' => TRUE,

 *        ),

 *        'referencePart' => array(

 *            'reference' => TRUE,

 *            'microreference' => TRUE,

 *        ),

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

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

 *    ),

 *  );

 * @endcode

 *

 */

function get_partDefinition($taxonNameType) {

  static $default_part_definitions = null;

  if (!isset($default_part_definitions)) {

    $default_part_definitions= unserialize(CDM_PART_DEFINITIONS_DEFAULT);

  }

  static $part_definitions = null;

  if (!isset($part_definitions)) {

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

  }

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

    return $part_definitions[$taxonNameType];

  } else {

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

  }

}

/**

 * Renders the markup for a CDM TaxonName instance.

 *

 * The layout of the name representation is configured by the

 * part_definitions and render_templates (see get_partDefinition() and

 * get_nameRenderTemplate())

 *

 * @param $taxonName

 *    cdm TaxonNameBase instance

 * @param $sec

 *    the sec reference of a taxon having this name (optional)

 * @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.

 *

 * @return string

 *  The markup for a taxon name.

 *

 */

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

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

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

    $taxonName = $taxon_name_or_taxon_base->name;

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

    $taggedTitle = $taxon_name_or_taxon_base->taggedTitle;

  } else {

    // assuming this is a TaxonNameBase

    $taxonName = $taxon_name_or_taxon_base;

    $taggedTitle = $taxon_name_or_taxon_base->taggedName;

  }

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

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

  // Apply definitions to template.

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

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

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

    }

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

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

    }

  }

  $secref_tagged_text = split_secref_from_tagged_text($taggedTitle);

  $nom_status_tagged_text = split_nomstatus_from_tagged_text($taggedTitle);

  normalize_tagged_text($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;

  // 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']);

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

      // Find author and split off from name.

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

      /*

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

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

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

      }

      */

      // Remove all authors.

      $taggedNameNew = array();

      foreach ($taggedName as $element) {

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

          $taggedNameNew[] = $element;

        }

        else {

          $lastAuthorElementString = $element->text;

        }

      }

      $taggedName = $taggedNameNew;

      unset($taggedNameNew);

    }

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

  }

  else {

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

  }

  // Fill name into $renderTemplate.

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

  // Fill with authorTeam.

  /*

  if($authorTeam){

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

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

  }

  */

  // Fill with reference.

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

    // 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;

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

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

    }

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

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

    // out of the reference.

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

      // If the nomenclaturalReference citation is not included in the

      // reference part but diplay of the microreference

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

      $citation = '';

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

        $separator = ": ";

        $citation = $taxonName->nomenclaturalMicroReference;

      }

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

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

    }

  }

  $is_reference_year = false;

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

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

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

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

      $is_reference_year = true;

    }

  }

  // Fill with status.

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

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

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

        array_setr('status', '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, 'span', '', array('postSeparator')) . '</span>', $renderTemplate);

      }

    }

  }

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

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

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

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

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

      };

      array_setr('secReference',

        $post_separator_markup

          . ' <span class="sec_reference">'

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

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

    }

  }

  // Fill with protologues etc...

  $descriptionHtml = '';

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

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

    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;

          $descriptionHtml .= theme("cdm_media", array(

              'descriptionElement' => $description_element,

              'mimeTypePreference' => array(

                'application/pdf',

                'image/png',

                'image/jpeg',

                'image/gif',

                'text/html',

              )

            )

          );

        }

      }

    }

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

  }

  // Render.

  $out = '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base). '" data-cdm-ref="/name/' . $taxonName->uuid . '">';

  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;

}

/**

 * Renders the string of Homonyms for a given taxon.

 *

 * @param $taxon

 *    A CDM Taxon instance

 * @return String

 *    The string of homomyns

 *

 * @throws \Exception

 */

function cdm_name_relationships_of($taxon) {

// =========== START OF HOMONYMS ========== //

  RenderHints::pushToRenderStack('homonym');

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

  // Later homonym or treated as later homonym AND bloking names.

  // TODO apply filter ? $name_rels_to_show = variable_get('name_relationships_to_show', NULL);

  $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);

  $homonyms_array = array();

  if ($name_relations) {

    foreach ($name_relations as $element) {

      $taxon_html = NULL;

      switch ($element->type->uuid) {

        case UUID_LATER_HOMONYM :

          $elementTaxonBasesUuid = isset ($element->toName->taxonBases [0]->uuid) ? $element->toName->taxonBases [0]->uuid : '';

          //from relation ships -> only shown at fromName-synonym

          if ($taxon->name->uuid == $element->fromName->uuid) {

            $taxon_html =render_taxon_or_name($element->toName,

              url(path_to_name($element->toName->uuid, $taxon->uuid, $elementTaxonBasesUuid))

            );

          }

          break;

        case UUID_TREATED_AS_LATER_HOMONYM :

          $elementTaxonBasesUuid = isset ($element->toName->taxonBases [0]->uuid) ? $element->toName->taxonBases [0]->uuid : '';

          //from relation ships -> only shown at fromName-synonym

          if ($taxon->name->uuid == $element->fromName->uuid) {

            $taxon_html = render_taxon_or_name($element->toName, url(path_to_name($element->toName->uuid)));

          }

          break;

        case UUID_BLOCKING_NAME_FOR :

          $elementTaxonBasesUuid = isset ($element->fromName->taxonBases [0]->uuid) ? $element->fromName->taxonBases [0]->uuid : '';

          //to relation ships -> only shown at toName-synonym

          if ($taxon->name->uuid == $element->toName->uuid) {

            $taxon_html = render_taxon_or_name($element->fromName,

              url(path_to_name($element->fromName->uuid, $taxon->uuid, $elementTaxonBasesUuid))

            );

          }

          break;

        default:

          $taxon_html = NULL;

      }

      if (isset($taxon_html) && $taxon_html) {

        if (count($homonyms_array)) {

          $homonyms_array [] = 'nec ' . $taxon_html;

        }

        else {

          $homonyms_array [] = 'non ' . $taxon_html;

        }

      }

    }

  }

  RenderHints::popFromRenderStack();

  return (count($homonyms_array) ?'[' . trim(join(" ", $homonyms_array)) . ']' : '');

}

  /**

 * 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;

}