EDIT

<?php

/**

 * @file

 * Name theming functions.

 *

 * @copyright

 *   (C) 2007-2012 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

 */

/**

 * 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;

}

/**

 * Renders and array of CDM TypeDesignations

 *

 * @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">';

  $typeDesignation_footnotes = FALSE;

  $is_lectotype = FALSE;

  $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)){

    uksort($name_type_designations, "compare_type_designation_status");

    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)) {

        $citation_footnote_str = theme('cdm_reference', array('reference' => $specimen_type_designation->citation, 'doIconLink' => true));

        $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 .........................

  if(!empty($textual_type_designations)) {

    foreach ($textual_type_designations as $textual_type_designation) {

      $encasement =  $textual_type_designation->verbatim ? '"' : '';

      $out .= '<' . $element_tag . ' class="' . html_class_attribute_ref($textual_type_designation) . '">' . type_designation_status_label_markup(null)

        . ': ' .  $encasement . $textual_type_designation->text_L10n->text . $encasement . '</' . $element_tag . '>';

      $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,

          'add_footnote_keys' => false,

          'bibliography_aware' => false),

      '',

        RenderHints::getFootnoteListKey() // passing a defined key to avoid separate annotation footnote key see https://dev.e-taxonomy.eu/redmine/issues/8543

        );

      $out .= $annotations_and_sources['foot_note_keys'];

        if(is_array( $annotations_and_sources['source_references'])){

          $citation_markup = join(', ', $annotations_and_sources['source_references']);

        }

    }

  }

  // 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;

}

/**

 * 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>'

    ;

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function theme_cdm_homotypicSynonymLine($variables) {

  $taxon = $variables['taxon'];

  $out = '';

  $out .= '<li class="synonym">' . cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

  return $out;

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function theme_cdm_heterotypicSynonymyGroup($variables) {

  $homotypical_group = $variables['homotypicalGroup'];

  RenderHints::pushToRenderStack('heterotypicSynonymyGroup');

  $out = '';

  $out = '<div class="heterotypic-synonymy-group"><ul class="heterotypicSynonymyGroup">';

  $footnoteListKey = (isset($homotypical_group[0]) ? $homotypical_group[0]->uuid : 'NULL');

  RenderHints::setFootnoteListKey($footnoteListKey);

  $type_designations= type_designations_for_synonymy_group($homotypical_group);

  $is_first_entry = TRUE;

  foreach ($homotypical_group as $synonym) {

    if ($is_first_entry) {

      $is_first_entry = FALSE;

      // Is first list entry.

      $out .= '<li class="firstentry synonym">' . cdm_related_taxon($synonym, UUID_HETEROTYPIC_SYNONYM_OF) . '</li>';

    }

    else {

      $out .= '<li class="synonym">' . cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

    }

  }

  if (count($type_designations) > 0) {

    $out .= render_type_designations($type_designations);

  }

  $out .= '</ul>';

  // ------- footnotes ------- //

  $out .= '<ul class="footnotes">';

  $out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= '</ul>';

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Renders the homotypic synonymy group for the accepted taxon in the synonymy.

 *

 * Foonotes of the accepted taxon will also be rendered here in the

 * homotypic synonymy group even if the synonymList or prependedSynonyms are

 * empty. Therefore  the homotypic group and accepted taxon share the  same

 * footnote key.

 *

 * @param $variables

 *   an associative array:

 *   - synonymList: the list of cdm Synonym entities

 *   - accepted_taxon_uuid: the uuid of the accepted taxon

 *   - prependedSynonyms: further synonyms which should be prepended

 *      before the actual list of synonyms

 */

function theme_cdm_homotypicSynonymyGroup($variables) {

  $synonymList = $variables['synonymList'];

  $accepted_taxon_name_uuid = $variables['accepted_taxon_name_uuid'];

  $prependedSynonyms = $variables['prependedSynonyms'];

  RenderHints::pushToRenderStack('homotypicSynonymyGroup');

  $type_designations_in_group = NULL;

  $out = '<div class="homotypic-synonymy-group">';

  $type_designations = type_designations_for_synonymy_group($synonymList, $accepted_taxon_name_uuid);

  if (count($type_designations) > 0 || is_array($prependedSynonyms) || is_array($synonymList)) {

    $out .= '<ul class="homotypicSynonyms">';

  if (!empty($prependedSynonyms)) {

    foreach ($prependedSynonyms as $taxon) {

      $out .= '<li class="synonym">' . cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

    }

  }

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

    foreach ($synonymList as $synonym) {

      $out .= '<li class="synonym">' . cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';

    }

  }

  if (count($type_designations) > 0) {

    $out .= theme('cdm_typedesignations', array('typeDesignations' => $type_designations));

  }

  }

  $out .= '</ul>';

  // ------- footnotes ------- //

  // all foonotes of the homotypic group and also of the accepted taxon are

  // rendered here, both should have the same footnote key

  $out .= '<ul class="footnotes">';

  $out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'li'));

  $out .= '</ul>';

  $out .= '</div>';

  RenderHints::popFromRenderStack();

  return $out;

}