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 array $variables

 *   - typeDesignations: an array of cdm TypeDesignation entities to render

 */

function theme_cdm_typedesignations($variables) {

  $typeDesignations = $variables['typeDesignations'];

  // need to add element to render path since type designations

  // need other name render template

  RenderHints::pushToRenderStack('typedesignations');

  $out = '<ul class="typeDesignations">';

  $typeDesignation_footnotes = FALSE;

  $is_lectotype = FALSE;

  $specimen_type_designations = array();

  $separator = ',';

  foreach ($typeDesignations as $typeDesignation) {

    if ($typeDesignation->class == 'SpecimenTypeDesignation') {

      // SpecimenTypeDesignations should be ordered. Collect theme here only.

      $specimen_type_designations[] = $typeDesignation;

    }

    // It is a lectotype?

    else {

      if (isset($typeDesignation->typeStatus->uuid) && $typeDesignation->typeStatus->uuid == UUID_NTD_LECTOTYPE) {

        $is_lectotype = TRUE;

      }

      // It's a NameTypeDesignation.

      if ($typeDesignation->notDesignated) {

        $out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>: ' . t('not designated') . '</li>';

      }

      elseif ($typeDesignation->typeName) {

        $link_to_name_page = url(path_to_name($typeDesignation->typeName->uuid));

        $out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>';

        if ($typeDesignation->citation) {

          $out .= type_designation_citation_layout($typeDesignation, $separator);

        }

        $referenceUri = '';

        if (isset($typeDesignation->typeName->nomenclaturalReference)) {

          $referenceUri = url(path_to_reference($typeDesignation->typeName->nomenclaturalReference->uuid));

        }

        $out .= ': ' . render_taxon_or_name($typeDesignation->typeName, $link_to_name_page, $referenceUri, TRUE, TRUE);

      }

    }

  }

  if (!empty($specimen_type_designations)) {

    // Sorting might be different for dataportals so this has to be

    // parameterized.

    usort($specimen_type_designations, "compare_specimenTypeDesignationStatus");

    foreach ($specimen_type_designations as $type_designation) {

      $typeReference = '';

      if (!empty($type_designation->citation)) {

        $citation_footnote_str = theme('cdm_reference', array('reference' => $type_designation->citation));

        $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $type_designation->citation->uuid);

        if(isset($author_team->titleCache)){

          $authorteam_str = $author_team->titleCache . partialToYear($type_designation->citation->datePublished->start);

          if($authorteam_str == $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 = '';

        }

        $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,

           ));

        }

        $typeReference .= '&nbsp;(' . t('designated by') . '&nbsp;<span class="typeReference">'. $authorteam_str . '</span>';

        if (!empty($type_designation->citationMicroReference)) {

          $typeReference .= ':' . $type_designation->citationMicroReference;

        }

        $typeReference .= $footnote_key_markup . ')';

      }

      $derivedUnitFacadeInstance = null;

      $out .= '<li class="specimenTypeDesignation">';

      $out .= '<span class="status">'

        . ((isset($type_designation->typeStatus->representation_L10n)) ? $type_designation->typeStatus->representation_L10n : t('Type'))

        . $typeReference

        . '</span>';

      if (isset($type_designation->typeSpecimen)) {

        $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);

      }

      if ( isset($derivedUnitFacadeInstance ) ){

        $out .= ': ' . $derivedUnitFacadeInstance->titleCache; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));

      }

      // Footnotes for collection acronyms.

      // 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 .= '</li>';

    }

  }

  $out .= '</ul>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * FIXME this definitively has to be in another spot.

 * just didn't know where to put it right now.

 * Compares the status of two SpecimenTypeDesignations

 *

 * @param string $a

 *   A SpecimenTypeDesignations.

 * @param string $b

 *   SpecimenTypeDesignations.

 */

function compare_specimenTypeDesignationStatus($a, $b) {

  /*

  This is the desired sort order as of now: Holotype Isotype Lectotype

  Isolectotype Syntype.

  TODO Basically, what we are trying to do is, we define

  an ordered array of TypeDesignation-states and use the index of this array

  for comparison. This array has to be filled with the cdm- TypeDesignation

  states and the order should be parameterisable inside the dataportal.

  */

  // Make that static for now.

  $typeOrder = array(

    'Holotype',

    'Isotype',

    'Lectotype',

    'Isolectotype',

    'Syntype',

  );

  $aQuantifier = FALSE;

  $bQuantifier = FALSE;

  if (isset($a->typeStatus->label) && isset($b->typeStatus->label)) {

    $aQuantifier = array_search($a->typeStatus->label, $typeOrder);

    $bQuantifier = array_search($b->typeStatus->label, $typeOrder);

  }

  if ($aQuantifier == $bQuantifier) {

    // Sort alphabetically.

    return (isset($a->typeStatus->label) && isset($b->typeStatus->label) && $a->typeStatus->label < $b->typeStatus->label) ? -1 : 1;

  }

  return ($aQuantifier < $bQuantifier) ? -1 : 1;

}

/**

 * @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) {

  $homotypicalGroup = $variables['homotypicalGroup'];

  RenderHints::pushToRenderStack('heterotypicSynonymyGroup');

  $out = '';

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

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

  RenderHints::setFootnoteListKey($footnoteListKey);

  $is_first_entry = TRUE;

  $typeDesignations = NULL;

  foreach ($homotypicalGroup as $synonym) {

    if ($is_first_entry) {

      $is_first_entry = FALSE;

      $typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);

      // 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 ($typeDesignations) {

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

  }

  $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');

  $homonym_typeDesignations = NULL;

  // TODO improve typeDesignations retrieval: wouldn't it be suffcient to retrieve all typeDesignations

  // only from the accepted taxon?

  $accepted_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $accepted_taxon_name_uuid);

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

  if (isset ($accepted_typeDesignations) || is_array($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>';

    }

  }

  $homonym_typeDesignations = NULL;

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

    foreach ($synonymList as $synonym) {

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

    }

    $homonym_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);

  }

  // type designations

  if ($accepted_typeDesignations) {

    $type_designations = filter_cdm_entity_list($homonym_typeDesignations, $accepted_typeDesignations);

  }

  else {

    $type_designations = $homonym_typeDesignations;

  }

  if ($type_designations) {

    $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;

}