EDIT

<?php

/**

 * @file

 * Page 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

 */

/**

 * Returns HTML for the default title of a taxon page.

 *  * The returned title is a formatted taxon name.

 *

 * @param array $variables

 *   An associative array containing:

 *   - taxon: The taxon name being formatted for the title.

 *   - uuid: UUID for the taxon.

 *

 * @return string

 *  Markup for a taxon page title

 *

 * @ingroup themeable

 */

function theme_cdm_taxon_page_title($variables) {

  $taxon = $variables['taxon'];

  RenderHints::pushToRenderStack('taxon_page_title');

  $referenceUri = '';

  $out = '';

  if (isset($taxon->name->nomenclaturalReference)) {

    $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

  }

  $out .= render_taxon_or_name($taxon, NULL, $referenceUri, FALSE);

  RenderHints::popFromRenderStack();

  return '<span class="' . $taxon->class . '">' . $out . '</span>';

}

/**

 * Returns HTML for the default title of a specimen page.

 *  * The returned title is a the identifier of the specimen.

 *

 * @param array $variables

 *   An associative array containing:

 *   - specimen: The specimen being formatted for the title.

 *

 * @return string

 *  Markup for the title of a specimen page

 *

 * @ingroup themeable

 */

function theme_cdm_specimen_page_title($variables)

{

    $specimen = $variables['specimen'];

    RenderHints::pushToRenderStack('specimen_page_title');

    $referenceUri = '';

    $out = '';

    $collection = null;

    if ($specimen->collection) {

        if ($specimen->collection->code) {

            $collection = $specimen->collection->code;

        } elseif ($specimen->collection->name) {

            $collection = $specimen->collection->name;

        }

    }

    if($specimen->accessionNumber){

        $specimenID = $specimen->accessionNumber;

    }

    elseif($specimen->barcode){

      $specimenID = $specimen->barcode;

    }

    elseif($specimen->catalogNumber) {

      $specimenID = $specimen->catalogNumber;

    }

    elseif($specimen->titleCache) {

        $specimenID = $specimen->titleCache;

    }

    if(!isset($specimenID) and !isset($collection)){

      $specimenID = $specimen->uuid;

    }

  $out .= "Specimen ";

  if($collection){

    $out .= $collection." ";

  }

  $out .= $specimenID;

  RenderHints::popFromRenderStack();

  return '<span class="' . $specimen->class . '">' . $out . '</span>';

}

/**

 * Returns HTML for the default title for a name page.

 *

 * The returned title is a formatted name.

 *

 * @param array $variables

 *   An associative array containing:

 *   - taxon_name: The taxon name object.

 *

 * @return string

 *  Markup for the title of a name page

 *

 * @ingroup themeable

 */

function theme_cdm_name_page_title($variables) {

  $taxon_name = $variables['taxon_name'];

  RenderHints::pushToRenderStack('taxon_page_title');

  $referenceUri = NULL;

  if (isset($taxon_name->nomenclaturalReference)) {

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

  }

  $out = '<span class="' . $taxon_name->class . '">'

    . render_taxon_or_name($taxon_name, NULL, $referenceUri, FALSE)

    . '</span>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Returns HTML containing the synonymy for the accepted taxon.

 *

 * Shows the whole synonymy for the accepted taxon.

 * The synonymy list is headed by the complete scientific name

 * of the accepted taxon with nomenclatural reference.

 *

 * @param object $taxon

 * @param boolean $add_accepted_taxon

 *

 * @return array

 *  Drupal render array for the synonymy

 *

 * @throws Exception

 *

 * @ingroup compose

 */

function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {

  RenderHints::pushToRenderStack('taxon_page_synonymy');

  // footnote key for the homotypic group and accepted taxon,

  // both should have the same footnote key

  RenderHints::setFootnoteListKey(RenderHints::getRenderPath());

  $synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));

  $out = '';

  // Render accepted taxon.

  //

  // foonotes of the accepted taxon will be rendered in the homotypic group section

  // even if there are not synonyms in the homotypic group

  // homotypic group and accepted taxon should have the same footnote key

  $referenceUri = '';

  if ($add_accepted_taxon) {

    // remember the last part of the render path

    $synonymy_render_path = RenderHints::getRenderPath();

    // set new render path for the accepted taxon so

    // it can be styled differently via the name render part definitions

    RenderHints::pushToRenderStack('accepted_taxon');

    $accepted_name = '';

    if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {

      $label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);

      $accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';

    }

    if (isset($taxon->name->nomenclaturalReference)) {

      $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

    }

    $accepted_name .= '<div class="accepted-name">';

    $accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);

    $name_relations = cdm_name_relationships_for_taxon($taxon);

    $name_relationships = render_name_relationships_of($name_relations, $taxon->name->uuid, $taxon->uuid);

    // Render relationships of accepted name.

    if($name_relationships){

      $accepted_name .= ' <span class="name_relationships">' . $name_relationships . '</span>';

    }

      // handle annotations of the name and taxon

    $special_annotations_array = array();

    $special_annotations_array[] = $taxon->name;

    $special_annotations_array[] = $taxon;

    $accepted_name .= theme('cdm_annotations_as_footnotekeys', array(

        'cdmBase_list' => $special_annotations_array,

        'footnote_list_key' => $synonymy_render_path . '-annotations')

      );

    $accepted_name .= '</div>';

    RenderHints::popFromRenderStack();

  }

  // --- Render homotypic synonymy group

  if (!empty($accepted_name)) {

    $out .= $accepted_name;

  }

  // Render the homotypicSynonymyGroup including the type information.

  $out .= theme(

      'cdm_homotypicSynonymyGroup',

      array(

          'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,

          'accepted_taxon_name_uuid' => $taxon->name->uuid

      )

    );

  // Render accepted taxon heterotypic synonymy groups.

  if ($synomymie->heterotypicSynonymyGroups) {

    foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {

      $out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));

    }

  }

  // Render taxon relationships.

  if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {

    $taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);

    $out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);

  }

  RenderHints::popFromRenderStack();

  return markup_to_render_array($out);

}

/**

 * Returns HTML for the given result page including a pager.

 *

 * @param array $variables

 *   An associative array containing:

 *   - pager: The cdmlib pager object containing the result set of cdm base

 *     objects (currently this function can only handle taxon instances =>

 *     TODO)

 *   - path: The target path for the pager links, this will usually point to

 *     'cdm_dataportal/search/results/taxon'

 *

 * @return string

 *  Markup for the result page

 *

 * @throws Exception

 *

 * @ingroup themeable

 */

function theme_cdm_search_taxa_results($variables)

{

  $pager = $variables['pager'];

  $path = $variables['path'];

  $freetextSearchResults = array();

  // If the pager contains records of SearchResults, extract the taxa and use

  // them as records instead.

  if (isset($pager->records[0]) && $pager->records[0]->class == "SearchResult") {

    $freetextSearchResults = $pager->records;

    $taxa = array();

    // $highlightedFragments = array();

    foreach ($pager->records as $searchResult) {

      $taxa[] = &$searchResult->entity;

      /*

       if(!isset($searchResult->fieldHighlightMap)){

      $searchResult->fieldHighlightMap = NULL;

      }

      $fragmentHighlighting[] = $searchResult->fieldHighlightMap;

      */

    }

    $pager->records = $taxa;

  }

  // Add thumbnails checkbox and refine search link.

  $out = '<div class="page_options">';

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

    if (cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) {

      $out .= '<div id="backButton">' . l(t('Modify search'), cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) . '</div>';

    }

  }

  if (variable_get(SEARCH_RESULTS_SHOW_THUMBNAIL_CHECKBOX, SEARCH_RESULTS_SHOW_THUMBNAIL_CHECKBOX_DEFAULT)) {

    $out .= '<form name="pageoptions"><div id="showThumbnails"><input class="showThumbnails" type="checkbox" name="showThumbnails" ' . (do_showThumbnails() == 1 ? 'checked="checked"' : '') . '> ' . t('Display image thumbnails') . '</div></form>';

  }

  $out .= '</div>';

  $classification = cdm_dataportal_searched_in_classification();

  if (  count(cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY)) > 1 ) { // FIXME use a count REST method for this!!!

    $out .= '<div id="search-summary">' . t('results for') . ' ';

    if ($classification != NULL) {

      $out .=  $classification->titleCache ;

    } else {

     $out .= t('any classification');

    }

    $out .= ':</div>';

  }

  // List results.

  if (isset($pager->records) && count($pager->records) > 0) {

    $out .= '<div id="search_results">';

    $list_of_taxa = compose_list_of_taxa($pager->records, $freetextSearchResults, $classification === NULL);

    $out .= drupal_render($list_of_taxa);

    $out .= '</div>';

    $out .= theme('cdm_pager', array(

        'pager' => $pager,

        'path' => $path,

        'parameters' => $_REQUEST,

    ));

  } else {

    $out .= '<h4 class="error">' . t('Sorry, no matching entries found.') . '</h4>';

  }

  return $out;

}

/**

 * TODO Implementation of Hook taxon_image_gallery()

 *

 * @param object $taxon

 * @param object $media

 *

 * @return string

 *  Markup for the default media gallery

 */

function taxon_image_gallery_default($taxon, $media) {

  $hasImages = isset($media[0]);

  if ($hasImages) {

    $maxExtend = 150;

    $cols = 3;

    $maxRows = FALSE;

    $alternativeMediaUri = NULL;

    /* Comment @WA: was in D5:

    $captionElements = array(

      'title',

      'rights',

      '#uri' => t('Open Image'),

    );

    */

    $captionElements = array(

      'title',

      'description',

      'artist',

      'location',

      'rights',

      '#uri' => t('Open image'),

    );

    $gallery_name = $taxon->uuid;

    $mediaLinkType = 'LIGHTBOX';

    // $gallery_settings = getGallerySettings(CDM_DATAPORTAL_MEDIA_GALLERY_NAME);

    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_TAXON_MEDIA_GALLERY_NAME_TAB);

    $out = '<div class="image-gallerie">';

    $out .= compose_cdm_media_gallerie(array(

      'mediaList' => $media,

      'galleryName' => $gallery_name,

      'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],

      'cols' => $gallery_settings['cdm_dataportal_media_cols'],

      'maxRows' => 0, // Ignore maxrows settings.

      'captionElements' => $captionElements,

      'mediaLinkType' => $mediaLinkType,

      'alternativeMediaUri' => NULL,

      'galleryLinkUri' => NULL,

      'showCaption' => $gallery_settings['cdm_dataportal_show_thumbnail_captions'],

    ));

    $out .= '</div>';

  }

  else {

    $out = 'No images available.';

  }

  return $out;

}

/**

 * TODO Implementation of Hook taxon_image_gallery()

 *

 * @param object $taxon

 * @param object $media

 *

 * @return string

 *  Markup for the fsi media gallery

 *

 * @throws Exception

 */

function taxon_image_gallery_fsi($taxon, $media) {

  $flashLink = isset($media[0]);

  if ($flashLink) {

    if (module_exists("fsi_gallery")) {

      $out = theme("fsi_gallery", array('taxon' => $taxon, 'media' => $media));

    }

    else {

      $message = t('In order to use the FSI gallery you must enable the according ') . l(t("module"), "admin/modules");

      drupal_set_message($message, "error");

      $out = '<h3>' . $message . '</h3>';

    }

  }

  else {

    $out = 'No images available.';

  }

  return $out;

}

/**

 * Returns a drupal render array for a single reference page.

 *

 * Composes a page with all data on a single reference.

 *

 * @param string $uuid

 *   An uuid for a cdm reference.

 *

 * @return array

 *  A drupal render array

 *

 * @throws Exception

 *

 * @ingroup compose

 */

function compose_cdm_reference_page($uuid) {

  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);

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

    drupal_set_title($reference->titleCache, PASS_THROUGH);

  }

  $field_order = array(

    "title",

    "abbrevTitle",

    // "titleCache" abbrevTitleCache

    // "citation",

    "authorship",

    "editor",

    "publisher",

    "placePublished",

    "datePublished",

    "year",

    "edition",// Class Book.

    "volume",// Class Article.

    "seriesPart",

    "inReference",

    "nomRefBase", // Class BookSection, Book, Article.

    "pages",// Class Article.

    "series",// Class Article, PrintSeries.

    "school",// Class Thesis.

    "institution",// Class Report.

    "organization",// Class Proceedings.

    "nextVersion",

    "previousVersion",

    "isbn",// Class Book.

    "issn",// Class Journal.

    "doi",

    "uri"

  );

  $table_rows = array();

  if (!isset($reference->authorship)) {

    $authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);

    $reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';

  }

  if (!isset($reference->inReference)) {

    $reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(

      $reference->uuid,

      "inReference",

    ));

  }

  foreach ($field_order as $fieldname) {

    if (isset($reference->$fieldname)) {

      if ($fieldname == "datePublished") {

        $period = $reference->$fieldname;

        $datePublished = timePeriodToString($period);

        if (isset($datePublished) && $datePublished != '') {

          $table_rows[] = array(

            t("Date published"),

            $datePublished,

          );

        }

        // $datePublished = array(t(ucfirst(strtolower($fieldname))),

        // $datePublished);

      }

      elseif ($fieldname == "doi" && is_object($reference->doi)) {

        $table_rows[] = array(

          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),

          cdm_doi($reference->doi, false)

        );

      }

      elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {

        $table_rows[] = array(

          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),

          cdm_external_uri($reference->uri, false)

        );

      }

      elseif (is_object($reference->$fieldname)) {

        if ($fieldname == "authorship") {

          $dump = $reference->$fieldname;

          $teammembers = "teamMembers";

          $team = $dump->$teammembers;

          $nameArray = array();

          foreach ($team as $member) {

            if (strlen($member->lastname) > 0) {

              $nname = $member->lastname;

              $name = $nname;

              if (strlen($member->firstname) > 0) {

                $vname = $member->firstname;

                $name = $vname . " " . $nname;

              }

              $nameArray[] = $name;

            }

            else {

              if (strlen($member->titleCache) > 0) {

                $nameArray[] = $member->titleCache;

              }

            }

          }

          $value = join($nameArray, ", ");

        }

        elseif ($fieldname == "inReference") {

          $type = $reference->$fieldname->type;

          $value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));

          switch ($type) {

            case "Book":

              $fieldname = "in book";

              break;

            case "Journal":

              $fieldname = "in journal";

              break;

            case "Proceedings":

              $fieldname = "in proceedings";

              break;

          }

        }

        else {

          $value = $reference->$fieldname->titleCache;

        }

        if (isset($value) && $value != '') {

          $table_rows[] = array(

            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),

            $value,

          );

        }

      }

      else {

        if (isset($reference->$fieldname) && $reference->$fieldname != '') {

          $table_rows[] = array(

            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),

            $reference->$fieldname,

          );

        }

      }

    }

  }

  $out = theme_table(array(

      'header' => array(),

      'rows' => $table_rows,

      'attributes' => array(

        'class' => html_class_attribute_ref($reference)

      ),

      'caption' => NULL,

      'colgroups' => NULL,

      'sticky' => NULL,

      'empty' => NULL,

  ));

  if($reference->referenceAbstract){

    $out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';

  }

  // Annotations below the table.

  $annotations = cdm_ws_getAnnotationsFor($reference);

  $out .= theme("cdm_annotations", array('annotations' => $annotations));

  $registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));

  if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){

    $out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list\">";

    foreach($registration_working_set->registrationDTOs as $registration_dto){

      if($registration_dto->status == "PUBLISHED"){

        $registration_render_a = compose_registation_dto($registration_dto, false, true);

        $registration_render_a["#prefix"] = "<div class=\"item\">";

        $registration_render_a["#suffix"] = "</div>";

        $out .= drupal_render($registration_render_a);

      }

    }

    $out .= "</div>";

  }

  return markup_to_render_array($out);

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_media_page($variables) {

  $media = $variables['media'];

  $mediarepresentation_uuid = $variables['mediarepresentation_uuid'];

  $partId = $variables['partId'];

  $out = '';

  // Determine which representation and which part to show

  $active_representation_index = 0;

  if (!$mediarepresentation_uuid) {

    // no representation requested by the method parameters, find the best one

    $representations = cdm_preferred_media_representations($media, array('image/png', 'image/jpeg', 'image/gif'), null, null);

    if($representations  && count($representations) > 0){

      $preferred_representation = array_shift($representations);

      $mediarepresentation_uuid = $preferred_representation->uuid;

    }

  }

  if($mediarepresentation_uuid){

    foreach ($media->representations as $representation) {

      if ($representation->uuid == $mediarepresentation_uuid) {

        break;

      }

      $active_representation_index++;

    }

  }

  $active_part_index = 0;

  if (is_uuid($partId)) {

    foreach ($media->representations[$active_representation_index]->parts as $part) {

      if ($part->uuid == $partId) {

        break;

      }

      $active_part_index++;

    }

  }

  else if(is_numeric($partId)){

    $active_part_index = $partId;

  }

  $media_metadata = read_media_metadata($media);

  // $title = $media->titleCache;

  $title = $media_metadata['title'];

  $imageMaxExtend = variable_get('image-page-maxextend', 400);

  if (!$title) {

    $title = 'Media ' . $media->uuid . '';

  }

  drupal_set_title($title, PASS_THROUGH);

  $out .= '<div class="media cdm_media_viewer_image">';

  if(preg_match('/cdm_dataportal\/taxon\//', $_SERVER['HTTP_REFERER']) ){

    if(variable_get('cdm_dataportal_taxonpage_tabs', 1)){

      // taxon page with tabs

      $out .= '<div id="backToGalleryButton">' . l(t('Back to images'), $_SESSION['cdm']['last_gallery']) . '</div>';

    } else {

      // tabless mode

      $out .= '<div id="backToGalleryButton">' . l(t('Back to taxon page'), $_SESSION['cdm']['last_gallery']) . '</div>';

    }

  }

  $out .= '<div class="viewer">';

  $out .= cdm_openlayers_image($media->representations[$active_representation_index]->parts[$active_part_index], $imageMaxExtend);

  $out .= '</div>';

  // General media metadata.

  $metadataToPrint = theme('cdm_media_caption', array('media' => $media, 'sources_as_content' => true));

  $out .= $metadataToPrint;

  $cdm_standard_image_viewer_settings = get_array_variable_merged(CDM_STANDARD_IMAGE_VIEWER, CDM_STANDARD_IMAGE_VIEWER_DEFAULT);

  if ($cdm_standard_image_viewer_settings['media_representation_details_enabled'] == 1){

    // Tabs for the different representations.

    // Representation(-part) specific metadata.

    $thumbnailMaxExtend = 100;

    $out .= '<h3>' .t('Media representations') .'</h3><ul id="media-representations">';

    $r_i = 0;

    foreach ($media->representations as $representation) {

      $out .= '<li><strong>'. t('Representation') . ' ' . $r_i . "</strong> ($representation->mimeType)" ;

      // parts

      $active_part_index = 0;

      $table_class_attribute = '';

      if($partIdx == $active_part_index && $active_representation_index == $r_i ){

        $table_class_attribute = 'class="active"';

      }

      $out .= "<table $table_class_attribute>";

      foreach ($representation->parts as $part) {

        $out .= '<tr><th>' . t('Part') . ' ' . ($active_part_index + 1) . '</th></tr><tr><td>';

        switch ($part->class) {

          case 'ImageFile':

            $out .= $part->width . 'x' . $part->height . ' px - ' . $part->size . ' kB';

            break;

          case 'AudioFile':

          case 'MovieFile':

            $out .= t('Duration') . ': ' . $part->duration . 's - ' . $part->size . ' kB';

            break;

          default:

            $out .= $part->size . 'k';

        }

        $out .= '</td><td><a href="' . url(path_to_media($media->uuid, $representation->uuid, $active_part_index)) . '">'

          . cdm_media_gallerie_image($part, $thumbnailMaxExtend, TRUE);

        $active_part_index++;

      }

      $out .= '</table>';

      $out .=  '</li>';

      $r_i++;

    }

    $out .= '</ul>';

  }

  $out .= '</div>';

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function theme_cdm_polytomousKey_page($variables) {

  $polytomousKey = $variables['polytomousKey'];

  drupal_set_title($polytomousKey->titleCache, PASS_THROUGH);

  $out = theme("cdm_IdentificationKey", array(

    'identificationKey' => $polytomousKey,

    'doLinkToKeyPage' => FALSE,

    'showIdentificationKeyTitle' => FALSE,

    ));

  // Key nodes in linked style.

  $out .= theme('cdm_polytomousKey', array('polytomousKey' => $polytomousKey));

  /*

   * FIXME implement node type for keys !!!

   * (wrapping the content in the cdm_dataportal.node becomes obsolete then).

   */

  return '<div id="identificationKey">' . $out . '</div>';

}