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.

 *

 * @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 .= theme('cdm_taxonName', array(

    'taxonName' => $taxon->name,

    'nameLink' => NULL,

    'refenceLink' => $referenceUri,

    'show_annotations' => FALSE,

  ));

  RenderHints::popFromRenderStack();

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

 *

 * @ingroup themeable

 */

function theme_cdm_name_page_title($variables) {

  $taxon_name = $variables['taxon_name'];

  RenderHints::pushToRenderStack('taxon_page_title');

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

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

  }

  $out = '<span class="' . $taxon_name->class . '">' . theme('cdm_taxonName', array(

    'taxonName' => $taxon_name,

    'nameLink' => NULL,

    'refenceLink' => $referenceUri,

    'show_annotations' => FALSE,

  )) . '</span>';

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Returns HTML for a taxon page.

 *

 * A wrapper function that groups available information to show by default,

 * when a taxon page is requested by the browser.

 * Individual themeing has to decide what this page should include (see methods

 * beneath) and what information should go into tabs or should not be shown

 * at all.

 *

 * It is headed by the name of the accepted taxon without author and reference.

 *

 * @param array $variables

 *   An associative array containing:

 *   - taxon: The taxon object for which to theme the page.

 *   - page_part: Name of the part to display, valid values are:

 *   'description', 'images', 'synonymy', 'all'.

 *

 * @ingroup themeable

 */

function theme_cdm_taxon_page($variables) {

  _add_js_footnotes();

  $page_part = $variables['page_part'];

  global $theme;

  $weight = 0; // the weight for the render array elements

  $page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';

  $hideImages = FALSE;

    $hideImages = ($rankCompare > -1);

  }

  // --- GET specimensOrObservations --- //

  $specimensOrObservationsCount = is_array($specimensOrObservations) ? count($specimensOrObservations) : 0;

  if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {

  // --- GET polytomousKeys --- //

  $polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");

  $identificationKeyCount = 0;

  if ($polytomousKeysPager) {

    $identificationKeyCount += $polytomousKeysPager->count;

  }

  if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {

  if ($tabsToDisplay["Synonymy"] == '0') {

  // -------------------------------------------- //

  $render_array['back_to_search'] = markup_to_render_array(theme('cdm_back_to_search_result_button'), $weight++);

      $render_array['accepted_for'] = markup_to_render_array(theme('cdm_acceptedFor', array('acceptedFor' => $_REQUEST['acceptedFor'])), $weight++);

  // --- PAGE PART: DESCRIPTION --- //

  if ($page_part == 'description' || $page_part == 'all') {

    $markerTypesEmpty = array();

    $markerTypesEmpty['markerTypes'] = '';

    $nonStructuredDescriptions = array();

    if ($taxonDescriptions != NULL) {

      foreach ($taxonDescriptions as $taxonDescription) {

        // Check if structured description.

        $hasStructuredData = cdm_ws_get(CDM_WS_DESCRIPTION_HAS_STRUCTRURED_DATA, $taxonDescription->uuid);

        if (isset($hasStructuredData->Boolean)) {

          $hasStructuredData = $hasStructuredData->Boolean == 'TRUE';

        }

        if ($hasStructuredData) {

          $structured_description_featuretree_uuid = variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, FALSE);

          if($structured_description_featuretree_uuid) {

            // if a feature tree for natural language generation has been defined use it,

            // otherwise natural language generation is skipped

            $naturallanguage_textData = cdm_ws_get(CDM_WS_DESCRIPTION_NATURALLANGUAGE_DESCRIPTION, array(

              $taxonDescription->uuid,

              $structured_description_featuretree_uuid,

            ));

            if (!isset($naturallanguage_textData)) {

              drupal_set_message(

                t(

                "The 'FeatureTree' for the generation of natural language representations is not configured correctly,"

                ." please select a 'FeatureTree' in the !settings",

                array(

                  ),

                'warning');

              $taxonDescription->elements = NULL;

              $taxonDescription->elements = array(

                $naturallanguage_textData,

              );

            }

          }

        }

        $nonStructuredDescriptions[] = $taxonDescription;

      }

      // Release memory.

      $taxonDescriptions = NULL;

    }

    $mergedTrees = cdm_ws_descriptions_by_featuretree(get_profile_featureTree(), $nonStructuredDescriptions, variable_get('cdm_dataportal_descriptions_separated', FALSE));

    $profile_html .= theme('cdm_taxon_page_profile', array(

      'mergedTrees' => $mergedTrees,

      'media' => $media,

      'hideImages' => $hideImages,

      ));

    $render_array['profile'] = markup_to_render_array($profile_html, $weight++);

  // --- PAGE PART: IMAGES --- //

  if ((!$hideImages && $page_part == 'images' || $page_part == 'all')) {

    // Get the image gallery as configured by the admin.

    $taxon_image_gallery = call_user_func_array('taxon_image_gallery_' . variable_get('image_gallery_viewer', 'default'), array(

      $taxon,

      $media,

    ));

    $images_html .= '</div>';

    $render_array['images'] = markup_to_render_array($images_html, $weight++);

  // --- PAGE PART: SYNONYMY --- //

  if (($page_part == 'synonymy' || $page_part == 'all')) {

    $addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);

    $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);

  // --- PAGE PART: SPECIMENS --- //

  if ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all')) {

        '#prefix' => '<div id="specimens">' . ($page_part == 'all' ? '<h2>' . t('Specimens') . '</h2>' : ''),

    );

  // --- PAGE PART: KEYS --- //

    drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));

  }

  else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {

    $keys_html .= '</div>';

    $render_array['keys'] = markup_to_render_array($keys_html, $weight++);

  return $render_array;

/**

 * Returns HTML containing descriptive data and preferred picture.

 *

 * Outputs all descriptive data and shows the preferred picture of the

 * accepted taxon.

 *

 * @param array $variables

 *   An associative array containing:

 *   - taxon

 *   - mergedTrees

 *   - media:

 *   - hideImages

 *

 * @ingroup themeable

 */

function theme_cdm_taxon_page_profile($variables) {

  $taxon = $variables['taxon'];

  $mergedTrees = $variables['mergedTrees'];

  $media = $variables['media'];

  $hideImages = $variables['hideImages'];

  $out = '';

  if ($taxon_profile_image_settings['show'] && !$hideImages) {

    $attributes = array();

    if (isset($media[0]->representations[0]->parts[0])) {

      $representationPart = $media[0]->representations[0]->parts[0];

      $attributes['alt'] = $representationPart->uri;

      if(!empty($taxon_profile_image_settings['media_uri_query'])){

        $representationPart->uri = $representationPart->uri

            . (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')

            . $taxon_profile_image_settings['media_uri_query'];

      }

    }

    else {

      // show placeholder image instead

      if(!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])){

        // use the user provided image

        $profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);

        $url = file_create_url($profile_image_file->uri);

        $image_info = image_get_info($profile_image_file->uri);

        $representationPart->width = $image_info['width'];

        $representationPart->height = $image_info['height'];

        $representationPart->uri = $url;

      } else {

        // use the hard coded default

        $representationPart->width = 184;

        $representationPart->height = 144;

        $representationPart->uri = base_path() .  drupal_get_path('module', 'cdm_dataportal') . '/images/no_picture.png';

      }

      $attributes['alt'] = "no image available";

    }

    $profile_image = theme('cdm_media_gallerie_image', array(

        'mediaRepresentationPart' => $representationPart,

        'maxExtend' => $taxon_profile_image_settings['maxextend'],

        'addPassePartout' => FALSE,

        'attributes' => $attributes,

    ));

    $out .= '<div id="taxonProfileImage">' . $profile_image. '</div>';

  // Description TOC.

  $out .= theme('cdm_featureTreeTOCs', array('mergedTrees' => $mergedTrees));

  // Description.

  $out .= theme('cdm_featureTrees', array('mergedTrees' => $mergedTrees, 'taxon' => $taxon));

  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 array $variables

 *   An associative array containing:

 *   - taxon

 *   - addAcceptedTaxon

 *

 * @ingroup themeable

 */

function theme_cdm_taxon_page_synonymy($variables) {

  $taxon = $variables['taxon'];

  $addAcceptedTaxon = $variables['addAcceptedTaxon'];

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

  // both should have the same footnote key

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

  $skip = array(

    UUID_BASIONYM,

  );

  $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

  if ($addAcceptedTaxon) {

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

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

    }

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

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

      'taxonName' => $taxon->name,

      'nameLink' => NULL,

      'refenceLink' => $referenceUri,

      ));

    $accepted_name .= '</span>';

    $special_annotations_array[] = $taxon->name;

    $special_annotations_array[] = $taxon;

        'footnote_list_key' => RenderHints::getRenderPath() . '-annotations')

      );

    $out .= $accepted_name;

  }

  $out .= theme('cdm_homotypicSynonymyGroup', array('synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup, 'accepted_taxon_uuid' => $taxon->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)) {

    $taxonRelationships = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS, $taxon->uuid);

    $out .= theme('cdm_taxonRelationships', array('taxonRelationships' => $taxonRelationships, 'focusedTaxon' => $taxon));

  }

  // Render name relationships.

  $name_rels_to_show = variable_get('name_relationships_to_show', NULL);

  $skip = array();

  if ($name_rels_to_show) {

    foreach ($name_rels_to_show as $key => $value) {

      if ($value === 0) {

        $skip[] = $key;

      }

    }

    if (sizeof($name_rels_to_show) != sizeof($skip)) {

      $nameRelationships = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);

      $out .= theme('cdm_nameRelationships', array('nameRelationships' => $nameRelationships, 'skipTypes' => $skip));

    }

  }

  RenderHints::popFromRenderStack();

  return $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

 * @ingroup themeable

 */

function theme_cdm_search_results($variables) {

  $pager = $variables['pager'];

  $freetextSearchResults = array();

  // 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;

  }

  $out = '';

  // 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>';

    }

  }

  $out .= '<form name="pageoptions"><input id="showThumbnails" type="checkbox" name="showThumbnails" ' . (do_showThumbnails() == 1 ? 'checked="checked"' : '') . '> ' . t('Show Thumbnails') . '</form>';

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

  $classification = cdm_dataportal_searched_in_classification();

  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">';

        array(

          'records' => $pager->records,

          'freetextSearchResults' => $freetextSearchResults,

          'show_classification' => $classification === NULL

        )

      );

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

        'pager' => $pager,

        'path' => $path,

  }

  else {

    $out .= '<h4 class="error">Sorry, no matching entries found.</h4>';

  }

  return $out;

}

 * TODO Implementation of Hook taxon_image_gallery()

 *

 * @param unknown_type $taxon

 * @param unknown_type $media

 *

 * @return unknown_type

 */

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 .= theme('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 unknown_type $taxon

 * @param unknown_type $media

 *

 * @return unknown_type

 */

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 HTML for a single reference page.

 *

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

 *

 * @param array $variables

 *   An associative array containing:

 *   - reference: Object.

 *

 * @ingroup themeable

 */

function theme_cdm_reference_page($variables) {

  $reference = $variables['reference'];

  $out = '';

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

    drupal_set_title($reference->titleCache, PASS_THROUGH);

  }

  $field_order = array(

    "title",

    // "titleCache",

    // "citation",

    "authorTeam",

    "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.

    "uri",

  );

  $header = array(

    t('Field'),

    t('Value'),

  );

  $table_rows = array();

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

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

    $reference->authorTeam = isset($authorTeam->titleCache) ? $authorTeam->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(ucfirst(strtolower($fieldname))),

            $datePublished,

          );

        }

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

        // $datePublished);

      }

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

        if ($fieldname == "authorTeam") {

          $dump = $reference->$fieldname;