EDIT

<?php

/**

 * @file

 * Overrides of generic themeing functions in cdm_dataportal.theme.php.

 */

/**

 * @todo Please document this function.

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

 */

function palmweb_2_cdm_descriptionElementDistribution($variables) {

  $descriptionElements = $variables['descriptionElements'];

  $enclosingTag = $variables['enclosingTag'];

  $out = '';

  $separator = ', ';

  RenderHints::pushToRenderStack('descriptionElementDistribution');

  RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);

  $itemCnt = 0;

  foreach ($descriptionElements as $descriptionElement) {

    /*

    $out .= ($descriptionElement->class);

    // Annotations as footnotes.

    $annotationFootnoteKeys = theme('cdm_annotations_as_footnotekeys', $descriptionElement);

    // Source references as footnotes.

    $sourcesFootnoteKeyList = '';

    foreach($descriptionElement->sources as $source){

      $_fkey = FootnoteManager::addNewFootnote(UUID_DISTRIBUTION, theme('cdm_OriginalSource', $source, FALSE));

      $sourcesFootnoteKeyList .= theme('cdm_footnote_key', $_fkey, ($sourcesFootnoteKeyList ? $separator : ''));

    }

    if($annotationFootnoteKeys && $sourcesFootnoteKeyList){

      $annotationFootnoteKeys .= $separator;

    }

    */

        $out .= '<' . $enclosingTag . ' class="DescriptionElement DescriptionElement-' . $descriptionElement->class . '">';

        // $out .= $descriptionElement->area->representation_L10n . $annotationFootnoteKeys . $sourcesFootnoteKeyList;

        $out .= $descriptionElement->area->representation_L10n;

        if (++$itemCnt < count($descriptionElements)) {

          $out .= $separator;

        }

        $out .= "</" . $enclosingTag . ">";

  }

  $taxonTrees = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY);

  $reference = new stdClass();

  foreach ($taxonTrees as $taxonTree) {

    if ($taxonTree->uuid == variable_get('cdm_taxonomictree_uuid')) {

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

        $reference = $taxonTree->reference;

      }

      break;

    }

  }

  $referenceCitation = '';

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

    $referenceCitation .= '(<span class="reference">';

    $referenceCitation .= l(t('World Checklist of Monocotyledons'), path_to_reference($reference->uuid), array('attributes' => array('class' => array('reference'))));

    $referenceCitation .= '</span>)';

  }

  else {

    // Comment @WA Added for compatibility with D5, but I think it is better to

    // remove this to not show a link rather than the wrong one.

    $referenceCitation .= '(<span class="reference">';

    $referenceCitation .= l(t('World Checklist of Monocotyledons'), '', array('attributes' => array('class' => array('reference'))));

    $referenceCitation .= '</span>)';

  }

  $sourceRefs = '';

  if ($out && strlen($out) > 0) {

    $sourceRefs = ' ' . $referenceCitation;

  }

  if (strlen($sourceRefs) > 0) {

    $sourceRefs = '<span class="sources">' . $sourceRefs . '</span>';

  }

  RenderHints::popFromRenderStack();

  return $out . $sourceRefs;

}

/**

 * @todo Please document this function.

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

 */

function palmweb_2_cdm_feature_nodesTOC($variables){

  $featureNodes = $variables['featureNodes'];

  $out = '';

  global $theme;

  $out .= '<ul>';

  $countFeatures = 0;

  $numberOfChildren = count(cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array (

    get_taxonomictree_uuid_selected(),

    substr(strrchr($_GET["q"],'/'), 1),

  )));

  if ($numberOfChildren != 0) {

    $out .= '<li>';

    $out .= l(t(theme('cdm_feature_name', array('feature_name' => 'Number of Taxa'))), $_GET['q'], array(

      'attributes' => array('class' => array('toc')),

      'fragment' => generalizeString('Number Of Taxa'),

    ));

    $out .= '</li>';

  }

  foreach ($featureNodes as $node) {

    if (hasFeatureNodeDescriptionElements($node)) {

      $featureRepresentation = isset($node->feature->representation_L10n) ? $node->feature->representation_L10n : 'Feature';

      // HACK to implement images for taxa, should be removed.

      if ($node->feature->uuid != UUID_IMAGE && $node->feature->uuid != UUID_USE) {

        $countFeatures++;

        $countFeatures++;

        $out .= '<li>' . l(t(theme('cdm_feature_name', array('feature_name' => $featureRepresentation))), $_GET['q'],

            array('attributes' => array('class' => array('toc')),'fragment' => generalizeString($featureRepresentation))) . '</li>';

      }

    }

  }

  // Setting the Anchor to the Bibliography section if the option is enabled.

  $show_bibliography = variable_get('cdm_show_bibliography', 1);

  $markerTypes['markerTypes'] = UUID_MARKERTYPE_USE;

  $useDescriptions = cdm_ws_get(CDM_WS_PORTAL_TAXON_DESCRIPTIONS, substr(strrchr($_GET["q"], '/'), 1), queryString($markerTypes));

  if (!empty($useDescriptions)) {

    $out .= '<li>';

    $out .= l(t(theme('cdm_feature_name', array('feature_name' => 'Uses'))), $_GET['q'], array(

      'attributes' => array('class' => array('toc')),

      'fragment' => 'userecords',

    ));

    $out .= '</li>';

  }

  if ($show_bibliography && $countFeatures != 0) {

    $out .= '<li>' . l(t(theme('cdm_feature_name', array('feature_name' => 'Bibliography'))), $_GET['q'], array('attributes' => array('class' => array('toc')), 'fragment' => 'bibliography')) . '</li>';

  }

  $out .= '</ul>';

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function palmweb_2_cdm_feature_nodes($variables){

  $mergedFeatureNodes = $variables['mergedFeatureNodes'];

  $taxon = $variables['taxon'];

  $out = '';

  RenderHints::pushToRenderStack('feature_nodes');

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME);

  // Creating an array to place the description elements in.

  $bibliographyOut = array();

  $countFeatures = 0;

  $numberOfChildren = count(cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array (get_taxonomictree_uuid_selected(), $taxon->uuid)));

  if ($taxon->name->rank->titleCache == "Genus") {

    $subRank = "species";

  }

  if ($taxon->name->rank->titleCache == "Species") {

    $subRank = "infraspecific taxa";

  }

  if ($numberOfChildren != 0) {

    $out .= '<a name="number_of_taxa"> </a><H2>Number of Taxa</H2><div class="content"> <ul class="description">';

    $out .= '<li class=\"descriptionText DescriptionElement\">' . $numberOfChildren . " " . $subRank . '</li></ul>';

  }

  foreach ($mergedFeatureNodes as $node) {

    if (hasFeatureNodeDescriptionElements($node)) {

      $featureRepresentation = isset($node->feature->representation_L10n) ? $node->feature->representation_L10n : 'Feature';

      $block = new stdClass();

      $block->module = 'cdm_dataportal';

      // If the option is enabled the description elements will be added

      // to the array.

      $show_bibliography = variable_get('cdm_show_bibliography', 1);

      if ($show_bibliography) {

        $bibliographyOut[] = $node->descriptionElements;

      }

      $media_list = array();

      if ($node->feature->uuid != UUID_IMAGE && $node->feature->uuid != UUID_USE) {

        $countFeatures++;

        $countFeatures++;

        $block->delta = generalizeString($featureRepresentation);

        $block->subject = '<span class="' . html_class_atttibute_ref($node->feature) . '">' . theme('cdm_feature_name',  array('feature_name' => $featureRepresentation)) . '</span>';

        $block->module = "cdm_dataportal-feature";

        $block->content = '';

        /*

        Content/DISTRIBUTION.

        */

        if ($node->feature->uuid == UUID_DISTRIBUTION) {

          if (variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)) {

            $distributionTextDataList = array();

            $distributionElementsList = array();

            foreach ($node->descriptionElements as $descriptionElement) {

              if ($descriptionElement->class == "TextData") {

                $distributionTextDataList[] = $descriptionElement;

              }

              else {

                $distributionElementsList[] = $descriptionElement;

              }

            }

            if (count($distributionTextDataList) > 0) {

              $node->descriptionElements = $distributionElementsList;

              $block->content .= theme('cdm_descriptionElements', array(

                'descriptionElements' => $distributionTextDataList,

                'featureUuid' => $node->feature->uuid,

                'taxon_uuid' => $taxon->uuid,

              ));

            }

          }

          // Display cdm distribution map.

          // TODO this is a HACK to a proper generic implementation?

          $block->content .= theme('cdm_distribution_map', array('taxon' => $taxon));

          $block->content .= theme('cdm_descriptionElements', array(

            'descriptionElements' => $node->descriptionElements,

            'featureUuid' => $node->feature->uuid,

            'taxon_uuid' => $taxon->uuid,

          ));

        }

        /*

        Content/COMMON_NAME.

        */

        elseif ($node->feature->uuid == UUID_COMMON_NAME) {

          // TODO why is theme_cdm_descriptionElement_CommonTaxonName

          // not beeing used???

          $block->content .= theme('cdm_common_names', array('elements' => $node->descriptionElements));

        /*

        }else if($node->feature->uuid == UUID_IMAGE_SOURCES) {

          $block->content .= theme('cdm_image_sources', $node->descriptionElements);

        */

        }

        /*

        Content/ALL OTHER FEATURES.

        */

        elseif ($node->feature->uuid == UUID_USE_RECORD) {

          $block->content .= theme('cdm_block_Uses', $taxon->uuid);

          // $block->content .= theme('cdm_descriptionElements', $node->descriptionElements, $node->feature->uuid, $taxon->uuid),

        }

        else {

          $block->content .= theme('cdm_descriptionElements', array(

            'descriptionElements' => $node->descriptionElements,

            'featureUuid' => $node->feature->uuid,

            'taxon_uuid' => $taxon->uuid,

          ));

          /*

          Content/ALL OTHER FEATURES/Subordinate Features

          subordinate features are printed inline in one floating text,

          it is expected that subordinate features only "contain" TextData

          elements.

          */

          // TODO move into own theme.

          if (count($node->children) > 0) {

            // TODO support more than one level of children.

            // @see http://dev.e-taxonomy.eu/trac/ticket/2393/

            $text = '';

            foreach ($node->children as $child) {

             if (is_array($child->descriptionElements)) {

               foreach ($child->descriptionElements as $element) {

                 if (is_array($element->media)) {

                   // Append media of subordinate elements to the list of

                   // main features.

                   $media_list = array_merge($media_list, $element->media);

                 }

                 $description = str_replace("\n", "<br/>", $element->multilanguageText_L10n->text);

                // TODO use localized version of feature name, the locale must

                // match the locale of the multilanguage text

                // (http://dev.e-taxonomy.eu/trac/ticket/2394).

                 $description = str_replace($element->feature->titleCache, '<em>' . $element->feature->titleCache . '</em>', $description);

               }

               $text .= " " . $description;

               $description = '';

             }

            }

            $block->content .= $text;

          }

        }

        /*

        Media/ALL FEATURES.

        */

        $media_list = array_merge($media_list, cdm_dataportal_media_from_descriptionElements($node->descriptionElements));

        $gallery = theme('cdm_media_gallerie', array(

           'mediaList' => $media_list,

           'galleryName' => CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME . '_' . $node->feature->uuid,

           'maxExtend' => isset($gallery_settings['cdm_dataportal_media_maxextend']) ? $gallery_settings['cdm_dataportal_media_maxextend'] : NULL ,

           'cols' => isset($gallery_settings['cdm_dataportal_media_cols']) ? $gallery_settings['cdm_dataportal_media_cols'] : NULL ,

           'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? $gallery_settings['cdm_dataportal_media_maxRows'] : NULL ,

           'captionElements' => isset($captionElements) ? $captionElements : NULL ,

           )

        );

        $block->content .= $gallery;

        $block->content .= theme('cdm_footnotes', array('footnoteListKey' => $node->feature->uuid));

        $block->content .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $node->feature->uuid));

        // Add anchor to subject.

        $block->subject = '<a name="' . $block->delta . '"></a>' . $block->subject;

        $block->region = FALSE;

        $out .= theme('block', array('elements' => array(

          '#block' => $block,

          '#children' => $block->content,

        )));

      }

    }

  }

  // Calling the theme function for Bibliography to add it to the output.

  // Add the display of the number of taxa in the selected genus.

  $out .= theme('cdm_block_Uses', array('taxonUuid' => $taxon->uuid));

  $show_bibliography = variable_get('cdm_show_bibliography', 1);

  if ($show_bibliography && $countFeatures != 0) {

    $out .= theme('cdm_descriptionElementBibliography', array('descriptionElementsBibliography' => $bibliographyOut));

  }

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function palmweb_2_cdm_search_results($variables){

  $pager = $variables['pager'];

  $path = $variables['path'];

  $out = '';

  $showThumbnails = isset($_SESSION['pageoption']['searchtaxa']['showThumbnails']) ? $_SESSION['pageoption']['searchtaxa']['showThumbnails'] : 0;

  if (!is_numeric($showThumbnails)) {

    // AT RBG KEW - 14/11/2011 - Set the show thumbnails to 0 by default.

    $showThumbnails = 0;

  }

  $setSessionUri = url('cdm_api/setvalue/session', array('query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => '')));

  drupal_add_js('jQuery(document).ready(function() {

        // Init.

        if(' . $showThumbnails . ' == 1){

              jQuery(\'.media_gallery\').show(20);

        } else {

          jQuery(\'.media_gallery\').hide(20);

        }

        // Add change hander.

        jQuery(\'#showThumbnails\').change(

          function(event){

            var state = 0;

            if(jQuery(this).is(\':checked\')){

              jQuery(\'.media_gallery\').show(20);

              state = 1;

            } else {

              jQuery(\'.media_gallery\').hide(20);

            }

            // Store state in session variable.

            var uri = \'' . $setSessionUri . '\' + state;

            jQuery.get(uri);

          });

        });', "inline");

  drupal_set_title(t('Search results'));

  // AT RBG KEW - 14/11/2011 - Changed the wording of the Show Thumbnails

  // tickbox text.

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

  $out .= '<form name="pageoptions">';

  $out .= '<input id="showThumbnails" type="checkbox" name="showThumbnails" ';

  $out .= $showThumbnails == 1 ? 'checked="checked"' : '';

  $out .= '> ' . t('Show Image Thumbnails') . '</form></div>';

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

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

    $out .= theme('cdm_list_of_taxa', array('records' => $pager->records));

    $out .= '</div>';

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

      'pager' => $pager,

      'path' => $path,

      'parameters' => $_REQUEST,

    ));

  }

  else {

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

  }

  return $out;

}

/*

Comment @WA: theme function moved to cdm_dataportal module,

theme/cdm_dataportal.bibliography.theme so this can be used by other portals

as well.

@TODO: should this not be part of the palmweb_2 featuretree and be treated

as a normal description feature?

function theme_cdm_descriptionElementBibliography

function formatReference_for_Bibliography($references) {

 */

/**

 * @todo Please document this function.

 */

function palmweb_2_cdm_media_caption($variables){

  $media = $variables['media'];

  $elements = $variables['elements'];

  $fileUri = $variables['fileUri'];

  $media_metadata = cdm_read_media_metadata($media);

  $doTitle = !$elements || array_search('title', $elements) !== FALSE;

  $doDescription = !$elements || array_search('description', $elements) !== FALSE;

  $doArtist = !$elements || array_search('artist', $elements) !== FALSE;

  $doLocation = !$elements || array_search('location', $elements) !== FALSE;

  $doRights = !$elements || array_search('rights', $elements) !== FALSE;

  $descriptionPrefix = "";

  $out = '<dl class="media-caption">';

  // Title.

  if ($doTitle) {

    if ($media_metadata['title']) {

      $out .= '<dt class = "title">' . t('Title') . '</dt> <dd class = "title">' . $media_metadata['title'] . '</dd>';

      $descriptionPrefix = "- ";

    }

    elseif (!($doDescription && $media_metadata['description'])) {

      // Use filename as fallbackoption if no description will be shown.

      $out .= '<dt class = "title">' . t('Title') . '</dt> <dd class = "title">' . $media_metadata['filename'] . '</dd>';

      $descriptionPrefix = "- ";

    }

  }

  // Description.

  if ($media_metadata['description'] && $doDescription) {

    $out .= '<dt class = "description">' . t('Description') . '</dt> <dd class = "description">' . $descriptionPrefix . $media_metadata['description'] . '</dd>';

  }

  // Artist.

  if ($media_metadata['artist'] && $doArtist) {

    $out .= '<dt class = "artist">' . t('Artist') . '</dt> <dd class = "astist">' . str_replace("'","", $media_metadata['artist']) . '</dd>';

  }

  // Location.

  if ($doLocation) {

    $location = '';

    $location .= $media_metadata['location']['sublocation'];

    if ($location && $media_metadata['location']['city']) {

      $location .= ', ';

    }

    $location .= $media_metadata['location']['city'];

    if ($location && $media_metadata['location']['province']) {

      $location .= ', ';

    }

    $location .= $media_metadata['location']['province'];

    if ($location && $media_metadata['location']['country']) {

      $location .= ' (' . $media_metadata['location']['country'] . ')';

    }

    else {

      $location .= $media_metadata['location']['country'];

    }

    if ($location) {

      $out .= '<dt class = "location">' . t('Location') . '</dt> <dd class = "location">' . $location  . '</dd>';

    }

  }

  // Rights.

  if ($doRights) {

    $rights = '';

    // Copyrights.

    $cnt = count($media_metadata['rights']['copyright']['agentNames']);

    if ($cnt > 0) {

      $rights .= '<dt class="rights">&copy;</dt> <dd class="rights"> ';

      for ($i = 0; $i < $cnt; $i++) {

        $rights .= str_replace("'","", $media_metadata['rights']['copyright']['agentNames'][$i]);

        if ($i + 1 < $cnt) {

          $rights .= ' / ';

        }

      }

      $rights .= '</dd>';

    }

    // License.

    $cnt = count($media_metadata['rights']['license']['agentNames']);

    if ($cnt > 0) {

      $rights .= '<dt class ="license">' . t('License') . '</dt> <dd class = "license">';

      for ($i = 0; $i < $cnt; $i++) {

        $rights .= $media_metadata['rights']['license']['agentNames'][$i];

        if ($i + 1 < $cnt) {

          $rights .= ' / ';

        }

      }

      $rights .= '</dd>';

    }

    if ($rights) {

      $out .= $rights . '</dt>';

    }

  }

  // TODO add all other metadata elemenst generically.

  $out .= '</dl>';

  // Return value.

  return $out;

}

/**

 * @todo document this function.

 */

function palmweb_2_cdm_reference($variables) {

  $reference = $variables['reference'];

  $microReference = $variables['microReference'];

  $doLink = $variables['doLink'];

  $referenceStyle = $variables['referenceStyle'];

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

  $year = '';

  if (isset($reference->datePublished->start)) {

    $year = partialToYear($reference->datePublished->start);

  }

  $citation = _short_form_of_author_team ($author_team->titleCache) . (!empty($year) ? '. ' . $year : '');

  $citation = str_replace('..', '.', $citation);

  if ($doLink) {

    $out = '<span class="reference">';

    $out .= l($citation, path_to_reference($reference->uuid), array(

    'attributes' => array('class' => 'reference'),

    'absolute' => TRUE,

    'html' => TRUE,

    ));

    $out .= '</span>';

  }

  else {

    $out = '<span class="reference">' . $citation . '</span>';

  }

  // FIXME use microreference webservice instead.

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

    $out .= ': ' . $descriptionElementSource->citationMicroReference;

  }

  return $out;

}

/**

 * Sets the body-tag class attribute.

 *

 * Adds 'sidebar-left', 'sidebar-right' or 'sidebars' classes as needed.

 */

function phptemplate_body_class($sidebar_left, $sidebar_right) {

  if ($sidebar_left != '' && $sidebar_right != '') {

    $class = 'sidebars';

  }

  else {

    if ($sidebar_left != '') {

      $class = 'sidebar-left';

    }

    if ($sidebar_right != '') {

      $class = 'sidebar-right';

    }

  }

  if (isset($class)) {

    print ' class="' . $class . '"';

  }

}

/**

 * Allow themeable wrapping of all comments.

 */

function phptemplate_comment_wrapper($content, $type = NULL) {

  static $node_type;

  if (isset($type)) {

    $node_type = $type;

  }

  if (!$content || $node_type == 'forum') {

    return '<div id="comments">' . $content . '</div>';

  }

  else {

    return '<div id="comments"><h2 class="comments">' . t('Comments') . '</h2>' . $content . '</div>';

  }

}

/**

 * Override or insert PHPTemplate variables into the templates.

 */

function _phptemplate_variables($hook, $vars) {

  if ($hook == 'page') {

    if ($secondary = menu_secondary_local_tasks()) {

      $output = '<span class="clear"></span>';

      $output .= "<ul class=\"tabs secondary\">\n" . $secondary . "</ul>\n";

      $vars['tabs2'] = $output;

    }

    // Hook into color.module

    if (module_exists('color')) {

      _color_page_alter($vars);

    }

    return $vars;

  }

  return array();

}

/**

 * Returns the rendered local tasks. The default implementation renders

 * them as tabs.

 *

 * @ingroup themeable

 */

function phptemplate_menu_local_tasks() {

  $output = '';

  if ($primary = menu_primary_local_tasks()) {

    $output .= "<ul class=\"tabs primary\">\n" . $primary . "</ul>\n";

  }

  return $output;

}

/**

 *  @deprecated define name render templates via the layout settings

 */

function palmweb_2_get_partDefinition($variables) {

  return array(

    'BotanicalName'=> array(

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

        'authorshipPart' => array(),

        'referencePart' => array('reference' => TRUE, 'microreference' => TRUE),

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

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

    ),

    'ZoologicalName' => array(

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

          'referencePart' => array('authors' => TRUE),

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

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

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

      ),

    '#DEFAULT' => array(

        'namePart' => array(

            'name' => TRUE,

            'authors' => TRUE

        ),

        'referencePart' => array(

            'reference' => TRUE

        ),

        'microreferencePart' => array(

            'microreference' => TRUE,

        ),

        'statusPart' => array(

            'status' => TRUE,

        ),

        'descriptionPart' => array(

            'description' => TRUE,

        ),

      )

  );

}

/**

 *  @deprecated define name render templates via the layout settings

 */

function palmweb_2_get_nameRenderTemplate($variables){

  return array(

    'acceptedFor' =>

      $template = array(

        'namePart' => array('#uri'=>TRUE),

      ),

    'typedesignations' => array(

        'namePart' => array('#uri'=>TRUE),

        'referencePart' => TRUE,

      ),

    'taxon_page_title,list_of_taxa,taxon_page_synonymy,related_taxon,polytomousKey' => array(

        'namePart' => array('#uri'=>TRUE),

        'referencePart' => TRUE,

        'descriptionPart' => TRUE,

        'statusPart' => TRUE,

      ),

    '#DEFAULT' => array(

        'namePart' => array('#uri'=>TRUE),

        'referencePart' => TRUE,

        'descriptionPart' => TRUE,

        'statusPart' => TRUE,

     )

  );

}

/**

 * @todo Please document this function.

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

 */

function palmweb_2_cdm_feature_name($variables){

  $feature_name = $variables['feature_name'];

  switch ($feature_name) {

    case "Protologue": return t("Original Publication");

    default: return t(ucfirst($feature_name));

  }

}

/**

 * Implements hook_preprocess_HOOK() for theme_page().

 *

 * Assign the css classes primary-links and secondary-links to the menus and

 * process the 'Login' menu item, to change into 'My account' after login and

 * change the tab title for the IMCE file browser.

 *

 * @author W.Addink <w.addink@eti.uva.nl>

 */

function palmweb_2_preprocess_page(&$vars) {

  if (isset($vars['main_menu'])) {

    // For the Palmae theme we want to change the menu item 'Login' into

    // 'My account' if a user is logged in.

    global $user;

    foreach ($vars['main_menu'] as $key => $value) {

        if ($value['href'] == 'user' && !empty($user->name)) {

            $vars['main_menu'][$key]['title'] = t('My account');

            $vars['main_menu'][$key]['href'] = 'user/' . $user->uid;

        }

    }

    // Theme the main menu with the desired css classes.

    $vars['primary_nav'] = theme('links__system_main_menu', array(

      'links' => $vars['main_menu'],

      'attributes' => array(

        'class' => array('links', 'inline', 'main-menu', 'primary-links'),

      ),

      'heading' => array(

        'text' => t('Main menu'),

        'level' => 'h2',

        'class' => array('element-invisible'),

      )));

  }

  else {

    $vars['primary_nav'] = FALSE;

  }

  if (isset($vars['secondary_menu'])) {

    $vars['secondary_nav'] = theme('links__system_secondary_menu', array(

      'links' => $vars['secondary_menu'],

      'attributes' => array(

        'class' => array('links', 'inline', 'secondary-menu', 'secondary-links'),

      ),

      'heading' => array(

        'text' => t('Secondary menu'),

        'level' => 'h2',

        'class' => array('element-invisible'),

      )));

  }

  else {

    $vars['secondary_nav'] = FALSE;

  }

  // Change IMCE tab to 'Personal Files'.

  if (!empty($vars['tabs']['#primary'])) {

    foreach ($vars['tabs']['#primary'] as $key => $value) {

      if ($value['#link']['path'] == 'user/%/imce') {

        $vars['tabs']['#primary'][$key]['#link']['title'] = t('Personal Files');

      }

    }

  }

  /* Display node title as page title for the comment form.

  * Comment @WA: it would probably be better to select $uuid from node_cdm

  * table and link to cdm_dataportal/taxon/%uuid instead.

  */

  if (arg(0) == 'comment' && arg(1) == 'reply') {

      $node = $vars['page']['content']['system_main']['comment_node']['#node'];

      $vars['title'] = l(check_plain($node->title),'node/' . $node->nid);

  }

}

/**

 * Implements hook_preprocess_HOOK() for theme_node().

 *

 * Fixes file urls in nodes. In nodes, relative urls are used to include files

 * like <img src="/files/..

 *

 * Portals can be installed in configurations with

 * sub-directories however, in which case these urls need to be adjusted.

 * Examples: mysite.org, mysite.org/myportal, mysite.org/portals/myportal.

 *

 * Therefore preprocess nodes and replace these urls with a the appropriate url

 * for the current setup.

 *

 * @author W.Addink <w.addink@eti.uva.nl>

 */

function palmweb_2_preprocess_node(&$vars) {

  $body = '';

// Warning: use #markup value, for which filters like php, html etc are applied!

  if (isset($vars['content']['body'][0]['#markup'])) {

    $body = $vars['content']['body'][0]['#markup'];

  }

  else {

    $vars['fixed_body'] = '';

    return;

  }

  $file_path = '/' . variable_get('file_public_path', conf_path() . '/files');

  global $base_url;

  if ($base_url == '/') {

    drupal_set_message(t('

      The $base_url in this portal could not be set, please set the $base_url

      manually your Drupal settings.php file.', 'error'

    ));

  }

  $fixed_file_path = $base_url . $file_path;

  $preg_file_path = preg_quote($file_path, '/');

  $body = preg_replace ('/src\s*=\s*["]\s*' . $preg_file_path . '/', 'src="' . $fixed_file_path , $body);

  $body = preg_replace ('/src\s*=\s*[\']\s*' . $preg_file_path . '/', 'src=\'' . $fixed_file_path , $body);