EDIT

<?php

/**

 * @file

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

 */

/**

 * This operride theme function ignores the original sources and annotations

 * and renders a hardcoded citation string at the end of the list of distibution

 * elements.

 * TODO the same output could also be achieved by collection all source citations

 * as it is done by the footnodesystem and to print the list of citations at the end

 * of the area list. The footnote key must be omitted in this case of course.

 *

 */

function palmweb_2_cdm_descriptionElement_Distribution($variables) {

  $descriptionElements = $variables['descriptionElements'];

  $enclosingTag = $variables['enclosingTag'];

  $out = '';

  $separator = ', ';

  RenderHints::pushToRenderStack('descriptionElementDistribution');

  RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);

  $itemCnt = 0;

  foreach ($descriptionElements as $descriptionElement) {

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

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

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

      $out .= $separator;

    }

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

  }

  $taxonTrees = cdm_ws_fetch_all(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_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.

  // =============== SPECIAL NUMBER OF TAXA  ================= //

  $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") {

    if($numberOfChildren==1){

      $subRank = "infraspecific taxon";

    }

    else{

      $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>';

  }

  // =============== END SPECIAL NUMBER OF TAXA ================= //

  foreach ($mergedFeatureNodes as $node) {

    if (isset($node->descriptionElements['#type']) || has_feature_node_description_elements($node)) {

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

      $block = new stdclass(); // Empty object.

      $block->module = 'cdm_dataportal';

      $media_list = array();

      // =============== SPECIAL bibliography ================= //

      // 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;

      }

      // =============== SPECIAL bibliography ================= //

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

        $countFeatures++;

        $countFeatures++;

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

        $block->subject = '<span class="' . html_class_attribute_ref($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) {

          $distributionElements = null;

          $distribution_info_dto = null;

          $text_data_out_array = array();

          $distribution_sortOutArray = FALSE;

          if (variable_get('distribution_sort', 'NO_SORT') != 'NO_SORT') {

            $distribution_glue = '';

            $distribution_enclosingTag = 'dl';

          }

          else {

            $distribution_glue = '';

            $distribution_enclosingTag = 'ul';

          }

          if(!isset($node->descriptionElements['#type']) || !$node->descriptionElements['#type']=='DTO') {

            // skip the DISTRIBUTION section if there is no DTO type element

            continue;

          }

          if(isset($node->descriptionElements['TextData'])){

            // --- TextData

            $text_data_glue = '';

            $text_data_sort = FALSE;

            $text_data_enclosingTag = 'ul';

            foreach ($node->descriptionElements['TextData'] as $text_data_element){

              $asListElement = FALSE;

              $repr = theme('cdm_descriptionElementTextData', array(

                  'element' => $text_data_element,

                  'asListElement' => $asListElement,

                  'feature_uuid' => $text_data_element->feature->uuid,

              ));

              if (!array_search($repr, $text_data_out_array)) {

                $text_data_out_array[] = $repr;

                // TODO HINT: sorting in theme_cdm_feature_block_elements will

                // not work since this array contains html attributes with uuids

                // !!!!

                $text_data_sort = TRUE;

                $text_data_glue = '<br/> ';

                $text_data_enclosingTag = 'p';

              }

            }

          }

          if ($text_data_out_array && variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)) {

            $tmp_render_array = compose_cdm_feature_block_elements(

              $text_data_out_array,

              $node->feature,

              $text_data_glue,

              $text_data_sort,

              $text_data_enclosingTag

            );

            $block->content .= $tmp_render_array['#markup'];

          }

          // --- Distribution map

          $distribution_map_query_parameters = null;

          if(isset($node->descriptionElements['DistributionInfoDTO'])) {

            $distribution_map_query_parameters = $node->descriptionElements['DistributionInfoDTO']->mapUriParams;

          }

          $map_render_element = compose_distribution_map($taxon, $distribution_map_query_parameters);

          $block->content .= $map_render_element['#markup'];

            // --- tree or list

              $dto_out_array = array();

          if(isset($node->descriptionElements['DistributionInfoDTO'])) {

            $distribution_info_dto = $node->descriptionElements['DistributionInfoDTO'];

            // --- tree

            if (is_object($distribution_info_dto->tree)) {

              $dto_out_array[] = theme('cdm_description_ordered_distributions', array('distribution_tree' => $distribution_info_dto->tree));

            }

            // --- sorted element list

            if( is_array($distribution_info_dto->elements) && count($distribution_info_dto->elements) > 0 ) {

              foreach ($distribution_info_dto->elements as $descriptionElement){

                if (is_object($descriptionElement->area)) {

                  $sortKey = $descriptionElement->area->representation_L10n;

                  $distributionElements[$sortKey] = $descriptionElement;

                }

              }

              ksort($distributionElements);

              $dto_out_array[] = theme('cdm_descriptionElement_Distribution', array(

                  'descriptionElements' => $distributionElements,

              ));

            }

            //

            $tmp_render_array = compose_cdm_feature_block_elements(

                $dto_out_array,

                $node->feature,

                $distribution_glue,

                $distribution_sortOutArray,

                $distribution_enclosingTag

            );

            $block->content .= $tmp_render_array['#markup'];

          }

          // --- TextData at the bottom

          if ($text_data_out_array && !variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)) {

            $tmp_render_array = compose_cdm_feature_block_elements(

                $text_data_out_array,

                $node->feature,

                $text_data_glue,

                $text_data_sort,

                $text_data_enclosingTag

            );

            $block->content .= $tmp_render_array['#markup'];

          }

        }

        /*

        Content/COMMON_NAME.

        */

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

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

        }

        /*

         * Content/ALL OTHER FEATURES.

        */

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

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

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

        }

        else {

          $block->content .= compose_cdm_descriptionElements($node->descriptionElements, $node->feature->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 (isset($node->childNodes[0])) {

            // TODO support more than one level of children.

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

            $text = '';

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

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

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

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

                    // Append media of supordinate elements to list of main

                    // feature.

                   $media_list = array_merge($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,

        )));

      }

    }

  }

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

  //

// !!!!!! no longer needed !!!!

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

//  $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'];

  $media_metadata = cdm_read_media_metadata($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;

}

/**

 * Overrive of the original theme_cdm_reference()

 * the main difference here seems to be that

 * this function is completely omitting the citation title cache

 * and only sets the authorTeam as the

 * _short_form_of_author_team() as $citation.

 *

 * If the authorteam is not set citation was empty,

 * this has been fixed for http://dev.e-taxonomy.eu/trac/ticket/4261

 *

 * TODO can this be made configuable via the dataportal

 *      settings so that we can remove this function?

 */

function xxx_palmweb_2_cdm_reference($variables) {

  $reference = $variables['reference'];

  $microReference = $variables['microReference'];

  $doLink = $variables['doLink'];

  $referenceStyle = $variables['referenceStyle'];

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

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

  } else {

    $author_team = $reference->authorTeam;

  }

  $year = '';

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

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

  }

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

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

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

  } else {

    $citation = $reference->titleCache;

  }

  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;

}

/**

 * @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);

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

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

  $vars['fixed_body'] = $body;

}

/**

 * Implements hook_form_FORM_ID_alter() for comment_form().

 *

 * Alter the comment form to make it look like a D5 style comment form.

 *

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

 */

function palmweb_2_form_comment_form_alter(&$form, &$form_state) {

  if (!isset($form['comment_preview'])) {

    $form['header'] = array(

      '#markup' => '<h2>' . t('Reply') . '</h2>',

      '#weight' => -2,

    );

  }

  $form['subject']['#title'] = $form['subject']['#title'] . ':';

  $form['comment_body']['und'][0]['#title'] = $form['comment_body']['und'][0]['#title'] . ':';

  if (isset($form['author']['_author']['#title'])) {

    $form['author']['_author']['#title'] = $form['author']['_author']['#title'] . ':';

  }

  $form['actions']['submit']['#value'] = t('Post comment');

  $form['actions']['submit']['#weight'] = 1000;

  $form['actions']['preview']['#value'] = t('Preview comment');

}

/**

 * Implements hook_preprocess_HOOK() for theme_comment().

 *

 * Alter the comment display to make it look like a D5 style comment.

 *

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

 */

function palmweb_2_preprocess_comment(&$variables) {

  $comment = $variables['elements']['#comment'];