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 xxx_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_search_taxa_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('Display image thumbnails') . '</form></div>';

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

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

    $list_of_taxa = compose_list_of_taxa($pager->records);

    $out .= drupal_render($list_of_taxa);

    $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;

}

/**

 * @todo Please document this function.

 */

function xxx_palmweb_2_cdm_media_caption($variables){

  $media = $variables['media'];

  $elements = $variables['elements'];

  $media_metadata = read_media_metadata($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 authorship 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'];

  $doTextLink = $variables['doTextLink'];

  $doIconLink = $variables['doIconLink'];

  $referenceStyle = $variables['referenceStyle'];

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

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

  } else {

    $author_team = $reference->authorship;

  }

  $year = '';

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

    $year = timePeriodToString($reference->datePublished, true, 'YYYY');

  }

  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 ($doTextLink) {

    $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'];

  if (isset($comment->subject)) {

    // Print title without link.

    $variables['title'] = $comment->subject;

    if ($variables['status'] == 'comment-preview') {

      // Add 'new' to preview.

      $variables['new'] = t('new');

    }

  }

}