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 garland_cichorieae_cdm_descriptionElementTextData($variables) {

  $element = $variables['element'];

  $asListElement = $variables['asListElement'];

  $feature_uuid = $variables['feature_uuid'];

  $description = '';

  if (isset($element->multilanguageText_L10n->text)) {

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

  }

  $sourceRefs = '';

  $do_links = TRUE;

  $default_theme = variable_get('theme_default', 'garland_cichorieae');

  if (($default_theme == 'flora_malesiana' || $default_theme == 'flore_afrique_centrale' || $default_theme == 'flore_gabon') && $element->feature->titleCache == 'Citation') {

    $asListElement = TRUE;

  }

  elseif ($element->feature->uuid == UUID_CHROMOSOMES_NUMBERS) {

    $asListElement = TRUE;

  }

  else {

    $asListElement = FALSE;

  }

  // Printing annotations footnotes.

  $annotation_fkeys = theme('cdm_annotations_as_footnotekeys', array(

    'cdmBase_list' => $element,

    'footnote_list_key' => $feature_uuid,

  ));

  if ($feature_uuid == UUID_NAME_USAGE || $feature_uuid == UUID_CHROMOSOMES) {

    $do_links = FALSE;

  }

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

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

      // Initialize some variables.

      if ($feature_uuid == UUID_NAME_USAGE) {

        $referenceCitation = cdm_ws_get(

          CDM_WS_NOMENCLATURAL_REFERENCE_CITATION,

          array($source->citation->uuid),

          "microReference=" . urlencode($source->citationMicroReference

        ));

        $referenceCitation = $referenceCitation->String;

      }

      else {

        $referenceCitation = theme('cdm_OriginalSource', array(

          'source' => $source,

          'doLink' => $do_links,

        ));

      }

      if ($description && strlen($description) > 0 && $referenceCitation) {

        $sourceRefs .= ' (' . $referenceCitation . ')';

      }

      elseif ($referenceCitation) {

        $sourceRefs = $referenceCitation;

      }

      // Generate the output.

      if (strlen($sourceRefs) > 0) {

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

      }

      $name_used_in_source_link_to_show = '';

      if (isset($source->nameUsedInSource->uuid) && ($feature_uuid != UUID_NAME_USAGE)) {

        // Do a link to name page.

        $name_used_in_source_link_to_show = l($source->nameUsedInSource->titleCache, path_to_name($source->nameUsedInSource->uuid), array(), NULL, NULL, FALSE, TRUE);

      }

      elseif (isset($source->nameUsedInSource->uuid) && ($feature_uuid == UUID_NAME_USAGE)) {

        // Do not do link for NAME USAGE feature.

        $name_used_in_source_link_to_show = $source->nameUsedInSource->titleCache;

      }

      elseif (isset($source->nameUsedInSource->originalNameString) && strlen($source->nameUsedInSource->originalNameString) > 0) {

        // Show a text without link.

        $name_used_in_source_link_to_show = $source->nameUsedInSource->originalNameString;

      }

      if ($asListElement && ($feature_uuid == UUID_NAME_USAGE)) {

        $out = '<li class="descriptionText">' . $name_used_in_source_link_to_show;

        // Adding ":" if necesary.

        if (!empty($name_used_in_source_link_to_show) && (!empty($description) || !empty($sourceRefs))) {

          $out .= ': ';

        }

        $out .= $description . $sourceRefs . theme('cdm_annotations_as_footnotekeys', array(

          'cdmBase_list' => $element,

          'footnote_list_key' => $feature_uuid,

        )) . $annotation_fkeys . '</li>';

      }

      elseif ($asListElement) {

        $out = '<li class="descriptionText DescriptionElement">';

        // Adding ":" if necessary.

        if (!empty($name_used_in_source_link_to_show)) {

          if ( (!empty($description)|| !empty($sourceRefs)) && $feature_uuid != UUID_CHROMOSOMES_NUMBERS) {

            $out .= $name_used_in_source_link_to_show . ': ';

          } else {

            $out .= $name_used_in_source_link_to_show . ' ';

          }

        }

        $out .= $description . $sourceRefs . theme('cdm_annotations_as_footnotekeys', array(

          'cdmBase_list' => $element,

          'footnote_list_key' => $feature_uuid,

        )) . $annotation_fkeys . '</li>';

        // Special handling for flora malesiana.

        // TODO: possible better way to implement this case?

      }

      else {

        if (isset($name_used_in_source_link_to_show)) {

          $name_used_in_source_link_to_show = ' (name in source: ' . $name_used_in_source_link_to_show . ')';

        }

        if (!isset($description)) {

          $description = '';

        }

        if (!isset($sourceRefs)) {

            $sourceRefs = '';

        }

        if (!isset($name_used_in_source_link_to_show)) {

            $name_used_in_source_link_to_show = '';

        }

        if (!isset($annotation_fkeys)) {

            $annotation_fkeys = '';

        }

        $out = '<span class="' . html_class_attribute_ref($element) . '"> ' . $description . $sourceRefs . $name_used_in_source_link_to_show . $annotation_fkeys . '</span>';

      }

    }

  }

  // If no sources, print the description.

  if (!isset($out)) {

    $out = '<span class="' . html_class_attribute_ref($element) . '"> ' . $description . $annotation_fkeys . '</span>';

  }

  /* Dead code:

   *

   * Disabled code; can this be removed?

  if ($feature_uuid == UUID_NAME_USAGE){ foreach($element->sources as

  $source){ $referenceCitation =

  cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION,

  array($source->citation->uuid),

  "microReference=".urlencode($source->citationMicroReference));

  $referenceCitation = $referenceCitation->String; if($description &&

  strlen($description) > 0 && $referenceCitation ){ $sourceRefs .= '

  ('.$referenceCitation.')' ; }else if ($referenceCitation){ $sourceRefs =

  $referenceCitation; } } }else{ foreach($element->sources as $source){

  $referenceCitation = theme('cdm_OriginalSource', $source,

  ($feature_uuid == UUID_NAME_USAGE) ? FALSE : TRUE); if($description &&

  strlen($description) > 0 && $referenceCitation ){ $sourceRefs .= '

  ('.$referenceCitation.')' ; }else if ($referenceCitation){ $sourceRefs =

  $referenceCitation; } } } if(strlen($sourceRefs) > 0){ $sourceRefs = '<span

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

  ($source->nameUsedInSource->uuid && ($feature_uuid != UUID_NAME_USAGE)){

  //do a link to name page $name_used_in_source_link_to_show =

  l($source->nameUsedInSource->titleCache,

  path_to_name($source->nameUsedInSource->uuid), array(), NULL, NULL, FALSE

  ,TRUE); }else if ($source->nameUsedInSource->uuid && ($feature_uuid ==

  UUID_NAME_USAGE)){ //do not do link for NAME USAGE feature

  $name_used_in_source_link_to_show = $source->nameUsedInSource->titleCache;

  }else if (strlen($source->nameUsedInSource->originalNameString) > 0){

  //show a text without link $name_used_in_source_link_to_show =

  $source->nameUsedInSource->originalNameString; } if($asListElement &&

  ($feature_uuid == UUID_NAME_USAGE)){ $out = '<li class="descriptionText">'

  . $name_used_in_source_link_to_show; //adding ":" if necesary if

  ($name_used_in_source_link_to_show && ($description || $sourceRefs)){ $out

  .= ': '; } $out .= $description . $sourceRefs .

  theme('cdm_annotations_as_footnotekeys', $element) . '</li>'; }else if

  ($asListElement){ $out = '<li class="descriptionText">' .

  $name_used_in_source_link_to_show; //adding ":" if necesary if

  ($name_used_in_source_link_to_show && ($description || $sourceRefs)){ $out

  .= ': '; } $out .= $description . $sourceRefs .

  theme('cdm_annotations_as_footnotekeys', $element) . '</li>'; //special

  handling for flora malesiana TODO: possible better way to implement this

  case? }else{ if ($name_used_in_source_link_to_show){

  $name_used_in_source_link_to_show = ' (name in source: '.

  $name_used_in_source_link_to_show . ')'; } $out = $description .

  $sourceRefs . $name_used_in_source_link_to_show; $out .=

  theme('cdm_annotations_as_footnotekeys', $element); }

  */

  // Add annotations as footnote key.

  // $out .= theme('cdm_annotations_as_footnotekeys', $element); move above.

  return $out;

}

// NO LONGER NEEDED - since term representation is changed now in the cdm for

// the cichorieae

// ====> delete

// /**

// * @overrides theme_cdm_taggedtext2html in order to replace t.infr and

// t.infgen. with '[unranked]'

// */

// function garland_cichorieae_cdm_taggedtext2html(array &$taggedtxt, $tag =

// 'span', $glue = ' ', $skiptags = array()){

// $out = '';

// $i = 0;

// foreach($taggedtxt as $tt){

// if(!in_array($tt->type, $skiptags) && strlen($tt->text) > 0){

// $out .= (strlen($out) > 0 && ++$i < count($taggedtxt)? $glue : '').'<'.$tag.'

// class="'.$tt->type.'">';

// if($tt->type == "rank" && ($tt->text == "t.infr." || $tt->text ==

// "t.infgen.")){

// $out .= t('[unranked]');

// }else{

// $out .= t($tt->text);

// }

// $out .= '</'.$tag.'>';

// }

// }

// return $out;

// }

/**

 * Returns HTML for a cdm_feature_block_elements.

 *

 * @param array $variables

 *   An associative array containing:

 *   - elementArray: The array with CDM description elements being formatted.

 *   - feature: The description feature container object for the

 *     description element array.

 *   - glue: String for joining the description elements together.

 *   - sortArray: Boolean, TRUE if the array should be sorted before themeing.

 *   - enclosingHTML: HTML tag, e.g. 'div', in which to wrap the description.

 *

 * @ingroup themeable

 */

function garland_cichorieae_cdm_feature_block_elements($variables) {

  $elementArray = $variables['elementArray'];

  $feature = $variables['feature'];

  $glue = $variables['glue'];

  $sortArray = $variables['sortArray'];

  $enclosingHtml = $variables['enclosingHtml'];

  $enclosingHtml = 'div';

  $out = '<' . $enclosingHtml . ' class="feature-block-elements" id="' . $feature->representation_L10n . '">';

  if ($sortArray) {

    sort($elementArray);

  }

  $out .= '<span class="feature-block-element">' . join($elementArray, '<span class="feature-block-element">' . $glue . '</span>') . '</span>';

  $out .= '</' . $enclosingHtml . '>';

  return $out;

}

/*

  ***** GARLAND OVERRIDES *****

*/

/**

 * 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 themable 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 HTML for 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;

}

/**

 * Returns HTML for taxon list thumbnails.

 *

 * Theme specific mods:

 * $captionElements = array('title', '#uri'=>t('open Image'));

 * $mediaLinkType:

 * "NORMAL": link to the image page or to the $alternativeMediaUri if it is

 * defined instead of

 * "LIGHTBOX": open the link in a light box,

 * TODO expose those in admin section, by adding 'em to gallery_settings see

 * http://dev.e-taxonomy.eu/trac/ticket/2494.

 *

 * @param array $variables

 *   An associative array containing:

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

 *

 * @ingroup themeable

 */

function garland_cichorieae_cdm_taxon_list_thumbnails($variables) {

  $out = '';

  $taxon = $variables['taxon'];

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);

  $mediaLinkType = 'NORMAL';

  $showCaption = $gallery_settings['cdm_dataportal_show_thumbnail_captions'];

  $captionElements = array();

  if ($showCaption) {

    $captionElements = array('title', '#uri' => t('open Image'));

  }

  $gallery_name = $taxon->uuid;

  $galleryLinkUri = path_to_taxon($taxon->uuid, 'images');

  $mediaList = $mediaList = _load_media_for_taxon($taxon);

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

    'mediaList' => $mediaList,

    'galleryName' => $gallery_name,

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

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

    'maxRows' => $gallery_settings['cdm_dataportal_media_maxRows'],

    'captionElements' => $captionElements,

    'mediaLinkType' => $mediaLinkType,

    'alternativeMediaUri' => $galleryLinkUri,

    'showCaption' => NULL,

  ));

  return $out;

}

/**

 * @todo Please document this function.

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

 */

function garland_cichorieae_cdm_feature_name($variables) {

  $feature_name = $variables['feature_name'];

  switch ($feature_name) {

    case "Protologue":

      return t("Original Publication");

    default:

      return ucfirst($feature_name);

  }

}

/*

======== Special functions for subtheme handling=============

*/

/**

 * @todo Please document this function.

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

 */

function sub_theme() {

  global $user, $custom_theme;

  // Only select the user selected theme if it is available in the

  // list of enabled themes.

  $themes = list_themes();

  $theme = $user->theme && $themes[$user->theme]->status ? $user->theme : variable_get('theme_default', 'garland');

  // Allow modules to override the present theme... only select custom theme

  // if it is available in the list of installed themes.

  $theme = $custom_theme && $themes[$custom_theme] ? $custom_theme : $theme;

  return $theme;

}

/**

 * Return the path to the currently selected sub theme.

 */

function path_to_sub_theme() {

  $themes = list_themes();

  $theme = sub_theme();

  return dirname($themes[$theme]->filename);

}

/**

 * Implements hook_preprocess_HOOK() for theme_page().

 *

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

 * Modify primary-links if cdm_api module exists.

 */

function garland_cichorieae_preprocess_page(&$vars) {

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

    /*

    obsolete, see http://dev.e-taxonomy.eu/trac/ticket/2191

    if(module_exists('cdm_api')){ foreach($vars['main_menu'] as $key =>

    $menu_item){ // nb this makes each menu item you click opening a new

    browser window..

    $menu_item['attributes']['target']=generalizeString($menu_item['title']);

    $main_menu[] = $menu_item; }; }else{ $main_menu = $vars['main_menu'] ; };

    */

    $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;

  }

  /*

  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 garland_cichorieae_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 garland_cichorieae_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 garland_cichorieae_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');

    }

  }

}