EDIT

<?php

// $Id$

/**

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

 */

/**

 * The description page is supposed to be the front page for a taxon.

 *

 * @param TaxonTO $taxonTO

 * @return

 */

function garland_cichorieae_cdm_taxon_page_description($taxon, $mergedTrees, $media, $hideImages = false){

  // description TOC

  $out = theme('cdm_featureTreeTOCs', $mergedTrees);

  // preferred image

  // 2 lines hard coded for testing

  if(!$hideImages){

    //$defaultPreferredImage = drupal_get_path('theme', 'garland_cichorieae').'/images/nopic_400x300.jpg';

    $defaultRepresentationPart = false;

    $defaultRepresentationPart->width = 400;

    $defaultRepresentationPart->height = 300;

    $defaultRepresentationPart->uri = drupal_get_path('theme', 'garland_cichorieae').'/images/nopic_400x300.jpg';

    $imageUriParams = '&width=400&height=300&quality=95&format=jpeg'; 

    $imageMaxExtend = 400;

    $out .= '<div class="preferredImage">'.theme('cdm_preferredImage', $media, $defaultRepresentationPart, $imageMaxExtend, $imageUriParams).'</div>';

  }

  // description

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

  return $out;

}

function garland_cichorieae_cdm_descriptionElementTextData($element){

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

  $referenceCitation = '';

  if($element->reference){

    // disabling references for cichorieae description Elements because they all have faulty references

    //$referenceCitation = '; '.theme('cdm_fullreference', $element->reference, TRUE);

  }

  return '<p class="descriptionText">' . $description . $referenceCitation.'</p>';

}

function garland_cichorieae_cdm_taxon_page_images($taxon, $media){

  $flashLink = isset($media[0]);

  if($flashLink){

    $taggedName = $taxon->name->taggedName;

    $nameArray = array();

    foreach($taggedName as $taggedText){

      if($taggedText->type == 'name'){

        $nameArray[] = $taggedText->text;

      }

    }

    $query = join("%5F", $nameArray) . '%20AND%20EditWP6%20AND%20jpg';

  $out = '

<script type="text/javascript" src="http://media.bgbm.org/erez/js/fsiwriter.js"></script>

<script type="text/javascript">

<!--

	writeFlashCode( "http://media.bgbm.org/erez/fsi/fsi.swf?&cfg=showcase_presets/showcase_info.fsi&effects=%26quality%3D95&showcase_query='.$query.'&skin=silver&showcase_labeltextheight=50&textbox_textfrom=IPTC_WP6&textbox_height=50&param_backgroundcolor=454343&publishwmode=opaque&showcase_hscroll=true&showcase_basecolor=454343&plugins=textbox,fullscreen",

		"http://media.bgbm.org/erez/erez?src=erez-private/flashrequired.svg&tmp=Large&quality=97&width=620&height=400",

		"width=620;height=400;bgcolor=454343;wmode=opaque");

// -->

</script>

<noscript>

	<object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" codebase="http://download.macromedia.com/pub/shockwave/cabs/flash/swflash.cab#version=6,0,65,0" width="470" height="400">

		<param name="movie" value="http://media.bgbm.org/erez/fsi/fsi.swf?&cfg=showcase_presets/showcase_info.fsi&effects=%26quality%3D95&showcase_query='.$query.'&skin=silver&showcase_labeltextheight=50&textbox_textfrom=IPTC_WP6&textbox_height=50&param_backgroundcolor=454343&publishwmode=opaque&showcase_hscroll=true&showcase_basecolor=454343plugins=textbox,fullscreen"/>

		<param name="bgcolor" value="454343" />

		<param name="wmode" value="opaque" />

		<param name="allowscriptaccess" value="always" />

		<param name="allowfullscreen" value="true" />

		<param name="quality" value="high" />

		<embed src="http://media.bgbm.org/erez/fsi/fsi.swf?&cfg=showcase_presets/showcase_info.fsi&effects=%26quality%3D95&showcase_query='.$query.'&skin=silver&showcase_labeltextheight=50&textbox_textfrom=IPTC_WP6&textbox_height=50&param_backgroundcolor=454343&publishwmode=opaque&showcase_hscroll=true&showcase_basecolor=454343plugins=PrintSave,textbox,fullscreen"

			width="620"

			height="400"

			bgcolor="454343"

			wmode="opaque"

			allowscriptaccess="always"

			allowfullscreen="true"

			quality="high"

			type="application/x-shockwave-flash"

			pluginspage="http://www.adobe.com/go/getflashplayer">

		</embed>

	</object>

</noscript>';

  }else{

    $out = 'No images available.';

  }

  return $out;

}

function garland_cichorieae_cdm_taxon_page_images_cichorieae_copyright(){

	$out = '<div id="cichorieae-copyright">';

	$out .= '<p>';

	$out .= '&copy; Images used on this website remain copyright of the individual photographer.<br> To obtain permission to use images in publications or websites please contact the network at <a href="edit-wp6-cichorieae@bgbm.org">edit-wp6-cichorieae@bgbm.org</a>. Images may be used for personal use, such as PowerPoint presentations, without permission.';

	$out .= '</p>';

    $out .= '</div>';

	return $out;

}

/**

 * @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;

}

function garland_cichorieae_cdm_descriptionElementArray($elementArray, $feature, $glue = '', $sortArray = false, $enclosingHtml = 'ul'){

  $enclosingHtml = 'div';

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

  if($sortArray) sort($elementArray);

  $out .= join($elementArray, $glue);

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

  return $out;

}

/**

 * all reference links switched of

 */

function garland_cichorieae_cdm_nomenclaturalReferenceSTO($referenceSTO, $doLink = FALSE, $cssClass = '', $separator = '<br />' , $enclosingTag = 'li'){

  $doLink = FALSE;

  if(isset($referenceSTO->microReference)){

    // it is a ReferenceTO

    $nomref_citation = theme('cdm_fullreference', $referenceSTO);

  } else {

    // it is ReferenceSTO

    $nomref_citation = $referenceSTO->fullCitation;

  }

  $is_IN_reference = str_beginsWith($nomref_citation, 'in');

  if($doLink){

    $nomref_citation = l($nomref_citation, "/cdm_dataportal/reference/".$referenceSTO->uuid, array(), NULL, NULL, FALSE, TRUE);

  }

  if(!empty($nomref_citation)){

    $nomref_citation = ($is_IN_reference ? ' ':', ') . $nomref_citation;

  }

  return $nomref_citation;

}

/***** 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 .'"';

  }

}

/**

 * Return a themed breadcrumb trail.

 *

 * @param $breadcrumb

 *   An array containing the breadcrumb links.

 * @return a string containing the breadcrumb output.

 */

function phptemplate_breadcrumb($breadcrumb) {

  if (!empty($breadcrumb)) {

    return '<div class="breadcrumb">'. implode(' › ', $breadcrumb) .'</div>';

  }

}

/**

 * 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 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;

}

function garland_cichorieae_get_partDefinition($nameType){

  if($nameType == 'BotanicalName'){

    return array(

        'namePart' => array(

          'name' => true

    ),

        'nameAuthorPart' => array(

          'name' => true,

          'authors' => true

    ),

        'referencePart' => array(

          'reference' => true,

          'microreference' => true,

    ),

        'statusPart' => array(

          'status' => true,

    ),

        'descriptionPart' => array(

          'description' => true,

    ),

    );

  }

  return false;

}

function garland_cichorieae_get_nameRenderTemplate($renderPath){

  switch($renderPath) {

    case 'taxon_page_title':

      $template = array(

            'namePart' => array('#uri'=>true)

      );

      break;

    case 'taxon_page_synonymy':

    case 'related_taxon':

      $template = array(

          'nameAuthorPart' => array('#uri'=>true),

          'referencePart' => true,

          'statusPart' => true,

          'descriptionPart' => true

      );

      break;

    case 'acceptedFor':

      $template = array(

            'nameAuthorPart' => array('#uri'=>true),

            'referencePart' => true

      );

      break;

    case 'typedesignations':

    case 'list_of_taxa':

    case '#DEFAULT':

      $template = array(

            'nameAuthorPart' => array('#uri'=>true),

            'referencePart' => true

      );

  }

  return $template;

}

/**

 */

function garland_cichorieae_cdm_taxon_list_thumbnails($taxon){

    $gallery_name = $taxon->uuid;

    $showCaption = variable_get('cdm_dataportal_findtaxa_show_thumbnail_captions', 0);

    $prefMimeTypeRegex = 'image:.*';

    $prefMediaQuality = '*';

    $cols = variable_get('cdm_dataportal_findtaxa_media_cols', 3);

    $maxRows = variable_get('cdm_dataportal_findtaxa_media_maxRows', 1);

    $maxExtend = variable_get('cdm_dataportal_findtaxa_media_maxextend', 120);

    if($showCaption){

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

    }

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

    $mediaList = cdm_ws_get(CDM_WS_PORTAL_TAXON_MEDIA, array($taxon->uuid, $prefMimeTypeRegex, $prefMediaQuality));

    $out .= theme('cdm_media_gallerie', $mediaList, $gallery_name ,$maxExtend, $cols, $maxRows, $captionElements, 'NORMAL', $galleryLinkUri, null);

    return $out;

}