EDIT

<?php

/**

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

 *

 * @param TaxonTO $taxonTO

 * @return

 */

function palmweb_2_cdm_taxon_page_description($taxon, $mergedTrees, $media, $hideImages = false){

  if(!$hideImages){

    // preferred image

    // hardcoded for testing;

    $defaultRepresentationPart = false;

    $defaultRepresentationPart->width = 184;

    $defaultRepresentationPart->height = 144;

    $defaultRepresentationPart->uri = drupal_get_path('theme', 'palmweb_2').'/images/no_picture.png';

    // preferred image size 184px × 144

    $imageMaxExtend = 184;

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

  }

  // description TOC

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

  // description

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

  return $out;

}

function _disabled_palmweb_2_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=PrintSave,textbox",

		"http://media.bgbm.org/erez/erez?src=erez-private/flashrequired.svg&tmp=Large&quality=97&width=500&height=323",

		"width=500;height=323;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="500" height="323">

		<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=PrintSave,textbox"/>

		<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"

			width="500"

			height="323"

			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 palmweb_2_cdm_descriptionElementDistribution($descriptionElements) {

  $out = '';

  $separator = ', ';

    RenderHints::pushToRenderStack('descriptionElementDistribution');

    RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);

    foreach($descriptionElements as $descriptionElement){

        // 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_DescriptionElementSource', $source, false));

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

//        }

//        if($annotationFootnoteKeys && $sourcesFootnoteKeyList){

//            $annotationFootnoteKeys .= $separator;

//        }

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

    }

  $taxonTrees =  cdm_ws_get(CDM_WS_PORTAL_TAXONOMY);

  foreach($taxonTrees as $taxonTree){

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

      $reference = $taxonTree->reference;

      break;

    }

  }

  $out = substr($out, 0, strlen($out)-strlen($separator) );

  $referenceCitation = '('.l('<span class="reference">World Checklist of Monocotyledons</span>', path_to_reference($reference->uuid), array("class"=>"reference"), NULL, NULL, FALSE ,TRUE).')';

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

    $sourceRefs .= ' '.$referenceCitation;

  }

  if(strlen($sourceRefs) > 0){

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

  }

    RenderHints::popFromRenderStack();

  return $out. $sourceRefs ;

}

/**

 * 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 palmweb_2_get_partDefinition($nameType){

  if($nameType == 'BotanicalName'){

    return array(

        'namePart' => array(

          'name' => true,

          'authors' => true,

        ),

        'authorshipPart' => array(

        ),

        'referencePart' => array(

          'reference' => true,

          'microreference' => true

        ),

        'statusPart' => array(

          'status' => true,

        ),

        'descriptionPart' => array(

          'description' => true,

        ),

      );

  }

  return false;

}

function palmweb_2_get_nameRenderTemplate($renderPath){

  switch($renderPath) {

      case 'acceptedFor':

        $template = array(

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

        );

        break;

      case 'typedesignations':

        $template = array(

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

          'referencePart' => true

        );

      case 'taxon_page_title':

      case 'list_of_taxa':

      case 'taxon_page_synonymy':

      case 'related_taxon':

      case 'polytomousKey':

      case '#DEFAULT':

        $template = array(

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

          'referencePart' => true,

          'descriptionPart' => true,

          'statusPart' => true

        );

  }

  return $template;

}

function palmweb_2_cdm_feature_name($feature_name){

  switch($feature_name){

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

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

  }

}

function palmweb_2_cdm_taxon_page_title($taxon, $uuid, $synonym_uuid){

	RenderHints::pushToRenderStack('taxon_page_title');

	$synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $synonym_uuid);

	if(isset($taxon->name->nomenclaturalReference)){

		$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));

	}

	$out = theme('cdm_taxonName', $taxon->name, null, $referenceUri, false);

	RenderHints::popFromRenderStack();

	if ($synonym->name->titleCache){

	$result = '<span class = "synonym_title">' .$synonym->name->titleCache . ' is synonym of ' .'</span>'.

		   '<span class="'.$taxon->class.'">'.$out.'</span>';

	}else{

		$result = '<span class="'.$taxon->class.'">'.$out.'</span>';

	}

	return $result;

}

function palmweb_2_cdm_uri_to_synonym($synonymUuid, $acceptedUuid, $pagePart = null) {

	$acceptedPath = path_to_taxon($acceptedUuid, true);

	return url($acceptedPath . ($pagePart ? '/'.$pagePart : '') . '/'.$synonymUuid, 'highlite='.$synonymUuid);

	//return url($acceptedPath.($pagePart ? '/'.$pagePart : ''), 'highlite='.$synonymUuid, $synonymUuid."/$synonymUuid");

	//return url("$acceptedPath/$synonymUuid".($pagePart ? '/'.$pagePart : ''), 'highlite='.$synonymUuid);

}