EDIT

/**

 * Creates markup for a taxon which is the accepted of another one

 *

 * @param $accepted_for_uuid

 *   The uuid of the accepted taxon

 */

function cdm_accepted_for($accepted_for_uuid) {

  if(!is_uuid($accepted_for_uuid)){

    return '';

  }

  RenderHints::pushToRenderStack('acceptedFor');

  $out = '';

  $synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $accepted_for_uuid);

  if ($synonym) {

    $out .= '<span class="acceptedFor">';

    $out .= t('is accepted for ');

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

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

    }

    $out .= render_taxon_or_name($synonym->name, NULL, $referenceUri);

    $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $synonym));

    $out .= '</span>';

  }

  RenderHints::popFromRenderStack();

  return $out;

}

/**

 * Compose function for a list of taxa.

 *

 * This function is for example used toi display search results or the taxa for a taxon name in the name page.

 *

 * @param $taxon_list array

 *   The list of CDM Taxon entities. e.g. The records array as contained in a pager object.

 * @param $freetext_search_results array

 * @param $show_classification boolean

 *

 * @ingroup compose

 *

 */

function compose_list_of_taxa($taxon_list, $freetext_search_results = array(), $show_classification = false) {

  $unclassified_snippet = '<span class="unclassified">' . t('unclassified') . '</span>';

  RenderHints::pushToRenderStack('list_of_taxa');

  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);

  $showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];

  $showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];

  $searched_in_classification = cdm_dataportal_searched_in_classification();

  $searched_in_classification_uuid = null;

  if(isset($searched_in_classification->uuid)){

    $searched_in_classification_uuid = $searched_in_classification->uuid;

  }

  // .. Well, for sure not as performant as before, but better than nothing.

  $synonym_uuids = array();

  $misappied_uuids = array();

  foreach ($taxon_list as $taxon) {

    if ($taxon->class == "Synonym") {

      if (!array_key_exists($taxon->uuid, $synonym_uuids)) {

        $synonym_uuids[$taxon->uuid] = $taxon->uuid;

      }

    }

    elseif (!_cdm_dataportal_acceptedByCurrentView($taxon)) {

      // Assuming that it is a misappied name, will be further examined below.

      $misappied_uuids[$taxon->uuid] = $taxon->uuid;

    }

  }

  // Batch service not jet implemented:

  // $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED,

  // join(',', $synonym_uuids));

  // thus ...

  $table_of_accepted = array();

  foreach ($synonym_uuids as $relatedUuid) {

    $table_of_accepted[$relatedUuid] = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array(

      $relatedUuid,

      $searched_in_classification_uuid,

    ));

  }

  foreach ($misappied_uuids as $relatedUuid) {

    $taxonRelations = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS, array(

      $relatedUuid,

    ));

    foreach ($taxonRelations as $relation) {

      if ($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR && _cdm_dataportal_acceptedByCurrentView($relation->toTaxon)) {

        $table_of_accepted[$relatedUuid][] = $relation->toTaxon;

      }

    }

  }

  $out = '<ul class="cdm_names" style="background-image: none;">';

  $itemCnt = -1;

  foreach ($taxon_list as $taxon) {

    $itemCnt++;

    if (isset($table_of_accepted[$taxon->uuid])) {

      // Its a synonym or misapplied name.

      $is_synonym = isset($synonym_uuids[$taxon->uuid]); //TODO better use the $taxon->class attribute?

      $taxon_type = $is_synonym ? "Synonym" : "misapplied-name";

      $acceptedTaxa = $table_of_accepted[$taxon->uuid];

      if (count($acceptedTaxa) == 1) {

        $acceptedTaxon = $acceptedTaxa[0];

        $taxonUri = uri_to_synonym($taxon->uuid, $acceptedTaxon->uuid, 'synonymy');

        $referenceUri = '';

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

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

        }

        $taxon_or_name = $is_synonym ? $taxon->name : $taxon;

        // $taxon_or_name this is a trick to suppress the sec reference for sysnonyms

        // supplying the name will cause render_taxon_or_name() to not show the sec reference

        $out .= '<li class="' . $taxon_type . '">' . render_taxon_or_name($taxon_or_name, $taxonUri, $referenceUri);

        if ($show_classification) {

          $classifications = get_classifications_for_taxon($taxon);

          $classification_titles = array();

          foreach ($classifications as $classification) {

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

              $classification_titles[] = $classification->titleCache;

            }

          }

          if(count($classification_titles) == 0){

            $classification_titles[] = $unclassified_snippet;

          }

          $out .= ' : <span class="classifications">' . implode(', ', $classification_titles) . '</span>';

        }

        $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));

        if ($showMedia_synonyms) {

          $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $acceptedTaxon));

        }

      }

      else {

        // TODO avoid using Ajax in the cdm_dynabox .... why?

        // TODO add media.

        $out .= cdm_dynabox(

          $taxon->uuid,

          render_taxon_or_name($taxon->name, NULL, NULL, FALSE),

          cdm_compose_url(CDM_WS_PORTAL_TAXON_ACCEPTED,

            array(

              $taxon->uuid,

              $searched_in_classification_uuid

            )

          ),

          'cdm_list_of_taxa',

          'show accepted taxa of this ' . $taxon_type,

          array('li', 'ul'),

          array('class' => array($taxon_type))

         );

      }

    }

    else {

      // Its a Taxon.

      $taxonUri = url(path_to_taxon($taxon->uuid));

      $referenceUri = '';

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

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

      }

      $out .= '<li class="Taxon">' . render_taxon_or_name($taxon, $taxonUri, $referenceUri);

      if ($show_classification) {

        $classifications = get_classifications_for_taxon($taxon);

        $classification_titles = array();

        foreach ($classifications as $classification) {

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

            $classification_titles[] = $classification->titleCache;

          }

        }

        if(count($classification_titles) == 0){

          $classification_titles[] = $unclassified_snippet;

        }

        $out .= ' : <span class="classifications">' . implode(', ', $classification_titles) . '</span>';

      }

      $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));

      if ($showMedia_taxa) {

        $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));

      }

    }

    /*

     * the score field will be empty in case of MultiTermQueries like

     * WildcardQueries, since these are  constant score by default

     * since Lucene 2.9

     */

    if(isset($freetext_search_results[$itemCnt]) && $freetext_search_results[$itemCnt]->score && $freetext_search_results[$itemCnt]->maxScore){

      $percentage =  ( $freetext_search_results[$itemCnt]->score / $freetext_search_results[$itemCnt]->maxScore ) * 100;

      $out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';

      $out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';

    }

    // Render highlighted fragments, these are made available by free text

    // searches.

    if (isset($freetext_search_results[$itemCnt]->fieldHighlightMap)) {

      $field_fragments = (array) $freetext_search_results[$itemCnt]->fieldHighlightMap;

      if (count($field_fragments) > 0) {

        $fragments_out = '';

        foreach ($field_fragments as $fieldName => $fragments) {

          $fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';

        }

        $out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';

      }

    }

    $out .= '</li>';

  }

  $out .= '</ul>';

  RenderHints::popFromRenderStack();

  return markup_to_render_array($out); // TODO create render array of all list items in function

}