EDIT

<?php

// $Id$

/**

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy

 * http://www.e-taxonomy.eu

 *

 * The contents of this file are subject to the Mozilla Public License Version 1.1

 * See http://www.mozilla.org/MPL/MPL-1.1.html for the full license terms.

 */

function theme_cdm_search_results($pager, $path, $parameters){

	$showThumbnails = $_SESSION['pageoptions']['searchtaxa']['showThumbnails'];

	if( !is_numeric($showThumbnails)){

		$showThumbnails = 1;

	}

	$setSessionUri = url('cdm_api/setvalue/session', "var=[pageoption][searchtaxa][showThumbnails]&val=");

	drupal_add_js('$(document).ready(function() {

        // init

        if('.$showThumbnails.' == 1){

              $(\'.media_gallery\').show(20);

        } else {

          $(\'.media_gallery\').hide(20);

        }

        // add change hander

        $(\'#showThumbnails\').change(

          function(event){

            var state = 0;

            if($(this).is(\':checked\')){

              $(\'.media_gallery\').show(20);

              state = 1;

            } else {

              $(\'.media_gallery\').hide(20);

            }

            // store state in session variable

            var uri = \''.$setSessionUri.'\' + state;

            jQuery.get(uri);

          });

        });', "inline");

	drupal_set_title(t('Search results'));

	$out = ''; //l('Advanced Search', '/cdm_dataportal/search');

	$out = '<div class="page_options"><form name="pageoptions"><input id="showThumbnails" type="checkbox" name="showThumbnails" '.($showThumbnails == 1? 'checked="checked"': '').'> '.t('Show Thumbnails').'</form></div>';

	if(count($pager->records) > 0){

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

		$out .= theme('cdm_list_of_taxa', $pager->records);

		$out .= '</div>';

		$out .= theme('cdm_pager', $pager, $path, $parameters);

	} else {

		$out = '<h4 class="error">Sorry, no matching entries found.</h4>';

	}

	return $out;

}

/**

 * renders misapplied names and invalid designations.

 * Both relation types are currently treated the same!

 *

 * @param unknown_type $taxonRelationships

 * @return unknown

 */

function theme_cdm_taxonRelationships($taxonRelationships){

	if(!$taxonRelationships){

		return;

	}

	RenderHints::pushToRenderStack('taxonRelationships');

	$footnoteListKey = 'taxonRelationships';

	RenderHints::setFootnoteListKey($footnoteListKey);

	$misapplied = array();

	$joinedAuthorTeams = array();

	$taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));

	// aggregate misapplied names having the same fullname:

	foreach($taxonRelationships as $taxonRelation){

	    if( in_array($taxonRelation->type->uuid, $taxon_relationship_types)) {

    		if( $taxonRelation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxonRelation->type->uuid == UUID_INVALID_DESIGNATION_FOR ){

    			$name = $taxonRelation->fromTaxon->name->titleCache;

    			$author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $taxonRelation->fromTaxon->sec->uuid);

    			$authorteam = $author_team->titleCache;

    			if(!isset($misapplied[$name])){

    				$misapplied[$name]['out'] =

    				  '<span class="misapplied">'

    				  .theme('cdm_related_taxon',$taxonRelation->fromTaxon, UUID_MISAPPLIED_NAME_FOR).

    				  '</span>';

    			}

    			// collect all authors for this fullname

    			if(isset($authorteam)){

    				$misapplied[$name]['authorteam'][$authorteam] = '';

    				$joinedAuthorTeams[$authorteam] = 'sensu '.theme('cdm_reference', $taxonRelation->fromTaxon->sec);

    			}

    		}

	    } else {

	       $taxonRelationshipsLines[] = theme('cdm_related_taxon',$taxonRelation->fromTaxon, $taxonRelation->type->uuid, $taxonRelation->type->representation_L10n_abbreviatedLabel);

	    }

	}

	// sort the joinedAuthorTeams and create footnotes and footnotekeys

	ksort($joinedAuthorTeams);

	foreach($joinedAuthorTeams as $authorteam=>$sensuCitation){

		$footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, $sensuCitation);

		$joinedAuthorTeams[$authorteam] = '<span class="sensu">sensu '.$authorteam. theme('cdm_footnote_key', $footnoteKey).'</span>';

	}

	// generate output

	$out = '<ul class="misapplied">';

	foreach($misapplied as $misapplied_name){

		$out .= '<li class="synonym">'.$misapplied_name['out'] . " ";

		if(isset($misapplied_name['authorteam'])){

			// fill authors with the renderedFootnoteKey and sorting 'em

			foreach($misapplied_name['authorteam'] as $authorteam=>&$renderedFootnoteKey) {

				$renderedFootnoteKey = $joinedAuthorTeams[$authorteam];

			}

				ksort($misapplied_name['authorteam']);

				$out .= join('; ', $misapplied_name['authorteam']);

		}

		$out .= '</li>';

	}

	$out .= '</ul>';

	$tr_footnotes = theme('cdm_footnotes', $footnoteListKey, 'li');

	$tr_footnotes_exploded = explode('sensu', $tr_footnotes);

	$tr_footnotes_aux = '';

	foreach ($tr_footnotes_exploded as $element){

		$tr_footnotes_aux .= $element;

	}

	$out .= '<ul>' . $tr_footnotes_aux . '</ul>';

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

	RenderHints::popFromRenderStack();

	return $out;

}

function theme_cdm_acceptedFor(){

	RenderHints::pushToRenderStack('acceptedFor');

	$out = '';

	if(isset($_REQUEST['acceptedFor'])){

		$synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $_REQUEST['acceptedFor']);

		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 .= theme('cdm_taxonName', $synonym->name, null, $referenceUri);

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

			$out .= '</span>';

		}

	}

	RenderHints::popFromRenderStack();

	return $out;

}

function theme_cdm_list_of_taxa($records, $showMedia = false){

	RenderHints::pushToRenderStack('list_of_taxa');

	$form_name = 'search_gallery';

	//$default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);

    //$gallery_settings = variable_get($form_name, $default_values);

    $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'];

	//$showMedia_taxa = variable_get('cdm_dataportal_findtaxa_show_taxon_thumbnails', 1);

	//$showMedia_synonyms = variable_get('cdm_dataportal_findtaxa_show_synonym_thumbnails', 0);

	$classification_uuid = get_taxonomictree_uuid_selected();

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

	$synonym_uuids = array();

	foreach($records as $taxon){

		if($taxon->class != "Taxon"){

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

				$synonym_uuids[$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 $synUuid){

		$table_of_accepted[$synUuid] = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($synUuid, $classification_uuid));

	}

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

	foreach($records as $taxon){

		// its a Taxon

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

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

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

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

			}

			$out .= '<li class="Taxon">'.theme('cdm_taxonName', $taxon->name, $taxonUri, $referenceUri);

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

			if($showMedia_taxa){

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

			}

			$out .= '</li>';

		} else {

			// its a synonym

			$uuid = $taxon->uuid;

			$acceptedTaxa = $table_of_accepted[$uuid];

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

				$acceptedTaxon = $acceptedTaxa[0];

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

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

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

				}

				$out .= '<li class="Synonym">'.theme('cdm_taxonName', $taxon->name, $taxonUri, $referenceUri);

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

				if($showMedia_synonyms){

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

				}

				$out .= '</li>';

			} else {

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

				//TODO add media

				$out .= cdm_dynabox(

				  theme('cdm_taxonName', $taxon->name, null, null, false),

				  cdm_compose_url(CDM_WS_PORTAL_TAXON_ACCEPTED, array($taxon->uuid, $classification_uuid)),

				  'cdm_list_of_taxa',

				  'Click for accepted taxon');

			}

		}

	}

	$out .= '</ul>';

	RenderHints::popFromRenderStack();

	return $out;

}

function theme_cdm_related_taxon($taxon, $reltype_uuid = false, $relsign = null){

	static $relsign_homo = '≡';

	static $relsign_hetero = '=';

	static $relsign_invalid = '–';

  $relsign = '';

	$name_prefix = '';

	$name_postfix = '';

	$skiptags = array();

	if(!$relsign) {

       	switch ($reltype_uuid){

    		case UUID_HETEROTYPIC_SYNONYM_OF:

    		case UUID_SYNONYM_OF:

    			$relsign = $relsign_hetero;

    			break;

    		case UUID_HOMOTYPIC_SYNONYM_OF:

    			$relsign = $relsign_homo;

    			break;

    		case UUID_MISAPPLIED_NAME_FOR:

    		case UUID_INVALID_DESIGNATION_FOR:

    			$skiptags[] = 'authors';

    			$relsign = $relsign_invalid;

    			$name_prefix = '"';

    			$name_postfix = '"';

    			break;

    		default :

    			$relsign = $relsign_invalid;

	    }

	}

	/*

	 * names with status invalid or nudum are to be displayed with the $relsign_invalid,

	 * these names appear at the end of all names in their homotypic group

	 * (ordered correctly by the java cdm_lib)

	 */

	if ( is_array($taxon->name->status)) {

		foreach($taxon->name->status as $status){

			if ($status->type->uuid == UUID_NOMENCLATURALSTATUS_TYPE_INVALID || $status->type->uuid == UUID_NOMENCLATURALSTATUS_TYPE_NUDUM){

				$relsign = $relsign_invalid;

			}

		}

	}

	// now rendering starts ..

	RenderHints::pushToRenderStack('related_taxon');

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

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

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

	}

	//printing the taxonName and the handling the special case of annotations

	$nameHtml = theme('cdm_taxonName', $taxon->name, $taxonUri, $referenceUri, true, false, $skiptags);

	$special_annotations_array = array();

	$special_annotations_array[] = $taxon->name;

	$special_annotations_array[] = $taxon;

	$nameHtml .= theme('cdm_annotations_as_footnotekeys', $special_annotations_array);

	//later homonym or trated as later homonym AND bloking names

	$from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);

	$to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);

	//first the FROM RELS

	if ($from_name_relations){

		foreach($from_name_relations as $element){

			switch ($element->type->representation_L10n){

				case 'later homonym for':

					if(isset($name_relations_html)){

						$name_relations_html .= ' nec ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

						    'cdm_dataportal/name/' . $element->toName->uuid . '/' . $taxon->uuid . '/' . $element->toName->taxonBases[0]->uuid);

					}else{

						$name_relations_html = ' non ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

                        'cdm_dataportal/name/' . $element->toName->uuid . '/' . $taxon->uuid . '/' . $element->toName->taxonBases[0]->uuid)

						. ' ' . $element->toName->datePublished->start;

					}

					break;

				case 'treated as later homonym for':

					if(isset($name_relations_html)){

						$name_relations_html = ' nec ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

                              'cdm_dataportal/name/' . $element->toName->uuid);

					}else{

						$name_relations_html = ' non ' . l($element->toName->titleCache . ' ' .  substr($element->toName->nomenclaturalReference->datePublished->start, 0, 4),

					                   'cdm_dataportal/name/' . $element->toName->uuid);

					}

					break;

			}

		}

		//second the TO RELS

		if ($to_name_relations){

			foreach($to_name_relations as $element){

				switch ($element->type->representation_L10n){

					case 'blocking name for':

						if(isset($name_relations_html) ){

							$name_relations_html .= ' nec ' . l($element->fromName->titleCache . ' ' .  substr($element->fromName->nomenclaturalReference->datePublished->start, 0, 4),

                'cdm_dataportal/name/' . $element->fromName->uuid . '/' . $taxon->uuid . '/' . $element->fromName->taxonBases[0]->uuid);

						}else{

							$name_relations_html = ' non ' . l($element->fromName->titleCache . ' ' .  substr($element->fromName->nomenclaturalReference->datePublished->start, 0, 4),

                        'cdm_dataportal/name/' . $element->fromName->uuid . '/' . $taxon->uuid . '/' . $element->fromName->taxonBases[0]->uuid)

							. ' ' . $element->fromName->datePublished->start;

						}

						break;

				}

			}

		}

    //rels output

		if(isset($name_relations_html)){

			$name_relations_html = '['. $name_relations_html .']';

		}

	}

  //geneal output

	$out = '<span class="relation_sign">'.$relsign.'</span>'.$name_prefix . $nameHtml . $name_postfix . $name_relations_html;

	$out = uuid_anchor($taxon->uuid, $out);

	RenderHints::popFromRenderStack();

	return $out;

}

/**

 */

function theme_cdm_taxon_list_thumbnails($taxon){

	$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);

	$showCaption = $gallery_settings['cdm_dataportal_show_thumbnail_captions'];

	if($showCaption){

		$captionElements = array('title', 'rights');

	}

	$gallery_name = $taxon->uuid;

 	$mediaQueryParameters = array("type"=>"ImageFile");

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

	// cdm_dataportal_show_media = ???? TODO

	$selectShowMedia = variable_get('cdm_dataportal_show_media', 0);

	if ($selectShowMedia == 0){

		$mediaList = cdm_ws_get(CDM_WS_PORTAL_TAXON_MEDIA, array($taxon->uuid), queryString( $mediaQueryParameters ));

	}else{

		$mediaList = cdm_ws_get(CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA, array($taxon->uuid), queryString( $mediaQueryParameters ));

	}

	$out .= theme('cdm_media_gallerie', $mediaList, $gallery_name ,

    	$gallery_settings['cdm_dataportal_media_maxextend'],

    	$gallery_settings['cdm_dataportal_media_cols'],

    	$gallery_settings['cdm_dataportal_media_maxRows'],

    	$captionElements, 'LIGHTBOX', null, $galleryLinkUri);

	return $out;

}