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.

 */

/**

 * This function prints the lectotype citation with the correct layout

 * Lectotypes are renderized in the synonymy tab of a taxon if they exist

 * @param $typeDesignation_citation The lectotype citation to print

 * @return html valid string

 */

function type_designation_citation_layout($typeDesignation, $footnote_separator = ','){

	$res = '';

	$citation = $typeDesignation->citation;

	$pages = $typeDesignation->citationMicroReference;

	$data_type = variable_get('cdm_dataportal_data_type', 'BIOLOGY');

	if($data_type == 'ZOOLOGY'){

		if ($typeDesignation->typeStatus->uuid == UUID_ORIGINAL_DESIGNATION ||

		    $typeDesignation->typeStatus->uuid == UUID_MONOTYPE){

			$res = ' ('. $typeDesignation->typeStatus->representation_L10n . ')';

			return $res;

		 }	 

	}

	if ($citation){

    //$type = $typeDesignation_citation->type;

    $year = substr($citation->datePublished->start, 0, 4);

    $author = $citation->authorTeam->titleCache;

    $res .= ' (designated by ';

    $res .= $author;

    $res .= ($year ? ' '.$year : '');

    $res .= ($pages ? ': '. $pages : '');

    //$res .= ')';

    $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations', $typeDesignation->citation->titleCache);

    $res .= theme('cdm_footnote_key', $fkey_typeDesignation, $footnote_separator, true, true) . ')';

    }		

	return $res;

}

function theme_cdm_typedesignations($typeDesignations = array()){

	/*

	 if(isset($renderTemplate['referencePart']['reference']) && $taxonName->nomenclaturalReference){

	 $microreference = null;

	 if(isset($renderTemplate['referencePart']['microreference'])){

	 $microreference = $taxonName->nomenclaturalMicroReference;

	 }

	 $citation = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array($typeDesignation->uuid), "microReference=".urlencode($microreference));

	 $citation = $citation->String;

	 */

	RenderHints::pushToRenderStack('typedesignations');

	//_add_js_cluetip();

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

	$typeDesignation_footnotes = false;

	$is_lectotype = false;

	$specimenTypeDesignations = array();

	$separator = ',';

	foreach($typeDesignations as $typeDesignation){

		if($typeDesignation->class == 'SpecimenTypeDesignation'){

			// SpecimenTypeDesignations should be ordered. collect theme here only

			$specimenTypeDesignations[] = $typeDesignation;

		}else{ //it is a lectotype?

			if(strcmp($typeDesignation->typeStatus->titleCache, 'lectotype') == 0){

        $is_lectotype = true;

      }

			// it's a NameTypeDesignation

			if($typeDesignation->notDesignated){

				$out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>: ' . t('not designated'). '</li>';

				//$out .= '<li class="nameTypeDesignation"><span class="status">Lectotype</span>: '.t('not designated'). '</li>';

			}else if($typeDesignation->typeName){

				$link_to_name_page = '?q=' . path_to_name($typeDesignation->typeName->uuid);

				$out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>';

				if($typeDesignation->citation){

					$out .= type_designation_citation_layout($typeDesignation, $separator);

					//footnotes

					//$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, $typeDesignation->citation->titleCache);

				/*

				  $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations', $typeDesignation->citation->titleCache);

					$out .= theme('cdm_footnote_key', $fkey_typeDesignation, $separator, true, true) . ')';

				*/

				}

				if($typeDesignation->typeName->nomenclaturalReference){

					$referenceUri = url(path_to_reference($typeDesignation->typeName->nomenclaturalReference->uuid));

				}

				$out .= ': ' . theme('cdm_taxonName', $typeDesignation->typeName, $link_to_name_page, $referenceUri, true, true);

			}

		}

	}

	if(!empty($specimenTypeDesignations)){

		// sorting might be different for dataportals so this has to be parameterized

		usort($specimenTypeDesignations, "compare_specimenTypeDesignationStatus");

		foreach($specimenTypeDesignations as $std){

			$typeReference = '';

			//show citation only for Lectotype or Neotype

			$showCitation = isset($std->typeStatus) && ($std->typeStatus->uuid == UUID_NEOTYPE || $std->typeStatus->uuid == UUID_LECTOTYPE);

			if($showCitation && !empty($std->citation)){

				//$shortCitation = $std->citation->authorTeam->titleCache;

				$author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $std->citation->uuid);

				$shortCitation = $author_team->titleCache;

				$shortCitation .= (strlen($shortCitation) > 0 ? ' ' : '' ). partialToYear($std->citation->datePublished->start);

				if(strlen($shortCitation) == 0){

					$shortCitation = theme('cdm_reference', $std->citation);

					$missingShortCitation = true;

				}

				$typeReference .= ' (' . t('designated by');

				$typeReference .= '&nbsp;<span class="typeReference '.($missingShortCitation ? '' : 'cluetip').' no-print" title="'. htmlspecialchars('|'.theme('cdm_reference',$std->citation ).'|') .'">';

				$typeReference .= $shortCitation.'</span>';

				$typeReference .= ':'. $std->citationMicroReference .')';

				$_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-lectotypes', $std->citation->titleCache);

				$typeReference .= theme('cdm_footnote_key', $_fkey2, $separator, true, true);

			}

			$derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $std->typeSpecimen->uuid);

			$out .= '<li class="specimenTypeDesignation">';

			$out .= '<span class="status">'

			     .(($std->typeStatus->representation_L10n) ? $std->typeStatus->representation_L10n : t('Type'))

			     .$typeReference.'</span>: '.$derivedUnitFacadeInstance->titleCache;

			$out .= theme('cdm_specimen', $derivedUnitFacadeInstance); 

			//footnotes for synonymy acronyms

			$_fkey = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-acronyms', $derivedUnitFacadeInstance->collection->titleCache);

			$out .= theme('cdm_footnote_key', $_fkey, $separator);

			$out .= '</li>';

			if (!empty($std->citation)){

				$render_footnote_lectotypes = true;

			 //$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-lectotypes');

			}

		}

	}

	$out .= '</ul>';

	//render the footnotes at the end of the page

	if ($render_footnote_lectotypes){

		$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-lectotypes');

	}

	$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-acronyms', 'li');

	$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations', 'li');

	//$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, 'li');

	RenderHints::popFromRenderStack();

	return $out;

}

/**

 * FIXME this definitively has to be in another spot. just didn't know where to put it right now.

 * Compares the status of two SpecimenTypeDesignations

 * @param String $a 	a SpecimenTypeDesignations

 * @param String $b		another SpecimenTypeDesignations

 */

function compare_specimenTypeDesignationStatus($a, $b){

	/* this is the desired sort oder as of now:

	 * 	Holotype

	 * 	Isotype

	 * 	Lectotype

	 * 	Isolectotype

	 * 	Syntype

	 *

	 * TODO

	 * Basically, what we are trying to do is, we define an ordered array of TypeDesignation-states

	 * and use the index of this array for comparison. This array has to be filled with the cdm-

	 * TypeDesignation states and the order should be parameterisable inside the dataportal.

	 */

	// make that static for now

	$typeOrder = array('Holotype', 'Isotype', 'Lectotype', 'Isolectotype', 'Syntype');

	$aQuantifier = array_search($a->typeStatus->label, $typeOrder);

	$bQuantifier = array_search($b->typeStatus->label, $typeOrder);

	if ($aQuantifier == $bQuantifier) {

		// sort alphabetically

		return ($a->typeStatus->label < $b->typeStatus->label) ? -1 : 1;

	}

	return ($aQuantifier < $bQuantifier) ? -1 : 1;

}

function theme_cdm_nameRelationships($nameRelationships, $skipTypes = false){

	if(!$nameRelationships){

		return;

	}

	RenderHints::pushToRenderStack('nameRelationships');

	$footnoteListKey = 'nameRelationships';

	RenderHints::setFootnoteListKey($footnoteListKey);

	// group by relationship type

	$relationshipGroups = array();

	foreach($nameRelationships as $nameRelationship){

		if(!array_key_exists($nameRelationship->type->uuid, $relationshipGroups)){

			$relationshipGroups[$nameRelationship->type->uuid] = array();

		}

		$relationshipGroups[$nameRelationship->type->uuid][] = $nameRelationship;

	}

	// generate output

	$out = '';

	foreach($relationshipGroups as $group){

		$type = $group[0]->type;

		if(is_array($skipTypes) && in_array($type->uuid, $skipTypes)){

			continue;

		}

		$block->module = 'cdm_dataportal';

		$block->subject = t(ucfirst($type->inverseRepresentation_L10n));

		$block->delta = generalizeString(strtolower($type->inverseRepresentation_L10n));

		foreach($group as $relationship){

			$relatedNames[] = cdm_taggedtext2html($relationship->fromName->taggedName);

		}

		$block->content .= implode('; ', $relatedNames);

		$out .= theme('block', $block);

	}

	$out .= theme('cdm_footnotes', $footnoteListKey, 'li');

	RenderHints::popFromRenderStack();

	return $out;

}

function theme_cdm_homotypicSynonymLine($taxon){

	$out = '';

	$out .= '<li class="synonym">'.theme('cdm_related_taxon', $taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

	return $out;

}

function theme_cdm_heterotypicSynonymyGroup($homotypicalGroup){

	RenderHints::pushToRenderStack('heterotypicSynonymyGroup');

	$out = '';

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

	$footnoteListKey = ( isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');

	RenderHints::setFootnoteListKey($footnoteListKey);

	$is_first_entry = true;

	$typeDesignations = null;

	foreach($homotypicalGroup as $synonym){

		if($is_first_entry){

			$is_first_entry = false;

			$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);

			// is first list entry

			$out .= '<li class="firstentry synonym">'.theme('cdm_related_taxon',$synonym, UUID_HETEROTYPIC_SYNONYM_OF).'</li>';

		} else {

			$out .= '<li class="synonym">'.theme('cdm_related_taxon',$synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

		}

	}

	//$test =  theme('cdm_annotation_footnotes', $footnoteListKey, 'li');

	//tuypedesignations footnotes

	if($typeDesignations){

		$out .= theme('cdm_typedesignations', $typeDesignations);

	}

	//annotation footnotes

	//$annotation_key = ( isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');

	//$fkey_annotations = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-annotations-' . $annotation_key, $annotation_key);

	//$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-annotations-' . $annotation_key);

	$out .= theme('cdm_annotation_footnotes', $footnoteListKey, 'li');

	//$out .= theme('cdm_annotation_footnotes', $footnoteListKey);

	$out .= '</ul>';

	RenderHints::popFromRenderStack();

	return $out;

}

function theme_cdm_homotypicSynonymyGroup($synonymList, $prependedSynonyms = array()){

	RenderHints::pushToRenderStack('homotypicSynonymyGroup');

	$footnoteListKey = isset($prependedSynonyms[0]) ? $prependedSynonyms[0]->uuid : (isset($synonymList[0]) ? $synonymList[0]->uuid : 'NULL');

	$accepted_taxon_footnoteListKey = RenderHints::getFootnoteListKey();

	RenderHints::setFootnoteListKey($footnoteListKey);

	if(! is_array($synonymList) || count($synonymList) == 0){

		return;

	}

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

	if(!empty($prependedSynonyms)){

		foreach($prependedSynonyms as $taxon){

			$out .= '<li class="synonym">'.theme('cdm_related_taxon', $taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

		}

	}

	foreach($synonymList as $synonym){

		$out .= '<li class="synonym">'.theme('cdm_related_taxon', $synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';

	}

	$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);

	if($typeDesignations){

		$out .= theme('cdm_typedesignations', $typeDesignations);

	}

  if($accepted_taxon_footnoteListKey){// to avoiding drupal warnings (#1830) why false???

  	 $out .= theme('cdm_footnotes', $accepted_taxon_footnoteListKey, 'li');

  }

	$out .= theme('cdm_annotation_footnotes', $footnoteListKey, 'li');

	$out .= '</ul>';

	RenderHints::popFromRenderStack();

	return $out;

}

function theme_cdm_taxonName($taxonName, $nameLink = NULL, $refenceLink = NULL,

                   $show_annotations = true, $is_type_designation = false, $skiptags = array()){

	$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);

	$partDefinition = get_partDefinition($taxonName->class);

	// apply defintions to template

	foreach($renderTemplate as $part=>$uri){

		if(isset($partDefinition[$part])){

			$renderTemplate[$part] = $partDefinition[$part];

		}

		if(is_array($uri)){

			$renderTemplate[$part]['#uri'] = $uri['#uri'];

		}

	}

	$firstEntryIsValidNamePart = is_array($taxonName->taggedName)

	&& is_string($taxonName->taggedName[0]->text)

	&& $taxonName->taggedName[0]->text != ''

	&& $taxonName->taggedName[0]->type == 'name';

	// got to use second entry as first one, see ToDo comment below ...

	if($firstEntryIsValidNamePart){

		$taggedName = $taxonName->taggedName;

		$lastAuthorElementString = false;

		$hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);

		$hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);

		if(!($hasNamePart_with_Authors || $hasNameAuthorPart_with_Authors)){

			//      // find author and split off from name

			//      // TODO expecting to find the author as the last element

			//      if($taggedName[count($taggedName)- 1]->type == 'authors'){

			//        $authorTeam = $taggedName[count($taggedName)- 1]->text;

			//        unset($taggedName[count($taggedName)- 1]);

			//      }

			// remove all authors

			$taggedNameNew = array();

			foreach($taggedName as $element){

				if($element->type != 'authors'){

					$taggedNameNew[] = $element;

				} else {

					$lastAuthorElementString = $element->text;

				}

			}

			$taggedName = $taggedNameNew;

		}

		$name = '<span class="'.$taxonName->class.'">'.theme('cdm_taggedtext2html', $taggedName, 'span', ' ', $skiptags).'</span>';

	} else {

		$name = '<span class="'.$taxonName->class.'_titleCache">'.$taxonName->titleCache.'</span>';

	}

	// fill name into $renderTemplate

	array_setr('name', $name, $renderTemplate);

	//  // fill with authorTeam

	//  if($authorTeam){

	//    $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';

	//    array_setr('authorTeam', $authorTeamHtml, $renderTemplate);

	//  }

	// fill with reference

	if(isset($renderTemplate['referencePart']) && !$is_type_designation){

		// [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,

		// Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."

		if(isset($renderTemplate['referencePart']['reference']) && $taxonName->nomenclaturalReference){

			$microreference = null;

			if(isset($renderTemplate['referencePart']['microreference'])){

				$microreference = $taxonName->nomenclaturalMicroReference;

			}

			$citation = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array($taxonName->nomenclaturalReference->uuid), "microReference=".urlencode($microreference));

			$citation = $citation->String;

			// find preceding element of the refrence

			$precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);

			if(str_beginsWith($citation, ", in")){

				$citation = substr($citation, 2);

				$separator = ' ';

			} else if(!str_beginsWith($citation, "in") && $precedingKey == 'authors'){

				$separator = ', ';

			} else {

				$separator = ' ';

			}

			$referenceArray['#separator'] = $separator;

			$referenceArray['#html'] = '<span class="reference">'.$citation.'</span>';

			array_setr('reference', $referenceArray, $renderTemplate);

		}

		// if authors have been removed from the name part the last named authorteam

		// should be added to the reference citation, otherwise, keep the separator

		// out of the reference

		if(isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString){

			// if the nomenclaturalReference cintation is not included in the reference part but diplay of the microreference

			// is whanted append the microreference to the authorTeam

			if(!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])){

				$separator = ": ";

				$citation = $taxonName->nomenclaturalMicroReference;

			}

			$referenceArray['#html'] = ' <span class="reference">'.$lastAuthorElementString.$separator.$citation.'</span>';

			array_setr('authors', $referenceArray, $renderTemplate);

		}

	}

	// fill with status

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

	if(array_setr('status', true, $renderTemplate)){

		if(isset($taxon->name->status[0])){

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

				$statusHtml .= ', '.$status->type->representation_L10n;

			}

		}

		array_setr('status', ' <span class="nomenclatural_status">'.$statusHtml.'</span>', $renderTemplate);

	}

	}

	// fill with protologues etc...

	if(array_setr('description', true, $renderTemplate)){

		$descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);

		foreach($descriptions as $description){

			if(!empty($description)){

				foreach($description->elements as $description_element){

					$second_citation = '';

					if ($description_element->multilanguageText_L10n->text){

						$second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';

					}

					$descriptionHtml .= $second_citation;

					$descriptionHtml .= theme("cdm_media", $description_element, array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html'));

				}

			}

		}

		array_setr('description', $descriptionHtml, $renderTemplate);

	}

	// render

	$out = '<span ref="/name/'.$taxonName->uuid.'">';

	foreach($renderTemplate as $partName=>$part){

		$separator = '';

		$partHtml = '';

		$uri = false;

		if(!is_array($part)){

			continue;

		}

		if(isset($part['#uri']) && is_string($part['#uri'])){

			$uri = $part['#uri'];

			unset($part['#uri']);

		}

		foreach($part as $key=>$content){

			$html = '';

			if(is_array($content)){

				$html = $content['#html'];

				$separator = $content['#separator'];

			} else if(is_string($content)){

				$html = $content;

			}

			$partHtml .= '<span class="'.$key.'">'.$html.'</span>';

		}

		if($uri){

			$out .= $separator.'<a href="'.$uri.'" class="'.$partName.'">'.$partHtml.'</a>';

		} else {

			$out .= $separator.$partHtml;

		}

	}

	$out .= '</span>';

	if ($show_annotations){

    //$out .= theme('cdm_annotations_as_footnotekeys', $taxonName);

	}

	return $out;

}

/**

 * Recursively searches the array for the $key and sets the given value

 * @param $key

 * @param $value

 * @param $array

 * @return true if the key has been found

 */

function &array_setr($key, $value, array &$array){

	foreach($array as $k=>&$v){

		if($key == $k){

			$v = $value;

			return $array;

		} else if(is_array($v)){

			$innerArray = array_setr($key, $value, $v);

			if($innerArray){

				return $array;

			}

		}

	}

	return null;

}

function &get_preceding_contentElement($contentElementKey, array &$renderTemplate){

	$precedingElement = null;

	foreach($renderTemplate as &$part){

		foreach($part as $key=>&$element){

			if($key == $contentElementKey){

				return $precedingElement;

			}

			$precedingElement = $element;

		}

	}

	return null;

}

function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate){

	$precedingKey = null;

	foreach($renderTemplate as &$part){

		if(is_array($part)){

			foreach($part as $key=>&$element){

				if($key == $contentElementKey){

					return $precedingKey;

				}

				if(!str_beginsWith($key, '#')){

					$precedingKey = $key;

				}

			}

		}

	}

	return null;

}