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<?php
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// $Id$
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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See http://www.mozilla.org/MPL/MPL-1.1.html for the full license terms.
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*/
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/**
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* This function prints the lectotype citation with the correct layout
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* Lectotypes are renderized in the synonymy tab of a taxon if they exist
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* @param $typeDesignation_citation The lectotype citation to print
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* @return html valid string
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*/
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function type_designation_citation_layout($typeDesignation){
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$res = '';
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$citation = $typeDesignation->citation;
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$pages = $typeDesignation->citationMicroReference;
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if ($citation){
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//$type = $typeDesignation_citation->type;
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$year = substr($citation->datePublished->start, 0, 4);
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$author = $citation->authorTeam->titleCache;
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$res .= ' (designated by ';
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$res .= $author;
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$res .= ($year ? ' '.$year : '');
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$res .= ($pages ? ': '. $pages : '');
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//$res .= ')';
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}
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return $res;
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}
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function theme_cdm_typedesignations($typeDesignations = array()){
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/*
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if(isset($renderTemplate['referencePart']['reference']) && $taxonName->nomenclaturalReference){
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$microreference = null;
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if(isset($renderTemplate['referencePart']['microreference'])){
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$microreference = $taxonName->nomenclaturalMicroReference;
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}
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$citation = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array($typeDesignation->uuid), "microReference=".urlencode($microreference));
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$citation = $citation->String;
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*/
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RenderHints::pushToRenderStack('typedesignations');
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//_add_js_cluetip();
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$out = '<ul class="typeDesignations">';
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$typeDesignation_footnotes = false;
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$is_lectotype = false;
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$specimenTypeDesignations = array();
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$separator = ',';
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foreach($typeDesignations as $typeDesignation){
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if($typeDesignation->class == 'SpecimenTypeDesignation'){
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// SpecimenTypeDesignations should be ordered. collect theme here only
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$specimenTypeDesignations[] = $typeDesignation;
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}else{ //it is a lectotype?
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if(strcmp($typeDesignation->typeStatus->titleCache, 'lectotype') == 0){
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$is_lectotype = true;
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}
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// it's a NameTypeDesignation
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if($typeDesignation->notDesignated){
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$out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>: ' . t('not designated'). '</li>';
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//$out .= '<li class="nameTypeDesignation"><span class="status">Lectotype</span>: '.t('not designated'). '</li>';
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}else if($typeDesignation->typeName){
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$link_to_name_page = '?q=' . path_to_name($typeDesignation->typeName->uuid);
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$out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>';
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if($typeDesignation->citation){
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$out .= type_designation_citation_layout($typeDesignation);
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//footnotes
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//$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, $typeDesignation->citation->titleCache);
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$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations', $typeDesignation->citation->titleCache);
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$out .= theme('cdm_footnote_key', $fkey_typeDesignation, $separator, true, true) . ')';
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}
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if($typeDesignation->typeName->nomenclaturalReference){
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$referenceUri = url(path_to_reference($typeDesignation->typeName->nomenclaturalReference->uuid));
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}
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$out .= ': ' . theme('cdm_taxonName', $typeDesignation->typeName, $link_to_name_page, $referenceUri, true, true);
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}
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}
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}
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if(!empty($specimenTypeDesignations)){
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// sorting might be different for dataportals so this has to be parameterized
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usort($specimenTypeDesignations, "compare_specimenTypeDesignationStatus");
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foreach($specimenTypeDesignations as $std){
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$typeReference = '';
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//show citation only for Lectotype or Neotype
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$showCitation = isset($std->typeStatus) && ($std->typeStatus->uuid == UUID_NEOTYPE || $std->typeStatus->uuid == UUID_LECTOTYPE);
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if($showCitation && !empty($std->citation)){
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//$shortCitation = $std->citation->authorTeam->titleCache;
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$author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $std->citation->uuid);
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$shortCitation = $author_team->titleCache;
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$shortCitation .= (strlen($shortCitation) > 0 ? ' ' : '' ). partialToYear($std->citation->datePublished->start);
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if(strlen($shortCitation) == 0){
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$shortCitation = theme('cdm_reference', $std->citation);
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$missingShortCitation = true;
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}
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$typeReference .= ' (' . t('designated by');
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$typeReference .= ' <span class="typeReference '.($missingShortCitation ? '' : 'cluetip').' no-print" title="'. htmlspecialchars('|'.theme('cdm_reference',$std->citation ).'|') .'">';
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$typeReference .= $shortCitation.'</span>';
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$typeReference .= ':'. $std->citationMicroReference .')';
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$_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-lectotypes', $std->citation->titleCache);
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$typeReference .= theme('cdm_footnote_key', $_fkey2, $separator, true, true);
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}
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$derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $std->typeSpecimen->uuid);
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$out .= '<li class="specimenTypeDesignation">';
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$out .= '<span class="status">'.(($std->typeStatus->representation_L10n) ? $std->typeStatus->representation_L10n : t('Type')) .$typeReference.'</span>: '.$derivedUnitFacadeInstance->titleCache;
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$out .= theme('cdm_specimen', $derivedUnitFacadeInstance);
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//footnotes for synonymy acronyms
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$_fkey = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-acronyms', $derivedUnitFacadeInstance->collection->titleCache);
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$out .= theme('cdm_footnote_key', $_fkey, $separator);
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$out .= '</li>';
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if (!empty($std->citation)){
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$render_footnote_lectotypes = true;
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//$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-lectotypes');
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}
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}
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}
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$out .= '</ul>';
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//render the footnotes at the end of the page
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if ($render_footnote_lectotypes){
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$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-lectotypes');
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}
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$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-acronyms', 'li');
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$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations', 'li');
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//$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, 'li');
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RenderHints::popFromRenderStack();
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return $out;
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}
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/**
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* FIXME this definitively has to be in another spot. just didn't know where to put it right now.
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* Compares the status of two SpecimenTypeDesignations
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* @param String $a a SpecimenTypeDesignations
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* @param String $b another SpecimenTypeDesignations
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*/
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function compare_specimenTypeDesignationStatus($a, $b){
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/* this is the desired sort oder as of now:
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* Holotype
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* Isotype
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* Lectotype
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* Isolectotype
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* Syntype
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*
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* TODO
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* Basically, what we are trying to do is, we define an ordered array of TypeDesignation-states
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* and use the index of this array for comparison. This array has to be filled with the cdm-
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* TypeDesignation states and the order should be parameterisable inside the dataportal.
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*/
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// make that static for now
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$typeOrder = array('Holotype', 'Isotype', 'Lectotype', 'Isolectotype', 'Syntype');
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$aQuantifier = array_search($a->typeStatus->label, $typeOrder);
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$bQuantifier = array_search($b->typeStatus->label, $typeOrder);
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if ($aQuantifier == $bQuantifier) {
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// sort alphabetically
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return ($a->typeStatus->label < $b->typeStatus->label) ? -1 : 1;
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}
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return ($aQuantifier < $bQuantifier) ? -1 : 1;
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}
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function theme_cdm_nameRelationships($nameRelationships, $skipTypes = false){
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if(!$nameRelationships){
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return;
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}
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RenderHints::pushToRenderStack('nameRelationships');
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$footnoteListKey = 'nameRelationships';
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RenderHints::setFootnoteListKey($footnoteListKey);
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// group by relationship type
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$relationshipGroups = array();
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foreach($nameRelationships as $nameRelationship){
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if(!array_key_exists($nameRelationship->type->uuid, $relationshipGroups)){
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$relationshipGroups[$nameRelationship->type->uuid] = array();
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}
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$relationshipGroups[$nameRelationship->type->uuid][] = $nameRelationship;
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}
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// generate output
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$out = '';
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foreach($relationshipGroups as $group){
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$type = $group[0]->type;
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if(is_array($skipTypes) && in_array($type->uuid, $skipTypes)){
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continue;
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}
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$block->module = 'cdm_dataportal';
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$block->subject = t(ucfirst($type->inverseRepresentation_L10n));
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$block->delta = generalizeString(strtolower($type->inverseRepresentation_L10n));
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foreach($group as $relationship){
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$relatedNames[] = cdm_taggedtext2html($relationship->fromName->taggedName);
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}
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$block->content .= implode('; ', $relatedNames);
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$out .= theme('block', $block);
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}
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$out .= theme('cdm_footnotes', $footnoteListKey, 'div');
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RenderHints::popFromRenderStack();
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return $out;
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}
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function theme_cdm_homotypicSynonymLine($taxon){
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$out = '';
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$out .= '<li class="synonym">'.theme('cdm_related_taxon', $taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
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return $out;
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}
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function theme_cdm_heterotypicSynonymyGroup($homotypicalGroup){
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RenderHints::pushToRenderStack('heterotypicSynonymyGroup');
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$out = '';
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$out = '<ul class="heterotypicSynonymyGroup">';
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$footnoteListKey = ( isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');
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RenderHints::setFootnoteListKey($footnoteListKey);
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$is_first_entry = true;
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$typeDesignations = null;
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foreach($homotypicalGroup as $synonym){
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if($is_first_entry){
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$is_first_entry = false;
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$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);
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// is first list entry
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$out .= '<li class="firstentry synonym">'.theme('cdm_related_taxon',$synonym, UUID_HETEROTYPIC_SYNONYM_OF).'</li>';
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} else {
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$out .= '<li class="synonym">'.theme('cdm_related_taxon',$synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
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}
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}
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//$test = theme('cdm_annotation_footnotes', $footnoteListKey, 'li');
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//tuypedesignations footnotes
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if($typeDesignations){
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$out .= theme('cdm_typedesignations', $typeDesignations);
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}
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//annotation footnotes
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//$annotation_key = ( isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');
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//$fkey_annotations = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-annotations-' . $annotation_key, $annotation_key);
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//$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-annotations-' . $annotation_key);
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$out .= theme('cdm_annotation_footnotes', $footnoteListKey, 'li');
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//$out .= theme('cdm_annotation_footnotes', $footnoteListKey);
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$out .= '</ul>';
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RenderHints::popFromRenderStack();
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return $out;
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}
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function theme_cdm_homotypicSynonymyGroup($synonymList, $prependedSynonyms = array()){
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RenderHints::pushToRenderStack('homotypicSynonymyGroup');
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$footnoteListKey = isset($prependedSynonyms[0]) ? $prependedSynonyms[0]->uuid : (isset($synonymList[0]) ? $synonymList[0]->uuid : 'NULL');
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$accepted_taxon_footnoteListKey = RenderHints::getFootnoteListKey();
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RenderHints::setFootnoteListKey($footnoteListKey);
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if(! is_array($synonymList) || count($synonymList) == 0){
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return;
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}
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$out = '<ul class="homotypicSynonyms">';
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if(!empty($prependedSynonyms)){
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foreach($prependedSynonyms as $taxon){
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$out .= '<li class="synonym">'.theme('cdm_related_taxon', $taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
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}
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}
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foreach($synonymList as $synonym){
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$out .= '<li class="synonym">'.theme('cdm_related_taxon', $synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
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}
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$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);
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if($typeDesignations){
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$out .= theme('cdm_typedesignations', $typeDesignations);
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}
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$out .= theme('cdm_footnotes', $accepted_taxon_footnoteListKey, 'li');
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$out .= theme('cdm_annotation_footnotes', $footnoteListKey, 'li');
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$out .= '</ul>';
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RenderHints::popFromRenderStack();
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return $out;
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}
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function theme_cdm_taxonName($taxonName, $nameLink = NULL, $refenceLink = NULL, $show_annotations = true, $is_type_designation = false){
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$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
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$partDefinition = get_partDefinition($taxonName->class);
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// apply defintions to template
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foreach($renderTemplate as $part=>$uri){
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if(isset($partDefinition[$part])){
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$renderTemplate[$part] = $partDefinition[$part];
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}
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if(is_array($uri)){
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$renderTemplate[$part]['#uri'] = $uri['#uri'];
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}
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}
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$firstEntryIsValidNamePart = is_array($taxonName->taggedName)
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&& is_string($taxonName->taggedName[0]->text)
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&& $taxonName->taggedName[0]->text != ''
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&& $taxonName->taggedName[0]->type == 'name';
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// got to use second entry as first one, see ToDo comment below ...
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if($firstEntryIsValidNamePart){
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$taggedName = $taxonName->taggedName;
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$lastAuthorElementString = false;
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$hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
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$hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
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if(!($hasNamePart_with_Authors || $hasNameAuthorPart_with_Authors)){
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// // find author and split off from name
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// // TODO expecting to find the author as the last element
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// if($taggedName[count($taggedName)- 1]->type == 'authors'){
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// $authorTeam = $taggedName[count($taggedName)- 1]->text;
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// unset($taggedName[count($taggedName)- 1]);
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// }
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// remove all authors
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$taggedNameNew = array();
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foreach($taggedName as $element){
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if($element->type != 'authors'){
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$taggedNameNew[] = $element;
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} else {
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$lastAuthorElementString = $element->text;
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}
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}
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$taggedName = $taggedNameNew;
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}
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$name = '<span class="'.$taxonName->class.'">'.theme('cdm_taggedtext2html', $taggedName).'</span>';
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} else {
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$name = '<span class="'.$taxonName->class.'_titleCache">'.$taxonName->titleCache.'</span>';
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}
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// fill name into $renderTemplate
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array_setr('name', $name, $renderTemplate);
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// // fill with authorTeam
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// if($authorTeam){
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// $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
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// array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
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// }
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// fill with reference
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if(isset($renderTemplate['referencePart']) && !$is_type_designation){
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// [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
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// Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
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382
|
if(isset($renderTemplate['referencePart']['reference']) && $taxonName->nomenclaturalReference){
|
383
|
$microreference = null;
|
384
|
if(isset($renderTemplate['referencePart']['microreference'])){
|
385
|
$microreference = $taxonName->nomenclaturalMicroReference;
|
386
|
}
|
387
|
$citation = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array($taxonName->nomenclaturalReference->uuid), "microReference=".urlencode($microreference));
|
388
|
$citation = $citation->String;
|
389
|
// find preceding element of the refrence
|
390
|
$precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
|
391
|
if(str_beginsWith($citation, ", in")){
|
392
|
$citation = substr($citation, 2);
|
393
|
$separator = ' ';
|
394
|
} else if(!str_beginsWith($citation, "in") && $precedingKey == 'authors'){
|
395
|
$separator = ', ';
|
396
|
} else {
|
397
|
$separator = ' ';
|
398
|
}
|
399
|
|
400
|
$referenceArray['#separator'] = $separator;
|
401
|
$referenceArray['#html'] = '<span class="reference">'.$citation.'</span>';
|
402
|
array_setr('reference', $referenceArray, $renderTemplate);
|
403
|
}
|
404
|
|
405
|
// if authors have been removed from the name part the last named authorteam
|
406
|
// should be added to the reference citation, otherwise, keep the separator
|
407
|
// out of the reference
|
408
|
if(isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString){
|
409
|
// if the nomenclaturalReference cintation is not included in the reference part but diplay of the microreference
|
410
|
// is whanted append the microreference to the authorTeam
|
411
|
if(!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])){
|
412
|
$separator = ": ";
|
413
|
$citation = $taxonName->nomenclaturalMicroReference;
|
414
|
}
|
415
|
$referenceArray['#html'] = ' <span class="reference">'.$lastAuthorElementString.$separator.$citation.'</span>';
|
416
|
array_setr('authors', $referenceArray, $renderTemplate);
|
417
|
}
|
418
|
|
419
|
}
|
420
|
|
421
|
// fill with status
|
422
|
if(array_setr('status', true, $renderTemplate)){
|
423
|
if(isset($taxon->name->status[0])){
|
424
|
foreach($taxon->name->status as $status){
|
425
|
$statusHtml .= ', '.$status->type->representation_L10n;
|
426
|
}
|
427
|
}
|
428
|
array_setr('status', ' <span class="nomenclatural_status">'.$statusHtml.'</span>', $renderTemplate);
|
429
|
}
|
430
|
|
431
|
// fill with protologues etc...
|
432
|
if(array_setr('description', true, $renderTemplate)){
|
433
|
$descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
|
434
|
foreach($descriptions as $description){
|
435
|
if(!empty($description)){
|
436
|
foreach($description->elements as $description_element){
|
437
|
$second_citation = '';
|
438
|
if ($description_element->multilanguageText_L10n->text){
|
439
|
$second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
|
440
|
}
|
441
|
$descriptionHtml .= $second_citation;
|
442
|
$descriptionHtml .= theme("cdm_media", $description_element, array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html'));
|
443
|
}
|
444
|
}
|
445
|
}
|
446
|
array_setr('description', $descriptionHtml, $renderTemplate);
|
447
|
}
|
448
|
|
449
|
// render
|
450
|
$out = '<span ref="/name/'.$taxonName->uuid.'">';
|
451
|
|
452
|
foreach($renderTemplate as $partName=>$part){
|
453
|
$separator = '';
|
454
|
$partHtml = '';
|
455
|
$uri = false;
|
456
|
if(!is_array($part)){
|
457
|
continue;
|
458
|
}
|
459
|
if(isset($part['#uri']) && is_string($part['#uri'])){
|
460
|
$uri = $part['#uri'];
|
461
|
unset($part['#uri']);
|
462
|
}
|
463
|
foreach($part as $key=>$content){
|
464
|
$html = '';
|
465
|
if(is_array($content)){
|
466
|
$html = $content['#html'];
|
467
|
$separator = $content['#separator'];
|
468
|
} else if(is_string($content)){
|
469
|
$html = $content;
|
470
|
}
|
471
|
$partHtml .= '<span class="'.$key.'">'.$html.'</span>';
|
472
|
}
|
473
|
if($uri){
|
474
|
$out .= $separator.'<a href="'.$uri.'" class="'.$partName.'">'.$partHtml.'</a>';
|
475
|
} else {
|
476
|
$out .= $separator.$partHtml;
|
477
|
}
|
478
|
}
|
479
|
$out .= '</span>';
|
480
|
if ($show_annotations){
|
481
|
//$out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
|
482
|
}
|
483
|
return $out;
|
484
|
}
|
485
|
|
486
|
/**
|
487
|
* Recursively searches the array for the $key and sets the given value
|
488
|
* @param $key
|
489
|
* @param $value
|
490
|
* @param $array
|
491
|
* @return true if the key has been found
|
492
|
*/
|
493
|
function &array_setr($key, $value, array &$array){
|
494
|
foreach($array as $k=>&$v){
|
495
|
if($key == $k){
|
496
|
$v = $value;
|
497
|
return $array;
|
498
|
} else if(is_array($v)){
|
499
|
$innerArray = array_setr($key, $value, $v);
|
500
|
if($innerArray){
|
501
|
return $array;
|
502
|
}
|
503
|
}
|
504
|
}
|
505
|
return null;
|
506
|
}
|
507
|
|
508
|
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate){
|
509
|
$precedingElement = null;
|
510
|
foreach($renderTemplate as &$part){
|
511
|
foreach($part as $key=>&$element){
|
512
|
if($key == $contentElementKey){
|
513
|
return $precedingElement;
|
514
|
}
|
515
|
$precedingElement = $element;
|
516
|
}
|
517
|
}
|
518
|
return null;
|
519
|
}
|
520
|
|
521
|
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate){
|
522
|
$precedingKey = null;
|
523
|
foreach($renderTemplate as &$part){
|
524
|
foreach($part as $key=>&$element){
|
525
|
if($key == $contentElementKey){
|
526
|
return $precedingKey;
|
527
|
}
|
528
|
if(!str_beginsWith($key, '#')){
|
529
|
$precedingKey = $key;
|
530
|
}
|
531
|
}
|
532
|
}
|
533
|
return null;
|
534
|
}
|
535
|
|
536
|
|
537
|
|
538
|
|
539
|
|
540
|
|
541
|
|