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806baeb2
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Andreas Kohlbecker
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<?php
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// $Id$
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/**
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75b05e16
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f.revilla
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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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806baeb2
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Andreas Kohlbecker
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13 |
75b05e16
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f.revilla
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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 $typeDesignation_citation The lectotype citation to print
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* @return html valid string
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*/
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44b1626d
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f.revilla
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function type_designation_citation_layout($typeDesignation, $footnote_separator = ','){
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75b05e16
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f.revilla
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$res = '';
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12196fd5
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f.revilla
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$citation = $typeDesignation->citation;
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$pages = $typeDesignation->citationMicroReference;
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8aabc503
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f.revilla
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if ($typeDesignation->typeStatus->uuid == UUID_ORIGINAL_DESIGNATION ||
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$typeDesignation->typeStatus->uuid == UUID_MONOTYPE){
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$res = ' ('. $typeDesignation->typeStatus->representation_L10n . ')';
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return $res;
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}
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44b1626d
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f.revilla
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if ($citation){
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8aabc503
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f.revilla
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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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$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations', $typeDesignation->citation->titleCache);
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$res .= theme('cdm_footnote_key', $fkey_typeDesignation, $footnote_separator, true, true) . ')';
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2efb8f43
|
Andreas Kohlbecker
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8aabc503
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f.revilla
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}
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return $res;
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75b05e16
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f.revilla
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}
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46 |
806baeb2
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Andreas Kohlbecker
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b32739d9
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f.revilla
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function contains_type_designation ($element, $collection){
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$result = false;
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foreach ($collection as $a){
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if($a->uuid == $element->uuid){
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$result = true;
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}
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}
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return $result;
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}
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function cdm_add_type_designations ($source, $extra) {
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a515d38e
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f.revilla
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if (is_array($source)){
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75aa3e52
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f.revilla
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$result = $source;
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if ($extra){
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ac168ae1
|
Andreas Kohlbecker
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foreach ($extra as $element) {
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75aa3e52
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f.revilla
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if (!contains_type_designation($element, $source)){
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$result[] = $element;
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}
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a515d38e
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f.revilla
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}
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75aa3e52
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f.revilla
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}
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a515d38e
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f.revilla
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}else {
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75aa3e52
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f.revilla
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$result = $extra;
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a515d38e
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f.revilla
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}
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ac168ae1
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Andreas Kohlbecker
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b32739d9
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f.revilla
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return $result;
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}
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806baeb2
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Andreas Kohlbecker
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function theme_cdm_typedesignations($typeDesignations = array()){
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6d589240
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f.revilla
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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 = $citation->String;
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*/
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ac168ae1
|
Andreas Kohlbecker
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RenderHints::pushToRenderStack('typedesignations');
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806baeb2
|
Andreas Kohlbecker
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$out = '<ul class="typeDesignations">';
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6d589240
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f.revilla
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$typeDesignation_footnotes = false;
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300375f2
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f.revilla
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$is_lectotype = false;
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806baeb2
|
Andreas Kohlbecker
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$specimenTypeDesignations = array();
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1f5b7a24
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f.revilla
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$separator = ',';
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806baeb2
|
Andreas Kohlbecker
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foreach($typeDesignations as $typeDesignation){
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if($typeDesignation->class == 'SpecimenTypeDesignation'){
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75b05e16
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f.revilla
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// SpecimenTypeDesignations should be ordered. collect theme here only
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806baeb2
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Andreas Kohlbecker
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$specimenTypeDesignations[] = $typeDesignation;
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300375f2
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f.revilla
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}else{ //it is a lectotype?
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if(strcmp($typeDesignation->typeStatus->titleCache, 'lectotype') == 0){
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8aabc503
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f.revilla
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$is_lectotype = true;
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}
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806baeb2
|
Andreas Kohlbecker
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// it's a NameTypeDesignation
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d74aa4df
|
Andreas Kohlbecker
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if($typeDesignation->notDesignated){
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300375f2
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f.revilla
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$out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>: ' . t('not designated'). '</li>';
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//$out .= '<li class="nameTypeDesignation"><span class="status">Lectotype</span>: '.t('not designated'). '</li>';
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806baeb2
|
Andreas Kohlbecker
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}else if($typeDesignation->typeName){
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75b05e16
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f.revilla
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$link_to_name_page = '?q=' . path_to_name($typeDesignation->typeName->uuid);
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300375f2
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f.revilla
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$out .= '<li class="nameTypeDesignation"><span class="status">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>';
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b32739d9
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f.revilla
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6d589240
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f.revilla
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if($typeDesignation->citation){
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44b1626d
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f.revilla
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$out .= type_designation_citation_layout($typeDesignation, $separator);
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6d589240
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f.revilla
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//footnotes
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f0df1f96
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f.revilla
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//$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, $typeDesignation->citation->titleCache);
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8aabc503
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f.revilla
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/*
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44b1626d
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f.revilla
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$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations', $typeDesignation->citation->titleCache);
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8aabc503
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f.revilla
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$out .= theme('cdm_footnote_key', $fkey_typeDesignation, $separator, true, true) . ')';
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*/
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6d589240
|
f.revilla
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}
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806baeb2
|
Andreas Kohlbecker
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if($typeDesignation->typeName->nomenclaturalReference){
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$referenceUri = url(path_to_reference($typeDesignation->typeName->nomenclaturalReference->uuid));
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}
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300375f2
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f.revilla
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$out .= ': ' . theme('cdm_taxonName', $typeDesignation->typeName, $link_to_name_page, $referenceUri, true, true);
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120 |
806baeb2
|
Andreas Kohlbecker
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}
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}
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}
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if(!empty($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($std->citation)){
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3147f061
|
f.revilla
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//$shortCitation = $std->citation->authorTeam->titleCache;
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15f11e83
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f.revilla
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75b05e16
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f.revilla
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$author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $std->citation->uuid);
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$shortCitation = $author_team->titleCache;
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15f11e83
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f.revilla
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806baeb2
|
Andreas Kohlbecker
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$shortCitation .= (strlen($shortCitation) > 0 ? ' ' : '' ). partialToYear($std->citation->datePublished->start);
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if(strlen($shortCitation) == 0){
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48650990
|
Andreas Kohlbecker
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$shortCitation = theme('cdm_reference', $std->citation);
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806baeb2
|
Andreas Kohlbecker
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$missingShortCitation = true;
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}
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75b05e16
|
f.revilla
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143 |
806baeb2
|
Andreas Kohlbecker
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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 .= $shortCitation.'</span>';
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21f49347
|
f.revilla
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$typeReference .= ':'. $std->citationMicroReference .')';
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75b05e16
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f.revilla
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$_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-lectotypes', $std->citation->titleCache);
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e5d101f3
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f.revilla
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$typeReference .= theme('cdm_footnote_key', $_fkey2, $separator, true, true);
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75b05e16
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f.revilla
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}
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151 |
806baeb2
|
Andreas Kohlbecker
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152 |
75b05e16
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f.revilla
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$derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $std->typeSpecimen->uuid);
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6d589240
|
f.revilla
|
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154 |
806baeb2
|
Andreas Kohlbecker
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$out .= '<li class="specimenTypeDesignation">';
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44b1626d
|
f.revilla
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$out .= '<span class="status">'
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8aabc503
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f.revilla
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.(($std->typeStatus->representation_L10n) ? $std->typeStatus->representation_L10n : t('Type'))
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.$typeReference.'</span>: '.$derivedUnitFacadeInstance->titleCache;
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$out .= theme('cdm_specimen', $derivedUnitFacadeInstance);
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21f49347
|
f.revilla
|
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160 |
75b05e16
|
f.revilla
|
//footnotes for synonymy acronyms
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aa582de0
|
Andreas Kohlbecker
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$_fkey = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-acronyms', $derivedUnitFacadeInstance->collection->titleCache);
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1f5b7a24
|
f.revilla
|
$out .= theme('cdm_footnote_key', $_fkey, $separator);
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163 |
806baeb2
|
Andreas Kohlbecker
|
$out .= '</li>';
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164 |
6d589240
|
f.revilla
|
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165 |
21f49347
|
f.revilla
|
if (!empty($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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169 |
806baeb2
|
Andreas Kohlbecker
|
}
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}
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$out .= '</ul>';
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173 |
ac168ae1
|
Andreas Kohlbecker
|
|
174 |
317b632e
|
f.revilla
|
//render the footnotes at the end of the page
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175 |
75b05e16
|
f.revilla
|
if ($render_footnote_lectotypes){
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$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-lectotypes');
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}
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178 |
f0df1f96
|
f.revilla
|
$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-acronyms', 'li');
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$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations', 'li');
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180 |
1f5b7a24
|
f.revilla
|
//$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, 'li');
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181 |
8aabc503
|
f.revilla
|
|
182 |
80e0aa8e
|
Andreas Kohlbecker
|
RenderHints::popFromRenderStack();
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183 |
19216886
|
f.revilla
|
|
184 |
806baeb2
|
Andreas Kohlbecker
|
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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190 |
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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 $b another SpecimenTypeDesignations
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*/
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194 |
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function compare_specimenTypeDesignationStatus($a, $b){
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195 |
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/* this is the desired sort oder as of now:
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196 |
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* Holotype
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* Isotype
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198 |
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* Lectotype
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199 |
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* Isolectotype
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200 |
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* Syntype
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*
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* TODO
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203 |
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* Basically, what we are trying to do is, we define an ordered array of TypeDesignation-states
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204 |
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* and use the index of this array for comparison. This array has to be filled with the cdm-
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205 |
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* TypeDesignation states and the order should be parameterisable inside the dataportal.
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*/
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207 |
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// make that static for now
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$typeOrder = array('Holotype', 'Isotype', 'Lectotype', 'Isolectotype', 'Syntype');
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209 |
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210 |
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$aQuantifier = array_search($a->typeStatus->label, $typeOrder);
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$bQuantifier = array_search($b->typeStatus->label, $typeOrder);
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212 |
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213 |
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if ($aQuantifier == $bQuantifier) {
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214 |
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// sort alphabetically
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215 |
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return ($a->typeStatus->label < $b->typeStatus->label) ? -1 : 1;
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}
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217 |
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return ($aQuantifier < $bQuantifier) ? -1 : 1;
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218 |
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219 |
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}
|
220 |
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221 |
0387c539
|
Andreas Kohlbecker
|
function theme_cdm_nameRelationships($nameRelationships, $skipTypes = false){
|
222 |
806baeb2
|
Andreas Kohlbecker
|
|
223 |
75b05e16
|
f.revilla
|
if(!$nameRelationships){
|
224 |
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return;
|
225 |
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}
|
226 |
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|
227 |
0387c539
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('nameRelationships');
|
228 |
75b05e16
|
f.revilla
|
$footnoteListKey = 'nameRelationships';
|
229 |
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RenderHints::setFootnoteListKey($footnoteListKey);
|
230 |
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|
231 |
806baeb2
|
Andreas Kohlbecker
|
// group by relationship type
|
232 |
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$relationshipGroups = array();
|
233 |
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foreach($nameRelationships as $nameRelationship){
|
234 |
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if(!array_key_exists($nameRelationship->type->uuid, $relationshipGroups)){
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235 |
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$relationshipGroups[$nameRelationship->type->uuid] = array();
|
236 |
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}
|
237 |
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$relationshipGroups[$nameRelationship->type->uuid][] = $nameRelationship;
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238 |
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}
|
239 |
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|
240 |
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// generate output
|
241 |
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$out = '';
|
242 |
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foreach($relationshipGroups as $group){
|
243 |
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$type = $group[0]->type;
|
244 |
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245 |
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if(is_array($skipTypes) && in_array($type->uuid, $skipTypes)){
|
246 |
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continue;
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247 |
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}
|
248 |
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249 |
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$block->module = 'cdm_dataportal';
|
250 |
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$block->subject = t(ucfirst($type->inverseRepresentation_L10n));
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251 |
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$block->delta = generalizeString(strtolower($type->inverseRepresentation_L10n));
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252 |
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253 |
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foreach($group as $relationship){
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254 |
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$relatedNames[] = cdm_taggedtext2html($relationship->fromName->taggedName);
|
255 |
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}
|
256 |
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257 |
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$block->content .= implode('; ', $relatedNames);
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258 |
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$out .= theme('block', $block);
|
259 |
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}
|
260 |
eec5d691
|
f.revilla
|
$out .= theme('cdm_footnotes', $footnoteListKey, 'li');
|
261 |
75b05e16
|
f.revilla
|
|
262 |
0387c539
|
Andreas Kohlbecker
|
RenderHints::popFromRenderStack();
|
263 |
806baeb2
|
Andreas Kohlbecker
|
return $out;
|
264 |
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}
|
265 |
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266 |
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267 |
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268 |
|
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function theme_cdm_homotypicSynonymLine($taxon){
|
269 |
|
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$out = '';
|
270 |
b9438135
|
Andreas Kohlbecker
|
$out .= '<li class="synonym">'.cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
|
271 |
75b05e16
|
f.revilla
|
|
272 |
806baeb2
|
Andreas Kohlbecker
|
return $out;
|
273 |
|
|
}
|
274 |
|
|
|
275 |
|
|
function theme_cdm_heterotypicSynonymyGroup($homotypicalGroup){
|
276 |
75b05e16
|
f.revilla
|
|
277 |
80e0aa8e
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('heterotypicSynonymyGroup');
|
278 |
75b05e16
|
f.revilla
|
|
279 |
806baeb2
|
Andreas Kohlbecker
|
$out = '';
|
280 |
|
|
$out = '<ul class="heterotypicSynonymyGroup">';
|
281 |
75b05e16
|
f.revilla
|
$footnoteListKey = ( isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');
|
282 |
0387c539
|
Andreas Kohlbecker
|
RenderHints::setFootnoteListKey($footnoteListKey);
|
283 |
75b05e16
|
f.revilla
|
|
284 |
806baeb2
|
Andreas Kohlbecker
|
$is_first_entry = true;
|
285 |
|
|
$typeDesignations = null;
|
286 |
|
|
foreach($homotypicalGroup as $synonym){
|
287 |
|
|
if($is_first_entry){
|
288 |
|
|
$is_first_entry = false;
|
289 |
12196fd5
|
f.revilla
|
$typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonym->name->uuid);
|
290 |
806baeb2
|
Andreas Kohlbecker
|
// is first list entry
|
291 |
b9438135
|
Andreas Kohlbecker
|
$out .= '<li class="firstentry synonym">'.cdm_related_taxon($synonym, UUID_HETEROTYPIC_SYNONYM_OF).'</li>';
|
292 |
806baeb2
|
Andreas Kohlbecker
|
} else {
|
293 |
b9438135
|
Andreas Kohlbecker
|
$out .= '<li class="synonym">'.cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
|
294 |
806baeb2
|
Andreas Kohlbecker
|
}
|
295 |
|
|
}
|
296 |
1f5b7a24
|
f.revilla
|
//$test = theme('cdm_annotation_footnotes', $footnoteListKey, 'li');
|
297 |
75b05e16
|
f.revilla
|
//tuypedesignations footnotes
|
298 |
d74aa4df
|
Andreas Kohlbecker
|
|
299 |
806baeb2
|
Andreas Kohlbecker
|
if($typeDesignations){
|
300 |
|
|
$out .= theme('cdm_typedesignations', $typeDesignations);
|
301 |
6d589240
|
f.revilla
|
|
302 |
806baeb2
|
Andreas Kohlbecker
|
}
|
303 |
d74aa4df
|
Andreas Kohlbecker
|
|
304 |
75b05e16
|
f.revilla
|
//annotation footnotes
|
305 |
|
|
//$annotation_key = ( isset($homotypicalGroup[0]) ? $homotypicalGroup[0]->uuid : 'NULL');
|
306 |
|
|
//$fkey_annotations = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-annotations-' . $annotation_key, $annotation_key);
|
307 |
6d589240
|
f.revilla
|
//$out .= theme('cdm_footnotes', RenderHints::getRenderPath() . '-annotations-' . $annotation_key);
|
308 |
|
|
$out .= theme('cdm_annotation_footnotes', $footnoteListKey, 'li');
|
309 |
1f5b7a24
|
f.revilla
|
//$out .= theme('cdm_annotation_footnotes', $footnoteListKey);
|
310 |
806baeb2
|
Andreas Kohlbecker
|
$out .= '</ul>';
|
311 |
75b05e16
|
f.revilla
|
|
312 |
|
|
|
313 |
|
|
RenderHints::popFromRenderStack();
|
314 |
806baeb2
|
Andreas Kohlbecker
|
return $out;
|
315 |
|
|
}
|
316 |
|
|
|
317 |
|
|
|
318 |
|
|
|
319 |
b32739d9
|
f.revilla
|
function theme_cdm_homotypicSynonymyGroup($synonymList, $accepted_taxon_uuid, $prependedSynonyms = array()){
|
320 |
75b05e16
|
f.revilla
|
|
321 |
80e0aa8e
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('homotypicSynonymyGroup');
|
322 |
75b05e16
|
f.revilla
|
|
323 |
0387c539
|
Andreas Kohlbecker
|
$footnoteListKey = isset($prependedSynonyms[0]) ? $prependedSynonyms[0]->uuid : (isset($synonymList[0]) ? $synonymList[0]->uuid : 'NULL');
|
324 |
f0df1f96
|
f.revilla
|
$accepted_taxon_footnoteListKey = RenderHints::getFootnoteListKey();
|
325 |
0387c539
|
Andreas Kohlbecker
|
RenderHints::setFootnoteListKey($footnoteListKey);
|
326 |
d74aa4df
|
Andreas Kohlbecker
|
|
327 |
806baeb2
|
Andreas Kohlbecker
|
if(! is_array($synonymList) || count($synonymList) == 0){
|
328 |
|
|
return;
|
329 |
|
|
}
|
330 |
|
|
|
331 |
|
|
$out = '<ul class="homotypicSynonyms">';
|
332 |
|
|
|
333 |
|
|
if(!empty($prependedSynonyms)){
|
334 |
|
|
foreach($prependedSynonyms as $taxon){
|
335 |
b9438135
|
Andreas Kohlbecker
|
$out .= '<li class="synonym">'.cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
|
336 |
806baeb2
|
Andreas Kohlbecker
|
}
|
337 |
|
|
}
|
338 |
|
|
|
339 |
|
|
foreach($synonymList as $synonym){
|
340 |
b9438135
|
Andreas Kohlbecker
|
$out .= '<li class="synonym">'.cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
|
341 |
806baeb2
|
Andreas Kohlbecker
|
}
|
342 |
ac168ae1
|
Andreas Kohlbecker
|
|
343 |
b32739d9
|
f.revilla
|
$homonym_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);
|
344 |
|
|
$accepted_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_TAXON_NAMETYPEDESIGNATIONS, $accepted_taxon_uuid);
|
345 |
|
|
if($accepted_typeDesignations){
|
346 |
|
|
$typeDesignations = cdm_add_type_designations($homonym_typeDesignations, $accepted_typeDesignations);
|
347 |
|
|
}else {
|
348 |
|
|
$typeDesignations = $homonym_typeDesignations;
|
349 |
|
|
}
|
350 |
806baeb2
|
Andreas Kohlbecker
|
if($typeDesignations){
|
351 |
|
|
$out .= theme('cdm_typedesignations', $typeDesignations);
|
352 |
|
|
}
|
353 |
8aabc503
|
f.revilla
|
if($accepted_taxon_footnoteListKey){// to avoiding drupal warnings (#1830) why false???
|
354 |
|
|
$out .= theme('cdm_footnotes', $accepted_taxon_footnoteListKey, 'li');
|
355 |
|
|
}
|
356 |
ac168ae1
|
Andreas Kohlbecker
|
|
357 |
b5e773ef
|
Andreas Kohlbecker
|
$out .= theme('cdm_annotation_footnotes', $footnoteListKey, 'li');
|
358 |
806baeb2
|
Andreas Kohlbecker
|
$out .= '</ul>';
|
359 |
75b05e16
|
f.revilla
|
|
360 |
80e0aa8e
|
Andreas Kohlbecker
|
RenderHints::popFromRenderStack();
|
361 |
806baeb2
|
Andreas Kohlbecker
|
return $out;
|
362 |
|
|
}
|
363 |
|
|
|
364 |
6cb938a3
|
Andreas Kohlbecker
|
function get_nameRenderTemplate($renderPath, $nameLink = NULL, $refenceLink = NULL){
|
365 |
|
|
//TODO implement admin user interface to replace switch statement
|
366 |
|
|
// preliminar solution: using themes
|
367 |
|
|
|
368 |
|
|
$template = null;
|
369 |
|
|
// find best matching default RenderTemplate in theme
|
370 |
|
|
//echo "<br/><br/>RENDER PATH: ".$renderPath;
|
371 |
|
|
//var_dump('RENDER PATH: ' . $renderPath);
|
372 |
2264b60d
|
Andreas Kohlbecker
|
|
373 |
|
|
// preserve renderPath_base
|
374 |
|
|
if( ($separatorPos = strpos($renderPath, '.')) >= 0 ){
|
375 |
|
|
} else {
|
376 |
|
|
$separatorPos = strlen($renderPath);
|
377 |
|
|
}
|
378 |
|
|
$renderPath_base = substr($renderPath, 0, $separatorPos);
|
379 |
|
|
|
380 |
|
|
// find in theme function if it exists
|
381 |
|
|
if(theme_get_function('get_nameRenderTemplate')){
|
382 |
|
|
while(!is_array($template) && strlen($renderPath) > 0){
|
383 |
|
|
$template = theme('get_nameRenderTemplate', $renderPath);
|
384 |
|
|
$renderPath = substr($renderPath, 0, strrpos($renderPath, '.'));
|
385 |
|
|
// if(!is_array($template)){
|
386 |
|
|
// echo "<br/>->".$renderPath;
|
387 |
|
|
// }
|
388 |
|
|
}
|
389 |
6cb938a3
|
Andreas Kohlbecker
|
}
|
390 |
|
|
|
391 |
|
|
// otherwise get default RenderTemplate from theme
|
392 |
|
|
if(!is_array($template)){
|
393 |
|
|
$template = theme('get_nameRenderTemplate', '#DEFAULT');
|
394 |
|
|
}
|
395 |
|
|
// otherwise get system default RenderTemplate
|
396 |
|
|
if(!is_array($template)){
|
397 |
2264b60d
|
Andreas Kohlbecker
|
switch($renderPath_base){
|
398 |
6cb938a3
|
Andreas Kohlbecker
|
case 'list_of_taxa':
|
399 |
2264b60d
|
Andreas Kohlbecker
|
case 'acceptedFor':
|
400 |
6cb938a3
|
Andreas Kohlbecker
|
case 'taxon_page_synonymy':
|
401 |
|
|
case 'typedesignations':
|
402 |
|
|
case 'taxon_page_title':
|
403 |
2264b60d
|
Andreas Kohlbecker
|
case 'polytomousKey':
|
404 |
6cb938a3
|
Andreas Kohlbecker
|
case 'na': $template = array(
|
405 |
|
|
'namePart' => array('#uri'=>true),
|
406 |
|
|
//'authorshipPart' => true,
|
407 |
|
|
);
|
408 |
|
|
break;
|
409 |
|
|
case 'nar': $template = array(
|
410 |
|
|
'namePart' => array('#uri'=>true),
|
411 |
|
|
//'authorshipPart' => true,
|
412 |
|
|
'referencePart' => array('#uri'=>true),
|
413 |
|
|
'microreferencePart' => true,
|
414 |
|
|
);
|
415 |
|
|
break;
|
416 |
|
|
default: $template = array(
|
417 |
|
|
'namePart' => array('#uri'=>true),
|
418 |
|
|
'authorshipPart' => true,
|
419 |
|
|
'referencePart' => array('#uri'=>true),
|
420 |
|
|
'microreferencePart' => true,
|
421 |
|
|
'statusPart' => true,
|
422 |
|
|
'descriptionPart' => true
|
423 |
|
|
);
|
424 |
|
|
}
|
425 |
|
|
}
|
426 |
|
|
|
427 |
|
|
if($nameLink && isset($template['nameAuthorPart']['#uri'])){
|
428 |
|
|
$template['nameAuthorPart']['#uri'] = $nameLink;
|
429 |
|
|
} else{
|
430 |
|
|
unset($template['nameAuthorPart']['#uri']);
|
431 |
|
|
}
|
432 |
|
|
|
433 |
|
|
if($nameLink && isset($template['namePart']['#uri'])){
|
434 |
|
|
$template['namePart']['#uri'] = $nameLink;
|
435 |
|
|
} else{
|
436 |
|
|
unset($template['namePart']['#uri']);
|
437 |
|
|
}
|
438 |
|
|
|
439 |
|
|
if($refenceLink && isset($template['referencePart']['#uri'])){
|
440 |
|
|
$template['referencePart']['#uri'] = $refenceLink;
|
441 |
|
|
}else{
|
442 |
|
|
unset($template['referencePart']['#uri']);
|
443 |
|
|
}
|
444 |
|
|
|
445 |
|
|
return $template;
|
446 |
|
|
}
|
447 |
|
|
|
448 |
|
|
function get_partDefinition($taxonNameType){
|
449 |
2264b60d
|
Andreas Kohlbecker
|
|
450 |
6cb938a3
|
Andreas Kohlbecker
|
//TODO implement admin user interface to allow specify the partdefinitions for any type
|
451 |
|
|
// preliminar solution: using themes
|
452 |
|
|
|
453 |
|
|
$partdef = theme('get_partDefinition', $taxonNameType);
|
454 |
|
|
|
455 |
|
|
if(!is_array($partdef)){
|
456 |
|
|
switch($taxonNameType){
|
457 |
|
|
case 'ZoologicalName': $partdef = array(
|
458 |
|
|
'namePart' => array(
|
459 |
|
|
'name' => true,
|
460 |
|
|
),
|
461 |
|
|
'referencePart' => array(
|
462 |
|
|
'authorTeam' => true
|
463 |
|
|
),
|
464 |
|
|
'microreferencePart' => array(
|
465 |
|
|
'microreference' => true,
|
466 |
|
|
),
|
467 |
|
|
'statusPart' => array(
|
468 |
|
|
'status' => true,
|
469 |
|
|
),
|
470 |
|
|
'descriptionPart' => array(
|
471 |
|
|
'description' => true,
|
472 |
|
|
),
|
473 |
|
|
);
|
474 |
|
|
break;
|
475 |
2264b60d
|
Andreas Kohlbecker
|
case 'BotanicalName':
|
476 |
|
|
default: $partdef = array(
|
477 |
6cb938a3
|
Andreas Kohlbecker
|
'namePart' => array(
|
478 |
|
|
'name' => true,
|
479 |
|
|
'authors' => true
|
480 |
|
|
),
|
481 |
|
|
'referencePart' => array(
|
482 |
|
|
'reference' => true,
|
483 |
|
|
'microreference' => true
|
484 |
|
|
),
|
485 |
|
|
'statusPart' => array(
|
486 |
|
|
'status' => true,
|
487 |
|
|
),
|
488 |
|
|
'descriptionPart' => array(
|
489 |
|
|
'description' => true,
|
490 |
|
|
),
|
491 |
|
|
);
|
492 |
|
|
break;
|
493 |
2264b60d
|
Andreas Kohlbecker
|
// default: $partdef = array(
|
494 |
|
|
// 'namePart' => array(
|
495 |
|
|
// 'name' => true,
|
496 |
|
|
// 'authorTeam' => true
|
497 |
|
|
// ),
|
498 |
|
|
// 'referencePart' => array(
|
499 |
|
|
// 'reference' => true
|
500 |
|
|
// ),
|
501 |
|
|
// 'microreferencePart' => array(
|
502 |
|
|
// 'microreference' => true,
|
503 |
|
|
// ),
|
504 |
|
|
// 'statusPart' => array(
|
505 |
|
|
// 'status' => true,
|
506 |
|
|
// ),
|
507 |
|
|
// 'descriptionPart' => array(
|
508 |
|
|
// 'description' => true,
|
509 |
|
|
// ),
|
510 |
|
|
// );
|
511 |
6cb938a3
|
Andreas Kohlbecker
|
}
|
512 |
|
|
}
|
513 |
|
|
return $partdef;
|
514 |
|
|
}
|
515 |
|
|
|
516 |
|
|
|
517 |
806baeb2
|
Andreas Kohlbecker
|
|
518 |
44b1626d
|
f.revilla
|
function theme_cdm_taxonName($taxonName, $nameLink = NULL, $refenceLink = NULL,
|
519 |
27b71dd0
|
f.revilla
|
$show_annotations = true, $is_type_designation = false, $skiptags = array()){
|
520 |
4411af64
|
Andreas Kohlbecker
|
|
521 |
75b05e16
|
f.revilla
|
$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
|
522 |
806baeb2
|
Andreas Kohlbecker
|
$partDefinition = get_partDefinition($taxonName->class);
|
523 |
|
|
|
524 |
|
|
// apply defintions to template
|
525 |
|
|
foreach($renderTemplate as $part=>$uri){
|
526 |
|
|
if(isset($partDefinition[$part])){
|
527 |
|
|
$renderTemplate[$part] = $partDefinition[$part];
|
528 |
|
|
}
|
529 |
|
|
if(is_array($uri)){
|
530 |
|
|
$renderTemplate[$part]['#uri'] = $uri['#uri'];
|
531 |
|
|
}
|
532 |
|
|
}
|
533 |
|
|
|
534 |
4411af64
|
Andreas Kohlbecker
|
normalize_TaggedName($taxonName->taggedName);
|
535 |
|
|
|
536 |
806baeb2
|
Andreas Kohlbecker
|
$firstEntryIsValidNamePart = is_array($taxonName->taggedName)
|
537 |
2264b60d
|
Andreas Kohlbecker
|
&& is_string($taxonName->taggedName[0]->text)
|
538 |
|
|
&& $taxonName->taggedName[0]->text != ''
|
539 |
|
|
&& $taxonName->taggedName[0]->type == 'name';
|
540 |
75b05e16
|
f.revilla
|
|
541 |
806baeb2
|
Andreas Kohlbecker
|
// got to use second entry as first one, see ToDo comment below ...
|
542 |
|
|
if($firstEntryIsValidNamePart){
|
543 |
|
|
|
544 |
|
|
$taggedName = $taxonName->taggedName;
|
545 |
75b05e16
|
f.revilla
|
|
546 |
806baeb2
|
Andreas Kohlbecker
|
$lastAuthorElementString = false;
|
547 |
|
|
$hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
|
548 |
|
|
$hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
|
549 |
|
|
|
550 |
|
|
if(!($hasNamePart_with_Authors || $hasNameAuthorPart_with_Authors)){
|
551 |
|
|
// // find author and split off from name
|
552 |
|
|
// // TODO expecting to find the author as the last element
|
553 |
|
|
// if($taggedName[count($taggedName)- 1]->type == 'authors'){
|
554 |
|
|
// $authorTeam = $taggedName[count($taggedName)- 1]->text;
|
555 |
|
|
// unset($taggedName[count($taggedName)- 1]);
|
556 |
|
|
// }
|
557 |
|
|
|
558 |
|
|
// remove all authors
|
559 |
|
|
$taggedNameNew = array();
|
560 |
|
|
foreach($taggedName as $element){
|
561 |
|
|
if($element->type != 'authors'){
|
562 |
|
|
$taggedNameNew[] = $element;
|
563 |
|
|
} else {
|
564 |
|
|
$lastAuthorElementString = $element->text;
|
565 |
|
|
}
|
566 |
|
|
}
|
567 |
|
|
$taggedName = $taggedNameNew;
|
568 |
|
|
|
569 |
|
|
}
|
570 |
44b1626d
|
f.revilla
|
$name = '<span class="'.$taxonName->class.'">'.theme('cdm_taggedtext2html', $taggedName, 'span', ' ', $skiptags).'</span>';
|
571 |
806baeb2
|
Andreas Kohlbecker
|
} else {
|
572 |
|
|
$name = '<span class="'.$taxonName->class.'_titleCache">'.$taxonName->titleCache.'</span>';
|
573 |
|
|
}
|
574 |
|
|
|
575 |
|
|
// fill name into $renderTemplate
|
576 |
|
|
array_setr('name', $name, $renderTemplate);
|
577 |
|
|
|
578 |
|
|
// // fill with authorTeam
|
579 |
|
|
// if($authorTeam){
|
580 |
|
|
// $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
|
581 |
|
|
// array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
|
582 |
|
|
// }
|
583 |
|
|
|
584 |
|
|
// fill with reference
|
585 |
300375f2
|
f.revilla
|
if(isset($renderTemplate['referencePart']) && !$is_type_designation){
|
586 |
806baeb2
|
Andreas Kohlbecker
|
|
587 |
|
|
// [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
|
588 |
|
|
// Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
|
589 |
|
|
if(isset($renderTemplate['referencePart']['reference']) && $taxonName->nomenclaturalReference){
|
590 |
|
|
$microreference = null;
|
591 |
|
|
if(isset($renderTemplate['referencePart']['microreference'])){
|
592 |
|
|
$microreference = $taxonName->nomenclaturalMicroReference;
|
593 |
|
|
}
|
594 |
a91d2f20
|
f.revilla
|
$citation = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array($taxonName->nomenclaturalReference->uuid), "microReference=".urlencode($microreference));
|
595 |
806baeb2
|
Andreas Kohlbecker
|
$citation = $citation->String;
|
596 |
|
|
// find preceding element of the refrence
|
597 |
|
|
$precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
|
598 |
|
|
if(str_beginsWith($citation, ", in")){
|
599 |
|
|
$citation = substr($citation, 2);
|
600 |
|
|
$separator = ' ';
|
601 |
|
|
} else if(!str_beginsWith($citation, "in") && $precedingKey == 'authors'){
|
602 |
|
|
$separator = ', ';
|
603 |
|
|
} else {
|
604 |
|
|
$separator = ' ';
|
605 |
|
|
}
|
606 |
|
|
|
607 |
|
|
$referenceArray['#separator'] = $separator;
|
608 |
|
|
$referenceArray['#html'] = '<span class="reference">'.$citation.'</span>';
|
609 |
|
|
array_setr('reference', $referenceArray, $renderTemplate);
|
610 |
|
|
}
|
611 |
|
|
|
612 |
|
|
// if authors have been removed from the name part the last named authorteam
|
613 |
|
|
// should be added to the reference citation, otherwise, keep the separator
|
614 |
|
|
// out of the reference
|
615 |
|
|
if(isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString){
|
616 |
|
|
// if the nomenclaturalReference cintation is not included in the reference part but diplay of the microreference
|
617 |
|
|
// is whanted append the microreference to the authorTeam
|
618 |
|
|
if(!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])){
|
619 |
|
|
$separator = ": ";
|
620 |
|
|
$citation = $taxonName->nomenclaturalMicroReference;
|
621 |
|
|
}
|
622 |
|
|
$referenceArray['#html'] = ' <span class="reference">'.$lastAuthorElementString.$separator.$citation.'</span>';
|
623 |
|
|
array_setr('authors', $referenceArray, $renderTemplate);
|
624 |
|
|
}
|
625 |
|
|
|
626 |
|
|
}
|
627 |
|
|
|
628 |
|
|
// fill with status
|
629 |
abf8a2db
|
Andreas Kohlbecker
|
if(is_array($taxonName->status)){
|
630 |
8aabc503
|
f.revilla
|
if(array_setr('status', true, $renderTemplate)){
|
631 |
abf8a2db
|
Andreas Kohlbecker
|
if(isset($taxonName->status[0])){
|
632 |
|
|
foreach($taxonName->status as $status){
|
633 |
3c99472c
|
Andreas Kohlbecker
|
$statusHtml .= ', '.$status->type->representation_L10n_abbreviatedLabel;
|
634 |
8aabc503
|
f.revilla
|
}
|
635 |
806baeb2
|
Andreas Kohlbecker
|
}
|
636 |
38e46518
|
Andreas Kohlbecker
|
array_setr('status', '<span class="nomenclatural_status">'.$statusHtml.'</span>', $renderTemplate);
|
637 |
806baeb2
|
Andreas Kohlbecker
|
}
|
638 |
44b1626d
|
f.revilla
|
}
|
639 |
abf8a2db
|
Andreas Kohlbecker
|
|
640 |
806baeb2
|
Andreas Kohlbecker
|
// fill with protologues etc...
|
641 |
|
|
if(array_setr('description', true, $renderTemplate)){
|
642 |
80e0aa8e
|
Andreas Kohlbecker
|
$descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
|
643 |
806baeb2
|
Andreas Kohlbecker
|
foreach($descriptions as $description){
|
644 |
|
|
if(!empty($description)){
|
645 |
|
|
foreach($description->elements as $description_element){
|
646 |
75b05e16
|
f.revilla
|
$second_citation = '';
|
647 |
7fc77599
|
f.revilla
|
if ($description_element->multilanguageText_L10n->text){
|
648 |
75b05e16
|
f.revilla
|
$second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
|
649 |
7fc77599
|
f.revilla
|
}
|
650 |
|
|
$descriptionHtml .= $second_citation;
|
651 |
806baeb2
|
Andreas Kohlbecker
|
$descriptionHtml .= theme("cdm_media", $description_element, array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html'));
|
652 |
|
|
}
|
653 |
|
|
}
|
654 |
|
|
}
|
655 |
|
|
array_setr('description', $descriptionHtml, $renderTemplate);
|
656 |
|
|
}
|
657 |
|
|
|
658 |
|
|
// render
|
659 |
2643c320
|
Katja Luther
|
$out = '<span ref="/name/'.$taxonName->uuid.'">';
|
660 |
75b05e16
|
f.revilla
|
|
661 |
806baeb2
|
Andreas Kohlbecker
|
foreach($renderTemplate as $partName=>$part){
|
662 |
|
|
$separator = '';
|
663 |
|
|
$partHtml = '';
|
664 |
|
|
$uri = false;
|
665 |
|
|
if(!is_array($part)){
|
666 |
|
|
continue;
|
667 |
|
|
}
|
668 |
|
|
if(isset($part['#uri']) && is_string($part['#uri'])){
|
669 |
|
|
$uri = $part['#uri'];
|
670 |
|
|
unset($part['#uri']);
|
671 |
|
|
}
|
672 |
|
|
foreach($part as $key=>$content){
|
673 |
|
|
$html = '';
|
674 |
|
|
if(is_array($content)){
|
675 |
|
|
$html = $content['#html'];
|
676 |
|
|
$separator = $content['#separator'];
|
677 |
|
|
} else if(is_string($content)){
|
678 |
|
|
$html = $content;
|
679 |
|
|
}
|
680 |
|
|
$partHtml .= '<span class="'.$key.'">'.$html.'</span>';
|
681 |
|
|
}
|
682 |
|
|
if($uri){
|
683 |
|
|
$out .= $separator.'<a href="'.$uri.'" class="'.$partName.'">'.$partHtml.'</a>';
|
684 |
|
|
} else {
|
685 |
|
|
$out .= $separator.$partHtml;
|
686 |
2efb8f43
|
Andreas Kohlbecker
|
|
687 |
806baeb2
|
Andreas Kohlbecker
|
}
|
688 |
|
|
}
|
689 |
75b05e16
|
f.revilla
|
$out .= '</span>';
|
690 |
1f5b7a24
|
f.revilla
|
if ($show_annotations){
|
691 |
8aabc503
|
f.revilla
|
//$out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
|
692 |
1f5b7a24
|
f.revilla
|
}
|
693 |
0387c539
|
Andreas Kohlbecker
|
return $out;
|
694 |
806baeb2
|
Andreas Kohlbecker
|
}
|
695 |
|
|
|
696 |
|
|
/**
|
697 |
|
|
* Recursively searches the array for the $key and sets the given value
|
698 |
|
|
* @param $key
|
699 |
|
|
* @param $value
|
700 |
|
|
* @param $array
|
701 |
|
|
* @return true if the key has been found
|
702 |
|
|
*/
|
703 |
|
|
function &array_setr($key, $value, array &$array){
|
704 |
|
|
foreach($array as $k=>&$v){
|
705 |
|
|
if($key == $k){
|
706 |
|
|
$v = $value;
|
707 |
|
|
return $array;
|
708 |
|
|
} else if(is_array($v)){
|
709 |
|
|
$innerArray = array_setr($key, $value, $v);
|
710 |
|
|
if($innerArray){
|
711 |
|
|
return $array;
|
712 |
|
|
}
|
713 |
|
|
}
|
714 |
|
|
}
|
715 |
|
|
return null;
|
716 |
|
|
}
|
717 |
|
|
|
718 |
|
|
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate){
|
719 |
|
|
$precedingElement = null;
|
720 |
|
|
foreach($renderTemplate as &$part){
|
721 |
|
|
foreach($part as $key=>&$element){
|
722 |
|
|
if($key == $contentElementKey){
|
723 |
|
|
return $precedingElement;
|
724 |
|
|
}
|
725 |
|
|
$precedingElement = $element;
|
726 |
|
|
}
|
727 |
|
|
}
|
728 |
|
|
return null;
|
729 |
|
|
}
|
730 |
|
|
|
731 |
|
|
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate){
|
732 |
|
|
$precedingKey = null;
|
733 |
|
|
foreach($renderTemplate as &$part){
|
734 |
d74aa4df
|
Andreas Kohlbecker
|
if(is_array($part)){
|
735 |
|
|
foreach($part as $key=>&$element){
|
736 |
|
|
if($key == $contentElementKey){
|
737 |
|
|
return $precedingKey;
|
738 |
|
|
}
|
739 |
|
|
if(!str_beginsWith($key, '#')){
|
740 |
|
|
$precedingKey = $key;
|
741 |
|
|
}
|
742 |
806baeb2
|
Andreas Kohlbecker
|
}
|
743 |
|
|
}
|
744 |
|
|
}
|
745 |
|
|
return null;
|
746 |
|
|
}
|
747 |
|
|
|
748 |
|
|
|
749 |
|
|
|
750 |
|
|
|
751 |
|
|
|
752 |
|
|
|
753 |
|
|
|