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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, $footnote_separator = ','){
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$res = '';
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$citation = $typeDesignation->citation;
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$pages = $typeDesignation->citationMicroReference;
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if ($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 $res;
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}
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if ($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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$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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}
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return $res;
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}
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function contains_type_designation ($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, $extra) {
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if (is_array($source)){
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$result = $source;
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if ($extra){
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foreach ($extra as $element) {
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if (!contains_type_designation($element, $source)){
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$result[] = $element;
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}
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}
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}
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}else {
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$result = $extra;
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}
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return $result;
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}
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function theme_cdm_typedesignations($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 = $citation->String;
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*/
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RenderHints::pushToRenderStack('typedesignations');
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$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, $separator);
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//footnotes
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//$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations-' . $typeDesignation->uuid, $typeDesignation->citation->titleCache);
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/*
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$fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getRenderPath() . '-typeDesignations', $typeDesignation->citation->titleCache);
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$out .= theme('cdm_footnote_key', $fkey_typeDesignation, $separator, true, true) . ')';
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*/
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}
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if($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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$out .= '<span class="status">'
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.(($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', $derivedUnitFacadeInstance);
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//footnotes for synonymy acronyms
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$_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, 'li');
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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">'.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">'.cdm_related_taxon($synonym, UUID_HETEROTYPIC_SYNONYM_OF).'</li>';
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} else {
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$out .= '<li class="synonym">'.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, $accepted_taxon_uuid, $prependedSynonyms = array()){
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RenderHints::pushToRenderStack('homotypicSynonymyGroup');
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$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">'.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">'.cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF).'</li>';
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}
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$homonym_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $synonymList[0]->name->uuid);
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$accepted_typeDesignations = cdm_ws_get(CDM_WS_PORTAL_TAXON_NAMETYPEDESIGNATIONS, $accepted_taxon_uuid);
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if($accepted_typeDesignations){
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$typeDesignations = cdm_add_type_designations($homonym_typeDesignations, $accepted_typeDesignations);
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}else {
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$typeDesignations = $homonym_typeDesignations;
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}
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if($typeDesignations){
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$out .= theme('cdm_typedesignations', $typeDesignations);
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}
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if($accepted_taxon_footnoteListKey){// to avoiding drupal warnings (#1830) why false???
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$out .= theme('cdm_footnotes', $accepted_taxon_footnoteListKey, 'li');
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}
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$out .= theme('cdm_annotation_footnotes', $footnoteListKey, 'li');
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$out .= '</ul>';
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RenderHints::popFromRenderStack();
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return $out;
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}
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function get_nameRenderTemplate($renderPath, $nameLink = NULL, $refenceLink = NULL){
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//TODO implement admin user interface to replace switch statement
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// preliminar solution: using themes
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$template = null;
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// find best matching default RenderTemplate in theme
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//echo "<br/><br/>RENDER PATH: ".$renderPath;
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//var_dump('RENDER PATH: ' . $renderPath);
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// preserve renderPath_base
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if( ($separatorPos = strpos($renderPath, '.')) >= 0 ){
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} else {
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$separatorPos = strlen($renderPath);
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}
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$renderPath_base = substr($renderPath, 0, $separatorPos);
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// find in theme function if it exists
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if(theme_get_function('get_nameRenderTemplate')){
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while(!is_array($template) && strlen($renderPath) > 0){
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$template = theme('get_nameRenderTemplate', $renderPath);
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$renderPath = substr($renderPath, 0, strrpos($renderPath, '.'));
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// if(!is_array($template)){
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// echo "<br/>->".$renderPath;
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|
// }
|
388
|
}
|
389
|
}
|
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
|
switch($renderPath_base){
|
398
|
case 'list_of_taxa':
|
399
|
case 'acceptedFor':
|
400
|
case 'taxon_page_synonymy':
|
401
|
case 'typedesignations':
|
402
|
case 'taxon_page_title':
|
403
|
case 'polytomousKey':
|
404
|
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
|
|
450
|
//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
|
case 'BotanicalName':
|
476
|
default: $partdef = array(
|
477
|
'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
|
// 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
|
}
|
512
|
}
|
513
|
return $partdef;
|
514
|
}
|
515
|
|
516
|
|
517
|
|
518
|
function theme_cdm_taxonName($taxonName, $nameLink = NULL, $refenceLink = NULL,
|
519
|
$show_annotations = true, $is_type_designation = false, $skiptags = array()){
|
520
|
|
521
|
$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
|
522
|
$partDefinition = get_partDefinition($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'] = $uri['#uri'];
|
531
|
}
|
532
|
}
|
533
|
|
534
|
normalize_TaggedName($taxonName->taggedName);
|
535
|
|
536
|
$firstEntryIsValidNamePart = is_array($taxonName->taggedName)
|
537
|
&& is_string($taxonName->taggedName[0]->text)
|
538
|
&& $taxonName->taggedName[0]->text != ''
|
539
|
&& $taxonName->taggedName[0]->type == 'name';
|
540
|
|
541
|
// got to use second entry as first one, see ToDo comment below ...
|
542
|
if($firstEntryIsValidNamePart){
|
543
|
|
544
|
$taggedName = $taxonName->taggedName;
|
545
|
|
546
|
$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
|
$name = '<span class="'.$taxonName->class.'">'.theme('cdm_taggedtext2html', $taggedName, 'span', ' ', $skiptags).'</span>';
|
571
|
} 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, $renderTemplate);
|
582
|
// }
|
583
|
|
584
|
// fill with reference
|
585
|
if(isset($renderTemplate['referencePart']) && !$is_type_designation){
|
586
|
|
587
|
// [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
|
588
|
// Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
|
589
|
if(isset($renderTemplate['referencePart']['reference']) && $taxonName->nomenclaturalReference){
|
590
|
$microreference = null;
|
591
|
if(isset($renderTemplate['referencePart']['microreference'])){
|
592
|
$microreference = $taxonName->nomenclaturalMicroReference;
|
593
|
}
|
594
|
$citation = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array($taxonName->nomenclaturalReference->uuid), "microReference=".urlencode($microreference));
|
595
|
$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, $renderTemplate);
|
624
|
}
|
625
|
|
626
|
}
|
627
|
|
628
|
// fill with status
|
629
|
if(is_array($taxonName->status)){
|
630
|
if(array_setr('status', true, $renderTemplate)){
|
631
|
if(isset($taxonName->status[0])){
|
632
|
foreach($taxonName->status as $status){
|
633
|
$statusHtml .= ', '.$status->type->representation_L10n_abbreviatedLabel;
|
634
|
}
|
635
|
}
|
636
|
array_setr('status', '<span class="nomenclatural_status">'.$statusHtml.'</span>', $renderTemplate);
|
637
|
}
|
638
|
}
|
639
|
|
640
|
// fill with protologues etc...
|
641
|
if(array_setr('description', true, $renderTemplate)){
|
642
|
$descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
|
643
|
foreach($descriptions as $description){
|
644
|
if(!empty($description)){
|
645
|
foreach($description->elements as $description_element){
|
646
|
$second_citation = '';
|
647
|
if ($description_element->multilanguageText_L10n->text){
|
648
|
$second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
|
649
|
}
|
650
|
$descriptionHtml .= $second_citation;
|
651
|
$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
|
$out = '<span ref="/name/'.$taxonName->uuid.'">';
|
660
|
|
661
|
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
|
|
687
|
}
|
688
|
}
|
689
|
$out .= '</span>';
|
690
|
if ($show_annotations){
|
691
|
//$out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
|
692
|
}
|
693
|
return $out;
|
694
|
}
|
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 &$part){
|
734
|
if(is_array($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
|
}
|
743
|
}
|
744
|
}
|
745
|
return null;
|
746
|
}
|
747
|
|
748
|
|
749
|
|
750
|
|
751
|
|
752
|
|
753
|
|