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<?php
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/**
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* @file
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* Name theming functions.
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*
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* @copyright
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* (C) 2007-2012 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 module are subject to the Mozilla
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* Public License Version 1.1.
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* @see http://www.mozilla.org/MPL/MPL-1.1.html
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*/
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/**
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* Return HTML for the lectotype citation with the correct layout.
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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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*
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* @param mixed $typeDesignation
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* Object containing the lectotype citation to print.
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*
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* @return string
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* Valid html string.
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*/
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function type_designation_citation_layout($typeDesignation, $footnote_separator = ',') {
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$res = '';
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$citation = $typeDesignation->citation;
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$pages = $typeDesignation->citationMicroReference;
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if(isset($typeDesignation->typeStatus->uuid) && isset($typeDesignation->typeStatus->representation_L10n)) {
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if ( $typeDesignation->typeStatus->uuid == UUID_NTD_ORIGINAL_DESIGNATION || $typeDesignation->typeStatus->uuid == UUID_NTD_MONOTYPY) {
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$res = ' (' . $typeDesignation->typeStatus->representation_L10n . ')';
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return $res;
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}
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}
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if ($citation) {
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// $type = $typeDesignation_citation->type;
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$year = isset($citation->datePublished->start) ? substr($citation->datePublished->start, 0, 4) : '';
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$author = isset($citation->authorTeam->titleCache) ? $citation->authorTeam->titleCache : '';
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$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(), $typeDesignation->citation->titleCache);
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$res .= theme('cdm_footnote_key', array(
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'footnoteKey' => $fkey_typeDesignation,
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'separator' => $footnote_separator,
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'highlightable' => TRUE,
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'separator_off' => TRUE,
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)) . ')';
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}
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return $res;
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function contains_type_designation($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 $result;
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function cdm_add_type_designations($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[] = $element;
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}
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}
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}
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}
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else {
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$result = $extra;
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}
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return $result;
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}
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/**
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* Renders and array of CDM TypeDesignations
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*
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* @param array $variables
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* - typeDesignations: an array of cdm TypeDesignation entities to render
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*/
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function theme_cdm_typedesignations($variables) {
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$typeDesignations = $variables['typeDesignations'];
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// need to add element to render path since type designations
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// need other name render template
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RenderHints::pushToRenderStack('typedesignations');
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$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[] = $typeDesignation;
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}
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// It is a lectotype?
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else {
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if (isset($typeDesignation->typeStatus->uuid) && $typeDesignation->typeStatus->uuid == UUID_NTD_LECTOTYPE) {
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$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">' . ($is_lectotype ? 'Lectotype' : 'Type') . '</span>: ' . t('not designated') . '</li>';
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}
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elseif ($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, $separator);
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}
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$referenceUri = '';
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if (isset($typeDesignation->typeName->nomenclaturalReference)) {
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$referenceUri = url(path_to_reference($typeDesignation->typeName->nomenclaturalReference->uuid));
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}
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$out .= ': ' . theme('cdm_taxonName', array(
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'taxonName' => $typeDesignation->typeName,
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'nameLink' => $link_to_name_page,
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'refenceLink' => $referenceUri,
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'show_annotations' => TRUE,
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'is_type_designation' => TRUE,
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));
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}
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}
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}
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if (!empty($specimenTypeDesignations)) {
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// Sorting might be different for dataportals so this has to be
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// 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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if (!empty($std->citation)) {
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$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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$missingShortCitation = FALSE;
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if (strlen($shortCitation) == 0) {
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$shortCitation = theme('cdm_reference', array('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', array('reference' => $std->citation)) . '|') . '">';
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$typeReference .= $shortCitation . '</span>';
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if (!empty($std->citationMicroReference)) {
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$typeReference .= ':' . $std->citationMicroReference;
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}
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$typeReference .= ')';
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$_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getRenderPath(), $std->citation->titleCache);
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$typeReference .= theme('cdm_footnote_key', array(
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'footnoteKey' => $_fkey2,
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'separator' => $separator,
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'highlightable' => TRUE,
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'separator_off' => TRUE,
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));
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}
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$derivedUnitFacadeInstance = null;
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$out .= '<li class="specimenTypeDesignation">';
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$out .= '<span class="status">'
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. ((isset($std->typeStatus->representation_L10n)) ? $std->typeStatus->representation_L10n : t('Type'))
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. $typeReference
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. '</span>: ';
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if (isset($std->typeSpecimen)) {
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$derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $std->typeSpecimen->uuid);
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}
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if ( isset($derivedUnitFacadeInstance ) ){
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$out .= $derivedUnitFacadeInstance->titleCache; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));
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}
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// Footnotes for collection acronyms.
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$_fkey = FootnoteManager::addNewFootnote(
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RenderHints::getRenderPath(),
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(isset($derivedUnitFacadeInstance->collection->titleCache) ? $derivedUnitFacadeInstance->collection->titleCache : FALSE)
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);
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$out .= theme('cdm_footnote_key', array('footnoteKey' => $_fkey, 'separator' => $separator));
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$out .= '</li>';
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}
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}
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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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/**
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* FIXME this definitively has to be in another spot.
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* just didn't know where to put it right now.
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* Compares the status of two SpecimenTypeDesignations
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*
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* @param string $a
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* A SpecimenTypeDesignations.
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* @param string $b
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* SpecimenTypeDesignations.
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*/
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function compare_specimenTypeDesignationStatus($a, $b) {
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/*
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This is the desired sort order as of now: Holotype Isotype Lectotype
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Isolectotype Syntype.
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TODO Basically, what we are trying to do is, we define
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an ordered array of TypeDesignation-states and use the index of this array
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for comparison. This array has to be filled with the cdm- TypeDesignation
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states and the order should be parameterisable inside the dataportal.
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*/
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// Make that static for now.
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$typeOrder = array(
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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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$aQuantifier = FALSE;
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$bQuantifier = FALSE;
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if (isset($a->typeStatus->label) && isset($b->typeStatus->label)) {
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$aQuantifier = array_search($a->typeStatus->label, $typeOrder);
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$bQuantifier = array_search($b->typeStatus->label, $typeOrder);
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}
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if ($aQuantifier == $bQuantifier) {
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// Sort alphabetically.
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return (isset($a->typeStatus->label) && isset($b->typeStatus->label) && $a->typeStatus->label < $b->typeStatus->label) ? -1 : 1;
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}
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return ($aQuantifier < $bQuantifier) ? -1 : 1;
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function theme_cdm_nameRelationships($variables) {
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$nameRelationships = $variables['nameRelationships'];
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$skipTypes = $variables['skipTypes'];
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if (!$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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$block = new stdclass(); // Empty object.
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foreach ($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', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));
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RenderHints::popFromRenderStack();
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return $out;
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function theme_cdm_homotypicSynonymLine($variables) {
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$taxon = $variables['taxon'];
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$out = '';
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$out .= '<li class="synonym">' . cdm_related_taxon($taxon, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';
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return $out;
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function theme_cdm_heterotypicSynonymyGroup($variables) {
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$homotypicalGroup = $variables['homotypicalGroup'];
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RenderHints::pushToRenderStack('heterotypicSynonymyGroup');
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$out = '';
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$out = '<div class="heterotypic-synonymy-group"><ul class="heterotypicSynonymyGroup">';
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$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($synonym, UUID_HETEROTYPIC_SYNONYM_OF) . '</li>';
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}
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else {
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$out .= '<li class="synonym">' . cdm_related_taxon($synonym, UUID_HOMOTYPIC_SYNONYM_OF) . '</li>';
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}
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}
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if ($typeDesignations) {
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$out .= theme('cdm_typedesignations', array('typeDesignations' => $typeDesignations));
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}
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$out .= '</ul>';
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// ------- footnotes ------- //
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$out .= '<ul class="footnotes">';
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$out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));
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$out .= '</ul>';
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$out .= '</div>';
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RenderHints::popFromRenderStack();
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return $out;
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}
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/**
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* @todo Please document this function.
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* @see http://drupal.org/node/1354
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*/
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function theme_cdm_homotypicSynonymyGroup($variables) {
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$synonymList = $variables['synonymList'];
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$accepted_taxon_uuid = $variables['accepted_taxon_uuid'];
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$prependedSynonyms = $variables['prependedSynonyms'];
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RenderHints::pushToRenderStack('homotypicSynonymyGroup');
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$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 = '<div class="homotypic-synonymy-group"><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, $accepted_typeDesignations);
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}
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else {
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$typeDesignations = $homonym_typeDesignations;
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}
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if ($typeDesignations) {
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$out .= theme('cdm_typedesignations', array('typeDesignations' => $typeDesignations));
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|
}
|
405
|
$out .= '</ul>';
|
406
|
|
407
|
// ------- footnotes ------- //
|
408
|
$out .= '<ul class="footnotes">';
|
409
|
// To avoiding drupal warnings (#1830).
|
410
|
if ($accepted_taxon_footnoteListKey) {
|
411
|
// Why FALSE???
|
412
|
$out .= theme('cdm_footnotes', array('footnoteListKey' => $accepted_taxon_footnoteListKey, 'enclosingTag' => 'li'));
|
413
|
}
|
414
|
$out .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));
|
415
|
$out .= theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getRenderPath(), 'enclosingTag' => 'li'));
|
416
|
$out .= '</ul>';
|
417
|
|
418
|
$out .= '</div>';
|
419
|
|
420
|
|
421
|
RenderHints::popFromRenderStack();
|
422
|
return $out;
|
423
|
}
|
424
|
|
425
|
/**
|
426
|
* Provides the name render template to be used within the page elements identified the the $renderPath.
|
427
|
*
|
428
|
* The render templates arrays contains one or more name render template to be used within the page elements identified the the
|
429
|
* renderPath. The renderPath is the key of the subelements whereas the value is the name render template.
|
430
|
* The following keys are curretly recogized:
|
431
|
*
|
432
|
* - list_of_taxa:
|
433
|
* - acceptedFor:
|
434
|
* - taxon_page_synonymy
|
435
|
* - typedesignations
|
436
|
* - taxon_page_title
|
437
|
* - polytomousKey
|
438
|
* - na: name + authorship
|
439
|
* - nar:name + authorship + reference
|
440
|
* - #DEFAULT
|
441
|
*
|
442
|
* A single render template can be used for multiple render paths. In this case the according key of the render templates
|
443
|
* array element should be the list of these render paths concatenated by ONLY a comma character without any whitespace.
|
444
|
*
|
445
|
* A render template is an associative array. The keys of this array are referring to the keys as defined in the part
|
446
|
* definitions array.
|
447
|
* @see get_partDefinition($taxonNameType) for more information
|
448
|
*
|
449
|
* The value of the render template element must be set to TRUE in order to let this part being rendered.
|
450
|
* The namePart, nameAuthorPart and referencePart can also hold an associative array with a single
|
451
|
* element: array('#uri' => TRUE). The value of the #uri element will be replaced by the according
|
452
|
* links if the paramters $nameLink or $refenceLink are set.
|
453
|
*
|
454
|
* @param string $renderPath
|
455
|
* The render path can consist of multiple dot separated elements
|
456
|
* @see RenderHints::getRenderPath()
|
457
|
* @param string $nameLink
|
458
|
* The link path ot URL to be used for name parts if a link is forseen in the template
|
459
|
* matching the given $renderPath.
|
460
|
* @param string $referenceLink
|
461
|
* The link path ot URL to be used for nomencaltural reference parts if a link is forseen
|
462
|
* in the template matching the given $renderPath.
|
463
|
* @return array
|
464
|
* An assciative array, the render template
|
465
|
*/
|
466
|
function get_nameRenderTemplate($renderPath, $nameLink = NULL, $refenceLink = NULL) {
|
467
|
|
468
|
$template = NULL;
|
469
|
|
470
|
static $default_render_templates = NULL;
|
471
|
if (!isset($default_render_templates)) {
|
472
|
$default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);
|
473
|
}
|
474
|
|
475
|
// get the base element of the renderPath
|
476
|
if (($separatorPos = strpos($renderPath, '.')) > 0) {
|
477
|
$renderPath_base = substr($renderPath, 0, $separatorPos);
|
478
|
} else {
|
479
|
$renderPath_base = $renderPath;
|
480
|
}
|
481
|
|
482
|
// --- preliminar solution: using themes.
|
483
|
$render_templates = theme('get_nameRenderTemplate', array());
|
484
|
if (!isset($render_templates)) {
|
485
|
// from the variables
|
486
|
$render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
|
487
|
}
|
488
|
|
489
|
// 1. try to find a template using the render path base element
|
490
|
if(array_key_exists($renderPath_base, $render_templates)){
|
491
|
$template = $render_templates[$renderPath_base];
|
492
|
}
|
493
|
|
494
|
// 2. Find best matching default RenderTemplate in theme
|
495
|
// by stripping the dot separated render path element by element
|
496
|
// is no matching template is found the DEFAULT will be used.
|
497
|
while (!is_array($template) && strlen($renderPath) > 0) {
|
498
|
|
499
|
foreach ($render_templates as $k => $t) {
|
500
|
if (strpos(',' . $k . ',', $renderPath ) !== FALSE) {
|
501
|
$template = $t;
|
502
|
break;
|
503
|
}
|
504
|
}
|
505
|
|
506
|
// shorten by one element
|
507
|
$renderPath = substr($renderPath, 0, strrpos($renderPath, '.'));
|
508
|
/*
|
509
|
if(!is_array($template)){
|
510
|
echo "<br/>->".$renderPath;
|
511
|
}
|
512
|
*/
|
513
|
}
|
514
|
|
515
|
// 3. Otherwise get default RenderTemplate from theme.
|
516
|
if (!is_array($template)) {
|
517
|
$template = $render_templates['#DEFAULT'];
|
518
|
}
|
519
|
|
520
|
// --- set the link uris to the according template fields if they exist
|
521
|
if ($nameLink && isset($template['nameAuthorPart']['#uri'])) {
|
522
|
$template['nameAuthorPart']['#uri'] = $nameLink;
|
523
|
}
|
524
|
else {
|
525
|
unset($template['nameAuthorPart']['#uri']);
|
526
|
}
|
527
|
|
528
|
if ($nameLink && isset($template['namePart']['#uri'])) {
|
529
|
$template['namePart']['#uri'] = $nameLink;
|
530
|
}
|
531
|
else {
|
532
|
unset($template['namePart']['#uri']);
|
533
|
}
|
534
|
|
535
|
if ($refenceLink && isset($template['referencePart']['#uri'])) {
|
536
|
$template['referencePart']['#uri'] = $refenceLink;
|
537
|
}
|
538
|
else {
|
539
|
unset($template['referencePart']['#uri']);
|
540
|
}
|
541
|
|
542
|
return $template;
|
543
|
}
|
544
|
|
545
|
/**
|
546
|
* The part definitions define the specific parts of which a rendered taxon name plus additional information will consist.
|
547
|
*
|
548
|
* A full taxon name plus additional information can consist of the following elements:
|
549
|
*
|
550
|
* - name: the taxon name inclugin rank nbut without author
|
551
|
* - authorTeam: The authors of a reference, also used in taxon names
|
552
|
* - authors: The authors of a reference, also used in taxon names
|
553
|
* - reference: the nomenclatural reference,
|
554
|
* - microreference: Volume, page number etc.
|
555
|
* - status: The nomenclatural status of a name
|
556
|
* - description: name descriptions like protologues etc ...
|
557
|
*
|
558
|
* These elements are combined in the part definitions array to from the specific parts to be rendered.
|
559
|
* Usually the following parts are formed:
|
560
|
*
|
561
|
* The name "Lapsana communis L., Sp. Pl.: 811. 1753" shall be an example here:
|
562
|
* - namePart: the name and rank (in example: "Lapsana communis")
|
563
|
* - authorshipPart: the author (in example: "L.")
|
564
|
* - nameAuthorPart: the combination of name and author part (in example: "Lapsana communis L.").
|
565
|
* This is useful for zoological names where the authorshipPart belongs to the name and both should
|
566
|
* be combined when a link to the taxon is rendered.
|
567
|
* - referencePart: the nomencaltural reference (in example: "Sp. Pl. 1753")
|
568
|
* - microreferencePart: usually the page number (in example ": 811.")
|
569
|
* - statusPart: the nomenclatorical status
|
570
|
* - descriptionPart:
|
571
|
*
|
572
|
* Each set of parts is dedicated to render a specific TaxonName type, the type names are used as keys for the
|
573
|
* specific parts part definitions:
|
574
|
*
|
575
|
* - BotanicalName
|
576
|
* - ZoologicalName
|
577
|
* - #DEFAULT: covers ViralNames and general NonViralNames
|
578
|
*
|
579
|
* An example:
|
580
|
* @code
|
581
|
* array(
|
582
|
* 'ZoologicalName' => array(
|
583
|
* 'namePart' => array('name' => TRUE),
|
584
|
* 'referencePart' => array('authorTeam' => TRUE),
|
585
|
* 'microreferencePart' => array('microreference' => TRUE),
|
586
|
* 'statusPart' => array('status' => TRUE),
|
587
|
* 'descriptionPart' => array('description' => TRUE),
|
588
|
* ),
|
589
|
* 'BotanicalName' => array(
|
590
|
* 'namePart' => array(
|
591
|
* 'name' => TRUE,
|
592
|
* 'authors' => TRUE,
|
593
|
* ),
|
594
|
* 'referencePart' => array(
|
595
|
* 'reference' => TRUE,
|
596
|
* 'microreference' => TRUE,
|
597
|
* ),
|
598
|
* 'statusPart' => array('status' => TRUE),
|
599
|
* 'descriptionPart' => array('description' => TRUE),
|
600
|
* ),
|
601
|
* );
|
602
|
* @endcode
|
603
|
*
|
604
|
* @todo document this function.
|
605
|
*/
|
606
|
function get_partDefinition($taxonNameType) {
|
607
|
|
608
|
static $default_part_definitions = null;
|
609
|
if (!isset($default_part_definitions)) {
|
610
|
$default_part_definitions= unserialize(CDM_PART_DEFINITIONS_DEFAULT);
|
611
|
}
|
612
|
|
613
|
// Preliminar solution: using themes.
|
614
|
// TODO remove this once all themes are using the newly introcuded part_definition settings
|
615
|
$part_definitions = theme('get_partDefinition', array());
|
616
|
|
617
|
// try to get get part definitions from variables
|
618
|
if(!is_array($part_definitions)) {
|
619
|
$part_definitions = variable_get(CDM_PART_DEFINITIONS, $default_part_definitions);
|
620
|
}
|
621
|
|
622
|
if (array_key_exists($taxonNameType, $part_definitions)) {
|
623
|
return $part_definitions[$taxonNameType];
|
624
|
} else {
|
625
|
return $part_definitions['#DEFAULT']; // covers ViralNames and general NonViralNames
|
626
|
}
|
627
|
|
628
|
}
|
629
|
|
630
|
/**
|
631
|
* @param $variables
|
632
|
* - taxonName : cdm TaxonNameBase instance
|
633
|
* - nameLink: URI to the taxon, @see path_to_taxon()
|
634
|
* - refenceLink: URI to the reference, @see path_to_reference()
|
635
|
* - show_annotations: ...
|
636
|
* - is_type_designation: ...
|
637
|
* - skiptags: an array of tags to skip ....
|
638
|
*
|
639
|
* @todo Please document this function.
|
640
|
* @see http://drupal.org/node/1354
|
641
|
*/
|
642
|
function theme_cdm_taxonName($variables) {
|
643
|
|
644
|
$taxonName = $variables['taxonName'];
|
645
|
$nameLink = $variables['nameLink'];
|
646
|
$refenceLink = $variables['refenceLink'];
|
647
|
$show_annotations = $variables['show_annotations'];
|
648
|
$is_type_designation = $variables['is_type_designation'];
|
649
|
$skiptags = $variables['skiptags'];
|
650
|
|
651
|
$renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
|
652
|
$partDefinition = get_partDefinition($taxonName->class);
|
653
|
|
654
|
// Apply definitions to template.
|
655
|
foreach ($renderTemplate as $part => $uri) {
|
656
|
|
657
|
if (isset($partDefinition[$part])) {
|
658
|
$renderTemplate[$part] = $partDefinition[$part];
|
659
|
}
|
660
|
if (is_array($uri) && isset($uri['#uri'])) {
|
661
|
$renderTemplate[$part]['#uri'] = $uri['#uri'];
|
662
|
}
|
663
|
}
|
664
|
|
665
|
normalize_TaggedName($taxonName->taggedName);
|
666
|
|
667
|
$firstEntryIsValidNamePart = isset($taxonName->taggedName) && is_array($taxonName->taggedName) && isset($taxonName->taggedName[0]->text) && is_string($taxonName->taggedName[0]->text) && $taxonName->taggedName[0]->text != '' && isset($taxonName->taggedName[0]->type) && $taxonName->taggedName[0]->type == 'name';
|
668
|
|
669
|
// Got to use second entry as first one, see ToDo comment below ...
|
670
|
if ($firstEntryIsValidNamePart) {
|
671
|
|
672
|
$taggedName = $taxonName->taggedName;
|
673
|
$lastAuthorElementString = FALSE;
|
674
|
$hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
|
675
|
$hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
|
676
|
|
677
|
if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {
|
678
|
// Find author and split off from name.
|
679
|
// TODO expecting to find the author as the last element.
|
680
|
/*
|
681
|
if($taggedName[count($taggedName)- 1]->type == 'authors'){
|
682
|
$authorTeam = $taggedName[count($taggedName)- 1]->text;
|
683
|
unset($taggedName[count($taggedName)- 1]);
|
684
|
}
|
685
|
*/
|
686
|
|
687
|
// Remove all authors.
|
688
|
$taggedNameNew = array();
|
689
|
foreach ($taggedName as $element) {
|
690
|
if ($element->type != 'authors') {
|
691
|
$taggedNameNew[] = $element;
|
692
|
}
|
693
|
else {
|
694
|
$lastAuthorElementString = $element->text;
|
695
|
}
|
696
|
}
|
697
|
$taggedName = $taggedNameNew;
|
698
|
}
|
699
|
$name = '<span class="' . $taxonName->class . '">' . theme('cdm_taggedtext2html', array(
|
700
|
'taggedtxt' => $taggedName,
|
701
|
'tag' => 'span',
|
702
|
'glue' => ' ',
|
703
|
'skiptags' => $skiptags,
|
704
|
)) . '</span>';
|
705
|
}
|
706
|
else {
|
707
|
$name = '<span class="' . $taxonName->class . '_titleCache">' . $taxonName->titleCache . '</span>';
|
708
|
}
|
709
|
|
710
|
// Fill name into $renderTemplate.
|
711
|
array_setr('name', $name, $renderTemplate);
|
712
|
|
713
|
// Fill with authorTeam.
|
714
|
/*
|
715
|
if($authorTeam){
|
716
|
$authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
|
717
|
array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
|
718
|
}
|
719
|
*/
|
720
|
|
721
|
// Fill with reference.
|
722
|
if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
|
723
|
|
724
|
// [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
|
725
|
// Komma nach dem Autornamen ist überall dort falsch, wo ein "in" folgt."
|
726
|
if (isset($renderTemplate['referencePart']['reference']) && isset($taxonName->nomenclaturalReference)) {
|
727
|
$microreference = NULL;
|
728
|
if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
|
729
|
$microreference = $taxonName->nomenclaturalMicroReference;
|
730
|
}
|
731
|
$citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);
|
732
|
|
733
|
// Find preceding element of the reference.
|
734
|
$precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
|
735
|
if (str_beginsWith($citation, ", in")) {
|
736
|
$citation = substr($citation, 2);
|
737
|
$separator = ' ';
|
738
|
}
|
739
|
elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
|
740
|
$separator = ', ';
|
741
|
}
|
742
|
else {
|
743
|
$separator = ' ';
|
744
|
}
|
745
|
|
746
|
$referenceArray['#separator'] = $separator;
|
747
|
$referenceArray['#html'] = '<span class="reference">' . $citation . '</span>';
|
748
|
array_setr('reference', $referenceArray, $renderTemplate);
|
749
|
}
|
750
|
|
751
|
// If authors have been removed from the name part the last named authorteam
|
752
|
// should be added to the reference citation, otherwise, keep the separator
|
753
|
// out of the reference.
|
754
|
if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {
|
755
|
// If the nomenclaturalReference citation is not included in the
|
756
|
// reference part but diplay of the microreference
|
757
|
// is wanted, append the microreference to the authorTeam.
|
758
|
if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {
|
759
|
$separator = ": ";
|
760
|
$citation = $taxonName->nomenclaturalMicroReference;
|
761
|
}
|
762
|
$referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';
|
763
|
array_setr('authors', $referenceArray, $renderTemplate);
|
764
|
}
|
765
|
}
|
766
|
|
767
|
// Fill with status.
|
768
|
$statusHtml = '';
|
769
|
if (isset($taxonName->status) && is_array($taxonName->status)) {
|
770
|
if (array_setr('status', TRUE, $renderTemplate)) {
|
771
|
if (isset($taxonName->status[0])) {
|
772
|
foreach ($taxonName->status as $status) {
|
773
|
$statusHtml .= ', ' . $status->type->representation_L10n_abbreviatedLabel;
|
774
|
}
|
775
|
}
|
776
|
array_setr('status', '<span class="nomenclatural_status">' . $statusHtml . '</span>', $renderTemplate);
|
777
|
}
|
778
|
}
|
779
|
|
780
|
// Fill with protologues etc...
|
781
|
$descriptionHtml = '';
|
782
|
if (array_setr('description', TRUE, $renderTemplate)) {
|
783
|
$descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
|
784
|
foreach ($descriptions as $description) {
|
785
|
if (!empty($description)) {
|
786
|
foreach ($description->elements as $description_element) {
|
787
|
$second_citation = '';
|
788
|
if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
|
789
|
$second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
|
790
|
}
|
791
|
$descriptionHtml .= $second_citation;
|
792
|
$descriptionHtml .= theme("cdm_media", array(
|
793
|
'descriptionElement' => $description_element,
|
794
|
'mimeTypePreference' => array(
|
795
|
'application/pdf',
|
796
|
'image/png',
|
797
|
'image/jpeg',
|
798
|
'image/gif',
|
799
|
'text/html',
|
800
|
)
|
801
|
)
|
802
|
);
|
803
|
|
804
|
}
|
805
|
}
|
806
|
}
|
807
|
array_setr('description', $descriptionHtml, $renderTemplate);
|
808
|
}
|
809
|
|
810
|
// Render.
|
811
|
$out = '<span ref="/name/' . $taxonName->uuid . '">';
|
812
|
|
813
|
foreach ($renderTemplate as $partName => $part) {
|
814
|
$separator = '';
|
815
|
$partHtml = '';
|
816
|
$uri = FALSE;
|
817
|
if (!is_array($part)) {
|
818
|
continue;
|
819
|
}
|
820
|
if (isset($part['#uri']) && is_string($part['#uri'])) {
|
821
|
$uri = $part['#uri'];
|
822
|
unset($part['#uri']);
|
823
|
}
|
824
|
foreach ($part as $key => $content) {
|
825
|
$html = '';
|
826
|
if (is_array($content)) {
|
827
|
$html = $content['#html'];
|
828
|
$separator = $content['#separator'];
|
829
|
}
|
830
|
elseif (is_string($content)) {
|
831
|
$html = $content;
|
832
|
}
|
833
|
$partHtml .= '<span class="' . $key . '">' . $html . '</span>';
|
834
|
}
|
835
|
if ($uri) {
|
836
|
$out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
|
837
|
}
|
838
|
else {
|
839
|
$out .= $separator . $partHtml;
|
840
|
}
|
841
|
}
|
842
|
$out .= '</span>';
|
843
|
if ($show_annotations) {
|
844
|
// $out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
|
845
|
}
|
846
|
return $out;
|
847
|
}
|
848
|
|
849
|
/**
|
850
|
* Recursively searches the array for the $key and sets the given value.
|
851
|
*
|
852
|
* @param mixed $key
|
853
|
* Key to search for.
|
854
|
* @param mixed $value
|
855
|
* Value to set.
|
856
|
* @param array $array
|
857
|
* Array to search in.
|
858
|
*
|
859
|
* @return bool
|
860
|
* True if the key has been found.
|
861
|
*/
|
862
|
function &array_setr($key, $value, array &$array) {
|
863
|
$res = NULL;
|
864
|
foreach ($array as $k => &$v) {
|
865
|
if ($key == $k) {
|
866
|
$v = $value;
|
867
|
return $array;
|
868
|
}
|
869
|
elseif (is_array($v)) {
|
870
|
$innerArray = array_setr($key, $value, $v);
|
871
|
if ($innerArray) {
|
872
|
return $array;
|
873
|
}
|
874
|
}
|
875
|
}
|
876
|
return $res;
|
877
|
}
|
878
|
|
879
|
/**
|
880
|
* @todo Please document this function.
|
881
|
* @see http://drupal.org/node/1354
|
882
|
*/
|
883
|
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
|
884
|
$res = NULL;
|
885
|
$precedingElement = NULL;
|
886
|
foreach ($renderTemplate as &$part) {
|
887
|
foreach ($part as $key => &$element) {
|
888
|
if ($key == $contentElementKey) {
|
889
|
return $precedingElement;
|
890
|
}
|
891
|
$precedingElement = $element;
|
892
|
}
|
893
|
}
|
894
|
return $res;
|
895
|
}
|
896
|
|
897
|
/**
|
898
|
* @todo Please document this function.
|
899
|
* @see http://drupal.org/node/1354
|
900
|
*/
|
901
|
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
|
902
|
$res = NULL;
|
903
|
$precedingKey = NULL;
|
904
|
foreach ($renderTemplate as &$part) {
|
905
|
if (is_array($part)) {
|
906
|
foreach ($part as $key => &$element) {
|
907
|
if ($key == $contentElementKey) {
|
908
|
return $precedingKey;
|
909
|
}
|
910
|
if (!str_beginsWith($key, '#')) {
|
911
|
$precedingKey = $key;
|
912
|
}
|
913
|
}
|
914
|
}
|
915
|
}
|
916
|
return $res;
|
917
|
}
|
918
|
|
919
|
/**
|
920
|
* Returns HTML for a name in your theme, when implemented.
|
921
|
*
|
922
|
* This function returns currently nothing, but can be used to override
|
923
|
* how names are rendered in your theme. See the code that is commented out
|
924
|
* for an example usage. it is used in the function get_nameRenderTemplate.
|
925
|
* See that function to find out how the create template is used.
|
926
|
*
|
927
|
* @see get_nameRenderTemplate()
|
928
|
*
|
929
|
* @deprecated define name render templates via the layout settings
|
930
|
*
|
931
|
* @ingroup: themeable
|
932
|
*/
|
933
|
function theme_get_nameRenderTemplate() {
|
934
|
/*
|
935
|
// Example usage:
|
936
|
// $render_path = $variables['renderPath'];
|
937
|
|
938
|
$templates = array(
|
939
|
'taxon_page_title,polytomousKey' => array(
|
940
|
'namePart' => array(
|
941
|
'#uri' => TRUE
|
942
|
)
|
943
|
),
|
944
|
'taxon_page_synonymy,related_taxon' => array(
|
945
|
'nameAuthorPart' => array(
|
946
|
'#uri' => TRUE
|
947
|
),
|
948
|
'referencePart' => TRUE,
|
949
|
'statusPart' => TRUE,
|
950
|
'descriptionPart' => TRUE
|
951
|
),
|
952
|
'acceptedFor' => array(
|
953
|
'nameAuthorPart' => array(
|
954
|
'#uri' => TRUE
|
955
|
),
|
956
|
'referencePart' => TRUE
|
957
|
),
|
958
|
'typedesignations,list_of_taxa' => array(
|
959
|
'nameAuthorPart' => array(
|
960
|
'#uri' => TRUE
|
961
|
), 'referencePart' => TRUE
|
962
|
),
|
963
|
'#DEFAULT'=> array(
|
964
|
'nameAuthorPart' => array(
|
965
|
'#uri' => TRUE
|
966
|
), 'referencePart' => TRUE
|
967
|
)
|
968
|
);
|
969
|
return $templates;
|
970
|
*/
|
971
|
|
972
|
}
|