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<?php
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/**
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* @file
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* Functions for dealing with CDM entities from the package model.taxon
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*
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* @copyright
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* (C) 2007-2016 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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* @author
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* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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*/
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/**
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* @defgroup compose Compose functions
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* @{
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* Functions which are composing Drupal render arrays
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*
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* The cdm_dataportal module needs to compose rather complex render arrays from
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* the data returned by the CDM REST service. The compose functions are
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* responsible for creating the render arrays.
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*
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* All these functions are also implementations of the compose_hook()
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* which is used in the proxy_content() function.
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* @}
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*/
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define('TAXON_TYPE_SYNONYM', 'Synonym');
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define('TAXON_TYPE_MISAPPLIEDNAME', 'MisappliedName');
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/**
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* Returns HTML for misapplied names and invalid designations.
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*
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* Both relation types are currently treated the same!
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*
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* @param object taxonRelationships
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* A TaxonRelationshipsDTO, see taxon/{uuid}/taxonRelationshipsDTO
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*
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* @param object focusedTaxon
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* The taxon being in the focus of the application
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*
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* @return string
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* the rendered html
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*/
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function cdm_taxonRelationships($taxonRelationshipsDTO, $focusedTaxon){
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static $relationship_type_order_weights = [
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//
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UUID_PROPARTE_MISAPPLIEDNAME_FOR => 0,
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UUID_PARTIAL_MISAPPLIEDNAME_FOR => 0,
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//
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UUID_MISAPPLIED_NAME_FOR => 1,
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//
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UUID_PROPARTE_SYNONYM_FOR => 2,
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UUID_PARTIAL_SYNONYM_FOR => 2
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];
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if (!$taxonRelationshipsDTO || $taxonRelationshipsDTO->size < 1) {
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return null;
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}
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static $dedup_rel_type_uuids = array(
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UUID_MISAPPLIED_NAME_FOR,
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UUID_PARTIAL_MISAPPLIEDNAME_FOR,
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UUID_PROPARTE_MISAPPLIEDNAME_FOR
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);
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RenderHints::pushToRenderStack('taxon_relationships');
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$footnote_list_key = 'taxon_relationships';
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RenderHints::setFootnoteListKey($footnote_list_key);
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$misapplied = array();
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$joined_refs = array();
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$taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));
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// Aggregate misapplied names having the same fullname:
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// - deduplicate misapplied names, so that the same name is not shown multiple times in case
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// the duplicates only have different sensu references with detail and appended phrase (see #5647)
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// - show only the author team as short citation for the sec reference
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// - show the according reference as footnote to this short citation
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//
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// Example:
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// "Xenoxylum foobar" sensu Grumbach¹; sensu Lem²
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// 1. Novel marsian species, Grumbach, 2022
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// 2. Flora solaris, Lem, 2019
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if (isset($taxonRelationshipsDTO->relations[0])) {
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foreach($taxonRelationshipsDTO->relations as $taxon_relation){
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if (in_array($taxon_relation->type->uuid, $taxon_relationship_types)) {
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if (in_array($taxon_relation->type->uuid, $dedup_rel_type_uuids)) {
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RenderHints::pushToRenderStack('misapplied_name_for'); // TODO the render path string should in future come from $taxonRelation->type->...
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// full name with relation symbol, rel sec as de-duplication key
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// the sensu part will be removed from the key below in case it is present
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$name_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('name')));
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$full_name_key = cdm_tagged_text_to_string($taxon_relation->taggedText, array('symbol', 'appendedPhrase'));
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$symbol_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('symbol')));
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$full_name_key = $name_text . ' ' . str_replace($name_text, '', $full_name_key) . ' ' . $symbol_text;
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cdm_taxonRelationships_process_relationship_dto($taxon_relation, $misapplied, $joined_refs, $relationship_type_order_weights , $full_name_key);
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RenderHints::popFromRenderStack();
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} else {
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RenderHints::pushToRenderStack('other_taxon_relationship');
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// All relationship types except misapplied_name_for and invalid_designation_for.
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$taxon_relationships_lines[] = cdm_tagged_text_to_markup($taxon_relation->taggedText);
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RenderHints::popFromRenderStack();
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}
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}
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} // END loop over $taxonRelationshipsDTO->relations
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}
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// Sort the $joined_refs and create footnotes and footnote keys.
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uasort($joined_refs, function($a, $b) {
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if ($a['order_by_key'] == $b['order_by_key']) {
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return 0;
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}
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return ($a['order_by_key'] < $b['order_by_key']) ? -1 : 1;
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});
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foreach ($joined_refs as $ref_key => $sensu_strings) {
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if(!empty($sensu_strings)) {
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$ref_key_tokens = explode('#', $ref_key);
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$sensu_uuid = $ref_key_tokens[0];
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$sensu_reference = cdm_ws_get(CDM_WS_REFERENCE, $sensu_uuid);
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if(!$sensu_reference){
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drupal_set_message("Problem fetching sensu reference with uuid " . $sensu_uuid, 'error');
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}
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if($sensu_strings['order_by_key'] != $sensu_reference->titleCache){
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$sensu_reference_markup = cdm_reference_markup($sensu_reference);
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$footnote_key = FootnoteManager::addNewFootnote($footnote_list_key, $sensu_reference_markup);
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$footnote_key = render_footnote_key($footnote_key);
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$joined_refs[$ref_key]['markup'] = '<span class="sensu">' . $sensu_strings['markup'] . $footnote_key . '</span>';
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}
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}
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}
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// ---- Generate output ---- //
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$out = '<div class="taxon-relationships">';
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if (count($misapplied) > 0) {
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ksort($misapplied); // order the misapplied by scientific name
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$out .= '<ul class="misapplied">';
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// create the list entries per misapplied name
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foreach ($misapplied as $misapplied_name) {
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$misapplied_name_markup = $misapplied_name['out'];
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// all sensu and auct. for this MAN
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if (isset($misapplied_name['sensu_uuids'])) {
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$sensu_refs_with_fkey = array();
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foreach ($misapplied_name['sensu_uuids'] as $sensu_data) {
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if($sensu_data['uuid']){
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$joined_ref_key = $sensu_data['uuid'] . ($sensu_data['citation_detail'] ? '#' . $sensu_data['citation_detail'] : '');
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$sensu_refs_with_fkey[$sensu_data['prefix'] . $joined_refs[$joined_ref_key]['order_by_key']] = $sensu_data['prefix'] . $joined_refs[$joined_ref_key]['markup'];
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} else {
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$sensu_refs_with_fkey[$sensu_data['prefix']] = $sensu_data['prefix'];
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}
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}
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ksort($sensu_refs_with_fkey);
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$sensu_refs_with_fkey_markup = join('; ', $sensu_refs_with_fkey);
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if(strpos($misapplied_name_markup, '{PLACEHOLDER_secReference}') !== false){
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$misapplied_name_markup = str_replace('{PLACEHOLDER_secReference}', $sensu_refs_with_fkey_markup, $misapplied_name_markup);
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// just remove the appendedPhrase placeholder as was included in the sensu_refs_with_fkey_markup
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$misapplied_name_markup = str_replace('{PLACEHOLDER_appendedPhrase}', '', $misapplied_name_markup);
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} else {
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// no sec ref so there could only be the appended phrase
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$misapplied_name_markup = str_replace('{PLACEHOLDER_appendedPhrase}', $sensu_refs_with_fkey_markup, $misapplied_name_markup);
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}
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}
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// append the err. sec. if there is any for this MAN
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if (isset($misapplied_name['relsec_uuids'])) {
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$relsec_refs_with_fkey = array();
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foreach ($misapplied_name['relsec_uuids'] as $relsec_data) {
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if($relsec_data['uuid']) {
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$relsec_refs_with_fkey[$relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['order_by_key']] = $relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['markup'];
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}
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}
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ksort($relsec_refs_with_fkey);
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$relsec_refs_with_fkey_markup = join('; ', $relsec_refs_with_fkey);
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$misapplied_name_markup = str_replace('{PLACEHOLDER_relSecReference}', $relsec_refs_with_fkey_markup, $misapplied_name_markup);
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}
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// final line
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$out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name_markup . ' </span></li>';
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}
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$out .= '</ul>';
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}
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if (isset($taxon_relationships_lines) && is_array($taxon_relationships_lines) && count($taxon_relationships_lines) > 0) {
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$out .= '<ul class="taxonRelationships">';
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foreach ($taxon_relationships_lines as $taxon_relationship_line) {
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$out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';
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}
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$out .= '</ul>';
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}
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$footnotes = render_footnotes($footnote_list_key, 'li');
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$out .= '<ul class="footnotes">' . $footnotes . '</ul>';
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$out .= '</div>';
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RenderHints::popFromRenderStack();
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return $out;
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}
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/**
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* Returns HTML for misapplied names and invalid designations.
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*
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* Both relation types are currently treated the same!
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*
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* @param object taxonRelationships
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* A TaxonRelationshipsDTO, see taxon/{uuid}/taxonRelationshipsDTO
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*
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* @param object focusedTaxon
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* The taxon being in the focus of the application
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*
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* @return string
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* the rendered html
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*/
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function cdm_new_taxonRelationships($taxonRelationshipsDTO, $focusedTaxon){
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static $relationship_type_order_weights = [
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//
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UUID_PROPARTE_MISAPPLIEDNAME_FOR => 0,
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UUID_PARTIAL_MISAPPLIEDNAME_FOR => 0,
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//
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UUID_MISAPPLIED_NAME_FOR => 1,
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//
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UUID_PROPARTE_SYNONYM_FOR => 2,
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UUID_PARTIAL_SYNONYM_FOR => 2
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];
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if (!$taxonRelationshipsDTO || $taxonRelationshipsDTO->count < 1) {
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return null;
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}
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static $dedup_rel_type_uuids = array(
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UUID_MISAPPLIED_NAME_FOR,
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UUID_PARTIAL_MISAPPLIEDNAME_FOR,
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UUID_PROPARTE_MISAPPLIEDNAME_FOR
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);
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RenderHints::pushToRenderStack('taxon_relationships');
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$footnote_list_key = 'taxon_relationships';
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RenderHints::setFootnoteListKey($footnote_list_key);
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$misapplied = array();
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$joined_refs = array();
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$taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));
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// Aggregate misapplied names having the same fullname:
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// - deduplicate misapplied names, so that the same name is not shown multiple times in case
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266
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// the duplicates only have different sensu references with detail and appended phrase (see #5647)
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267
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// - show only the author team as short citation for the sec reference
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// - show the according reference as footnote to this short citation
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//
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// Example:
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// "Xenoxylum foobar" sensu Grumbach¹; sensu Lem²
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// 1. Novel marsian species, Grumbach, 2022
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// 2. Flora solaris, Lem, 2019
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// if (isset($taxonRelationshipsDTO->relations[0])) {
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foreach($taxonRelationshipsDTO->items as $taxon_relation){
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if (in_array($taxon_relation->relTypeUuid, $taxon_relationship_types)) {
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if (in_array($taxon_relation->relTypeUuid, $dedup_rel_type_uuids)) {
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RenderHints::pushToRenderStack('misapplied_name_for'); // TODO the render path string should in future come from $taxonRelation->type->...
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// full name with relation symbol, rel sec as de-duplication key
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// the sensu part will be removed from the key below in case it is present
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$name_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedLabel, array('name')));
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$full_name_key = cdm_tagged_text_to_string($taxon_relation->taggedLabel, array('symbol', 'appendedPhrase'));
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$symbol_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedLabel, array('symbol')));
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$full_name_key = $name_text . ' ' . str_replace($name_text, '', $full_name_key) . ' ' . $symbol_text;
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cdm_new_taxonRelationships_process_relationship_dto($taxon_relation, $misapplied, $joined_refs, $relationship_type_order_weights , $full_name_key);
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RenderHints::popFromRenderStack();
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} else {
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RenderHints::pushToRenderStack('other_taxon_relationship');
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// All relationship types except misapplied_name_for and invalid_designation_for.
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$taxon_relationships_lines[] = cdm_tagged_text_to_markup($taxon_relation->taggedLabel);
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RenderHints::popFromRenderStack();
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}
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}
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} // END loop over $taxonRelationshipsDTO->relations
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//}
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// Sort the $joined_refs and create footnotes and footnote keys.
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uasort($joined_refs, function($a, $b) {
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if ($a['order_by_key'] == $b['order_by_key']) {
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return 0;
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}
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return ($a['order_by_key'] < $b['order_by_key']) ? -1 : 1;
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});
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foreach ($joined_refs as $ref_key => $sensu_strings) {
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if(!empty($sensu_strings)) {
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$ref_key_tokens = explode('#', $ref_key);
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$sensu_uuid = $ref_key_tokens[0];
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//TODO!!!
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//$sensu_reference = cdm_ws_get(CDM_WS_REFERENCE, $sensu_uuid);
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$sensu_reference = $sensu_strings['markup'];
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if(!$sensu_reference){
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drupal_set_message("Problem fetching sensu reference with uuid " . $sensu_uuid, 'error');
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}
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//TODO: Check whether this still needs to be handled
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326
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if($sensu_strings['order_by_key'] != $sensu_strings['longCitation']){
|
|
327
|
$sensu_reference_markup = $sensu_strings['markup'];
|
|
328
|
$footnote_key = FootnoteManager::addNewFootnote($footnote_list_key, $sensu_reference_markup);
|
|
329
|
$footnote_key = render_footnote_key($footnote_key);
|
|
330
|
$joined_refs[$ref_key]['markup'] = '<span class="sensu">' . $sensu_strings['shortCitation'] . $footnote_key . '</span>';
|
|
331
|
}
|
|
332
|
}
|
|
333
|
}
|
|
334
|
|
|
335
|
// ---- Generate output ---- //
|
|
336
|
$out = '<div class="taxon-relationships">';
|
|
337
|
if (count($misapplied) > 0) {
|
|
338
|
ksort($misapplied); // order the misapplied by scientific name
|
|
339
|
$out .= '<ul class="misapplied">';
|
|
340
|
|
|
341
|
// create the list entries per misapplied name
|
|
342
|
foreach ($misapplied as $misapplied_name) {
|
|
343
|
$misapplied_name_markup = $misapplied_name['out'];
|
|
344
|
// all sensu and auct. for this MAN
|
|
345
|
if (isset($misapplied_name['sensu_uuids'])) {
|
|
346
|
$sensu_refs_with_fkey = array();
|
|
347
|
foreach ($misapplied_name['sensu_uuids'] as $sensu_data) {
|
|
348
|
if($sensu_data['uuid']){
|
|
349
|
$joined_ref_key = $sensu_data['uuid'] . ($sensu_data['citation_detail'] ? '#' . $sensu_data['citation_detail'] : '');
|
|
350
|
$sensu_refs_with_fkey[$sensu_data['prefix'] . $joined_refs[$joined_ref_key]['shortCitation']] = $sensu_data['prefix'] . $joined_refs[$joined_ref_key]['markup'];
|
|
351
|
} else {
|
|
352
|
$sensu_refs_with_fkey[$sensu_data['prefix']] = $sensu_data['prefix'];
|
|
353
|
}
|
|
354
|
}
|
|
355
|
ksort($sensu_refs_with_fkey);
|
|
356
|
$sensu_refs_with_fkey_markup = join('; ', $sensu_refs_with_fkey);
|
|
357
|
if(strpos($misapplied_name_markup, '{PLACEHOLDER_secReference}') !== false){
|
|
358
|
$misapplied_name_markup = str_replace('{PLACEHOLDER_secReference}', $sensu_refs_with_fkey_markup, $misapplied_name_markup);
|
|
359
|
// just remove the appendedPhrase placeholder as was included in the sensu_refs_with_fkey_markup
|
|
360
|
$misapplied_name_markup = str_replace('{PLACEHOLDER_appendedPhrase}', '', $misapplied_name_markup);
|
|
361
|
} else {
|
|
362
|
// no sec ref so there could only be the appended phrase
|
|
363
|
$misapplied_name_markup = str_replace('{PLACEHOLDER_appendedPhrase}', $sensu_refs_with_fkey_markup, $misapplied_name_markup);
|
|
364
|
}
|
|
365
|
}
|
|
366
|
|
|
367
|
// append the err. sec. if there is any for this MAN
|
|
368
|
if (isset($misapplied_name['relsec_uuids'])) {
|
|
369
|
$relsec_refs_with_fkey = array();
|
|
370
|
foreach ($misapplied_name['relsec_uuids'] as $relsec_data) {
|
|
371
|
if($relsec_data['uuid']) {
|
|
372
|
$relsec_refs_with_fkey[$relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['order_by_key']] = $relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['markup'];
|
|
373
|
}
|
|
374
|
}
|
|
375
|
ksort($relsec_refs_with_fkey);
|
|
376
|
$relsec_refs_with_fkey_markup = join('; ', $relsec_refs_with_fkey);
|
|
377
|
$misapplied_name_markup = str_replace('{PLACEHOLDER_relSecReference}', $relsec_refs_with_fkey_markup, $misapplied_name_markup);
|
|
378
|
}
|
|
379
|
// final line
|
|
380
|
$out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name_markup . ' </span></li>';
|
|
381
|
}
|
|
382
|
$out .= '</ul>';
|
|
383
|
}
|
|
384
|
|
|
385
|
if (isset($taxon_relationships_lines) && is_array($taxon_relationships_lines) && count($taxon_relationships_lines) > 0) {
|
|
386
|
$out .= '<ul class="taxonRelationships">';
|
|
387
|
foreach ($taxon_relationships_lines as $taxon_relationship_line) {
|
|
388
|
$out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';
|
|
389
|
}
|
|
390
|
$out .= '</ul>';
|
|
391
|
}
|
|
392
|
|
|
393
|
$footnotes = render_footnotes($footnote_list_key, 'li');
|
|
394
|
|
|
395
|
$out .= '<ul class="footnotes">' . $footnotes . '</ul>';
|
|
396
|
$out .= '</div>';
|
|
397
|
|
|
398
|
RenderHints::popFromRenderStack();
|
|
399
|
return $out;
|
|
400
|
}
|
|
401
|
|
|
402
|
|
|
403
|
/**
|
|
404
|
* @param $taxon_relation
|
|
405
|
* @param $misapplied
|
|
406
|
* @param $joined_refs
|
|
407
|
* @param $relationship_type_weights
|
|
408
|
* @param $name_dedup_key
|
|
409
|
*/
|
|
410
|
function cdm_taxonRelationships_process_relationship_dto($taxon_relation, &$misapplied, &$joined_refs, $relationship_type_weights, $name_dedup_key) {
|
|
411
|
|
|
412
|
$appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('appendedPhrase')));
|
|
413
|
// remove/extract appendedPhrase, secReference, relSecReference and add placeholders if needed
|
|
414
|
tagged_text_extract($taxon_relation->taggedText, 'appendedPhrase', true);
|
|
415
|
$sensu_tagged_text = tagged_text_extract_reference_and_detail($taxon_relation->taggedText, "secReference", true);
|
|
416
|
$relsec_tagged_text = tagged_text_extract_reference_and_detail($taxon_relation->taggedText, "relSecReference", true);
|
|
417
|
|
|
418
|
// prepend the weight value for the relationship type to the $name_dedup_key so that the key can be used for ordering the
|
|
419
|
// entries in the $misapplied array
|
|
420
|
if(isset($relationship_type_weights[$taxon_relation->type->uuid])){
|
|
421
|
$reltype_weight = $relationship_type_weights[$taxon_relation->type->uuid];
|
|
422
|
} else {
|
|
423
|
$reltype_weight = 99;
|
|
424
|
}
|
|
425
|
$name_dedup_key = str_pad( $reltype_weight, 2, '0', STR_PAD_LEFT) . '-' . $name_dedup_key;
|
|
426
|
$skipTags = array();
|
|
427
|
$skipTags[] = "secMicroReference";
|
|
428
|
if (isset($sensu_tagged_text[1])) {
|
|
429
|
// for de-duplication everything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21
|
|
430
|
$name_dedup_key = str_replace(cdm_tagged_text_to_string($sensu_tagged_text), ' ', $name_dedup_key);
|
|
431
|
$appended_phrase_text = $appended_phrase_text . array_shift($sensu_tagged_text)->text; // remove first element which contains the "sensu", this will be added later in this code
|
|
432
|
$sensu_citation_detail = trim(join(' ', cdm_tagged_text_values($sensu_tagged_text, array('secMicroReference'))));
|
|
433
|
//TODO: add footnote placeholder in front of the secMicroReference
|
|
434
|
$sensu_citation_short_markup = cdm_tagged_text_to_markup($sensu_tagged_text);
|
|
435
|
//only one footnote for a reference undependent of detail
|
|
436
|
$sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text, array('secMicroReference'));
|
|
437
|
$sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid;
|
|
438
|
$name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
|
|
439
|
$misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);
|
|
440
|
$ref_key = $sensu_uuid . ($sensu_citation_detail ? '#' . $sensu_citation_detail : '');
|
|
441
|
if (!isset($joined_refs[$ref_key])) {
|
|
442
|
$joined_refs[$ref_key] = array(
|
|
443
|
'order_by_key' => $sensu_citation_short,
|
|
444
|
'markup' => $sensu_citation_short_markup // the footnote key will be appended later
|
|
445
|
);
|
|
446
|
}
|
|
447
|
} else if ($appended_phrase_text) {
|
|
448
|
// appended phrase without reference
|
|
449
|
$name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
|
|
450
|
$misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => null, 'prefix' => $appended_phrase_text);
|
|
451
|
}
|
|
452
|
|
|
453
|
if (isset($relsec_tagged_text[1])) {
|
|
454
|
$appended_phrase_text = array_shift($relsec_tagged_text)->text; // remove first element which contains the "err. sec", this will be added later in this code
|
|
455
|
$relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));
|
|
456
|
$relsec_citation_short_markup = cdm_tagged_text_to_markup($relsec_tagged_text);
|
|
457
|
$relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text, array('secMicroReference'));
|
|
458
|
$relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid;
|
|
459
|
$misapplied[$name_dedup_key]['relsec_uuids'][] = array('uuid' => $relsec_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $relsec_citation_detail);;
|
|
460
|
$ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : '');
|
|
461
|
if (!isset($joined_refs[$ref_key])) {
|
|
462
|
$joined_refs[$ref_key] = array(
|
|
463
|
'order_by_key' => $relsec_citation_short,
|
|
464
|
'markup' => $relsec_citation_short_markup // the footnote key will be appended later
|
|
465
|
);
|
|
466
|
}
|
|
467
|
}
|
|
468
|
|
|
469
|
if (!isset($misapplied[$name_dedup_key]['out'])) {
|
|
470
|
// helpful for debugging: // cdm_tagged_text_add_options($taxon_relation->taggedText, array(array('filter-type' => 'symbol', 'attributes' => array('title' => array($taxon_relation->type->representations[0]->label)))));
|
|
471
|
$misapplied[$name_dedup_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedText);
|
|
472
|
} else {
|
|
473
|
// We need to add the anchors for all of the other misapplied names not
|
|
474
|
// being rendered explicitly.
|
|
475
|
$misapplied[$name_dedup_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$name_dedup_key]['out']);
|
|
476
|
}
|
|
477
|
|
|
478
|
}
|
|
479
|
/**
|
|
480
|
* @param $taxon_relation
|
|
481
|
* @param $misapplied
|
|
482
|
* @param $joined_refs
|
|
483
|
* @param $relationship_type_weights
|
|
484
|
* @param $name_dedup_key
|
|
485
|
*/
|
|
486
|
function cdm_new_taxonRelationships_process_relationship_dto($taxon_relation, &$misapplied, &$joined_refs, $relationship_type_weights, $name_dedup_key) {
|
|
487
|
|
|
488
|
$appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedLabel, array('appendedPhrase')));
|
|
489
|
// remove/extract appendedPhrase, secReference, relSecReference and add placeholders if needed
|
|
490
|
tagged_text_extract($taxon_relation->taggedLabel, 'appendedPhrase', true);
|
|
491
|
$sensu_tagged_text = tagged_text_extract_reference_and_detail($taxon_relation->taggedLabel, "secReference", true);
|
|
492
|
$relsec_tagged_text = tagged_text_extract_reference_and_detail($taxon_relation->taggedLabel, "relSecReference", true);
|
|
493
|
|
|
494
|
// prepend the weight value for the relationship type to the $name_dedup_key so that the key can be used for ordering the
|
|
495
|
// entries in the $misapplied array
|
|
496
|
if(isset($relationship_type_weights[$taxon_relation->relTypeUuid])){
|
|
497
|
$reltype_weight = $relationship_type_weights[$taxon_relation->relTypeUuid];
|
|
498
|
} else {
|
|
499
|
$reltype_weight = 99;
|
|
500
|
}
|
|
501
|
$name_dedup_key = str_pad( $reltype_weight, 2, '0', STR_PAD_LEFT) . '-' . $name_dedup_key;
|
|
502
|
|
|
503
|
if (isset($sensu_tagged_text[1])) {
|
|
504
|
// for de-duplication everything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21
|
|
505
|
$name_dedup_key = str_replace(cdm_tagged_text_to_string($sensu_tagged_text), ' ', $name_dedup_key);
|
|
506
|
$appended_phrase_text = $appended_phrase_text . array_shift($sensu_tagged_text)->text; // remove first element which contains the "sensu", this will be added later in this code
|
|
507
|
$sensu_citation_detail = trim(join(' ', cdm_tagged_text_values($sensu_tagged_text, array('secMicroReference'))));
|
|
508
|
if (isset_not_empty($taxon_relation->secSource) && isset_not_empty($taxon_relation->secSource->label[0])){
|
|
509
|
$sensu_citation_long = $taxon_relation->secSource->label[0]->label;
|
|
510
|
}
|
|
511
|
$sensu_citation_long_markup = render_original_source($taxon_relation->secSource, FALSE);
|
|
512
|
$sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text);
|
|
513
|
$sensu_citation_short_without_detail = cdm_tagged_text_to_string($sensu_tagged_text, array('secMicroReference'));
|
|
514
|
$sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid;
|
|
515
|
$name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
|
|
516
|
$misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);
|
|
517
|
$ref_key = $sensu_uuid . ($sensu_citation_detail ? '#' . $sensu_citation_detail : '');
|
|
518
|
if (!isset($joined_refs[$ref_key])) {
|
|
519
|
$joined_refs[$ref_key] = array(
|
|
520
|
'order_by_key' => $sensu_citation_short_without_detail,
|
|
521
|
'markup' => $sensu_citation_long_markup,
|
|
522
|
'shortCitation' => $sensu_citation_short,
|
|
523
|
'longCitation' => $sensu_citation_long// the footnote key will be appended later
|
|
524
|
);
|
|
525
|
}
|
|
526
|
} else if ($appended_phrase_text) {
|
|
527
|
// appended phrase without reference
|
|
528
|
$name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
|
|
529
|
$misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => null, 'prefix' => $appended_phrase_text);
|
|
530
|
}
|
|
531
|
|
|
532
|
if (isset($relsec_tagged_text[1])) {
|
|
533
|
$appended_phrase_text = array_shift($relsec_tagged_text)->text; // remove first element which contains the "err. sec", this will be added later in this code
|
|
534
|
$relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));
|
|
535
|
$relsec_citation_long_markup = render_original_source($taxon_relation->relSource, FALSE);
|
|
536
|
if (isset_not_empty($taxon_relation->relSource) && isset_not_empty($taxon_relation->relSource->label[0])){
|
|
537
|
$relsec_citation_long = $taxon_relation->relSource->label[0]->label;
|
|
538
|
}
|
|
539
|
$relsec_citation_short_without_detail = cdm_tagged_text_to_string($relsec_tagged_text, array('secMicroReference'));
|
|
540
|
$relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text);
|
|
541
|
$relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid;
|
|
542
|
$misapplied[$name_dedup_key]['relsec_uuids'][] = array('uuid' => $relsec_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $relsec_citation_detail);;
|
|
543
|
$ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : '');
|
|
544
|
if (!isset($joined_refs[$ref_key])) {
|
|
545
|
$joined_refs[$ref_key] = array(
|
|
546
|
'order_by_key' => $relsec_citation_short_without_detail,
|
|
547
|
'markup' => $relsec_citation_long_markup,
|
|
548
|
'shortCitation' => $relsec_citation_short,
|
|
549
|
'longCitation' => $relsec_citation_long// the footnote key will be appended later
|
|
550
|
);
|
|
551
|
}
|
|
552
|
}
|
|
553
|
|
|
554
|
if (!isset($misapplied[$name_dedup_key]['out'])) {
|
|
555
|
// helpful for debugging: // cdm_tagged_text_add_options($taxon_relation->taggedText, array(array('filter-type' => 'symbol', 'attributes' => array('title' => array($taxon_relation->type->representations[0]->label)))));
|
|
556
|
$misapplied[$name_dedup_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedLabel);
|
|
557
|
$misapplied[$name_dedup_key]['out'] = uuid_anchor($taxon_relation->relTaxonUuid, $misapplied[$name_dedup_key]['out']);
|
|
558
|
} else {
|
|
559
|
// We need to add the anchors for all of the other misapplied names not
|
|
560
|
// being rendered explicitly. TODO!!
|
|
561
|
// $misapplied[$name_dedup_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$name_dedup_key]['out']);
|
|
562
|
}
|
|
563
|
|
|
564
|
}
|
|
565
|
|
|
566
|
|
|
567
|
/**
|
|
568
|
* Renders a representation of the given taxon relationship.
|
|
569
|
*
|
|
570
|
* According name relationships are also being rendered.
|
|
571
|
*
|
|
572
|
* @param $taxon
|
|
573
|
* The CDM TaxonBase entity
|
|
574
|
* @param $reltype_uuid
|
|
575
|
* The UUID of the TaxonRelationshipType
|
|
576
|
* @param $relsign
|
|
577
|
* Optional. Can be used to override the internal decision strategy on finding a suitable icon for the relationship
|
|
578
|
* @param $reltype_representation
|
|
579
|
* Optional: Defines the value for the title attribute of the html element enclosing the relsign
|
|
580
|
* @param $doubtful
|
|
581
|
* TODO
|
|
582
|
* @param $doLinkTaxon
|
|
583
|
* The taxon will be rendered as clickable link when true.
|
|
584
|
*
|
|
585
|
* @return string
|
|
586
|
* Markup for the taxon relationship.
|
|
587
|
*
|
|
588
|
* @throws Exception
|
|
589
|
*/
|
|
590
|
function cdm_related_taxon($taxon, $reltype_uuid = NULL) {
|
|
591
|
static $relsign_homo = '≡';
|
|
592
|
static $relsign_hetero = '=';
|
|
593
|
static $relsign_invalid = '–';
|
|
594
|
static $nom_status_invalid_type_uuids = array(
|
|
595
|
UUID_NOMENCLATURALSTATUS_TYPE_INVALID,
|
|
596
|
UUID_NOMENCLATURALSTATUS_TYPE_NUDUM,
|
|
597
|
UUID_NOMENCLATURALSTATUS_TYPE_COMBINATIONINVALID,
|
|
598
|
UUID_NOMENCLATURALSTATUS_TYPE_PROVISIONAL
|
|
599
|
);
|
|
600
|
|
|
601
|
// 'taxonRelationships';
|
|
602
|
$footnoteListKey = NULL;
|
|
603
|
|
|
604
|
$skip_render_template_keys = array();
|
|
605
|
|
|
606
|
$is_invalid = false;
|
|
607
|
|
|
608
|
|
|
609
|
switch ($reltype_uuid) {
|
|
610
|
case UUID_HETEROTYPIC_SYNONYM_OF:
|
|
611
|
case UUID_SYNONYM_OF:
|
|
612
|
$relsign = $relsign_hetero;
|
|
613
|
break;
|
|
614
|
|
|
615
|
case UUID_HOMOTYPIC_SYNONYM_OF:
|
|
616
|
$relsign = $relsign_homo;
|
|
617
|
break;
|
|
618
|
|
|
619
|
case UUID_MISAPPLIED_NAME_FOR:
|
|
620
|
$skip_render_template_keys[] = 'nameAuthorPart';
|
|
621
|
$is_invalid = true;
|
|
622
|
$relsign = $relsign_invalid;
|
|
623
|
|
|
624
|
break;
|
|
625
|
|
|
626
|
default:
|
|
627
|
$relsign = $relsign_invalid;
|
|
628
|
}
|
|
629
|
|
|
630
|
|
|
631
|
/*
|
|
632
|
Names with status invalid or nudum are to be displayed with the
|
|
633
|
$relsign_invalid, these names appear at the end of all names in their
|
|
634
|
homotypic group (ordered correctly by the java cdm_lib).
|
|
635
|
*/
|
|
636
|
if (isset($taxon->name->status) && is_array($taxon->name->status)) {
|
|
637
|
foreach ($taxon->name->status as $status) {
|
|
638
|
if (in_array($status->type->uuid , $nom_status_invalid_type_uuids)) {
|
|
639
|
$relsign = $relsign_invalid;
|
|
640
|
break;
|
|
641
|
}
|
|
642
|
}
|
|
643
|
}
|
|
644
|
|
|
645
|
// Now rendering starts ..
|
|
646
|
RenderHints::pushToRenderStack('related_taxon');
|
|
647
|
|
|
648
|
if (isset($taxon->name->nomenclaturalSource->citation)) {
|
|
649
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalSource->citation->uuid));
|
|
650
|
}
|
|
651
|
$taxonUri = '';
|
|
652
|
|
|
653
|
// Printing the taxonName and the handling the special case of annotations.
|
|
654
|
if (!isset($referenceUri)) {
|
|
655
|
$referenceUri = FALSE;
|
|
656
|
}
|
|
657
|
$out_taxon_part = render_taxon_or_name($taxon, $taxonUri, $referenceUri, TRUE, TRUE, FALSE, $skip_render_template_keys, $is_invalid);
|
|
658
|
$name_relations = cdm_name_relationships_for_taxon($taxon);
|
|
659
|
$name_relations_render_array = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
|
|
660
|
|
|
661
|
$out = '<span class="relation_sign">' . $relsign . '</span>'
|
|
662
|
. $out_taxon_part;
|
|
663
|
if(isset($name_relations_render_array['list']['items'][0])){
|
|
664
|
$out .= ' ' . drupal_render($name_relations_render_array);
|
|
665
|
}
|
|
666
|
|
|
667
|
$out = uuid_anchor($taxon->uuid, $out);
|
|
668
|
|
|
669
|
RenderHints::popFromRenderStack();
|
|
670
|
|
|
671
|
return $out;
|
|
672
|
}
|
|
673
|
/**
|
|
674
|
* Renders a representation of the given taxon relationship.
|
|
675
|
*
|
|
676
|
* According name relationships are also being rendered.
|
|
677
|
*
|
|
678
|
* @param $taxon_dto
|
|
679
|
* The CDM TaxonBase dto
|
|
680
|
* @param $reltype_uuid
|
|
681
|
* The UUID of the TaxonRelationshipType
|
|
682
|
* @param $relsign
|
|
683
|
* Optional. Can be used to override the internal decision strategy on finding a suitable icon for the relationship
|
|
684
|
* @param $reltype_representation
|
|
685
|
* Optional: Defines the value for the title attribute of the html element enclosing the relsign
|
|
686
|
* @param $doubtful
|
|
687
|
* TODO
|
|
688
|
* @param $doLinkTaxon
|
|
689
|
* The taxon will be rendered as clickable link when true.
|
|
690
|
*
|
|
691
|
* @return string
|
|
692
|
* Markup for the taxon relationship.
|
|
693
|
*
|
|
694
|
* @throws Exception
|
|
695
|
*/
|
|
696
|
function cdm_new_related_taxon($taxon_dto, $reltype_uuid = NULL) {
|
|
697
|
static $relsign_homo = '≡';
|
|
698
|
static $relsign_hetero = '=';
|
|
699
|
static $relsign_invalid = '–';
|
|
700
|
static $nom_status_invalid_type_uuids = array(
|
|
701
|
UUID_NOMENCLATURALSTATUS_TYPE_INVALID,
|
|
702
|
UUID_NOMENCLATURALSTATUS_TYPE_NUDUM,
|
|
703
|
UUID_NOMENCLATURALSTATUS_TYPE_COMBINATIONINVALID,
|
|
704
|
UUID_NOMENCLATURALSTATUS_TYPE_PROVISIONAL
|
|
705
|
);
|
|
706
|
|
|
707
|
// 'taxonRelationships';
|
|
708
|
$footnoteListKey = NULL;
|
|
709
|
|
|
710
|
$skip_render_template_keys = array();
|
|
711
|
|
|
712
|
$is_invalid = false;
|
|
713
|
|
|
714
|
|
|
715
|
switch ($reltype_uuid) {
|
|
716
|
case UUID_HETEROTYPIC_SYNONYM_OF:
|
|
717
|
case UUID_SYNONYM_OF:
|
|
718
|
$relsign = $relsign_hetero;
|
|
719
|
break;
|
|
720
|
|
|
721
|
case UUID_HOMOTYPIC_SYNONYM_OF:
|
|
722
|
$relsign = $relsign_homo;
|
|
723
|
break;
|
|
724
|
|
|
725
|
case UUID_MISAPPLIED_NAME_FOR:
|
|
726
|
$skip_render_template_keys[] = 'nameAuthorPart';
|
|
727
|
$is_invalid = true;
|
|
728
|
$relsign = $relsign_invalid;
|
|
729
|
|
|
730
|
break;
|
|
731
|
|
|
732
|
default:
|
|
733
|
$relsign = $relsign_invalid;
|
|
734
|
}
|
|
735
|
|
|
736
|
|
|
737
|
/*
|
|
738
|
Names with status invalid or nudum are to be displayed with the
|
|
739
|
$relsign_invalid, these names appear at the end of all names in their
|
|
740
|
homotypic group (ordered correctly by the java cdm_lib).
|
|
741
|
*/
|
|
742
|
//TODO: how it is implemented in new dto???
|
|
743
|
if (isset($taxon_dto->taggedLabel) ) {
|
|
744
|
//if ()
|
|
745
|
}
|
|
746
|
|
|
747
|
// Now rendering starts ..
|
|
748
|
RenderHints::pushToRenderStack('related_taxon');
|
|
749
|
//TODO: actually the uuid of the nomenclatural source is not available in taxon dto
|
|
750
|
/*if (isset($taxon_dto->name->nomenclaturalSource->citation)) {
|
|
751
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalSource->citation->uuid));
|
|
752
|
}*/
|
|
753
|
$taxonUri = '';
|
|
754
|
|
|
755
|
// Printing the taxonName and the handling the special case of annotations.
|
|
756
|
if (!isset($referenceUri)) {
|
|
757
|
$referenceUri = FALSE;
|
|
758
|
}
|
|
759
|
$out_taxon_part = render_new_taxon_or_name($taxon_dto, true, $taxonUri, $referenceUri, TRUE, FALSE, $skip_render_template_keys, $is_invalid);
|
|
760
|
$name_relations = cdm_name_relationships_for_taxon_new($taxon_dto);
|
|
761
|
//TODO the name uuid is not available!!!
|
|
762
|
$name_relations_render_array = compose_new_name_relationships_inline($name_relations, $taxon_dto->uuid, $taxon_dto->nameType);
|
|
763
|
|
|
764
|
$out = '<span class="relation_sign">' . $relsign . '</span>'
|
|
765
|
. $out_taxon_part;
|
|
766
|
if(isset($name_relations_render_array['list']['items'][0])){
|
|
767
|
$out .= ' ' . drupal_render($name_relations_render_array);
|
|
768
|
}
|
|
769
|
|
|
770
|
$out = uuid_anchor($taxon_dto->uuid, $out);
|
|
771
|
|
|
772
|
RenderHints::popFromRenderStack();
|
|
773
|
|
|
774
|
return $out;
|
|
775
|
}
|
|
776
|
/**
|
|
777
|
* Creates markup for a taxon which is the accepted of another one
|
|
778
|
*
|
|
779
|
* @param $accepted_for_uuid
|
|
780
|
* The uuid of the accepted taxon
|
|
781
|
*/
|
|
782
|
function cdm_accepted_for($accepted_for_uuid) {
|
|
783
|
|
|
784
|
if(!is_uuid($accepted_for_uuid)){
|
|
785
|
return '';
|
|
786
|
}
|
|
787
|
|
|
788
|
RenderHints::pushToRenderStack('acceptedFor');
|
|
789
|
$out = '';
|
|
790
|
|
|
791
|
$synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $accepted_for_uuid);
|
|
792
|
if ($synonym) {
|
|
793
|
$out .= '<span class="acceptedFor">';
|
|
794
|
$out .= t('is accepted for ');
|
|
795
|
$referenceUri = null;
|
|
796
|
if (isset($synonym->name->nomenclaturalSource->citation)) {
|
|
797
|
$referenceUri = url(path_to_reference($synonym->name->nomenclaturalSource->citation->uuid));
|
|
798
|
}
|
|
799
|
$out .= render_taxon_or_name($synonym->name, NULL, $referenceUri);
|
|
800
|
RenderHints::setAnnotationsAndSourceConfig(synonymy_annotations_and_source_config());
|
|
801
|
$annotations_and_sources = handle_annotations_and_sources($synonym);
|
|
802
|
$out .= $annotations_and_sources->footNoteKeysMarkup();
|
|
803
|
$out .= '</span>';
|
|
804
|
}
|
|
805
|
RenderHints::popFromRenderStack();
|
|
806
|
return $out;
|
|
807
|
}
|
|
808
|
|
|
809
|
/**
|
|
810
|
* Compose function for a list of taxa.
|
|
811
|
*
|
|
812
|
* This function is for used to:
|
|
813
|
*
|
|
814
|
* 1. Display search results
|
|
815
|
* 2. List the taxa for a taxon name in the name page.
|
|
816
|
*
|
|
817
|
* @param $taxon_list array
|
|
818
|
* The list of CDM Taxon entities. e.g. The records array as contained in a pager object.
|
|
819
|
* @param $freetext_search_results array
|
|
820
|
* @param $show_classification boolean
|
|
821
|
*
|
|
822
|
* @ingroup compose
|
|
823
|
*/
|
|
824
|
function compose_list_of_taxa($taxon_list, $freetext_search_results = array(), $show_classification = false) {
|
|
825
|
|
|
826
|
RenderHints::pushToRenderStack('list_of_taxa');
|
|
827
|
|
|
828
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);
|
|
829
|
|
|
830
|
$showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];
|
|
831
|
$showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];
|
|
832
|
$searched_in_classification = cdm_dataportal_searched_in_classification();
|
|
833
|
$searched_in_classification_uuid = null;
|
|
834
|
if(isset($searched_in_classification->uuid)){
|
|
835
|
$searched_in_classification_uuid = $searched_in_classification->uuid;
|
|
836
|
}
|
|
837
|
|
|
838
|
// .. Well, for sure not as performant as before, but better than nothing.
|
|
839
|
$synonym_uuids = array();
|
|
840
|
$misapplied_uuids = array();
|
|
841
|
foreach ($taxon_list as $taxon) {
|
|
842
|
if ($taxon->class == "Synonym") {
|
|
843
|
if (!array_key_exists($taxon->uuid, $synonym_uuids)) {
|
|
844
|
$synonym_uuids[$taxon->uuid] = $taxon->uuid;
|
|
845
|
}
|
|
846
|
}
|
|
847
|
elseif (!_cdm_dataportal_acceptedByCurrentView($taxon)) {
|
|
848
|
// Assuming that it is a misapplied name, will be further examined below.
|
|
849
|
$misapplied_uuids[$taxon->uuid] = $taxon->uuid;
|
|
850
|
}
|
|
851
|
}
|
|
852
|
|
|
853
|
// Batch service not jet implemented:
|
|
854
|
// $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED,
|
|
855
|
// join(',', $synonym_uuids));
|
|
856
|
// thus ...
|
|
857
|
$table_of_accepted = array();
|
|
858
|
|
|
859
|
foreach ($synonym_uuids as $misapplication_uuid) {
|
|
860
|
$classification_filter = '';
|
|
861
|
if($searched_in_classification_uuid){
|
|
862
|
$classification_filter = 'classificationFilter=' . $searched_in_classification_uuid;
|
|
863
|
}
|
|
864
|
$table_of_accepted[$misapplication_uuid] = cdm_ws_get(
|
|
865
|
CDM_WS_PORTAL_TAXON_ACCEPTED,
|
|
866
|
array($misapplication_uuid),
|
|
867
|
$classification_filter
|
|
868
|
);
|
|
869
|
}
|
|
870
|
|
|
871
|
foreach ($misapplied_uuids as $mispplication_uuid) {
|
|
872
|
$taxonRelationsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, array(
|
|
873
|
$mispplication_uuid,
|
|
874
|
));
|
|
875
|
if(isset($taxonRelationsDTO->relations)){
|
|
876
|
foreach ($taxonRelationsDTO->relations as $relation) {
|
|
877
|
if ($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR && _cdm_dataportal_matches_current_view($relation->classificationsUUIDs)) {
|
|
878
|
$table_of_accepted[$mispplication_uuid][] = cdm_ws_get(CDM_WS_TAXON, $relation->taxonUuid);
|
|
879
|
}
|
|
880
|
}
|
|
881
|
}
|
|
882
|
}
|
|
883
|
|
|
884
|
$out = '<div class="cdm-item-list" style="background-image: none;">';
|
|
885
|
$itemCnt = -1;
|
|
886
|
foreach ($taxon_list as $taxon) {
|
|
887
|
$itemCnt++;
|
|
888
|
|
|
889
|
if (isset($table_of_accepted[$taxon->uuid])) {
|
|
890
|
// Its a synonym or misapplied name.
|
|
891
|
$is_synonym = isset($synonym_uuids[$taxon->uuid]); //TODO better use the $taxon->class attribute?
|
|
892
|
$taxon_type = $is_synonym ? TAXON_TYPE_SYNONYM :TAXON_TYPE_MISAPPLIEDNAME;
|
|
893
|
|
|
894
|
$acceptedTaxa = $table_of_accepted[$taxon->uuid];
|
|
895
|
|
|
896
|
if (!is_array($acceptedTaxa)) {
|
|
897
|
$acceptedTaxa = array($acceptedTaxa);
|
|
898
|
}
|
|
899
|
|
|
900
|
foreach ($acceptedTaxa as $acceptedTaxon) {
|
|
901
|
if (is_object($acceptedTaxon)) {
|
|
902
|
|
|
903
|
$taxonUri = uri_to_synonym($taxon->uuid, $acceptedTaxon->uuid);
|
|
904
|
$referenceUri = '';
|
|
905
|
if (isset($acceptedTaxon->name->nomenclaturalSource->citation)) {
|
|
906
|
$referenceUri = url(path_to_reference($acceptedTaxon->name->nomenclaturalSource->citation->uuid));
|
|
907
|
}
|
|
908
|
$skip_render_template_parts = $is_synonym ? ['secReferencePart'] : [];
|
|
909
|
// $taxon_or_name this is a trick to suppress the sec reference for synonyms
|
|
910
|
// supplying the name will cause render_taxon_or_name() to not show the sec reference
|
|
911
|
$out .= "<div class=\"item " . $taxon_type . "\">" . render_taxon_or_name($taxon, $taxonUri, $referenceUri, true, false, $skip_render_template_parts);
|
|
912
|
if($taxon_type == TAXON_TYPE_MISAPPLIEDNAME && isset_not_empty($taxon->secSource) && isset_not_empty($taxon->secSource->citation)) {
|
|
913
|
if (isset($taxon->secSource->citation->authorship)) {
|
|
914
|
$authorship = $taxon->secSource->citation->authorship->titleCache;
|
|
915
|
}
|
|
916
|
else {
|
|
917
|
$authorship = $taxon->secSource->citation->titleCache;
|
|
918
|
}
|
|
919
|
$out .= ' sensu ' . $authorship;
|
|
920
|
}
|
|
921
|
if ($show_classification) {
|
|
922
|
$out .= render_classifications_for_taxon($taxon);
|
|
923
|
}
|
|
924
|
if ($showMedia_synonyms) {
|
|
925
|
$out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $acceptedTaxon));
|
|
926
|
}
|
|
927
|
}
|
|
928
|
}
|
|
929
|
}
|
|
930
|
else {
|
|
931
|
// Its a Taxon.
|
|
932
|
$taxonUri = url(path_to_taxon($taxon->uuid));
|
|
933
|
$referenceUri = '';
|
|
934
|
if (isset($taxon->name->nomenclaturalSource->citation)) {
|
|
935
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalSource->citation->uuid));
|
|
936
|
}
|
|
937
|
$out .= '<div class="item Taxon">' . render_taxon_or_name($taxon, $taxonUri, $referenceUri, false);
|
|
938
|
if ($show_classification) {
|
|
939
|
$out .= render_classifications_for_taxon($taxon);
|
|
940
|
}
|
|
941
|
if ($showMedia_taxa) {
|
|
942
|
$out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));
|
|
943
|
}
|
|
944
|
}
|
|
945
|
|
|
946
|
/*
|
|
947
|
* the score field will be empty in case of MultiTermQueries like
|
|
948
|
* WildcardQueries, since these are constant score by default
|
|
949
|
* since Lucene 2.9
|
|
950
|
*/
|
|
951
|
if(isset($freetext_search_results[$itemCnt]) && $freetext_search_results[$itemCnt]->score && $freetext_search_results[$itemCnt]->maxScore){
|
|
952
|
$percentage = ( $freetext_search_results[$itemCnt]->score / $freetext_search_results[$itemCnt]->maxScore ) * 100;
|
|
953
|
$out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';
|
|
954
|
$out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';
|
|
955
|
}
|
|
956
|
|
|
957
|
// Render highlighted fragments, these are made available by free text
|
|
958
|
// searches.
|
|
959
|
if (isset($freetext_search_results[$itemCnt]->fieldHighlightMap)) {
|
|
960
|
$field_fragments = (array) $freetext_search_results[$itemCnt]->fieldHighlightMap;
|
|
961
|
if (count($field_fragments) > 0) {
|
|
962
|
$fragments_out = '';
|
|
963
|
foreach ($field_fragments as $fieldName => $fragments) {
|
|
964
|
$fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';
|
|
965
|
}
|
|
966
|
$out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';
|
|
967
|
}
|
|
968
|
}
|
|
969
|
|
|
970
|
$out .= '</div>';
|
|
971
|
}
|
|
972
|
|
|
973
|
$out .= '</div>';
|
|
974
|
RenderHints::popFromRenderStack();
|
|
975
|
|
|
976
|
return markup_to_render_array($out); // TODO create render array of all list items in function
|
|
977
|
}
|
|
978
|
|
|
979
|
/**
|
|
980
|
* Compose function for a list of taxa.
|
|
981
|
*
|
|
982
|
* This function is for used to:
|
|
983
|
*
|
|
984
|
* 1. Display search results
|
|
985
|
* 2. List the taxa for a taxon name in the name page.
|
|
986
|
*
|
|
987
|
* @param $taxon_list array
|
|
988
|
* The list of CDM Taxon entities. e.g. The records array as contained in a pager object.
|
|
989
|
* @param $freetext_search_results array
|
|
990
|
* @param $show_classification boolean
|
|
991
|
*
|
|
992
|
* @ingroup compose
|
|
993
|
*/
|
|
994
|
function compose_list_of_taxon_search_result($taxon_list, $freetext_search_results = array(), $show_classification = false) {
|
|
995
|
|
|
996
|
RenderHints::pushToRenderStack('list_of_taxa');
|
|
997
|
|
|
998
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);
|
|
999
|
|
|
1000
|
$showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];
|
|
1001
|
$showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];
|
|
1002
|
$searched_in_classification = cdm_dataportal_searched_in_classification();
|
|
1003
|
$searched_in_classification_uuid = null;
|
|
1004
|
if(isset($searched_in_classification->uuid)){
|
|
1005
|
$searched_in_classification_uuid = $searched_in_classification->uuid;
|
|
1006
|
}
|
|
1007
|
|
|
1008
|
// .. Well, for sure not as performant as before, but better than nothing.
|
|
1009
|
$misapplied_uuids = array();
|
|
1010
|
foreach ($taxon_list as $taxon) {
|
|
1011
|
if ($taxon->entity->class == 'Taxon' && !_cdm_dataportal_acceptedByCurrentView($taxon)) {
|
|
1012
|
// Assuming that it is a misapplied name, will be further examined below.
|
|
1013
|
$misapplied_uuids[$taxon->entity->uuid] = $taxon->entity->uuid;
|
|
1014
|
}
|
|
1015
|
}
|
|
1016
|
|
|
1017
|
// Batch service not jet implemented:
|
|
1018
|
// $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED,
|
|
1019
|
// join(',', $synonym_uuids));
|
|
1020
|
// thus ...
|
|
1021
|
$table_of_accepted = array();
|
|
1022
|
foreach ($misapplied_uuids as $mispplication_uuid) {
|
|
1023
|
$taxonRelationsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, array(
|
|
1024
|
$mispplication_uuid,
|
|
1025
|
));
|
|
1026
|
if(isset($taxonRelationsDTO->relations)){
|
|
1027
|
$taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));
|
|
1028
|
foreach ($taxonRelationsDTO->relations as $relation) {
|
|
1029
|
if (in_array($relation->type->uuid, $taxon_relationship_types) && in_array($searched_in_classification->uuid,$relation->classificationsUUIDs) ) {
|
|
1030
|
//if (($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $relation->typeUuid == UUID_MISAPPLIED_NAME_FOR || $relation->type->uuid == UUID_PROPARTE_SYNONYM_FOR || $relation->typeUuid == UUID_PROPARTE_SYNONYM_FOR) && _cdm_dataportal_matches_current_view($relation->classificationsUUIDs)) {
|
|
1031
|
// $table_of_accepted[$mispplication_uuid][] = cdm_ws_get(CDM_WS_TAXON, $relation);
|
|
1032
|
$table_of_accepted[$mispplication_uuid][] = $relation;
|
|
1033
|
}
|
|
1034
|
}
|
|
1035
|
}
|
|
1036
|
}
|
|
1037
|
|
|
1038
|
$out = '<div class="cdm-item-list" style="background-image: none;">';
|
|
1039
|
$itemCnt = -1;
|
|
1040
|
foreach ($taxon_list as $taxon) {
|
|
1041
|
$itemCnt++;
|
|
1042
|
if ($taxon->entity->class == "Synonym") {
|
|
1043
|
$synonym = $taxon;
|
|
1044
|
$taxonUri = uri_to_synonym($synonym->entity->uuid, $synonym->acceptedTaxonUuid);
|
|
1045
|
$taxon_type = TAXON_TYPE_SYNONYM;
|
|
1046
|
$out .=createOutput($taxon_type, $taxon, $taxonUri, "");
|
|
1047
|
}else {
|
|
1048
|
if (isset($table_of_accepted[$taxon->entity->uuid])) {
|
|
1049
|
// Its a misapplied name.
|
|
1050
|
$taxon_type = TAXON_TYPE_MISAPPLIEDNAME;
|
|
1051
|
$relations = $table_of_accepted[$taxon->entity->uuid];
|
|
1052
|
|
|
1053
|
if (!is_array($relations)) {
|
|
1054
|
$relations = array($relations);
|
|
1055
|
}
|
|
1056
|
$taxa_count = count($relations)-1;
|
|
1057
|
$index = 0;
|
|
1058
|
foreach ($relations as $relation) {
|
|
1059
|
if (is_object($relation)) {
|
|
1060
|
$taxonUri = uri_to_synonym($taxon->entity->uuid, $relation->taxonUuid);
|
|
1061
|
$referenceUri = '';
|
|
1062
|
//if (isset($acceptedTaxon->name->nomenclaturalSource->citation)) {
|
|
1063
|
// $referenceUri = url(path_to_reference($acceptedTaxon->name->nomenclaturalSource->citation->uuid));
|
|
1064
|
//}
|
|
1065
|
$out .= createOutput($taxon_type, $taxon, $taxonUri, $referenceUri);
|
|
1066
|
$out .= " as ". cdm_tagged_text_to_markup($relation->taggedText, ['reference', 'secReference', 'relSecReference']);
|
|
1067
|
if ($index<$taxa_count) {
|
|
1068
|
$out .= "</div>";
|
|
1069
|
}
|
|
1070
|
$index++;
|
|
1071
|
}
|
|
1072
|
}
|
|
1073
|
}else{
|
|
1074
|
if (isset_not_empty($taxon->entity) && isset_not_empty($taxon->entity->uuid)){
|
|
1075
|
$taxonUri = url(path_to_taxon($taxon->entity->uuid));
|
|
1076
|
$taxon_type = "Taxon";
|
|
1077
|
$referenceUri = '';
|
|
1078
|
if (isset_not_empty($taxon->entity->name->nomenclaturalSource) && isset_not_empty($taxon->entity->name->nomenclaturalSource->citation)) {
|
|
1079
|
$referenceUri = url(path_to_reference($taxon->entity->name->nomenclaturalSource->citation->uuid));
|
|
1080
|
}
|
|
1081
|
$out .= createOutput($taxon_type, $taxon, $taxonUri, $referenceUri);
|
|
1082
|
}
|
|
1083
|
}
|
|
1084
|
|
|
1085
|
}
|
|
1086
|
|
|
1087
|
//$out .= '<div class="item Taxon">' . render_taxon_or_name($taxon, $taxonUri, $referenceUri, false);
|
|
1088
|
// $out = createOutput($taxon_type, $taxon, $taxonUri, $referenceUri, $out);
|
|
1089
|
if ($show_classification) {
|
|
1090
|
$out .= render_classifications_for_taxon($taxon-> entity);
|
|
1091
|
}
|
|
1092
|
if ($showMedia_taxa) {
|
|
1093
|
$out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));
|
|
1094
|
}
|
|
1095
|
|
|
1096
|
|
|
1097
|
|
|
1098
|
/*
|
|
1099
|
* the score field will be empty in case of MultiTermQueries like
|
|
1100
|
* WildcardQueries, since these are constant score by default
|
|
1101
|
* since Lucene 2.9
|
|
1102
|
*/
|
|
1103
|
if(isset($freetext_search_results[$itemCnt]) && $freetext_search_results[$itemCnt]->score && $freetext_search_results[$itemCnt]->maxScore){
|
|
1104
|
$percentage = ( $freetext_search_results[$itemCnt]->score / $freetext_search_results[$itemCnt]->maxScore ) * 100;
|
|
1105
|
$out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';
|
|
1106
|
$out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';
|
|
1107
|
}
|
|
1108
|
|
|
1109
|
// Render highlighted fragments, these are made available by free text
|
|
1110
|
// searches.
|
|
1111
|
if (isset($freetext_search_results[$itemCnt]->fieldHighlightMap)) {
|
|
1112
|
$field_fragments = (array) $freetext_search_results[$itemCnt]->fieldHighlightMap;
|
|
1113
|
if (count($field_fragments) > 0) {
|
|
1114
|
$fragments_out = '';
|
|
1115
|
foreach ($field_fragments as $fieldName => $fragments) {
|
|
1116
|
$fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';
|
|
1117
|
}
|
|
1118
|
$out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';
|
|
1119
|
}
|
|
1120
|
}
|
|
1121
|
|
|
1122
|
$out .= '</div>';
|
|
1123
|
}
|
|
1124
|
|
|
1125
|
$out .= '</div>';
|
|
1126
|
RenderHints::popFromRenderStack();
|
|
1127
|
|
|
1128
|
return markup_to_render_array($out); // TODO create render array of all list items in function
|
|
1129
|
}
|
|
1130
|
|
|
1131
|
/**
|
|
1132
|
* @param string $taxon_type
|
|
1133
|
* @param mixed $taxon
|
|
1134
|
* @param string $taxonUri
|
|
1135
|
* @param string $referenceUri
|
|
1136
|
* @param string $out
|
|
1137
|
* @return string
|
|
1138
|
*/
|
|
1139
|
function createOutput($taxon_type, $taxon, $taxonUri, $referenceUri): string
|
|
1140
|
{
|
|
1141
|
$out = "";
|
|
1142
|
$skip_render_template_parts = $taxon_type == TAXON_TYPE_SYNONYM ? ['secReferencePart'] : [];
|
|
1143
|
$skip_render_template_parts = $taxon_type == TAXON_TYPE_MISAPPLIEDNAME ? ['referencePart', 'secReferencePart'] : [];
|
|
1144
|
$out .= "<div class=\"item " . $taxon_type . "\">" . render_new_taxon_or_name($taxon, true, $taxonUri, $referenceUri, false, false, false, $skip_render_template_parts);
|
|
1145
|
return $out;
|
|
1146
|
}
|
|
1147
|
|
|
1148
|
|
|
1149
|
function render_classifications_for_taxon($taxon) {
|
|
1150
|
$unclassified_snippet = '<span class="unclassified">' . t('unclassified') . '</span>';
|
|
1151
|
|
|
1152
|
$classifications = get_classifications_for_taxon($taxon);
|
|
1153
|
$classification_titles = array();
|
|
1154
|
foreach ($classifications as $classification) {
|
|
1155
|
if (isset($classification->titleCache)) {
|
|
1156
|
$classification_titles[] = $classification->titleCache;
|
|
1157
|
}
|
|
1158
|
}
|
|
1159
|
if (count($classification_titles) == 0) {
|
|
1160
|
$classification_titles[] = $unclassified_snippet;
|
|
1161
|
}
|
|
1162
|
return '<span class="classifications"><span class="separator"> : </span>' . implode(', ', $classification_titles) . '</span>';
|
|
1163
|
}
|
|
1164
|
|
|
1165
|
/**
|
|
1166
|
* Compose function for the taxonomic children
|
|
1167
|
*
|
|
1168
|
* @param $taxon_uuid
|
|
1169
|
* The uuuid of the taxon to compose the list of taxonomic children for
|
|
1170
|
* @return
|
|
1171
|
* A drupal render array.
|
|
1172
|
*
|
|
1173
|
* @ingroup compose
|
|
1174
|
*/
|
|
1175
|
function compose_taxonomic_children($taxon_uuid){
|
|
1176
|
|
|
1177
|
$render_array = array();
|
|
1178
|
|
|
1179
|
if($taxon_uuid) {
|
|
1180
|
$children = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
|
|
1181
|
get_current_classification_uuid(),
|
|
1182
|
$taxon_uuid
|
|
1183
|
));
|
|
1184
|
if($children){
|
|
1185
|
$taxonomic_children = theme('cdm_taxontree', array('tree' => $children));
|
|
1186
|
$render_array = markup_to_render_array($taxonomic_children);
|
|
1187
|
}
|
|
1188
|
}
|
|
1189
|
return $render_array;
|
|
1190
|
}
|
|
1191
|
|