1 |
b7a20282
|
Andreas Kohlbecker
|
<?php
|
2 |
|
|
|
3 |
|
|
/**
|
4 |
|
|
* @file
|
5 |
|
|
* Functions for dealing with CDM entities from the package model.taxon
|
6 |
|
|
*
|
7 |
|
|
* @copyright
|
8 |
|
|
* (C) 2007-2016 EDIT
|
9 |
|
|
* European Distributed Institute of Taxonomy
|
10 |
|
|
* http://www.e-taxonomy.eu
|
11 |
|
|
*
|
12 |
|
|
* The contents of this module are subject to the Mozilla
|
13 |
|
|
* Public License Version 1.1.
|
14 |
|
|
* @see http://www.mozilla.org/MPL/MPL-1.1.html
|
15 |
|
|
*
|
16 |
|
|
* @author
|
17 |
|
|
* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
|
18 |
|
|
*/
|
19 |
|
|
|
20 |
|
|
/**
|
21 |
|
|
* @defgroup compose Compose functions
|
22 |
|
|
* @{
|
23 |
|
|
* Functions which are composing Drupal render arrays
|
24 |
|
|
*
|
25 |
|
|
* The cdm_dataportal module needs to compose rather complex render arrays from
|
26 |
|
|
* the data returned by the CDM REST service. The compose functions are
|
27 |
|
|
* responsible for creating the render arrays.
|
28 |
|
|
*
|
29 |
|
|
* All these functions are also implementations of the compose_hook()
|
30 |
|
|
* which is used in the proxy_content() function.
|
31 |
|
|
* @}
|
32 |
|
|
*/
|
33 |
|
|
|
34 |
|
|
|
35 |
|
|
/**
|
36 |
|
|
* Returns HTML for misapplied names and invalid designations.
|
37 |
|
|
*
|
38 |
|
|
* Both relation types are currently treated the same!
|
39 |
|
|
*
|
40 |
|
|
* @param taxonRelationships
|
41 |
|
|
* @param focusedTaxon
|
42 |
|
|
*
|
43 |
|
|
* @return string
|
44 |
|
|
* the rendered html
|
45 |
|
|
*/
|
46 |
|
|
function cdm_taxonRelationships($taxonRelationships, $focusedTaxon){
|
47 |
|
|
|
48 |
df6226aa
|
Andreas Kohlbecker
|
static $NULL_AUTHORTEAM = 'NULL_AUTHORTEAM';
|
49 |
|
|
|
50 |
b7a20282
|
Andreas Kohlbecker
|
if (!$taxonRelationships) {
|
51 |
|
|
return null;
|
52 |
|
|
}
|
53 |
|
|
|
54 |
df6226aa
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('taxon_relationships');
|
55 |
|
|
$footnoteListKey = 'taxon_relationships';
|
56 |
b7a20282
|
Andreas Kohlbecker
|
RenderHints::setFootnoteListKey($footnoteListKey);
|
57 |
|
|
|
58 |
|
|
$misapplied = array();
|
59 |
|
|
$joinedAuthorTeams = array();
|
60 |
|
|
|
61 |
|
|
$taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));
|
62 |
|
|
|
63 |
|
|
// Aggregate misapplied names having the same fullname:
|
64 |
763b610c
|
Andreas Kohlbecker
|
// - deduplicate misapplied names, so that the same name it not shown multiple times in case it
|
65 |
|
|
// the duplicates only have different sensu references/author teams (see #5647)
|
66 |
|
|
// - show the author team as sec reference
|
67 |
|
|
// - show the according reference as footnote to this author team
|
68 |
|
|
// - if the sec reference has no author team it should show instead the title cache
|
69 |
|
|
//
|
70 |
|
|
// Example:
|
71 |
|
|
// "Xenoxylum foobar" sensu Grumbach¹; sensu Lem²
|
72 |
|
|
// 1. Novel marsian species, Grumbach, 2022
|
73 |
|
|
// 2. Flora solaris, Lem, 2019
|
74 |
b7a20282
|
Andreas Kohlbecker
|
foreach ($taxonRelationships as $taxonRelation) {
|
75 |
|
|
|
76 |
|
|
if (in_array($taxonRelation->type->uuid, $taxon_relationship_types)) {
|
77 |
|
|
|
78 |
|
|
if ($taxonRelation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxonRelation->type->uuid == UUID_INVALID_DESIGNATION_FOR) {
|
79 |
|
|
|
80 |
df6226aa
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('misapplied_name_for'); // TODO the render path string should in future come from $taxonRelation->type->...
|
81 |
|
|
|
82 |
b7a20282
|
Andreas Kohlbecker
|
$name = $taxonRelation->fromTaxon->name->titleCache;
|
83 |
|
|
|
84 |
763b610c
|
Andreas Kohlbecker
|
$sensu_citation_footnote_str = null;
|
85 |
|
|
|
86 |
b7a20282
|
Andreas Kohlbecker
|
if(isset($taxonRelation->fromTaxon->sec)) {
|
87 |
763b610c
|
Andreas Kohlbecker
|
$sensu_citation_footnote_str = theme('cdm_reference', array('reference' => $taxonRelation->fromTaxon->sec));
|
88 |
b7a20282
|
Andreas Kohlbecker
|
$authorteam = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $taxonRelation->fromTaxon->sec->uuid);
|
89 |
763b610c
|
Andreas Kohlbecker
|
|
90 |
|
|
if(isset($authorteam->titleCache)){
|
91 |
|
|
$authorteam_str = $authorteam->titleCache;
|
92 |
|
|
if($taxonRelation->fromTaxon->sec->titleCache == $authorteam->titleCache){
|
93 |
|
|
// no need for a footnote in case the reference only consists of the author team
|
94 |
|
|
$sensu_citation_footnote_str = '';
|
95 |
|
|
}
|
96 |
|
|
} else {
|
97 |
|
|
$authorteam_str = $sensu_citation_footnote_str;
|
98 |
|
|
// no need for a footnote in case in case it is used as replacement for missing author teams
|
99 |
|
|
$sensu_citation_footnote_str = '';
|
100 |
|
|
}
|
101 |
|
|
} else {
|
102 |
|
|
// taxa not always are have a sec reference (e.g. doubtful taxa)
|
103 |
|
|
// use the NULL_AUTHORTEAM in this case
|
104 |
|
|
$authorteam_str = $NULL_AUTHORTEAM;
|
105 |
b7a20282
|
Andreas Kohlbecker
|
}
|
106 |
|
|
|
107 |
|
|
if (!isset($misapplied[$name])) {
|
108 |
|
|
// Render the first name found as representative for all others.
|
109 |
|
|
$misapplied[$name]['out'] = cdm_related_taxon($taxonRelation->fromTaxon, UUID_MISAPPLIED_NAME_FOR);
|
110 |
|
|
}
|
111 |
|
|
else {
|
112 |
df6226aa
|
Andreas Kohlbecker
|
// We need to add the anchors for all of the other misapplied names not
|
113 |
b7a20282
|
Andreas Kohlbecker
|
// being rendered explicitly.
|
114 |
|
|
$misapplied[$name]['out'] = uuid_anchor($taxonRelation->fromTaxon->uuid, $misapplied[$name]['out']);
|
115 |
|
|
}
|
116 |
|
|
|
117 |
|
|
// Collect all authors for this fullname.
|
118 |
763b610c
|
Andreas Kohlbecker
|
if (isset($authorteam_str) && $authorteam_str != $NULL_AUTHORTEAM) {
|
119 |
|
|
// prepare entry for the footnote key of the sensu citation footnote
|
120 |
|
|
$misapplied[$name]['authorteam'][$authorteam_str] = '';
|
121 |
|
|
// map sensu citation footnote to the authorteam string
|
122 |
|
|
$joinedAuthorTeams[$authorteam_str] = $sensu_citation_footnote_str;
|
123 |
|
|
|
124 |
b7a20282
|
Andreas Kohlbecker
|
}
|
125 |
df6226aa
|
Andreas Kohlbecker
|
|
126 |
b7a20282
|
Andreas Kohlbecker
|
}
|
127 |
|
|
else {
|
128 |
df6226aa
|
Andreas Kohlbecker
|
RenderHints::pushToRenderStack('other_taxon_relationship');
|
129 |
b7a20282
|
Andreas Kohlbecker
|
// All relationsship types but misapplied_name_for
|
130 |
|
|
// invalid_designation_for.
|
131 |
|
|
$taxon_relationships_lines[] = cdm_taxonRelationship($taxonRelation, TRUE, _is_invers_taxonRelationship($taxonRelation, $focusedTaxon));
|
132 |
|
|
}
|
133 |
df6226aa
|
Andreas Kohlbecker
|
|
134 |
|
|
RenderHints::popFromRenderStack();
|
135 |
b7a20282
|
Andreas Kohlbecker
|
}
|
136 |
|
|
}
|
137 |
|
|
|
138 |
|
|
// Sort the joinedAuthorTeams and create footnotes and footnotekeys.
|
139 |
|
|
ksort($joinedAuthorTeams);
|
140 |
6bb442fe
|
Andreas Kohlbecker
|
$author_team_cnt = 0;
|
141 |
763b610c
|
Andreas Kohlbecker
|
foreach ($joinedAuthorTeams as $authorteam_str => $sensu_citation) {
|
142 |
|
|
$footnoteKey = '';
|
143 |
|
|
if(!empty($sensu_citation)) {
|
144 |
|
|
$footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, 'sensu ' . $sensu_citation);
|
145 |
|
|
$footnoteKey = theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey));
|
146 |
|
|
}
|
147 |
|
|
$sensu = '';
|
148 |
|
|
if($authorteam_str != $NULL_AUTHORTEAM){
|
149 |
|
|
$sensu = ++$author_team_cnt == 0 ? '' : 'sensu ' . $authorteam_str;
|
150 |
|
|
}
|
151 |
|
|
$joinedAuthorTeams[$authorteam_str] = '<span class="sensu">' . $sensu . $footnoteKey .'</span>';
|
152 |
b7a20282
|
Andreas Kohlbecker
|
}
|
153 |
|
|
|
154 |
|
|
// ---- Generate output ---- //
|
155 |
|
|
|
156 |
|
|
$out = '<div class="taxon-relationships">';
|
157 |
|
|
if (is_array($misapplied) && count($misapplied) > 0) {
|
158 |
|
|
$out .= '<ul class="misapplied">';
|
159 |
|
|
foreach ($misapplied as $misapplied_name) {
|
160 |
|
|
|
161 |
|
|
$out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name['out'] . ' </span>';
|
162 |
|
|
|
163 |
|
|
if (isset($misapplied_name['authorteam'])) {
|
164 |
|
|
// Fill authors with the renderedFootnoteKey and sorting 'em.
|
165 |
763b610c
|
Andreas Kohlbecker
|
foreach ($misapplied_name['authorteam'] as $authorteam_str => &$renderedFootnoteKey) {
|
166 |
|
|
$renderedFootnoteKey = $joinedAuthorTeams[$authorteam_str];
|
167 |
b7a20282
|
Andreas Kohlbecker
|
}
|
168 |
|
|
ksort($misapplied_name['authorteam']);
|
169 |
|
|
$out .= join('; ', $misapplied_name['authorteam']);
|
170 |
|
|
}
|
171 |
|
|
$out .= '</li>';
|
172 |
|
|
}
|
173 |
|
|
$out .= '</ul>';
|
174 |
|
|
}
|
175 |
|
|
|
176 |
|
|
if (isset($taxon_relationships_lines) && is_array($taxon_relationships_lines) && count($taxon_relationships_lines) > 0) {
|
177 |
|
|
$out .= '<ul class="taxonRelationships">';
|
178 |
|
|
foreach ($taxon_relationships_lines as $taxon_relationship_line) {
|
179 |
|
|
$out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';
|
180 |
|
|
}
|
181 |
|
|
$out .= '</ul>';
|
182 |
|
|
}
|
183 |
|
|
|
184 |
|
|
$footnotes = theme('cdm_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));
|
185 |
|
|
$footnotes .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnoteListKey, 'enclosingTag' => 'li'));
|
186 |
|
|
|
187 |
|
|
// AK: why splitting footnotes at the sensu string ??? this is weired and hacky
|
188 |
|
|
// TODO remove below dead code
|
189 |
|
|
// $tr_footnotes_exploded = explode('sensu', $tr_footnotes);
|
190 |
|
|
// $tr_footnotes_aux = '';
|
191 |
|
|
// foreach ($tr_footnotes_exploded as $element) {
|
192 |
|
|
// $tr_footnotes_aux .= $element;
|
193 |
|
|
// }
|
194 |
|
|
|
195 |
|
|
$out .= '<ul class="footnotes">' . $footnotes . '</ul>';
|
196 |
|
|
|
197 |
|
|
$out .= '</div>';
|
198 |
|
|
|
199 |
|
|
RenderHints::popFromRenderStack();
|
200 |
|
|
return $out;
|
201 |
|
|
}
|
202 |
|
|
|
203 |
|
|
|
204 |
|
|
/**
|
205 |
|
|
* Renders a representation of the given taxon relationship.
|
206 |
|
|
*
|
207 |
|
|
* According name relationships are also being rendered.
|
208 |
|
|
*
|
209 |
763b610c
|
Andreas Kohlbecker
|
* @param $taxonRelationship
|
210 |
b7a20282
|
Andreas Kohlbecker
|
* @param boolean $doLinkTaxon
|
211 |
|
|
* whether to create a link to the related taxon
|
212 |
|
|
* @param boolean $inverse
|
213 |
|
|
* whether the $taxonRelationship should be treaded as invers relation
|
214 |
|
|
*
|
215 |
|
|
* @return void|string
|
216 |
|
|
*/
|
217 |
|
|
function cdm_taxonRelationship($taxonRelationship, $doLinkTaxon = FALSE, $inverse = FALSE) {
|
218 |
|
|
|
219 |
|
|
// Validate object.
|
220 |
|
|
if (!(isset($taxonRelationship->toTaxon) && isset($taxonRelationship->fromTaxon) && isset($taxonRelationship->type))) {
|
221 |
|
|
return null;
|
222 |
|
|
}
|
223 |
|
|
|
224 |
|
|
$taxonRelationType = $taxonRelationship->type;
|
225 |
|
|
|
226 |
|
|
if ($inverse) {
|
227 |
|
|
$toTaxon = $taxonRelationship->fromTaxon;
|
228 |
|
|
$relsign = $taxonRelationType->inverseRepresentation_L10n_abbreviatedLabel;
|
229 |
|
|
$reltype_representation = $taxonRelationType->inverseRepresentation_L10n;
|
230 |
|
|
}
|
231 |
|
|
else {
|
232 |
|
|
$toTaxon = $taxonRelationship->toTaxon;
|
233 |
|
|
$relsign = $taxonRelationType->representation_L10n_abbreviatedLabel;
|
234 |
|
|
$reltype_representation = $taxonRelationType->representation_L10n;
|
235 |
|
|
}
|
236 |
|
|
|
237 |
|
|
return cdm_related_taxon($toTaxon, NULL, $relsign, $reltype_representation, $taxonRelationship->doubtful, $doLinkTaxon);
|
238 |
|
|
}
|
239 |
|
|
|
240 |
|
|
/**
|
241 |
|
|
* Renders a representation of the given taxon relationship.
|
242 |
|
|
*
|
243 |
|
|
* According name relationships are also being rendered.
|
244 |
|
|
*
|
245 |
|
|
* @param $taxon
|
246 |
|
|
* The CDM TaxonBase entity
|
247 |
|
|
* @param $reltype_uuid
|
248 |
|
|
* The UUID of the TaxonRelationshipType
|
249 |
|
|
* @param $relsign
|
250 |
|
|
* Optional. Can be used to override the internal decision strategy on finding a suitable icon for the relationship
|
251 |
|
|
* @param $reltype_representation
|
252 |
|
|
* Optional: Defines the value for the title attribute of the html element enclosing the relsign
|
253 |
|
|
* @param $doubtful
|
254 |
|
|
* TODO
|
255 |
|
|
* @param $doLinkTaxon
|
256 |
|
|
* The taxon will be rendered as clickable link when true.
|
257 |
|
|
*
|
258 |
|
|
* @return string
|
259 |
|
|
* Markup for the taxon relationship.
|
260 |
|
|
*/
|
261 |
|
|
function cdm_related_taxon($taxon, $reltype_uuid = NULL, $relsign = NULL, $reltype_representation = NULL, $doubtful=false, $doLinkTaxon = FALSE) {
|
262 |
|
|
static $relsign_homo = '≡';
|
263 |
|
|
static $relsign_hetero = '=';
|
264 |
|
|
static $relsign_invalid = '–';
|
265 |
|
|
static $nom_status_invalid_type_uuids = array(
|
266 |
|
|
UUID_NOMENCLATURALSTATUS_TYPE_INVALID,
|
267 |
|
|
UUID_NOMENCLATURALSTATUS_TYPE_NUDUM,
|
268 |
|
|
UUID_NOMENCLATURALSTATUS_TYPE_COMBINATIONINVALID,
|
269 |
|
|
UUID_NOMENCLATURALSTATUS_TYPE_PROVISIONAL
|
270 |
|
|
);
|
271 |
|
|
|
272 |
|
|
// 'taxonRelationships';
|
273 |
|
|
$footnoteListKey = NULL;
|
274 |
|
|
|
275 |
|
|
$skip_tags = array();
|
276 |
|
|
|
277 |
|
|
$is_invalid = false;
|
278 |
|
|
|
279 |
|
|
if (!$relsign) {
|
280 |
|
|
|
281 |
|
|
switch ($reltype_uuid) {
|
282 |
|
|
case UUID_HETEROTYPIC_SYNONYM_OF:
|
283 |
|
|
case UUID_SYNONYM_OF:
|
284 |
|
|
$relsign = $relsign_hetero;
|
285 |
|
|
break;
|
286 |
|
|
|
287 |
|
|
case UUID_HOMOTYPIC_SYNONYM_OF:
|
288 |
|
|
$relsign = $relsign_homo;
|
289 |
|
|
break;
|
290 |
|
|
|
291 |
|
|
case UUID_MISAPPLIED_NAME_FOR:
|
292 |
|
|
case UUID_INVALID_DESIGNATION_FOR:
|
293 |
|
|
$skip_tags[] = 'authors';
|
294 |
|
|
$is_invalid = true;
|
295 |
|
|
$relsign = $relsign_invalid;
|
296 |
|
|
|
297 |
|
|
break;
|
298 |
|
|
|
299 |
|
|
default:
|
300 |
|
|
$relsign = $relsign_invalid;
|
301 |
|
|
}
|
302 |
|
|
|
303 |
|
|
}
|
304 |
|
|
|
305 |
|
|
if($doubtful) {
|
306 |
|
|
$relsign = '?' . $relsign;
|
307 |
|
|
}
|
308 |
|
|
|
309 |
|
|
/*
|
310 |
|
|
Names with status invalid or nudum are to be displayed with the
|
311 |
|
|
$relsign_invalid, these names appear at the end of all names in their
|
312 |
|
|
homotypic group (ordered correctly by the java cdm_lib).
|
313 |
|
|
*/
|
314 |
|
|
if (isset($taxon->name->status) && is_array($taxon->name->status)) {
|
315 |
|
|
foreach ($taxon->name->status as $status) {
|
316 |
|
|
if (in_array($status->type->uuid , $nom_status_invalid_type_uuids)) {
|
317 |
|
|
$relsign = $relsign_invalid;
|
318 |
|
|
break;
|
319 |
|
|
}
|
320 |
|
|
}
|
321 |
|
|
}
|
322 |
|
|
|
323 |
|
|
// Now rendering starts ..
|
324 |
|
|
RenderHints::pushToRenderStack('related_taxon');
|
325 |
|
|
|
326 |
|
|
if (isset($taxon->name->nomenclaturalReference)) {
|
327 |
|
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
|
328 |
|
|
}
|
329 |
|
|
$taxonUri = '';
|
330 |
|
|
if ($doLinkTaxon) {
|
331 |
|
|
$taxonUri = url(path_to_taxon($taxon->uuid, "synonymy"));
|
332 |
|
|
}
|
333 |
|
|
// Printing the taxonName and the handling the special case of annotations.
|
334 |
|
|
if (!isset($referenceUri)) {
|
335 |
|
|
$referenceUri = FALSE;
|
336 |
|
|
}
|
337 |
|
|
$out_taxon_part = render_taxon_or_name($taxon, $taxonUri, $referenceUri, TRUE, FALSE, $skip_tags, $is_invalid);
|
338 |
|
|
$taxon_footnotes = theme('cdm_annotations_as_footnotekeys',
|
339 |
|
|
array('cdmBase_list' => array(
|
340 |
|
|
$taxon->name,
|
341 |
|
|
$taxon,
|
342 |
|
|
),
|
343 |
|
|
'footnote_list_key' => $footnoteListKey)
|
344 |
|
|
);
|
345 |
|
|
|
346 |
|
|
$homonyms = cdm_name_relationships_of($taxon);
|
347 |
|
|
|
348 |
|
|
$out = '<span class="relation_sign" title="' . $reltype_representation . '">' . $relsign . '</span>'
|
349 |
|
|
. $out_taxon_part . $taxon_footnotes . ' ' . $homonyms;
|
350 |
|
|
|
351 |
|
|
$out = uuid_anchor($taxon->uuid, $out);
|
352 |
|
|
|
353 |
|
|
RenderHints::popFromRenderStack();
|
354 |
|
|
|
355 |
|
|
return $out;
|
356 |
|
|
}
|
357 |
|
|
|
358 |
87b304a7
|
Andreas Kohlbecker
|
|
359 |
|
|
/**
|
360 |
|
|
* Creates markup for a taxon which is the accepted of another one
|
361 |
|
|
*
|
362 |
|
|
* @param $accepted_for_uuid
|
363 |
|
|
* The uuid of the accepted taxon
|
364 |
|
|
*/
|
365 |
|
|
function cdm_accepted_for($accepted_for_uuid) {
|
366 |
|
|
|
367 |
|
|
if(!is_uuid($accepted_for_uuid)){
|
368 |
|
|
return '';
|
369 |
|
|
}
|
370 |
|
|
|
371 |
|
|
RenderHints::pushToRenderStack('acceptedFor');
|
372 |
|
|
$out = '';
|
373 |
|
|
|
374 |
|
|
$synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $accepted_for_uuid);
|
375 |
|
|
if ($synonym) {
|
376 |
|
|
$out .= '<span class="acceptedFor">';
|
377 |
|
|
$out .= t('is accepted for ');
|
378 |
|
|
if (isset($synonym->name->nomenclaturalReference)) {
|
379 |
|
|
$referenceUri = url(path_to_reference($synonym->name->nomenclaturalReference->uuid));
|
380 |
|
|
}
|
381 |
|
|
$out .= render_taxon_or_name($synonym->name, NULL, $referenceUri);
|
382 |
|
|
$out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $synonym));
|
383 |
|
|
$out .= '</span>';
|
384 |
|
|
}
|
385 |
|
|
RenderHints::popFromRenderStack();
|
386 |
|
|
return $out;
|
387 |
|
|
}
|
388 |
|
|
|
389 |
|
|
/**
|
390 |
|
|
* Compose function for a list of taxa.
|
391 |
|
|
*
|
392 |
bc400a17
|
Andreas Kohlbecker
|
* This function is for example used to display search results or the taxa for a taxon name in the name page.
|
393 |
87b304a7
|
Andreas Kohlbecker
|
*
|
394 |
|
|
* @param $taxon_list array
|
395 |
|
|
* The list of CDM Taxon entities. e.g. The records array as contained in a pager object.
|
396 |
|
|
* @param $freetext_search_results array
|
397 |
|
|
* @param $show_classification boolean
|
398 |
|
|
*
|
399 |
|
|
* @ingroup compose
|
400 |
|
|
*
|
401 |
|
|
*/
|
402 |
|
|
function compose_list_of_taxa($taxon_list, $freetext_search_results = array(), $show_classification = false) {
|
403 |
|
|
|
404 |
|
|
$unclassified_snippet = '<span class="unclassified">' . t('unclassified') . '</span>';
|
405 |
|
|
|
406 |
|
|
RenderHints::pushToRenderStack('list_of_taxa');
|
407 |
|
|
|
408 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);
|
409 |
|
|
|
410 |
|
|
$showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];
|
411 |
|
|
$showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];
|
412 |
|
|
$searched_in_classification = cdm_dataportal_searched_in_classification();
|
413 |
|
|
$searched_in_classification_uuid = null;
|
414 |
|
|
if(isset($searched_in_classification->uuid)){
|
415 |
|
|
$searched_in_classification_uuid = $searched_in_classification->uuid;
|
416 |
|
|
}
|
417 |
|
|
|
418 |
|
|
// .. Well, for sure not as performant as before, but better than nothing.
|
419 |
|
|
$synonym_uuids = array();
|
420 |
|
|
$misappied_uuids = array();
|
421 |
|
|
foreach ($taxon_list as $taxon) {
|
422 |
|
|
if ($taxon->class == "Synonym") {
|
423 |
|
|
if (!array_key_exists($taxon->uuid, $synonym_uuids)) {
|
424 |
|
|
$synonym_uuids[$taxon->uuid] = $taxon->uuid;
|
425 |
|
|
}
|
426 |
|
|
}
|
427 |
|
|
elseif (!_cdm_dataportal_acceptedByCurrentView($taxon)) {
|
428 |
|
|
// Assuming that it is a misappied name, will be further examined below.
|
429 |
|
|
$misappied_uuids[$taxon->uuid] = $taxon->uuid;
|
430 |
|
|
}
|
431 |
|
|
}
|
432 |
|
|
|
433 |
|
|
// Batch service not jet implemented:
|
434 |
|
|
// $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED,
|
435 |
|
|
// join(',', $synonym_uuids));
|
436 |
|
|
// thus ...
|
437 |
|
|
$table_of_accepted = array();
|
438 |
|
|
|
439 |
|
|
foreach ($synonym_uuids as $relatedUuid) {
|
440 |
|
|
$table_of_accepted[$relatedUuid] = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array(
|
441 |
|
|
$relatedUuid,
|
442 |
|
|
$searched_in_classification_uuid,
|
443 |
|
|
));
|
444 |
|
|
}
|
445 |
|
|
|
446 |
|
|
foreach ($misappied_uuids as $relatedUuid) {
|
447 |
|
|
$taxonRelations = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS, array(
|
448 |
|
|
$relatedUuid,
|
449 |
|
|
));
|
450 |
|
|
foreach ($taxonRelations as $relation) {
|
451 |
|
|
if ($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR && _cdm_dataportal_acceptedByCurrentView($relation->toTaxon)) {
|
452 |
|
|
$table_of_accepted[$relatedUuid][] = $relation->toTaxon;
|
453 |
|
|
}
|
454 |
|
|
}
|
455 |
|
|
}
|
456 |
|
|
|
457 |
|
|
$out = '<ul class="cdm_names" style="background-image: none;">';
|
458 |
|
|
$itemCnt = -1;
|
459 |
|
|
foreach ($taxon_list as $taxon) {
|
460 |
|
|
$itemCnt++;
|
461 |
|
|
if (isset($table_of_accepted[$taxon->uuid])) {
|
462 |
|
|
// Its a synonym or misapplied name.
|
463 |
|
|
$is_synonym = isset($synonym_uuids[$taxon->uuid]); //TODO better use the $taxon->class attribute?
|
464 |
|
|
$taxon_type = $is_synonym ? "Synonym" : "misapplied-name";
|
465 |
|
|
|
466 |
|
|
$acceptedTaxa = $table_of_accepted[$taxon->uuid];
|
467 |
|
|
|
468 |
|
|
if (count($acceptedTaxa) == 1) {
|
469 |
|
|
|
470 |
|
|
$acceptedTaxon = $acceptedTaxa[0];
|
471 |
9bbe3bcd
|
Andreas Kohlbecker
|
$taxonUri = uri_to_synonym($taxon->uuid, $acceptedTaxon->uuid);
|
472 |
87b304a7
|
Andreas Kohlbecker
|
$referenceUri = '';
|
473 |
|
|
if (isset($acceptedTaxon->name->nomenclaturalReference)) {
|
474 |
|
|
$referenceUri = url(path_to_reference($acceptedTaxon->name->nomenclaturalReference->uuid));
|
475 |
|
|
}
|
476 |
|
|
$taxon_or_name = $is_synonym ? $taxon->name : $taxon;
|
477 |
|
|
// $taxon_or_name this is a trick to suppress the sec reference for sysnonyms
|
478 |
|
|
// supplying the name will cause render_taxon_or_name() to not show the sec reference
|
479 |
|
|
$out .= '<li class="' . $taxon_type . '">' . render_taxon_or_name($taxon_or_name, $taxonUri, $referenceUri);
|
480 |
|
|
if ($show_classification) {
|
481 |
|
|
$classifications = get_classifications_for_taxon($taxon);
|
482 |
|
|
$classification_titles = array();
|
483 |
|
|
foreach ($classifications as $classification) {
|
484 |
|
|
if (isset($classification->titleCache)) {
|
485 |
|
|
$classification_titles[] = $classification->titleCache;
|
486 |
|
|
}
|
487 |
|
|
}
|
488 |
|
|
if(count($classification_titles) == 0){
|
489 |
|
|
$classification_titles[] = $unclassified_snippet;
|
490 |
|
|
}
|
491 |
|
|
$out .= ' : <span class="classifications">' . implode(', ', $classification_titles) . '</span>';
|
492 |
|
|
}
|
493 |
|
|
$out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));
|
494 |
|
|
if ($showMedia_synonyms) {
|
495 |
|
|
$out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $acceptedTaxon));
|
496 |
|
|
}
|
497 |
|
|
}
|
498 |
|
|
else {
|
499 |
|
|
|
500 |
|
|
// TODO avoid using Ajax in the cdm_dynabox .... why?
|
501 |
|
|
// TODO add media.
|
502 |
|
|
$out .= cdm_dynabox(
|
503 |
|
|
$taxon->uuid,
|
504 |
|
|
render_taxon_or_name($taxon->name, NULL, NULL, FALSE),
|
505 |
|
|
cdm_compose_url(CDM_WS_PORTAL_TAXON_ACCEPTED,
|
506 |
|
|
array(
|
507 |
|
|
$taxon->uuid,
|
508 |
|
|
$searched_in_classification_uuid
|
509 |
|
|
)
|
510 |
|
|
),
|
511 |
|
|
'cdm_list_of_taxa',
|
512 |
|
|
'show accepted taxa of this ' . $taxon_type,
|
513 |
|
|
array('li', 'ul'),
|
514 |
|
|
array('class' => array($taxon_type))
|
515 |
|
|
);
|
516 |
|
|
}
|
517 |
|
|
}
|
518 |
|
|
else {
|
519 |
|
|
// Its a Taxon.
|
520 |
|
|
$taxonUri = url(path_to_taxon($taxon->uuid));
|
521 |
|
|
$referenceUri = '';
|
522 |
|
|
if (isset($taxon->name->nomenclaturalReference)) {
|
523 |
|
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
|
524 |
|
|
}
|
525 |
|
|
$out .= '<li class="Taxon">' . render_taxon_or_name($taxon, $taxonUri, $referenceUri);
|
526 |
|
|
if ($show_classification) {
|
527 |
|
|
$classifications = get_classifications_for_taxon($taxon);
|
528 |
|
|
$classification_titles = array();
|
529 |
|
|
foreach ($classifications as $classification) {
|
530 |
|
|
if (isset($classification->titleCache)) {
|
531 |
|
|
$classification_titles[] = $classification->titleCache;
|
532 |
|
|
}
|
533 |
|
|
}
|
534 |
|
|
if(count($classification_titles) == 0){
|
535 |
|
|
$classification_titles[] = $unclassified_snippet;
|
536 |
|
|
}
|
537 |
|
|
$out .= ' : <span class="classifications">' . implode(', ', $classification_titles) . '</span>';
|
538 |
|
|
}
|
539 |
|
|
$out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));
|
540 |
|
|
|
541 |
|
|
if ($showMedia_taxa) {
|
542 |
|
|
$out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));
|
543 |
|
|
}
|
544 |
|
|
}
|
545 |
|
|
|
546 |
|
|
/*
|
547 |
|
|
* the score field will be empty in case of MultiTermQueries like
|
548 |
|
|
* WildcardQueries, since these are constant score by default
|
549 |
|
|
* since Lucene 2.9
|
550 |
|
|
*/
|
551 |
|
|
if(isset($freetext_search_results[$itemCnt]) && $freetext_search_results[$itemCnt]->score && $freetext_search_results[$itemCnt]->maxScore){
|
552 |
|
|
$percentage = ( $freetext_search_results[$itemCnt]->score / $freetext_search_results[$itemCnt]->maxScore ) * 100;
|
553 |
|
|
$out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';
|
554 |
|
|
$out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';
|
555 |
|
|
}
|
556 |
|
|
|
557 |
|
|
// Render highlighted fragments, these are made available by free text
|
558 |
|
|
// searches.
|
559 |
|
|
if (isset($freetext_search_results[$itemCnt]->fieldHighlightMap)) {
|
560 |
|
|
$field_fragments = (array) $freetext_search_results[$itemCnt]->fieldHighlightMap;
|
561 |
|
|
if (count($field_fragments) > 0) {
|
562 |
|
|
$fragments_out = '';
|
563 |
|
|
foreach ($field_fragments as $fieldName => $fragments) {
|
564 |
|
|
$fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';
|
565 |
|
|
}
|
566 |
|
|
$out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';
|
567 |
|
|
}
|
568 |
|
|
}
|
569 |
|
|
|
570 |
|
|
$out .= '</li>';
|
571 |
|
|
}
|
572 |
|
|
|
573 |
|
|
$out .= '</ul>';
|
574 |
|
|
RenderHints::popFromRenderStack();
|
575 |
|
|
|
576 |
|
|
return markup_to_render_array($out); // TODO create render array of all list items in function
|
577 |
|
|
}
|
578 |
|
|
|
579 |
bc400a17
|
Andreas Kohlbecker
|
|
580 |
|
|
function compose_taxonomic_children($taxon_uuid){
|
581 |
|
|
|
582 |
|
|
$render_array = array();
|
583 |
f58a08fa
|
Andreas Kohlbecker
|
|
584 |
|
|
if($taxon_uuid) {
|
585 |
|
|
$children = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
|
586 |
|
|
get_current_classification_uuid(),
|
587 |
|
|
$taxon_uuid
|
588 |
|
|
));
|
589 |
|
|
if($children){
|
590 |
|
|
$taxonomic_children = theme('cdm_taxontree', array('tree' => $children));
|
591 |
|
|
$render_array = markup_to_render_array($taxonomic_children);
|
592 |
|
|
}
|
593 |
bc400a17
|
Andreas Kohlbecker
|
}
|
594 |
|
|
return $render_array;
|
595 |
|
|
}
|