35 |
35 |
$detail_html .= "<strong>$specimenPageLink</strong><br>";
|
36 |
36 |
}
|
37 |
37 |
|
38 |
|
if($is_specimen_page) {
|
39 |
|
if($specimen->citation){
|
40 |
|
$detail_html .= "<br>".create_label("Citation") . $specimen->citation . "<br>";
|
|
38 |
if ($is_specimen_page) {
|
|
39 |
if ($specimen->citation) {
|
|
40 |
$detail_html .= "<br>" . create_label("Citation") . $specimen->citation . "<br>";
|
41 |
41 |
}
|
42 |
42 |
}
|
43 |
|
if($specimen->preferredStableUri){
|
44 |
|
$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
|
|
43 |
if ($specimen->preferredStableUri) {
|
|
44 |
$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
|
45 |
45 |
$detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
|
46 |
46 |
}
|
47 |
|
if($is_specimen_page){
|
|
47 |
if ($is_specimen_page) {
|
48 |
48 |
// associated taxa
|
49 |
|
if($specimen->associatedTaxa){
|
|
49 |
if ($specimen->associatedTaxa) {
|
50 |
50 |
$detail_html .= "<br>";
|
51 |
|
$detail_html .= create_label("Associated with");
|
52 |
|
if(sizeof($specimen->associatedTaxa)>1){
|
|
51 |
$detail_html .= create_label("Associated with");
|
|
52 |
if (sizeof($specimen->associatedTaxa) > 1) {
|
|
53 |
$detail_html .= "<br>";
|
|
54 |
}
|
|
55 |
foreach ($specimen->associatedTaxa as $associatedTaxon) {
|
|
56 |
$detail_html .= l($associatedTaxon->second, path_to_taxon($associatedTaxon->first, "specimens"));//$associatedTaxon->second."<br>";
|
|
57 |
}
|
53 |
58 |
$detail_html .= "<br>";
|
54 |
|
}
|
55 |
|
foreach($specimen->associatedTaxa as $associatedTaxon){
|
56 |
|
$detail_html .= l($associatedTaxon->second, path_to_taxon($associatedTaxon->first, "specimens"));//$associatedTaxon->second."<br>";
|
57 |
|
}
|
58 |
|
$detail_html .= "<br>";
|
59 |
59 |
}
|
60 |
60 |
}
|
61 |
|
// - type information
|
|
61 |
// - type information
|
62 |
62 |
$types = "";
|
63 |
63 |
if (isset($specimen->types)) {
|
64 |
64 |
//typed taxa
|
65 |
65 |
foreach ($specimen->types as $typeStatus => $typedTaxa) {
|
|
66 |
/* Updated upstream
|
66 |
67 |
if($specimen->types){
|
67 |
68 |
$detail_html .= "<i>".$typeStatus."</i> of ";
|
68 |
69 |
foreach($typedTaxa as $typedTaxon){
|
69 |
70 |
$detail_html .= $typedTaxon." ";
|
70 |
71 |
}
|
71 |
72 |
$detail_html .= "<br>";
|
|
73 |
*/
|
|
74 |
if ($is_specimen_page) {
|
|
75 |
if ($specimen->types) {
|
|
76 |
$detail_html .= "<i>" . $typeStatus . "</i>: ";
|
|
77 |
foreach ($typedTaxa as $typedTaxon) {
|
|
78 |
$detail_html .= $typedTaxon . " ";
|
|
79 |
}
|
|
80 |
$detail_html .= "<br>";
|
|
81 |
}
|
|
82 |
} else {
|
|
83 |
$types .= $typeStatus . " ";
|
|
84 |
|
72 |
85 |
}
|
73 |
86 |
}
|
74 |
87 |
}
|
... | ... | |
94 |
107 |
if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {
|
95 |
108 |
$molecularData .= create_html_link($contigFile->contigLink, true) . " ";
|
96 |
109 |
}
|
97 |
|
}
|
98 |
|
else {
|
|
110 |
} else {
|
99 |
111 |
$molecularData .= "no contig ";
|
100 |
112 |
}
|
101 |
113 |
//primer links
|
102 |
|
if(isset($contigFile->primerLinks)) {
|
|
114 |
if (isset($contigFile->primerLinks)) {
|
103 |
115 |
$molecularData .= create_html_links($contigFile->primerLinks, true);
|
104 |
116 |
}
|
105 |
117 |
}
|
... | ... | |
114 |
126 |
$detailImages = create_html_links($derivateDataDTO->detailImages, true);
|
115 |
127 |
|
116 |
128 |
if ($types) {
|
117 |
|
$detail_html .= $is_specimen_page?"<br>":"";
|
|
129 |
$detail_html .= $is_specimen_page ? "<br>" : "";
|
118 |
130 |
$detail_html .= create_label("Type(s)") . $types . "<br>";
|
119 |
131 |
}
|
120 |
132 |
if ($specimenScans and !$is_specimen_page) {
|
121 |
133 |
$detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
|
122 |
134 |
}
|
123 |
135 |
//specimen scan image gallery
|
124 |
|
if($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
|
|
136 |
if ($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
|
125 |
137 |
$detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
|
126 |
138 |
}
|
127 |
139 |
|
128 |
140 |
if ($molecularData) {
|
129 |
|
$detail_html .= $is_specimen_page?"<br>":"";
|
|
141 |
$detail_html .= $is_specimen_page ? "<br>" : "";
|
130 |
142 |
$detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
|
131 |
143 |
}
|
132 |
144 |
|
... | ... | |
135 |
147 |
}
|
136 |
148 |
|
137 |
149 |
//detail image gallery
|
138 |
|
if($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)){
|
|
150 |
if ($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {
|
139 |
151 |
$detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
|
140 |
152 |
}
|
141 |
153 |
|
142 |
154 |
//character data
|
143 |
155 |
if ($specimen->characterData) {
|
144 |
|
$detail_html .= $is_specimen_page?"<br>":"";
|
|
156 |
$detail_html .= $is_specimen_page ? "<br>" : "";
|
145 |
157 |
$detail_html .= create_label("Character Data");
|
146 |
|
if($is_specimen_page) {
|
|
158 |
if ($is_specimen_page) {
|
147 |
159 |
$detail_html .= "<br>";
|
148 |
160 |
foreach ($specimen->characterData as $characterStatePair) {
|
149 |
161 |
$detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;
|
150 |
162 |
$detail_html .= "<br>";
|
151 |
163 |
}
|
152 |
|
}
|
153 |
|
else{
|
154 |
|
$detail_html .= l("detail page", $pathToSpecimen,array('attributes' => array('target'=>'_blank')));
|
|
164 |
} else {
|
|
165 |
$detail_html .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
155 |
166 |
$detail_html .= "<br>";
|
156 |
167 |
}
|
157 |
168 |
}
|
158 |
169 |
return $detail_html;
|
159 |
170 |
}
|
160 |
171 |
|
161 |
|
function addImageGallery($galleryName, $imageUuids){
|
|
172 |
function addImageGallery($galleryName, $imageUuids)
|
|
173 |
{
|
162 |
174 |
$images = array();
|
163 |
175 |
foreach ($imageUuids as $uuid) {
|
164 |
176 |
$images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid);
|
... | ... | |
172 |
184 |
'rights',
|
173 |
185 |
);
|
174 |
186 |
$alternativeMediaUris = array();
|
175 |
|
foreach($images as $image){
|
176 |
|
$mediaUri = getMediaUri($image);
|
177 |
|
if($mediaUri){
|
178 |
|
$alternativeMediaUris[] = $mediaUri;
|
179 |
|
}
|
180 |
|
else{
|
181 |
|
$alternativeMediaUris[] = path_to_media($image->uuid);
|
182 |
|
}
|
|
187 |
foreach ($images as $image) {
|
|
188 |
$mediaUri = getMediaUri($image);
|
|
189 |
if ($mediaUri) {
|
|
190 |
$alternativeMediaUris[] = $mediaUri;
|
|
191 |
} else {
|
|
192 |
$alternativeMediaUris[] = path_to_media($image->uuid);
|
|
193 |
}
|
183 |
194 |
}
|
184 |
195 |
|
185 |
196 |
$gallery_html = compose_cdm_media_gallerie(array(
|
... | ... | |
194 |
205 |
'galleryLinkUri' => NULL,
|
195 |
206 |
));
|
196 |
207 |
}
|
197 |
|
return "<br>".create_label($galleryName)."<br>".$gallery_html;
|
|
208 |
return "<br>" . create_label($galleryName) . "<br>" . $gallery_html;
|
198 |
209 |
}
|
199 |
210 |
|
200 |
|
function getMediaUri($media){
|
201 |
|
if(isset($media->representations) && sizeof($media->representations)==1
|
202 |
|
&& isset($media->representations[0]->parts) &&
|
203 |
|
sizeof($media->representations[0]->parts)==1) {
|
204 |
|
return $media->representations[0]->parts[0]->uri;
|
205 |
|
}
|
206 |
|
return null;
|
|
211 |
function getMediaUri($media)
|
|
212 |
{
|
|
213 |
if (isset($media->representations) && sizeof($media->representations) == 1
|
|
214 |
&& isset($media->representations[0]->parts) &&
|
|
215 |
sizeof($media->representations[0]->parts) == 1) {
|
|
216 |
return $media->representations[0]->parts[0]->uri;
|
|
217 |
}
|
|
218 |
return null;
|
207 |
219 |
}
|
208 |
220 |
|
209 |
221 |
|
... | ... | |
213 |
225 |
*/
|
214 |
226 |
function create_label($label)
|
215 |
227 |
{
|
216 |
|
return "<span class='specimen_table_label'>".$label.": </span>";
|
|
228 |
return "<span class='specimen_table_label'>" . $label . ": </span>";
|
217 |
229 |
}
|
218 |
230 |
|
219 |
231 |
/**
|
... | ... | |
234 |
246 |
*
|
235 |
247 |
* @ingroup compose
|
236 |
248 |
*/
|
|
249 |
/*<<<<<<< Updated upstream
|
237 |
250 |
function compose_cdm_specimen_or_observation($specimenOrObservation, &$derivatives = null) {
|
238 |
251 |
|
239 |
252 |
$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
|
... | ... | |
264 |
277 |
|
265 |
278 |
$descriptions = null;
|
266 |
279 |
$derivedFrom = null;
|
|
280 |
=======*/
|
|
281 |
function compose_cdm_specimenOrObservation($specimenOrObservation, &$derivatives = null)
|
|
282 |
{
|
267 |
283 |
|
268 |
|
if (is_object($specimenOrObservation)) {
|
|
284 |
//>>>>>>> Stashed changes
|
|
285 |
$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
|
|
286 |
if (!isset($exclude_occurrence_fields)) {
|
|
287 |
$exclude_occurrence_fields = array(
|
|
288 |
// 'derivationEvents',
|
|
289 |
'titleCache',
|
|
290 |
'protectedTitleCache',
|
|
291 |
'derivedUnitMedia',
|
|
292 |
'created',
|
|
293 |
'publish',
|
|
294 |
'updated',
|
|
295 |
'class',
|
|
296 |
'uuid',
|
|
297 |
''
|
|
298 |
);
|
|
299 |
}
|
269 |
300 |
|
270 |
|
// request again for deeper initialization
|
271 |
|
$specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
|
272 |
301 |
|
|
302 |
// only show uuid it the user is logged in
|
|
303 |
if (user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE) {
|
|
304 |
unset($exclude_occurrence_fields[$a_idx]);
|
|
305 |
}
|
273 |
306 |
|
274 |
|
$type_label = $specimenOrObservation->class;
|
275 |
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);
|
|
307 |
if (!isset($derivatives)) {
|
|
308 |
$derivatives = array();
|
|
309 |
}
|
276 |
310 |
|
277 |
|
// collect typeStatus as label
|
278 |
|
if (isset($specimenOrObservation->specimenTypeDesignations)) {
|
279 |
|
$type_status = array();
|
280 |
|
foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {
|
281 |
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
282 |
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
|
311 |
$descriptions = null;
|
|
312 |
$derivedFrom = null;
|
|
313 |
$derivates = null;
|
|
314 |
|
|
315 |
if (is_object($specimenOrObservation)) {
|
|
316 |
|
|
317 |
// request again for deeper initialization
|
|
318 |
// $specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
|
|
319 |
|
|
320 |
|
|
321 |
$type_label = $specimenOrObservation->recordBase;
|
|
322 |
RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);
|
|
323 |
/*
|
|
324 |
* $label_html = cdm_dynabox(
|
|
325 |
$specimenOrObservation->uuid,
|
|
326 |
$type_label . $specimenOrObservation->titleCache,
|
|
327 |
$derived_unit_ws_request, //cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
|
|
328 |
'cdm_specimenOrObservation',
|
|
329 |
'Click for details',
|
|
330 |
array('div', 'div'),
|
|
331 |
array(),
|
|
332 |
null, // $content_element_selector
|
|
333 |
'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback
|
|
334 |
'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback
|
|
335 |
);
|
|
336 |
|
|
337 |
*/
|
|
338 |
// collect typeStatus as label
|
|
339 |
if (isset($specimenOrObservation->specimenTypeDesignations)) {
|
|
340 |
$type_status = array();
|
|
341 |
foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {
|
|
342 |
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
|
343 |
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
|
344 |
}
|
|
345 |
}
|
|
346 |
if (count($type_status) > 0) {
|
|
347 |
$type_label = implode(', ', $type_status);
|
|
348 |
}
|
283 |
349 |
}
|
284 |
|
}
|
285 |
|
if (count($type_status) > 0) {
|
286 |
|
$type_label = implode(', ', $type_status);
|
287 |
|
}
|
288 |
|
}
|
289 |
350 |
|
290 |
|
$title = $type_label . ': ' . $specimenOrObservation->titleCache;
|
|
351 |
$title = $type_label . ': ' . $specimenOrObservation->titleCache;
|
|
352 |
|
|
353 |
$groups = array();
|
|
354 |
// --- add initialized fields
|
|
355 |
foreach (get_object_vars($specimenOrObservation) as $field => $value) {
|
|
356 |
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
|
357 |
switch ($field) {
|
|
358 |
// case 'recordBasis':
|
|
359 |
// if ($value != '' /* FieldUnit' */) {
|
|
360 |
// @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
|
361 |
// }
|
|
362 |
// break;
|
|
363 |
/* ---- java.lang.Object --- */
|
|
364 |
case 'class':
|
|
365 |
if ($value != '' /* FieldUnit' */) {
|
|
366 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
|
367 |
}
|
|
368 |
break;
|
291 |
369 |
|
292 |
|
$groups = array();
|
293 |
|
// --- add initialized fields
|
294 |
|
foreach (get_object_vars($specimenOrObservation) as $field => $value) {
|
295 |
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
296 |
|
switch ($field) {
|
297 |
|
|
298 |
|
/* ---- java.lang.Object --- */
|
299 |
|
case 'class':
|
300 |
|
if ($value != '' /* FieldUnit' */) {
|
301 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
302 |
|
}
|
303 |
|
break;
|
|
370 |
case 'markers':
|
|
371 |
$dd_elements = array();
|
|
372 |
foreach ($value as $marker) {
|
|
373 |
$dd_elements[] = compose_cdm_marker($marker);
|
|
374 |
}
|
|
375 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
376 |
break;
|
304 |
377 |
|
305 |
|
case 'markers':
|
306 |
|
$dd_elements = array();
|
307 |
|
foreach ($value as $marker) {
|
308 |
|
$dd_elements[] = compose_cdm_marker($marker);
|
309 |
|
}
|
310 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
311 |
|
break;
|
312 |
378 |
|
|
379 |
case 'annotations':
|
|
380 |
$dd_elements = array();
|
|
381 |
foreach ($value as $annotation) {
|
|
382 |
// TODO respect annotation type filter settings
|
|
383 |
$dd_elements[] = $annotation->text;
|
|
384 |
}
|
|
385 |
@_description_list_group_add($groups, t('Notes'), $dd_elements);
|
|
386 |
break;
|
|
387 |
|
|
388 |
/* ---- SpecimenOrObservationBase --- */
|
|
389 |
case 'sex':
|
|
390 |
case 'lifeStage':
|
|
391 |
case 'kindOfUnit':
|
|
392 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n, NULL, 1);
|
|
393 |
break;
|
|
394 |
|
|
395 |
case 'definition':
|
|
396 |
// TODO
|
|
397 |
break;
|
|
398 |
|
|
399 |
case 'preferredStableUri':
|
|
400 |
|
|
401 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
|
402 |
break;
|
|
403 |
|
|
404 |
case 'specimenTypeDesignations':
|
|
405 |
@_description_list_group_add(
|
|
406 |
$groups,
|
|
407 |
cdm_occurrence_field_name_label($field),
|
|
408 |
array(
|
|
409 |
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
|
410 |
)
|
|
411 |
);
|
|
412 |
break;
|
|
413 |
|
|
414 |
case 'determinations':
|
|
415 |
$dd_elements = array();
|
|
416 |
$glue = ', ';
|
|
417 |
|
|
418 |
foreach ($value as $determinationEvent) {
|
|
419 |
$timeperiod_string = NULL;
|
|
420 |
if (isset($determinationEvent->timeperiod)) {
|
|
421 |
$timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
|
|
422 |
}
|
|
423 |
$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
|
|
424 |
// check key exists
|
|
425 |
while (array_key_exists($weight, $dd_elements)) {
|
|
426 |
$weight .= '0';
|
|
427 |
}
|
313 |
428 |
|
314 |
|
case 'annotations':
|
315 |
|
$dd_elements = array();
|
316 |
|
foreach ($value as $annotation) {
|
317 |
|
// TODO respect annotation type filter settings
|
318 |
|
$dd_elements[] = $annotation->text;
|
319 |
|
}
|
320 |
|
@_description_list_group_add($groups, t('Notes'), $dd_elements);
|
321 |
|
break;
|
322 |
|
|
323 |
|
/* ---- SpecimenOrObservationBase --- */
|
324 |
|
case 'sex':
|
325 |
|
case 'lifeStage':
|
326 |
|
case 'kindOfUnit':
|
327 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
|
328 |
|
break;
|
329 |
|
|
330 |
|
case 'definition':
|
331 |
|
// TODO
|
332 |
|
break;
|
333 |
|
|
334 |
|
case 'preferredStableUri':
|
335 |
|
|
336 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
337 |
|
break;
|
338 |
|
|
339 |
|
case 'specimenTypeDesignations':
|
340 |
|
@_description_list_group_add(
|
341 |
|
$groups,
|
342 |
|
cdm_occurrence_field_name_label($field),
|
343 |
|
array(
|
344 |
|
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
345 |
|
)
|
346 |
|
);
|
347 |
|
break;
|
348 |
|
|
349 |
|
case 'determinations':
|
350 |
|
$dd_elements = array();
|
351 |
|
$glue = ', ';
|
352 |
|
|
353 |
|
foreach ($value as $determinationEvent) {
|
354 |
|
$timeperiod_string = NULL;
|
355 |
|
if (isset($determinationEvent->timeperiod)) {
|
356 |
|
$timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
|
357 |
|
}
|
358 |
|
$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
|
359 |
|
// check key exists
|
360 |
|
while (array_key_exists($weight, $dd_elements)) {
|
361 |
|
$weight .= '0';
|
362 |
|
}
|
363 |
|
|
364 |
|
$taxon_name = '';
|
365 |
|
$name_link = '';
|
366 |
|
if ($determinationEvent->taxonName) {
|
367 |
|
$taxon_name = $determinationEvent->taxonName;
|
368 |
|
} else if ($determinationEvent->taxon) {
|
369 |
|
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
|
370 |
|
$name_link = path_to_taxon($determinationEvent->taxon->uuid);
|
371 |
|
}
|
372 |
|
if ($taxon_name) {
|
373 |
|
$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
374 |
|
$dd_elements[$weight] = $taxon_html;
|
375 |
|
}
|
376 |
|
if (isset($determinationEvent->modifier)) {
|
377 |
|
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
|
378 |
|
}
|
379 |
|
if ($timeperiod_string) {
|
380 |
|
$dd_elements[$weight] .= $glue . $timeperiod_string;
|
381 |
|
}
|
382 |
|
if (isset($determinationEvent->actor->titleCache)) {
|
383 |
|
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
|
384 |
|
}
|
385 |
|
if (isset($determinationEvent->description)) {
|
386 |
|
$dd_elements[$weight] .= $glue . $determinationEvent->description;
|
387 |
|
}
|
388 |
|
}
|
389 |
|
ksort($dd_elements);
|
390 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
391 |
|
break;
|
|
429 |
$taxon_name = '';
|
|
430 |
$name_link = '';
|
|
431 |
if ($determinationEvent->taxonName) {
|
|
432 |
$taxon_name = $determinationEvent->taxonName;
|
|
433 |
} else if ($determinationEvent->taxon) {
|
|
434 |
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
|
|
435 |
$name_link = path_to_taxon($determinationEvent->taxon->uuid);
|
|
436 |
}
|
|
437 |
if ($taxon_name) {
|
|
438 |
$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
|
439 |
$dd_elements[$weight] = $taxon_html;
|
|
440 |
}
|
|
441 |
if (isset($determinationEvent->modifier)) {
|
|
442 |
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
|
|
443 |
}
|
|
444 |
if ($timeperiod_string) {
|
|
445 |
$dd_elements[$weight] .= $glue . $timeperiod_string;
|
|
446 |
}
|
|
447 |
if (isset($determinationEvent->actor->titleCache)) {
|
|
448 |
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
|
|
449 |
}
|
|
450 |
if (isset($determinationEvent->description)) {
|
|
451 |
$dd_elements[$weight] .= $glue . $determinationEvent->description;
|
|
452 |
}
|
|
453 |
}
|
|
454 |
ksort($dd_elements);
|
|
455 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
|
456 |
break;
|
392 |
457 |
|
393 |
|
case 'descriptions':
|
394 |
|
$occurrence_featureTree = cdm_get_occurrence_featureTree();
|
395 |
|
$dd_elements = array();
|
|
458 |
case 'descriptions':
|
|
459 |
$occurrence_featureTree = cdm_get_occurrence_featureTree();
|
|
460 |
$dd_elements = array();
|
396 |
461 |
|
397 |
|
foreach ($value as $description) {
|
398 |
|
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
|
|
462 |
foreach ($value as $description) {
|
|
463 |
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
|
399 |
464 |
// if($description->imageGallery == TRUE) {
|
400 |
465 |
// continue;
|
401 |
466 |
// }
|
402 |
|
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
|
403 |
|
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));
|
404 |
|
$dd_elements[] = $description_render_elements;
|
405 |
|
}
|
|
467 |
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
|
|
468 |
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));
|
|
469 |
$dd_elements[] = $description_render_elements;
|
|
470 |
if ($description->isImageGallery) {
|
|
471 |
$mediaList = array();
|
|
472 |
if (is_array($description->elements)) {
|
|
473 |
$mediaList = $description->elements;
|
|
474 |
}
|
|
475 |
$gallery_html = '';
|
|
476 |
if (count($mediaList) > 0) {
|
|
477 |
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
|
478 |
$captionElements = array(
|
|
479 |
'#uri' => t('open media'),
|
|
480 |
);
|
|
481 |
|
|
482 |
$gallery_html = compose_cdm_media_gallerie(array(
|
|
483 |
'mediaList' => $mediaList,
|
|
484 |
'galleryName' => $gallery_name,
|
|
485 |
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
|
486 |
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
|
487 |
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
|
488 |
'captionElements' => $captionElements,
|
|
489 |
'mediaLinkType' => 'LIGHTBOX',
|
|
490 |
'alternativeMediaUri' => NULL,
|
|
491 |
'galleryLinkUri' => NULL,
|
|
492 |
));
|
|
493 |
}
|
406 |
494 |
|
407 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
408 |
|
break;
|
|
495 |
}
|
|
496 |
}
|
409 |
497 |
|
410 |
|
case 'sources':
|
411 |
|
$dd_elements = array();
|
412 |
|
foreach ($value as $identifiable_source) {
|
413 |
|
$dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));
|
414 |
|
}
|
415 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
416 |
|
break;
|
417 |
|
|
418 |
|
|
419 |
|
/* ---- DerivedUnitBase --- */
|
420 |
|
case 'derivedFrom':
|
421 |
|
$derivedFrom = $value;
|
422 |
|
break;
|
423 |
|
|
424 |
|
case 'collection':
|
425 |
|
$sub_dl_groups = array();
|
426 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
427 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
428 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
429 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
430 |
|
// TODO "superCollection"
|
431 |
|
// TODO may have media
|
432 |
|
|
433 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
434 |
|
array(
|
435 |
|
array('#markup' => $value->titleCache),
|
436 |
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
437 |
|
)
|
438 |
|
);
|
439 |
|
break;
|
|
498 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
499 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $gallery_html);
|
|
500 |
break;
|
440 |
501 |
|
441 |
|
case 'storedUnder':
|
442 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
443 |
|
break;
|
|
502 |
case 'sources':
|
|
503 |
$dd_elements = array();
|
|
504 |
foreach ($value as $identifiable_source) {
|
|
505 |
$dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));
|
|
506 |
}
|
|
507 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
|
508 |
break;
|
|
509 |
|
|
510 |
|
|
511 |
/* ---- DerivedUnitBase --- */
|
|
512 |
case 'derivedFrom':
|
|
513 |
$derivedFrom = $value;
|
|
514 |
break;
|
|
515 |
|
|
516 |
case 'collection':
|
|
517 |
$sub_dl_groups = array();
|
|
518 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
|
519 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
|
520 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
|
521 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
|
522 |
// TODO "superCollection"
|
|
523 |
// TODO may have media
|
|
524 |
|
|
525 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
526 |
array(
|
|
527 |
array('#markup' => $value->titleCache),
|
|
528 |
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
529 |
)
|
|
530 |
);
|
|
531 |
break;
|
|
532 |
|
|
533 |
case 'storedUnder':
|
|
534 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
|
535 |
break;
|
|
536 |
|
|
537 |
|
|
538 |
/* ---- Specimen --- */
|
|
539 |
case 'sequences':
|
|
540 |
$dd_elements = array();
|
|
541 |
foreach ($value as $sequence) {
|
|
542 |
$dd_elements[] = compose_cdm_sequence($sequence);
|
|
543 |
}
|
|
544 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
545 |
break;
|
|
546 |
|
|
547 |
// TODO preservation
|
|
548 |
// TODO exsiccatum
|
|
549 |
|
|
550 |
|
|
551 |
/* ---- FieldObservation --- */
|
|
552 |
case 'gatheringEvent':
|
|
553 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
|
|
554 |
@_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
|
|
555 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
|
556 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
|
|
557 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
|
|
558 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
|
559 |
if (isset($value->absoluteElevation)) {
|
|
560 |
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
|
561 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
|
562 |
}
|
|
563 |
if (isset($value->distanceToGround)) {
|
|
564 |
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
|
565 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
|
566 |
}
|
|
567 |
if (isset($value->distanceToWaterSurface)) {
|
|
568 |
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
|
569 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
|
570 |
}
|
444 |
571 |
|
|
572 |
if (isset($value->collectingAreas)) {
|
|
573 |
$area_representations = array();
|
|
574 |
foreach ($value->collectingAreas as $area) {
|
|
575 |
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
|
576 |
}
|
|
577 |
if (!empty($area_representations))
|
|
578 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
|
579 |
array(
|
|
580 |
array('#markup' => implode(', ', $area_representations))
|
|
581 |
)
|
|
582 |
);
|
|
583 |
}
|
|
584 |
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
|
585 |
$sub_dl_groups = array();
|
|
586 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
|
587 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
|
588 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
|
589 |
if (isset($value->exactLocation->referenceSystem)) {
|
|
590 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
|
591 |
}
|
445 |
592 |
|
446 |
|
/* ---- Specimen --- */
|
447 |
|
case 'sequences':
|
448 |
|
$dd_elements = array();
|
449 |
|
foreach ($value as $sequence) {
|
450 |
|
$dd_elements[] = compose_cdm_sequence($sequence);
|
451 |
|
}
|
452 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
453 |
|
break;
|
454 |
|
|
455 |
|
// TODO preservation
|
456 |
|
// TODO exsiccatum
|
457 |
|
|
458 |
|
|
459 |
|
/* ---- FieldObservation --- */
|
460 |
|
case 'gatheringEvent':
|
461 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
|
462 |
|
@_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
|
463 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
464 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
|
465 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
|
466 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
467 |
|
if (isset($value->absoluteElevation)) {
|
468 |
|
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
469 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
470 |
|
}
|
471 |
|
if (isset($value->distanceToGround)) {
|
472 |
|
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
473 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
474 |
|
}
|
475 |
|
if (isset($value->distanceToWaterSurface)) {
|
476 |
|
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
477 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
478 |
|
}
|
|
593 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
|
594 |
array(
|
|
595 |
array('#markup' => $value->exactLocation->sexagesimalString),
|
|
596 |
array(
|
|
597 |
'#theme' => 'description_list',
|
|
598 |
'#groups' => $sub_dl_groups
|
|
599 |
),
|
|
600 |
)
|
|
601 |
);
|
|
602 |
}
|
|
603 |
break;
|
|
604 |
|
|
605 |
/* ---- DerivationEvent --- */
|
|
606 |
case 'derivationEvents':
|
|
607 |
@_description_list_group_add($groups, t('Association type'), $value->description);
|
|
608 |
break;
|
|
609 |
case 'preservedSpecimenDTOs':
|
|
610 |
$derivates = $value;
|
|
611 |
break;
|
|
612 |
case 'derivates':
|
|
613 |
$derivates = $value;
|
|
614 |
break;
|
|
615 |
|
|
616 |
default:
|
|
617 |
if (is_object($value) || is_array($value)) {
|
|
618 |
drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
|
619 |
} else {
|
|
620 |
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
|
621 |
}
|
479 |
622 |
|
480 |
|
if (isset($value->collectingAreas)) {
|
481 |
|
$area_representations = array();
|
482 |
|
foreach ($value->collectingAreas as $area) {
|
483 |
|
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
484 |
|
}
|
485 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
486 |
|
array(
|
487 |
|
array('#markup' => implode(', ', $area_representations))
|
488 |
|
)
|
489 |
|
);
|
490 |
|
}
|
491 |
|
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
492 |
|
$sub_dl_groups = array();
|
493 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
494 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
495 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
496 |
|
if (isset($value->exactLocation->referenceSystem)) {
|
497 |
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
498 |
|
}
|
499 |
|
|
500 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
501 |
|
array(
|
502 |
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
503 |
|
array(
|
504 |
|
'#theme' => 'description_list',
|
505 |
|
'#groups' => $sub_dl_groups
|
506 |
|
),
|
507 |
|
)
|
508 |
|
);
|
509 |
|
}
|
510 |
|
break;
|
|
623 |
}
|
511 |
624 |
|
|
625 |
/*
|
|
626 |
*
|
512 |
627 |
default:
|
513 |
628 |
if (is_object($value) || is_array($value)) {
|
514 |
629 |
drupal_set_message("Unhandled type in compose_cdm_specimen_or_observation() for field " . $field, "warning");
|
515 |
630 |
} else {
|
516 |
631 |
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
|
632 |
*/
|
|
633 |
// Stashed changes
|
517 |
634 |
}
|
|
635 |
} // END of loop over $derivedUnitFacade fields
|
518 |
636 |
|
|
637 |
// Extensions
|
|
638 |
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimenOrObservation->uuid . '/extensions', array($specimenOrObservation->uuid));
|
|
639 |
if ($extensions && count($extensions)) {
|
|
640 |
|
|
641 |
$extensions_render_array = compose_extensions($extensions);
|
|
642 |
@_description_list_group_add($groups, t('Extensions') . ':',
|
|
643 |
$extensions_render_array,
|
|
644 |
'', 100);
|
519 |
645 |
}
|
520 |
646 |
|
521 |
|
}
|
522 |
|
} // END of loop over $derivedUnitFacade fields
|
523 |
647 |
|
524 |
|
// Extensions
|
525 |
|
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimenOrObservation->uuid . '/extensions', array($specimenOrObservation->uuid));
|
526 |
|
if ($extensions && count($extensions)) {
|
|
648 |
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
649 |
uasort($groups, 'element_sort');
|
527 |
650 |
|
528 |
|
$extensions_render_array = compose_extensions($extensions);
|
529 |
|
@_description_list_group_add($groups, t('Extensions') . ':',
|
530 |
|
$extensions_render_array,
|
531 |
|
'', 100);
|
532 |
|
}
|
|
651 |
$occurrence_elements = array(
|
|
652 |
'#title' => $title,
|
|
653 |
'#theme' => 'description_list',
|
|
654 |
'#groups' => $groups,
|
|
655 |
'#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),
|
|
656 |
);
|
|
657 |
$derivatives[] = $occurrence_elements;
|
|
658 |
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
|
|
659 |
$foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
|
|
660 |
if (!empty($foonote_li_elements)) {
|
|
661 |
$derivatives[] = array(
|
|
662 |
'#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
|
|
663 |
);
|
|
664 |
}
|
533 |
665 |
|
|
666 |
// --- recurse into originals
|
|
667 |
if (!isset($derivedFrom)) {
|
|
668 |
$derivedFrom = cdm_ws_get(
|
|
669 |
CDM_WS_OCCURRENCE,
|
|
670 |
array($specimenOrObservation->uuid, 'derivedFrom')
|
|
671 |
);
|
|
672 |
}
|
534 |
673 |
|
535 |
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
536 |
|
uasort($groups, 'element_sort');
|
|
674 |
if (isset($derivates)) {
|
|
675 |
if (isset($derivedFrom->originals)) {
|
|
676 |
$derived_from_label = t('derivated');
|
|
677 |
// $preposition = t('from');
|
|
678 |
if (isset($derivedFrom->type)) {
|
|
679 |
$derived_from_label = $derivedFrom->type->representation_L10n;
|
|
680 |
if (isset($derivedFrom->description)) {
|
|
681 |
$derived_from_label = $derivedFrom->description;
|
|
682 |
}
|
|
683 |
// if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
|
684 |
// $preposition = t('of');
|
|
685 |
// }
|
|
686 |
}
|
|
687 |
if (count($groups) > 0) {
|
|
688 |
// TODO annotations
|
537 |
689 |
|
538 |
|
$occurrence_elements = array(
|
539 |
|
'#title' => $title,
|
540 |
|
'#theme' => 'description_list',
|
541 |
|
'#groups' => $groups,
|
542 |
|
'#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),
|
543 |
|
);
|
544 |
|
$derivatives[] = $occurrence_elements;
|
545 |
|
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
|
546 |
|
$foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
|
547 |
|
if (!empty($foonote_li_elements)) {
|
548 |
|
$derivatives[] = array(
|
549 |
|
'#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
|
550 |
|
);
|
551 |
|
}
|
|
690 |
// only display the derived from information when the derivative has any element which will be diplayed
|
|
691 |
$derivatives[] = array(
|
|
692 |
'#markup' => '<div class="derived_from">' . $derived_from_label . ': </div>',//' ' . $preposition . ': </div>',
|
|
693 |
);
|
|
694 |
}
|
|
695 |
// foreach ($derivedFrom->originals as $original) {
|
552 |
696 |
|
553 |
|
// --- recurse into originals
|
554 |
|
if (!isset($derivedFrom)) {
|
555 |
|
$derivedFrom = cdm_ws_get(
|
556 |
|
CDM_WS_OCCURRENCE,
|
557 |
|
array($specimenOrObservation->uuid, 'derivedFrom')
|
558 |
|
);
|
559 |
|
}
|
560 |
697 |
|
561 |
|
if (isset($derivedFrom)) {
|
562 |
|
if (isset($derivedFrom->originals)) {
|
563 |
|
$derived_from_label = t('derived');
|
564 |
|
$preposition = t('from');
|
565 |
|
if(isset($derivedFrom->type)){
|
566 |
|
$derived_from_label = $derivedFrom->type->representation_L10n;
|
567 |
|
if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
568 |
|
$preposition = t('of');
|
569 |
|
}
|
570 |
|
}
|
571 |
|
if (count($groups) > 0) {
|
572 |
|
// TODO annotations
|
573 |
698 |
|
574 |
|
// only display the derived from information when the derivative has any element which will be diplayed
|
575 |
|
$derivatives[] = array(
|
576 |
|
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
|
577 |
|
);
|
|
699 |
}
|
578 |
700 |
}
|
|
701 |
/*<<<<<<< Updated upstream
|
579 |
702 |
foreach ($derivedFrom->originals as $original) {
|
580 |
703 |
compose_cdm_specimen_or_observation($original, $derivatives);
|
|
704 |
=======*/
|
|
705 |
if (isset($derivates )) {
|
|
706 |
|
|
707 |
foreach ($derivates as $derivate){
|
|
708 |
compose_cdm_specimenOrObservation($derivate, $derivatives);
|
|
709 |
}
|
|
710 |
//>>>>>>> Stashed changes
|
581 |
711 |
}
|
582 |
|
}
|
583 |
|
}
|
584 |
712 |
|
585 |
|
} // END of $specimenOrObservation exists
|
|
713 |
} // END of $specimenOrObservation exists
|
586 |
714 |
|
587 |
|
return $derivatives;
|
|
715 |
return $derivatives;
|
588 |
716 |
}
|
589 |
717 |
|
590 |
718 |
|
... | ... | |
600 |
728 |
*
|
601 |
729 |
* @ingroup compose
|
602 |
730 |
*/
|
603 |
|
function compose_cdm_sequence($sequence) {
|
604 |
|
|
605 |
|
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
606 |
|
if (!isset($exclude_sequence_fields)) {
|
607 |
|
$exclude_sequence_fields = array(
|
608 |
|
'titleCache',
|
609 |
|
'protectedTitleCache',
|
610 |
|
'microReference',
|
611 |
|
'created',
|
612 |
|
'updated',
|
613 |
|
'class',
|
614 |
|
);
|
615 |
|
}
|
|
731 |
function compose_cdm_sequence($sequence)
|
|
732 |
{
|
|
733 |
|
|
734 |
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
|
735 |
if (!isset($exclude_sequence_fields)) {
|
|
736 |
$exclude_sequence_fields = array(
|
|
737 |
'titleCache',
|
|
738 |
'protectedTitleCache',
|
|
739 |
'microReference',
|
|
740 |
'created',
|
|
741 |
'updated',
|
|
742 |
'class',
|
|
743 |
);
|
|
744 |
}
|
616 |
745 |
|
617 |
|
$groups = array();
|
|
746 |
$groups = array();
|
618 |
747 |
|
619 |
|
// -- retrieve additional data if neesscary
|
620 |
|
// TODO below call disabled since sequences are not yet supported,
|
621 |
|
// see #3347 (services and REST service controller for molecular classes implemented)
|
622 |
|
//
|
623 |
|
// cdm_load_annotations($sequence);
|
|
748 |
// -- retrieve additional data if neesscary
|
|
749 |
// TODO below call disabled since sequences are not yet supported,
|
|
750 |
// see #3347 (services and REST service controller for molecular classes implemented)
|
|
751 |
//
|
|
752 |
// cdm_load_annotations($sequence);
|
624 |
753 |
|
625 |
|
foreach (get_object_vars($sequence) as $field => $value) {
|
|
754 |
foreach (get_object_vars($sequence) as $field => $value) {
|
626 |
755 |
|
627 |
756 |
|
628 |
|
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
629 |
|
switch ($field) {
|
|
757 |
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
|
758 |
switch ($field) {
|
630 |
759 |
|
631 |
|
case 'geneticAccessionNumber';
|
632 |
|
$dd_elements = array();
|
633 |
|
foreach ($value as $accession) {
|
634 |
|
if (isset($accession->uri) ){
|
635 |
|
$dd_elements[] = l($accession->accessionNumber, $accession->uri);
|
636 |
|
} else {
|
637 |
|
$dd_elements[] = $accession->accessionNumber;
|
|
760 |
case 'geneticAccessionNumber';
|
|
761 |
$dd_elements = array();
|
|
762 |
foreach ($value as $accession) {
|
|
763 |
if (isset($accession->uri)) {
|
|
764 |
$dd_elements[] = l($accession->accessionNumber, $accession->uri);
|
|
765 |
} else {
|
|
766 |
$dd_elements[] = $accession->accessionNumber;
|
|
767 |
}
|
|
768 |
}
|
|
769 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 2);
|
|
770 |
break;
|
|
771 |
|
|
772 |
|
|
773 |
case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
|
774 |
if (isset($value->name)) {
|
|
775 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
|
776 |
}
|
|
777 |
if (isset($value->description)) {
|
|
778 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description'), $value->description, NULL, 4);
|
|
779 |
}
|
|
780 |
break;
|
|
781 |
|
|
782 |
case 'consensusSequence':
|
|
783 |
// format in genbank style, force linebreaks after each 70 nucleotites
|
|
784 |
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
|
785 |
@_description_list_group_add(
|
|
786 |
$groups,
|
|
787 |
cdm_occurrence_field_name_label($field),
|
|
788 |
array(
|
|
789 |
array(
|
|
790 |
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
|
791 |
'#wrapper_attributes' => array('class' => 'dna-sequence')
|
|
792 |
)
|
|
793 |
),
|
|
794 |
5);
|
|
795 |
break;
|
|
796 |
|
|
797 |
case 'dnaSample': // FIXME 3.3 implement
|
|
798 |
break;
|
|
799 |
case 'singleReads': // FIXME 3.3 implement
|
|
800 |
break;
|
|
801 |
case 'contigFile': // FIXME 3.3 implement - Media
|
|
802 |
break;
|
|
803 |
case 'pherograms': // FIXME 3.3 implement - Media
|
|
804 |
break;
|
|
805 |
case 'haplotype': // FIXME 3.3 implement
|
|
806 |
break;
|
|
807 |
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
|
808 |
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
|
809 |
break;
|
|
810 |
|
|
811 |
case 'barcode': // boolean
|
|
812 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes' : 'No', NULL, 7);
|
|
813 |
break;
|
|
814 |
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
|
815 |
break;
|
|
816 |
|
|
817 |
case 'citation':
|
|
818 |
@_description_list_group_add($groups,
|
|
819 |
cdm_occurrence_field_name_label($field),
|
|
820 |
theme('cdm_reference', array('reference' => $value, 'microReference' => $sequence->microReference)),
|
|
821 |
NULL,
|
|
822 |
8
|
|
823 |
);
|
|
824 |
break;
|
|
825 |
|
|
826 |
case 'publishedIn':
|
|
827 |
@_description_list_group_add($groups,
|
|
828 |
cdm_occurrence_field_name_label($field),
|
|
829 |
theme('cdm_reference', array('reference' => $value)),
|
|
830 |
NULL,
|
|
831 |
7
|
|
832 |
);
|
|
833 |
break;
|
|
834 |
|
|
835 |
case 'rights':
|
|
836 |
array_merge($groups, cdm_rights_as_dl_groups($value));
|
|
837 |
break;
|
|
838 |
|
|
839 |
case 'annotations':
|
|
840 |
$dd_elements = array();
|
|
841 |
foreach ($value as $annotation) {
|
|
842 |
// TODO respect annotation type filter settings
|
|
843 |
$dd_elements[] = $annotation->text;
|
|
844 |
}
|
|
845 |
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
|
846 |
break;
|
|
847 |
|
|
848 |
case 'markers':
|
|
849 |
$dd_elements = array();
|
|
850 |
foreach ($value as $marker) {
|
|
851 |
$dd_elements[] = compose_cdm_marker($marker);
|
|
852 |
}
|
|
853 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
|
854 |
break;
|
|
855 |
|
|
856 |
case 'chromatograms':
|
|
857 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
858 |
array(
|
|
859 |
'#markup' => compose_cdm_media_gallerie(array('medialist' => $value)),
|
|
860 |
),
|
|
861 |
NULL,
|
|
862 |
11);
|
|
863 |
break;
|
|
864 |
|
|
865 |
default:
|
|
866 |
if (is_object($value) || is_array($value)) {
|
|
867 |
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
|
868 |
} else {
|
|
869 |
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
|
870 |
}
|
638 |
871 |
}
|
639 |
|
}
|
640 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 1);
|
641 |
|
break;
|
642 |
|
|
643 |
|
|
644 |
|
case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
645 |
|
if (isset($value->name)) {
|
646 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
647 |
|
}
|
648 |
|
if (isset($value->description)) {
|
649 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description') , $value->description, NULL, 4);
|
650 |
|
}
|
651 |
|
break;
|
652 |
|
|
653 |
|
case 'consensusSequence':
|
654 |
|
// format in genbank style, force linebreaks after each 70 nucleotites
|
655 |
|
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
656 |
|
@_description_list_group_add(
|
657 |
|
$groups,
|
658 |
|
cdm_occurrence_field_name_label($field),
|
659 |
|
array(
|
660 |
|
array(
|
661 |
|
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb'). '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
662 |
|
'#wrapper_attributes' => array('class'=>'dna-sequence')
|
663 |
|
)
|
664 |
|
),
|
665 |
|
5);
|
666 |
|
break;
|
667 |
|
|
668 |
|
case 'dnaSample': // FIXME 3.3 implement
|
669 |
|
break;
|
670 |
|
case 'singleReads': // FIXME 3.3 implement
|
671 |
|
break;
|
672 |
|
case 'contigFile': // FIXME 3.3 implement - Media
|
673 |
|
break;
|
674 |
|
case 'pherograms': // FIXME 3.3 implement - Media
|
675 |
|
break;
|
676 |
|
case 'haplotype': // FIXME 3.3 implement
|
677 |
|
break;
|
678 |
|
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
679 |
|
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
680 |
|
break;
|
681 |
|
|
682 |
|
case 'barcode': // boolean
|
683 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes': 'No', NULL, 7);
|
684 |
|
break;
|
685 |
|
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
686 |
|
break;
|
687 |
|
|
688 |
|
case 'citation':
|
689 |
|
@_description_list_group_add($groups,
|
690 |
|
cdm_occurrence_field_name_label($field),
|
691 |
|
theme('cdm_reference', array('reference' =>$value, 'microReference' => $sequence->microReference)),
|
692 |
|
NULL,
|
693 |
|
8
|
694 |
|
);
|
695 |
|
break;
|
696 |
|
|
697 |
|
case 'publishedIn':
|
698 |
|
@_description_list_group_add($groups,
|
699 |
|
cdm_occurrence_field_name_label($field),
|
700 |
|
theme('cdm_reference', array('reference'=>$value)),
|
701 |
|
NULL,
|
702 |
|
7
|
703 |
|
);
|
704 |
|
break;
|
705 |
|
|
706 |
|
case 'rights':
|
707 |
|
array_merge($groups, cdm_rights_as_dl_groups($value));
|
708 |
|
break;
|
709 |
|
|
710 |
|
case 'annotations':
|
711 |
|
$dd_elements = array();
|
712 |
|
foreach ($value as $annotation) {
|
713 |
|
// TODO respect annotation type filter settings
|
714 |
|
$dd_elements[] = $annotation->text;
|
715 |
|
}
|
716 |
|
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
717 |
|
break;
|
718 |
|
|
719 |
|
case 'markers':
|
720 |
|
$dd_elements = array();
|
721 |
|
foreach ($value as $marker) {
|
722 |
|
$dd_elements[] = compose_cdm_marker($marker);
|
723 |
|
}
|
724 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
725 |
|
break;
|
726 |
|
|
727 |
|
case 'chromatograms':
|
728 |
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
729 |
|
array(
|
730 |
|
'#markup'=>compose_cdm_media_gallerie(array('medialist'=>$value)),
|
731 |
|
),
|
732 |
|
NULL,
|
733 |
|
11);
|
734 |
|
break;
|
735 |
|
|
736 |
|
default:
|
737 |
|
if(is_object($value) || is_array($value)){
|
738 |
|
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
739 |
|
} else {
|
740 |
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
741 |
|
}
|
742 |
|
}
|
|
872 |
}
|
743 |
873 |
}
|
744 |
|
}
|
745 |
874 |
|
746 |
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
747 |
|
uasort($groups, 'element_sort');
|
|
875 |
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
876 |
uasort($groups, 'element_sort');
|
748 |
877 |
|
749 |
|
$sequence_elements = array(
|
750 |
|
'#theme' => 'description_list',
|
751 |
|
'#groups' => $groups
|
752 |
|
);
|
|
878 |
$sequence_elements = array(
|
|
879 |
'#theme' => 'description_list',
|
|
880 |
'#groups' => $groups
|
|
881 |
);
|
753 |
882 |
|
754 |
|
return $sequence_elements;
|
|
883 |
return $sequence_elements;
|
755 |
884 |
}
|
756 |
885 |
|
757 |
886 |
|
first steps of specimen page with DTOs