| 34 |
34 |
* @param object $sob_dto
|
| 35 |
35 |
* the CDM FieldUnitDTO or DerivedUnitDTO to compose
|
| 36 |
36 |
* the render array for.
|
| 37 |
|
* @param bool $compact_mode
|
| 38 |
|
* Currently unused, but added for compatibility with
|
| 39 |
|
* compose_cdm_specimen_or_observation($specimen_or_observation,
|
| 40 |
|
* $isSpecimen_page = false, &$derivatives = null)
|
|
37 |
* @param bool $full_details
|
|
38 |
* Activates the display of additional data like: annotations, markers, ...
|
| 41 |
39 |
*
|
| 42 |
40 |
* @return array
|
| 43 |
41 |
* The render array for the SpecimenOrObservationDTO
|
| 44 |
42 |
*
|
| 45 |
43 |
* @ingroup compose
|
| 46 |
44 |
*/
|
| 47 |
|
function compose_cdm_specimen_or_observation_dto_details_grid($sob_dto, $compact_mode = FALSE) {
|
|
45 |
function compose_cdm_specimen_or_observation_dto_details_grid($sob_dto, $full_details = FALSE) {
|
| 48 |
46 |
$render_array = [];
|
| 49 |
47 |
if (!$sob_dto) {
|
| 50 |
48 |
return $render_array;
|
| 51 |
49 |
}
|
| 52 |
50 |
if ($sob_dto->type == 'FieldUnit') {
|
| 53 |
|
$render_array['field-unit'] = compose_cdm_field_unit_dto_details($sob_dto, $compact_mode);
|
|
51 |
$render_array['field-unit'] = compose_cdm_field_unit_dto_details($sob_dto, $full_details);
|
| 54 |
52 |
if (isset($sob_dto->gatheringEvent)) {
|
| 55 |
|
$render_array['gathering'] = compose_cdm_gathering_dto_details($sob_dto->gatheringEvent, $compact_mode);
|
|
53 |
$render_array['gathering'] = compose_cdm_gathering_dto_details($sob_dto->gatheringEvent, $full_details);
|
| 56 |
54 |
}
|
| 57 |
55 |
} else {
|
| 58 |
56 |
if(isset($sob_dto->derivationEvent)){
|
| 59 |
57 |
$render_array['derivation-event'] = compose_cdm_derivation_event($sob_dto->derivationEvent);
|
| 60 |
58 |
}
|
| 61 |
|
$render_array['storage'] = compose_cdm_derived_unit_dto_storage_details($sob_dto, $compact_mode);
|
| 62 |
|
$render_array['type-designations'] = compose_cdm_unit_dto_type_designations($sob_dto, $compact_mode);
|
|
59 |
$render_array['storage'] = compose_cdm_derived_unit_dto_storage_details($sob_dto, $full_details);
|
|
60 |
$render_array['type-designations'] = compose_cdm_unit_dto_type_designations($sob_dto, $full_details);
|
| 63 |
61 |
if($sob_dto->type == 'DnaSample'){
|
| 64 |
62 |
// FIXME:
|
| 65 |
|
$render_array['dna-sample'] = compose_cdm_derived_unit_dto_sequences($sob_dto, $compact_mode);
|
|
63 |
$render_array['dna-sample'] = compose_cdm_derived_unit_dto_sequences($sob_dto, $full_details);
|
| 66 |
64 |
} else if($sob_dto->type == 'MediaSpecimen' && isset_not_empty($sob_dto->mediaSpecimen)) {
|
| 67 |
65 |
$render_array['media-specimens'] = cdm_sob_dto_media_table($sob_dto->mediaSpecimen, $sob_dto, 'Media Specimens');
|
| 68 |
66 |
}
|
| 69 |
67 |
}
|
| 70 |
68 |
if(isset_not_empty($sob_dto->determinedNames)){
|
| 71 |
|
$render_array['determinations'] = compose_cdm_sob_dto_determinations($sob_dto, $compact_mode);
|
|
69 |
$render_array['determinations'] = compose_cdm_sob_dto_determinations($sob_dto, $full_details);
|
| 72 |
70 |
}
|
| 73 |
71 |
if(isset_not_empty($sob_dto->listOfMedia)){
|
| 74 |
72 |
$render_array['media'] = cdm_sob_dto_media_table($sob_dto->listOfMedia, $sob_dto, 'Media');;
|
| 75 |
73 |
}
|
| 76 |
74 |
|
|
75 |
if($full_details){
|
|
76 |
RenderHints::setAnnotationsAndSourceConfig([
|
|
77 |
'sources_as_content' => TRUE,
|
|
78 |
'link_to_name_used_in_source' => TRUE,
|
|
79 |
'link_to_reference' => FALSE,
|
|
80 |
'add_footnote_keys' => FALSE,
|
|
81 |
'bibliography_aware' => FALSE
|
|
82 |
]);
|
|
83 |
$annotations_and_sources = handle_annotations_and_sources($sob_dto);
|
|
84 |
if ($annotations_and_sources->hasSourceReferences()) {
|
|
85 |
$render_array['sources'] = compose_cdm_sob_dto_sources($sob_dto, $annotations_and_sources);
|
|
86 |
}
|
|
87 |
}
|
|
88 |
|
| 77 |
89 |
return $render_array;
|
| 78 |
90 |
}
|
| 79 |
91 |
/**
|
| 80 |
92 |
* Data rows with details for a SpecimenOrObservationDTO to be used in a table
|
| 81 |
93 |
* @param object $sob_dto
|
| 82 |
94 |
* the CDM SpecimenOrObservationDTO
|
| 83 |
|
* @param bool $compact_mode
|
|
95 |
* @param bool $full_details
|
| 84 |
96 |
* Currently unused,
|
| 85 |
97 |
*
|
| 86 |
98 |
* @return array
|
| 87 |
99 |
* The data rows
|
| 88 |
100 |
*/
|
| 89 |
|
function sob_dto_details_rows($sob_dto, $compact_mode = FALSE) {
|
|
101 |
function sob_dto_details_rows($sob_dto, $full_details = FALSE) {
|
| 90 |
102 |
|
| 91 |
103 |
$table_row_data = [];
|
| 92 |
104 |
|
| ... | ... | |
| 130 |
142 |
*
|
| 131 |
143 |
* @param object $derivation_event_dto
|
| 132 |
144 |
* the CDM DerivationEventDTO
|
| 133 |
|
* @param bool $compact_mode
|
|
145 |
* @param bool $full_details
|
| 134 |
146 |
* Currently unused,
|
| 135 |
147 |
*
|
| 136 |
148 |
* @return array
|
| ... | ... | |
| 138 |
150 |
*
|
| 139 |
151 |
* @ingroup compose
|
| 140 |
152 |
*/
|
| 141 |
|
function compose_cdm_derivation_event($derivation_event_dto, $compact_mode = FALSE){
|
|
153 |
function compose_cdm_derivation_event($derivation_event_dto, $full_details = FALSE){
|
| 142 |
154 |
|
| 143 |
155 |
$details_array = [];
|
| 144 |
156 |
// $markup = t("Derivation") . ': ';
|
| ... | ... | |
| 181 |
193 |
*
|
| 182 |
194 |
* @param object $fu_dto
|
| 183 |
195 |
* the CDM FieldUnitDTO
|
| 184 |
|
* @param bool $compact_mode
|
|
196 |
* @param bool $full_details
|
| 185 |
197 |
* Currently unused,
|
| 186 |
198 |
*
|
| 187 |
199 |
* @return array
|
| ... | ... | |
| 189 |
201 |
*
|
| 190 |
202 |
* @ingroup compose
|
| 191 |
203 |
*/
|
| 192 |
|
function compose_cdm_field_unit_dto_details($fu_dto, $compact_mode = FALSE) {
|
|
204 |
function compose_cdm_field_unit_dto_details($fu_dto, $full_details = FALSE) {
|
| 193 |
205 |
|
| 194 |
|
$table_row_data = sob_dto_details_rows($fu_dto, $compact_mode);
|
|
206 |
$table_row_data = sob_dto_details_rows($fu_dto, $full_details);
|
| 195 |
207 |
|
| 196 |
208 |
if (isset_not_empty($fu_dto->individualCount)) {
|
| 197 |
209 |
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('individualCount'), $fu_dto->individualCount);
|
| ... | ... | |
| 223 |
235 |
*
|
| 224 |
236 |
* @param object $du_dto
|
| 225 |
237 |
* the CDM DerivedUnitDTO
|
| 226 |
|
* @param bool $compact_mode
|
|
238 |
* @param bool $full_details
|
| 227 |
239 |
* Currently unused,
|
| 228 |
240 |
*
|
| 229 |
241 |
* @return array
|
| ... | ... | |
| 231 |
243 |
*
|
| 232 |
244 |
* @ingroup compose
|
| 233 |
245 |
*/
|
| 234 |
|
function compose_cdm_derived_unit_dto_storage_details($du_dto, $compact_mode = FALSE) {
|
|
246 |
function compose_cdm_derived_unit_dto_storage_details($du_dto, $full_details = FALSE) {
|
| 235 |
247 |
|
| 236 |
|
$table_row_data = sob_dto_details_rows($du_dto, $compact_mode);
|
|
248 |
$table_row_data = sob_dto_details_rows($du_dto, $full_details);
|
| 237 |
249 |
|
| 238 |
250 |
if (isset($du_dto->accessionNumber)) {
|
| 239 |
251 |
$table_row_data[] = cdm_sob_dto_table_row(
|
| ... | ... | |
| 299 |
311 |
*
|
| 300 |
312 |
* @param object $gathering_dto
|
| 301 |
313 |
* the CDM GatheringDTO object
|
| 302 |
|
* @param bool $compact_mode
|
|
314 |
* @param bool $full_details
|
| 303 |
315 |
* Currently unused,
|
| 304 |
316 |
*
|
| 305 |
317 |
* @return array
|
| ... | ... | |
| 307 |
319 |
*
|
| 308 |
320 |
* @ingroup compose
|
| 309 |
321 |
*/
|
| 310 |
|
function compose_cdm_gathering_dto_details($gathering_dto, $compact_mode = FALSE) {
|
|
322 |
function compose_cdm_gathering_dto_details($gathering_dto, $full_details = FALSE) {
|
| 311 |
323 |
|
| 312 |
324 |
$table_row_data = [];
|
| 313 |
325 |
if (isset_not_empty($gathering_dto->date)) {
|
| ... | ... | |
| 375 |
387 |
*
|
| 376 |
388 |
* @param object $sob_dto
|
| 377 |
389 |
* the CDM SpecimenOrObservationDTO
|
| 378 |
|
* @param bool $compact_mode
|
|
390 |
* @param bool $full_details
|
| 379 |
391 |
* Currently unused,
|
| 380 |
392 |
*
|
| 381 |
393 |
* @return array
|
| ... | ... | |
| 383 |
395 |
*
|
| 384 |
396 |
* @ingroup compose
|
| 385 |
397 |
*/
|
| 386 |
|
function compose_cdm_sob_dto_determinations($sob_dto, $compact_mode = FALSE) {
|
|
398 |
function compose_cdm_sob_dto_determinations($sob_dto, $full_details = FALSE) {
|
| 387 |
399 |
|
| 388 |
400 |
$table_row_data = [];
|
| 389 |
401 |
|
| ... | ... | |
| 396 |
408 |
return cdm_sob_dto_table($label, $table_row_data, $sob_dto, 1);
|
| 397 |
409 |
}
|
| 398 |
410 |
|
|
411 |
/**
|
|
412 |
* Compose an render array from the SpecimenOrObservationDTO.determinedNames.
|
|
413 |
*
|
|
414 |
* The resulting DOM block level element will have a header line and details.
|
|
415 |
*
|
|
416 |
* compose_hook() implementation
|
|
417 |
*
|
|
418 |
* @param \AnnotationsAndSources $annotations_and_sources
|
|
419 |
* see
|
|
420 |
*
|
|
421 |
* @return array
|
|
422 |
* The render array for the SpecimenOrObservationDTO.determinedNames
|
|
423 |
*
|
|
424 |
* @ingroup compose
|
|
425 |
*/
|
|
426 |
function compose_cdm_sob_dto_sources($sob_dto, $annotations_and_sources) {
|
|
427 |
|
|
428 |
$table_row_data = [];
|
|
429 |
|
|
430 |
foreach ($annotations_and_sources->getSourceReferences() as $source_ref) {
|
|
431 |
$table_row_data[] = cdm_sob_dto_table_row(NULL, $source_ref);
|
|
432 |
}
|
|
433 |
|
|
434 |
$label = count($table_row_data) > 1 ? t("Sources") : t("Source");
|
|
435 |
return cdm_sob_dto_table($label, $table_row_data, $sob_dto, 1);
|
|
436 |
}
|
|
437 |
|
| 399 |
438 |
/**
|
| 400 |
439 |
* Compose an render array from the DerivedUnitDTO.specimenTypeDesignations.
|
| 401 |
440 |
*
|
| ... | ... | |
| 405 |
444 |
*
|
| 406 |
445 |
* @param object $unit_dto
|
| 407 |
446 |
* the CDM DerivedUnitDTO
|
| 408 |
|
* @param bool $compact_mode
|
|
447 |
* @param bool $full_details
|
| 409 |
448 |
* Currently unused,
|
| 410 |
449 |
*
|
| 411 |
450 |
* @return array
|
| ... | ... | |
| 413 |
452 |
*
|
| 414 |
453 |
* @ingroup compose
|
| 415 |
454 |
*/
|
| 416 |
|
function compose_cdm_unit_dto_type_designations($unit_dto, $compact_mode = FALSE) {
|
|
455 |
function compose_cdm_unit_dto_type_designations($unit_dto, $full_details = FALSE) {
|
| 417 |
456 |
|
| 418 |
457 |
$table_row_data = [];
|
| 419 |
458 |
|
| ... | ... | |
| 466 |
505 |
*
|
| 467 |
506 |
* @param object $unit_dto
|
| 468 |
507 |
* the CDM DerivedUnitDTO
|
| 469 |
|
* @param bool $compact_mode
|
|
508 |
* @param bool $full_details
|
| 470 |
509 |
* Currently unused,
|
| 471 |
510 |
*
|
| 472 |
511 |
* @return array
|
| ... | ... | |
| 476 |
515 |
*
|
| 477 |
516 |
* TODO see #3347 (services and REST service controller for molecular classes implemented)
|
| 478 |
517 |
*/
|
| 479 |
|
function compose_cdm_derived_unit_dto_sequences($unit_dto, $compact_mode = FALSE) {
|
|
518 |
function compose_cdm_derived_unit_dto_sequences($unit_dto, $full_details = FALSE) {
|
| 480 |
519 |
|
| 481 |
520 |
$table_row_data = [];
|
| 482 |
521 |
if(isset_not_empty($unit_dto->sequences)){
|
| ... | ... | |
| 605 |
644 |
* @param object $sob_dto
|
| 606 |
645 |
* the CDM FieldUnit or DerivedUnit to compose
|
| 607 |
646 |
* the render array for.
|
| 608 |
|
* @param bool $isSpecimen_page
|
| 609 |
|
* @param array $derivatives
|
| 610 |
|
* the render array which contains the compositions of the derivatives
|
| 611 |
|
* of the supplied $specimenOrObservation
|
| 612 |
647 |
*
|
| 613 |
648 |
* @return array
|
| 614 |
649 |
* the supplied render array $derivatives to which the composition of the supplied
|
| 615 |
650 |
* $specimenOrObservation has been added to
|
| 616 |
651 |
*
|
| 617 |
|
* @throws \Exception
|
| 618 |
652 |
* @ingroup compose
|
| 619 |
653 |
*/
|
| 620 |
|
|
| 621 |
654 |
function compose_cdm_specimen_or_observation_new($sob_dto)
|
| 622 |
655 |
{
|
| 623 |
656 |
|
| ... | ... | |
| 649 |
682 |
'#attributes' => [
|
| 650 |
683 |
'class' => 'derived-unit-details-grid'
|
| 651 |
684 |
],
|
| 652 |
|
'children' => compose_cdm_specimen_or_observation_dto_details_grid($sob_dto)
|
|
685 |
'children' => compose_cdm_specimen_or_observation_dto_details_grid($sob_dto, true)
|
| 653 |
686 |
];;
|
| 654 |
687 |
|
| 655 |
688 |
$derivation_tree_roots = cdm_ws_get(CDM_WS_OCCURRENCE_FIELD_UNIT_DTOS, [$sob_dto->uuid]);
|
| ... | ... | |
| 662 |
695 |
/* TODO
|
| 663 |
696 |
case 'definition':
|
| 664 |
697 |
|
| 665 |
|
case 'annotations':
|
|
698 |
case 'annotations':
|
| 666 |
699 |
$dd_elements = array();
|
| 667 |
700 |
foreach ($value as $annotation) {
|
| 668 |
701 |
// TODO respect annotation type filter settings
|
| ... | ... | |
| 670 |
703 |
}
|
| 671 |
704 |
break;
|
| 672 |
705 |
|
| 673 |
|
case 'markers':
|
|
706 |
case 'markers':
|
| 674 |
707 |
$dd_elements = array();
|
| 675 |
708 |
foreach ($value as $marker) {
|
| 676 |
709 |
$dd_elements[] = compose_cdm_marker($marker);
|
| ... | ... | |
| 679 |
712 |
break;
|
| 680 |
713 |
|
| 681 |
714 |
@_description_list_group_add($groups, t('Notes:'), $dd_elements);
|
| 682 |
|
*
|
| 683 |
|
*/
|
|
715 |
|
| 684 |
716 |
|
| 685 |
717 |
|
| 686 |
718 |
|
| ... | ... | |
| 736 |
768 |
break;
|
| 737 |
769 |
*/
|
| 738 |
770 |
|
| 739 |
|
/* TODO
|
| 740 |
|
|
| 741 |
|
case 'sources':
|
| 742 |
|
RenderHints::setAnnotationsAndSourceConfig([
|
| 743 |
|
'sources_as_content' => TRUE,
|
| 744 |
|
'link_to_name_used_in_source' => TRUE,
|
| 745 |
|
'link_to_reference' => FALSE,
|
| 746 |
|
'add_footnote_keys' => FALSE,
|
| 747 |
|
'bibliography_aware' => FALSE
|
| 748 |
|
]);
|
| 749 |
|
$annotations_and_sources = handle_annotations_and_sources($sob_dto);
|
| 750 |
|
if ($annotations_and_sources->hasSourceReferences()) {
|
| 751 |
|
@_description_list_group_add($groups, t('Sources') . ':', join(', ', $annotations_and_sources->getSourceReferences()), '', 12);
|
| 752 |
|
}
|
| 753 |
|
break;
|
| 754 |
|
*/
|
| 755 |
|
|
| 756 |
|
|
| 757 |
|
|
| 758 |
771 |
/* TODO Extensions
|
| 759 |
772 |
// TODO: filter by using visible_extensions_sorted()
|
| 760 |
773 |
// TODO: treat as top level element, see https://dev.e-taxonomy.eu/redmine/issues/2985#note-23
|
| ... | ... | |
| 768 |
781 |
}
|
| 769 |
782 |
*/
|
| 770 |
783 |
|
| 771 |
|
|
| 772 |
|
|
| 773 |
784 |
$render_array['footnotes'] = markup_to_render_array(render_footnotes($footnote_list_key));
|
| 774 |
785 |
|
| 775 |
786 |
|
ref #6866 display of sources