Revision 0e617798
Added by Andreas Kohlbecker over 2 years ago
| modules/cdm_dataportal/cdm_api/cdm_api.module | ||
|---|---|---|
| 891 | 891 |
* |
| 892 | 892 |
* NOTE: Not all CDM Base types are yet supported. |
| 893 | 893 |
* |
| 894 |
* @param $cdmBase
|
|
| 894 |
* @param $cdm_entity
|
|
| 895 | 895 |
* The CDM entity to construct the annotations pager uri for |
| 896 | 896 |
*/ |
| 897 |
function cdm_compose_annotations_uri($cdmBase) {
|
|
| 897 |
function cdm_compose_annotations_uri($cdm_entity) {
|
|
| 898 |
|
|
| 899 |
$cdm_entity_type = $cdm_entity->class; |
|
| 900 |
|
|
| 901 |
if($cdm_entity_type == 'DerivedUnitFacade'){
|
|
| 902 |
// TODO we may want to implement a derivedUnitFacade/{uuid}/annotations service and use that instead
|
|
| 903 |
$cdm_entity_type = $cdm_entity->fieldUnitEntityReference->type; |
|
| 904 |
$cdm_entity_uuid = $cdm_entity->fieldUnitEntityReference->uuid; |
|
| 905 |
} else {
|
|
| 906 |
if (isset($cdm_entity->uuid)) {
|
|
| 907 |
$cdm_entity_uuid = $cdm_entity->uuid; |
|
| 908 |
} |
|
| 909 |
} |
|
| 898 | 910 |
|
| 899 |
if (!$cdmBase->uuid) {
|
|
| 911 |
if(!$cdm_entity_uuid){
|
|
| 912 |
// silently give up |
|
| 900 | 913 |
return; |
| 901 | 914 |
} |
| 902 | 915 |
|
| 903 |
$ws_base_uri = cdm_ws_base_uri($cdmBase->class);
|
|
| 916 |
$ws_base_uri = cdm_ws_base_uri($cdm_entity_type);
|
|
| 904 | 917 |
|
| 905 | 918 |
if($ws_base_uri === null){
|
| 906 |
trigger_error(check_plain('Unsupported CDM Class - no annotations available for ' . $cdmBase->class), E_USER_ERROR);
|
|
| 919 |
trigger_error(check_plain('Unsupported CDM Class - no annotations available for ' . $cdm_entity_type), E_USER_ERROR);
|
|
| 907 | 920 |
} |
| 908 | 921 |
return cdm_compose_url($ws_base_uri, array( |
| 909 |
$cdmBase->uuid,
|
|
| 922 |
$cdm_entity_uuid,
|
|
| 910 | 923 |
'annotations', |
| 911 | 924 |
)); |
| 912 | 925 |
} |
| ... | ... | |
| 1777 | 1790 |
* @return array |
| 1778 | 1791 |
* An array of Annotation objects or an empty array. |
| 1779 | 1792 |
*/ |
| 1780 |
function cdm_ws_getAnnotationsFor(&$cdm_entity, $include_types = FALSE) {
|
|
| 1793 |
function cdm_ws_fetch_annotations(&$cdm_entity, $include_types = FALSE) {
|
|
| 1781 | 1794 |
|
| 1782 | 1795 |
if(!isset($cdm_entity->annotations)){
|
| 1783 | 1796 |
$annotation_url = cdm_compose_annotations_uri($cdm_entity); |
| ... | ... | |
| 1816 | 1829 |
if(!$annotations_types_filter) {
|
| 1817 | 1830 |
$annotations_types_filter = unserialize(EXTENSION_TYPES_VISIBLE_DEFAULT); |
| 1818 | 1831 |
} |
| 1819 |
return cdm_ws_getAnnotationsFor($cdm_entity, variable_get(ANNOTATION_TYPES_VISIBLE, $annotations_types_filter));
|
|
| 1832 |
return cdm_ws_fetch_annotations($cdm_entity, variable_get(ANNOTATION_TYPES_VISIBLE, $annotations_types_filter));
|
|
| 1820 | 1833 |
} |
| 1821 | 1834 |
|
| 1822 | 1835 |
/** |
| ... | ... | |
| 1830 | 1843 |
*/ |
| 1831 | 1844 |
function cdm_load_annotations(&$annotatable_entity) {
|
| 1832 | 1845 |
if (isset($annotatable_entity) && !isset($annotatable_entity->annotations)) {
|
| 1833 |
$annotations = cdm_ws_getAnnotationsFor($annotatable_entity);
|
|
| 1846 |
$annotations = cdm_ws_fetch_annotations($annotatable_entity);
|
|
| 1834 | 1847 |
if (is_array($annotations)) {
|
| 1835 | 1848 |
$annotatable_entity->annotations = $annotations; |
| 1836 | 1849 |
} |
| ... | ... | |
| 2699 | 2712 |
return $query; |
| 2700 | 2713 |
} |
| 2701 | 2714 |
|
| 2702 |
/** |
|
| 2703 |
* Implementation of the magic method __clone to allow deep cloning of objects |
|
| 2704 |
* and arrays. |
|
| 2705 |
*/ |
|
| 2706 |
function __clone() {
|
|
| 2707 |
foreach ($this as $name => $value) {
|
|
| 2708 |
if (gettype($value) == 'object' || gettype($value) == 'array') {
|
|
| 2709 |
$this->$name = clone($this->$name); |
|
| 2710 |
} |
|
| 2711 |
} |
|
| 2712 |
} |
|
| 2713 |
|
|
| 2714 | 2715 |
/** |
| 2715 | 2716 |
* Compares the given CDM Term instances by the representationL10n. |
| 2716 | 2717 |
* |
| modules/cdm_dataportal/includes/descriptions.inc | ||
|---|---|---|
| 345 | 345 |
* @param $footnote_list_key_suggestion string |
| 346 | 346 |
* Optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined by the nested |
| 347 | 347 |
* method calls by calling RenderHints::getFootnoteListKey(). NOTE: the footnote key for annotations will be set to |
| 348 |
* RenderHints::getFootnoteListKey().'-annotations'. @return String |
|
| 348 |
* RenderHints::getFootnoteListKey().'-annotations'. |
|
| 349 |
* |
|
| 350 |
* @return String |
|
| 349 | 351 |
* The foot note keys |
| 350 | 352 |
* |
| 351 | 353 |
* @see cdm_entities_annotations_as_footnotekeys() |
| ... | ... | |
| 367 | 369 |
$sources = cdm_entity_sources_sorted($description_element); |
| 368 | 370 |
|
| 369 | 371 |
// Annotations as footnotes. |
| 370 |
$footNoteKeys = cdm_entity_annotations_as_footnotekeys($description_element, $footnote_list_key_suggestion);
|
|
| 372 |
$footnote_keys = cdm_entity_annotations_as_footnotekeys($description_element, $footnote_list_key_suggestion);
|
|
| 371 | 373 |
|
| 372 | 374 |
// Source references as footnotes. |
| 373 | 375 |
if($is_bibliography_aware){
|
| ... | ... | |
| 394 | 396 |
$original_source_footnote_tag |
| 395 | 397 |
); |
| 396 | 398 |
// Ensure uniqueness of the footnote keys. |
| 397 |
cdm_add_footnote_to_array($footNoteKeys, $fn_key);
|
|
| 399 |
cdm_add_footnote_to_array($footnote_keys, $fn_key);
|
|
| 398 | 400 |
} |
| 399 | 401 |
} |
| 400 | 402 |
// Sort and render footnote keys. |
| 401 |
$footnoteKeyListStr = ''; |
|
| 402 |
asort($footNoteKeys); |
|
| 403 |
foreach ($footNoteKeys as $footNoteKey) {
|
|
| 404 |
try{
|
|
| 405 |
$footnoteKeyListStr .= theme('cdm_footnote_key',
|
|
| 403 |
asort($footnote_keys); |
|
| 404 |
$footnotes_markup = footnote_keys_to_markup($footnote_keys, $separator); |
|
| 405 |
return $footnotes_markup; |
|
| 406 |
} |
|
| 407 |
|
|
| 408 |
/** |
|
| 409 |
* Creates markup for an array of foot note keys |
|
| 410 |
* |
|
| 411 |
* @param array $footnote_keys |
|
| 412 |
* @param string $separator |
|
| 413 |
* |
|
| 414 |
* @return string |
|
| 415 |
*/ |
|
| 416 |
function footnote_keys_to_markup(array $footnote_keys, string $separator): string {
|
|
| 417 |
|
|
| 418 |
$footnotes_markup = ''; |
|
| 419 |
foreach ($footnote_keys as $foot_note_key) {
|
|
| 420 |
try {
|
|
| 421 |
$footnotes_markup .= theme('cdm_footnote_key',
|
|
| 406 | 422 |
array( |
| 407 |
'footnoteKey' => $footNoteKey, |
|
| 408 |
'separator' => ($footnoteKeyListStr ? $separator : ''))); |
|
| 423 |
'footnoteKey' => $foot_note_key, |
|
| 424 |
'separator' => ($footnotes_markup ? $separator : '') |
|
| 425 |
)); |
|
| 409 | 426 |
} catch (Exception $e) {
|
| 410 |
drupal_set_message("Exception: " . $e->getMessage(), 'error');
|
|
| 427 |
drupal_set_message("Exception: " . $e->getMessage(), 'error');
|
|
| 411 | 428 |
} |
| 412 | 429 |
} |
| 413 |
return $footnoteKeyListStr;
|
|
| 430 |
return $footnotes_markup;
|
|
| 414 | 431 |
} |
| 415 | 432 |
|
| 416 | 433 |
|
| ... | ... | |
| 559 | 576 |
|
| 560 | 577 |
$annotations_and_sources = array( |
| 561 | 578 |
'foot_note_keys' => NULL, |
| 562 |
'source_references' => array(),
|
|
| 563 |
'names_used_in_source' => array()
|
|
| 579 |
'source_references' => [],
|
|
| 580 |
'names_used_in_source' => []
|
|
| 564 | 581 |
); |
| 565 | 582 |
|
| 566 | 583 |
// some entity types only have single sources: |
| ... | ... | |
| 596 | 613 |
} |
| 597 | 614 |
} // END of loop over sources |
| 598 | 615 |
|
| 599 |
// annotations footnotes separate. |
|
| 600 |
$annotations_and_sources['foot_note_keys'] = theme('cdm_entities_annotations_as_footnotekeys',
|
|
| 601 |
array( |
|
| 602 |
'cdmBase_list' => $entity, |
|
| 603 |
'footnote_list_key' => $footnote_list_key_suggestion, |
|
| 604 |
) |
|
| 616 |
// annotations footnotes separate from sources |
|
| 617 |
$annotations_and_sources['foot_note_keys'] = footnote_keys_to_markup( |
|
| 618 |
cdm_entity_annotations_as_footnotekeys($entity, $footnote_list_key_suggestion), ', ' |
|
| 605 | 619 |
); |
| 606 | 620 |
|
| 607 | 621 |
} // END of references inline |
| modules/cdm_dataportal/includes/name.inc | ||
|---|---|---|
| 694 | 694 |
$render_array['nomenclatural_act']['#weight'] + 10 ); |
| 695 | 695 |
} |
| 696 | 696 |
|
| 697 |
$render_array['footnotes'] = markup_to_render_array( |
|
| 698 |
theme('cdm_annotation_footnotes', ['footnoteListKey' => RenderHints::getFootnoteListKey() ]),
|
|
| 699 |
12 |
|
| 700 |
); |
|
| 701 |
|
|
| 697 | 702 |
// registration date and office |
| 698 | 703 |
$registration_date_insitute_markup = render_registration_date_and_institute($registration_dto); |
| 699 | 704 |
if($registration_date_insitute_markup){
|
| ... | ... | |
| 702 | 707 |
100); |
| 703 | 708 |
} |
| 704 | 709 |
|
| 710 |
|
|
| 705 | 711 |
return $render_array; |
| 706 | 712 |
} |
| 707 | 713 |
|
| ... | ... | |
| 864 | 870 |
/** |
| 865 | 871 |
* Renders and array of CDM TypeDesignations |
| 866 | 872 |
* |
| 873 |
* - NameTypeDesignation |
|
| 874 |
* - SpecimenTypeDesignation |
|
| 875 |
* - TextualTypeDesignation |
|
| 876 |
* |
|
| 867 | 877 |
* @param object $type_designations an array of cdm TypeDesignation entities |
| 868 | 878 |
* to render |
| 869 | 879 |
* @param string $enclosing_tag the tag element type to enclose the whole list |
| ... | ... | |
| 1084 | 1094 |
/** |
| 1085 | 1095 |
* Composes the TypedEntityReference to name type designations passed as associatve array. |
| 1086 | 1096 |
* |
| 1087 |
* @param $$type_entity_refs array
|
|
| 1097 |
* @param $type_entity_refs array |
|
| 1088 | 1098 |
* an associative array of name type type => TypedEntityReference for name type designations as |
| 1089 | 1099 |
* produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager |
| 1090 | 1100 |
* |
| ... | ... | |
| 1128 | 1138 |
|
| 1129 | 1139 |
$render_array = array(); |
| 1130 | 1140 |
|
| 1141 |
static $annotations_and_sources_config = [ |
|
| 1142 |
'sources_as_content' => TRUE, |
|
| 1143 |
'link_to_name_used_in_source' => FALSE, |
|
| 1144 |
'link_to_reference' => TRUE, |
|
| 1145 |
'add_footnote_keys' => FALSE, |
|
| 1146 |
'bibliography_aware' => FALSE |
|
| 1147 |
]; |
|
| 1148 |
|
|
| 1131 | 1149 |
$type_designation_list = array(); |
| 1132 | 1150 |
uksort($type_entity_refs, "compare_type_designation_status_labels"); |
| 1133 |
foreach($type_entity_refs as $type_status => $specimen_types){
|
|
| 1134 |
foreach($specimen_types as $specimen_type){
|
|
| 1151 |
foreach($type_entity_refs as $type_status => $type_designation_entity_refs){
|
|
| 1152 |
foreach($type_designation_entity_refs as $type_designation_entity_ref){
|
|
| 1135 | 1153 |
|
| 1136 |
$type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($specimen_type->uuid));
|
|
| 1154 |
$type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($type_designation_entity_ref->uuid));
|
|
| 1137 | 1155 |
$type_designation_list[] = $type_designation; // collect for the map |
| 1138 | 1156 |
|
| 1139 |
$derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
|
|
| 1157 |
$derived_unit_facade_dto = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
|
|
| 1140 | 1158 |
// the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately |
| 1141 | 1159 |
$mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen')); |
| 1142 | 1160 |
|
| ... | ... | |
| 1145 | 1163 |
$citation_markup = ''; |
| 1146 | 1164 |
$media = ''; |
| 1147 | 1165 |
|
| 1166 |
// annotations and sources for the $derived_unit_facade_dto |
|
| 1167 |
$annotations_and_sources = handle_annotations_and_sources( |
|
| 1168 |
$derived_unit_facade_dto, |
|
| 1169 |
$annotations_and_sources_config, |
|
| 1170 |
'', |
|
| 1171 |
null |
|
| 1172 |
); |
|
| 1173 |
$source_citations = $annotations_and_sources['source_references']; |
|
| 1174 |
$foot_note_keys = $annotations_and_sources['foot_note_keys']; |
|
| 1175 |
|
|
| 1148 | 1176 |
// preferredStableUri |
| 1149 | 1177 |
if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
|
| 1150 | 1178 |
$preferredStableUri = $type_designation->typeSpecimen->preferredStableUri; |
| ... | ... | |
| 1162 | 1190 |
); |
| 1163 | 1191 |
$media = compose_cdm_media_gallerie(array( |
| 1164 | 1192 |
'mediaList' => array($mediaSpecimen), |
| 1165 |
'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
|
|
| 1193 |
'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $type_designation_entity_ref->uuid,
|
|
| 1166 | 1194 |
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'], |
| 1167 | 1195 |
'cols' => $gallery_settings['cdm_dataportal_media_cols'], |
| 1168 | 1196 |
'captionElements' => $captionElements, |
| 1169 | 1197 |
)); |
| 1170 | 1198 |
} |
| 1171 |
// citation and detail |
|
| 1199 |
// citation and detail for the media specimen
|
|
| 1172 | 1200 |
$annotations_and_sources = handle_annotations_and_sources( |
| 1173 |
$mediaSpecimen, |
|
| 1174 |
array( |
|
| 1175 |
'sources_as_content' => true, |
|
| 1176 |
'link_to_name_used_in_source' => false, |
|
| 1177 |
'link_to_reference' => true, |
|
| 1178 |
'add_footnote_keys' => false, |
|
| 1179 |
'bibliography_aware' => false), |
|
| 1180 |
'', |
|
| 1181 |
null |
|
| 1201 |
$mediaSpecimen, |
|
| 1202 |
$annotations_and_sources_config, |
|
| 1203 |
'', |
|
| 1204 |
null |
|
| 1182 | 1205 |
); |
| 1183 | 1206 |
if(is_array( $annotations_and_sources['source_references'])){
|
| 1184 |
$citation_markup = join(', ', $annotations_and_sources['source_references']);
|
|
| 1207 |
$source_citations = array_merge($source_citations, $annotations_and_sources['source_references']); |
|
| 1208 |
} |
|
| 1209 |
if($annotations_and_sources['foot_note_keys']){
|
|
| 1210 |
$foot_note_keys .= ', ' . $annotations_and_sources['foot_note_keys']; |
|
| 1185 | 1211 |
} |
| 1186 | 1212 |
} |
| 1187 | 1213 |
|
| 1188 |
$specimen_markup = $derivedUnitFacadeInstance->titleCache; |
|
| 1189 |
if(isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
|
|
| 1190 |
$specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup); |
|
| 1214 |
$citation_markup = join(', ', $source_citations);
|
|
| 1215 |
|
|
| 1216 |
$specimen_markup = $derived_unit_facade_dto->titleCache; |
|
| 1217 |
if(isset($derived_unit_facade_dto->specimenLabel) && $derived_unit_facade_dto->specimenLabel){
|
|
| 1218 |
$specimen_markup = str_replace( |
|
| 1219 |
$derived_unit_facade_dto->specimenLabel, |
|
| 1220 |
l($derived_unit_facade_dto->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup); |
|
| 1191 | 1221 |
} |
| 1192 | 1222 |
|
| 1193 |
$type_designation_render_array = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type) . '">
|
|
| 1223 |
$type_designation_render_array = markup_to_render_array( |
|
| 1224 |
'<div class="type_designation_entity_ref ' . html_class_attribute_ref($type_designation_entity_ref) . '"> |
|
| 1194 | 1225 |
<span class="type-status">' . ucfirst($type_status) . "</span>: " |
| 1195 |
. $specimen_markup |
|
| 1226 |
. $specimen_markup . $foot_note_keys
|
|
| 1196 | 1227 |
. ($citation_markup ? ' '. $citation_markup : '') |
| 1197 | 1228 |
. ($preferredStableUri ? " ". l($preferredStableUri, $preferredStableUri) : '') |
| 1198 | 1229 |
. $media |
Also available in: Unified diff
ref #8850 showing fieldunit annotations in registration page