Revision c10f70e4
Added by Katja Luther over 5 years ago
| modules/cdm_dataportal/includes/occurrences.inc | ||
|---|---|---|
| 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 |
|
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