Revision 72d57201
Added by Katja Luther almost 5 years ago
| modules/cdm_dataportal/includes/occurrences.inc | ||
|---|---|---|
| 469 | 469 |
$taxon_name = cdm_ws_get(CDM_WS_NAME, $determinationEvent->taxonName->uuid); |
| 470 | 470 |
$taxon_name->taggedName = cdm_ws_get(CDM_WS_NAME, array($determinationEvent->taxonName->uuid, "taggedName")); |
| 471 | 471 |
$name_link = path_to_name($determinationEvent->taxonName->uuid); |
| 472 |
}else if ($determinationEvent->taxon) {
|
|
| 473 |
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
|
|
| 474 |
$name_link = path_to_taxon($determinationEvent->taxon->uuid);
|
|
| 472 |
} else if ($determinationEvent->taxon) {
|
|
| 473 |
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid); |
|
| 474 |
$name_link = path_to_taxon($determinationEvent->taxon->uuid); |
|
| 475 | 475 |
} |
| 476 | 476 |
if ($taxon_name) {
|
| 477 | 477 |
$taxon_html = render_taxon_or_name($taxon_name, $name_link); |
| ... | ... | |
| 501 | 501 |
foreach ($value as $description) {
|
| 502 | 502 |
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid); |
| 503 | 503 |
|
| 504 |
if($description->imageGallery == TRUE) {
|
|
| 505 |
continue; |
|
| 506 |
} |
|
| 504 |
if ($description->imageGallery == TRUE) {
|
|
| 505 |
continue;
|
|
| 506 |
}
|
|
| 507 | 507 |
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements); |
| 508 | 508 |
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null)); |
| 509 | 509 |
$dd_elements[] = $description_render_elements; |
| ... | ... | |
| 512 | 512 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements); |
| 513 | 513 |
break; |
| 514 | 514 |
case '_derivedUnitMedia': |
| 515 |
if ($isSpecimen_page){
|
|
| 515 |
if ($isSpecimen_page) {
|
|
| 516 | 516 |
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME); |
| 517 | 517 |
$captionElements = array( |
| 518 | 518 |
'#uri' => t('open media'),
|
| ... | ... | |
| 528 | 528 |
'alternativeMediaUri' => NULL, |
| 529 | 529 |
'galleryLinkUri' => NULL, |
| 530 | 530 |
)); |
| 531 |
@_description_list_group_add($groups, "Detail Images:" , markup_to_render_array($gallery_html),'',20);
|
|
| 531 |
@_description_list_group_add($groups, "Detail Images:", markup_to_render_array($gallery_html), '', 20);
|
|
| 532 | 532 |
} |
| 533 | 533 |
|
| 534 |
// $dd_elements[] = markup_to_render_array($gallery_html); |
|
| 534 |
// $dd_elements[] = markup_to_render_array($gallery_html);
|
|
| 535 | 535 |
|
| 536 | 536 |
break; |
| 537 | 537 |
case 'sources': |
| ... | ... | |
| 546 | 546 |
NULL, |
| 547 | 547 |
'' |
| 548 | 548 |
); |
| 549 |
if(!empty($annotations_and_sources['source_references'])){
|
|
| 550 |
@_description_list_group_add($groups, t('Sources') . ':', join(', ', $annotations_and_sources['source_references']),'',12 );
|
|
| 549 |
if (!empty($annotations_and_sources['source_references'])) {
|
|
| 550 |
@_description_list_group_add($groups, t('Sources') . ':', join(', ', $annotations_and_sources['source_references']), '', 12);
|
|
| 551 | 551 |
} |
| 552 | 552 |
break; |
| 553 | 553 |
|
| ... | ... | |
| 559 | 559 |
foreach ($derivedFrom->originals as $original) {
|
| 560 | 560 |
$pathToSpecimen = path_to_specimen($original->uuid); |
| 561 | 561 |
$description = ""; |
| 562 |
if (isset( $derivedFrom->description) && $derivedFrom->description != ''){
|
|
| 562 |
if (isset($derivedFrom->description) && $derivedFrom->description != '') {
|
|
| 563 | 563 |
$description = $derivedFrom->description . ": "; |
| 564 | 564 |
} |
| 565 | 565 |
|
| 566 | 566 |
$originals[] = markup_to_render_array(l($description . $original->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
| 567 |
if ($original->class == 'FieldUnit'){
|
|
| 567 |
if ($original->class == 'FieldUnit') {
|
|
| 568 | 568 |
$label = t('Field data');
|
| 569 |
}else{
|
|
| 569 |
} else {
|
|
| 570 | 570 |
$label = t('Derived from');
|
| 571 | 571 |
} |
| 572 | 572 |
@_description_list_group_add($groups, $label . ':', |
| ... | ... | |
| 588 | 588 |
} |
| 589 | 589 |
|
| 590 | 590 |
$derived_units[] = markup_to_render_array(l($description . $derived_unit->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
| 591 |
} |
|
| 592 |
} @_description_list_group_add($groups, t('Derivates') . ':',
|
|
| 591 |
} |
|
| 592 |
} |
|
| 593 |
@_description_list_group_add($groups, t('Derivates') . ':',
|
|
| 593 | 594 |
$derived_units, |
| 594 |
'', 100);
|
|
| 595 |
'', 100); |
|
| 595 | 596 |
|
| 596 | 597 |
} |
| 597 | 598 |
break; |
| ... | ... | |
| 616 | 617 |
case 'storedUnder': |
| 617 | 618 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
| 618 | 619 |
break; |
| 620 |
case 'dnaQuality': |
|
| 621 |
$sub_dl_groups = array(); |
|
| 622 |
|
|
| 623 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('purificationMethod'), $value->purificationMethod, NULL, 1);
|
|
| 624 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_230'), $value->ratioOfAbsorbance260_230, NULL, 2);
|
|
| 625 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_280'), $value->ratioOfAbsorbance260_280, NULL, 3);
|
|
| 626 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentration'), $value->concentration, NULL, 4);
|
|
| 627 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentrationUnit'), $value->concentrationUnit, NULL, 4);
|
|
| 628 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityTerm'), $value->qualityTerm, NULL, 4);
|
|
| 629 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityCheckDate'), $value->qualityCheckDate, NULL, 4);
|
|
| 630 |
|
|
| 631 |
if (is_array($sub_dl_groups) && sizeof($sub_dl_groups)>0) {
|
|
| 632 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), |
|
| 633 |
array( |
|
| 634 |
array('#markup' => $value->titleCache),
|
|
| 635 |
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
| 636 |
) |
|
| 637 |
); |
|
| 638 |
} |
|
| 639 |
break; |
|
| 640 |
|
|
| 641 |
case 'preservation': |
|
| 642 |
$sub_dl_groups = array(); |
|
| 619 | 643 |
|
| 644 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('medium'), $value->medium, NULL, 1);
|
|
| 645 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('temperature'), $value->temperature, NULL, 2);
|
|
| 646 |
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('definedMaterialOrMethod'), $value->definedMaterialOrMethod, NULL, 3);
|
|
| 647 |
|
|
| 648 |
if (is_array($sub_dl_groups) && sizeof($sub_dl_groups)>0) {
|
|
| 649 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), |
|
| 650 |
array( |
|
| 651 |
array('#markup' => $value->titleCache),
|
|
| 652 |
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
| 653 |
) |
|
| 654 |
); |
|
| 655 |
} |
|
| 656 |
break; |
|
| 620 | 657 |
|
| 621 | 658 |
/* ---- Specimen --- */ |
| 622 | 659 |
case 'sequences': |
| ... | ... | |
| 1064 | 1101 |
case 'kindOfUnit': |
| 1065 | 1102 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1); |
| 1066 | 1103 |
break; |
| 1067 |
|
|
| 1104 |
case 'accessionNumber': |
|
| 1105 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 0); |
|
| 1106 |
break; |
|
| 1068 | 1107 |
|
| 1069 | 1108 |
case 'preferredStableUri': |
| 1070 | 1109 |
|
| ... | ... | |
| 1092 | 1131 |
); |
| 1093 | 1132 |
$gallery_html = compose_cdm_media_gallerie(array( |
| 1094 | 1133 |
'mediaList' => $value, |
| 1095 |
'galleryName' => $specimen_or_observation->label,
|
|
| 1134 |
'galleryName' => $specimen_or_observation->uuid,
|
|
| 1096 | 1135 |
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'], |
| 1097 | 1136 |
'cols' => $gallery_settings['cdm_dataportal_media_cols'], |
| 1098 | 1137 |
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null, |
| ... | ... | |
| 1209 | 1248 |
case 'derivationEvents': |
| 1210 | 1249 |
//@_description_list_group_add($groups, t('Association type'), $value->description);
|
| 1211 | 1250 |
break; |
| 1251 |
case 'determinedNames': |
|
| 1252 |
$dd_elements = array(); |
|
| 1253 |
foreach ($value as $name) {
|
|
| 1254 |
$taxon_name = cdm_ws_get(CDM_WS_NAME, $name->key); |
|
| 1255 |
$taxon_name->taggedName = cdm_ws_get(CDM_WS_NAME, array($name->key, "taggedName")); |
|
| 1256 |
$name_link = path_to_name($name->key); |
|
| 1257 |
|
|
| 1258 |
//$taxon_html = render_taxon_or_name($taxon_name, $name_link); |
|
| 1259 |
$taxon_html = l($taxon_name->titleCache, $name_link, array('attributes' => array('target' => '_blank')));
|
|
| 1260 |
$dd_elements[] = $taxon_html; |
|
| 1261 |
} |
|
| 1262 |
@_description_list_group_add($groups, cdm_occurrence_field_name_label("Identification(s)"), $dd_elements,'', 100);
|
|
| 1263 |
break; |
|
| 1212 | 1264 |
|
| 1213 | 1265 |
|
| 1214 | 1266 |
default: |
| ... | ... | |
| 1240 | 1292 |
$output .= $gallery_html; |
| 1241 | 1293 |
} |
| 1242 | 1294 |
$pathToSpecimen = path_to_specimen($specimen_or_observation->uuid); |
| 1243 |
$output .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
|
| 1295 |
$output .= l("Detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
|
| 1244 | 1296 |
} // END of $specimenOrObservation exists |
| 1245 | 1297 |
|
| 1246 | 1298 |
return $output; |
| 1247 | 1299 |
} |
| 1248 | 1300 |
|
| 1249 | 1301 |
function compose_table_of_blast_result(array $data){
|
| 1302 |
// get icon images |
|
| 1303 |
$expand_icon = font_awesome_icon_markup( |
|
| 1304 |
'fa-plus-square-o', |
|
| 1305 |
array( |
|
| 1306 |
'alt' => 'Show details', |
|
| 1307 |
'class' => array('expand_icon')
|
|
| 1308 |
) |
|
| 1309 |
); |
|
| 1310 |
$collapse_icon = font_awesome_icon_markup( |
|
| 1311 |
'fa-minus-square-o', |
|
| 1312 |
array( |
|
| 1313 |
'alt' => 'Show details', |
|
| 1314 |
'class' => array('collapse_icon')
|
|
| 1315 |
) |
|
| 1316 |
); |
|
| 1317 |
//$detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
|
|
| 1318 |
$rowcount = 0; |
|
| 1319 |
$rows = array(); |
|
| 1250 | 1320 |
|
| 1251 | 1321 |
foreach ($data as $row_data){
|
| 1252 | 1322 |
$pathToSpecimen = path_to_specimen_by_accession_number($row_data['id']); |
| ... | ... | |
| 1254 | 1324 |
|
| 1255 | 1325 |
$rows[] = array( |
| 1256 | 1326 |
'data' => array( |
| 1327 |
array( |
|
| 1328 |
'data' => $expand_icon . $collapse_icon, |
|
| 1329 |
'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
|
|
| 1330 |
), |
|
| 1257 | 1331 |
array( |
| 1258 | 1332 |
'data' => $row_data['def'], |
| 1259 | 1333 |
), |
| ... | ... | |
| 1263 | 1337 |
array( |
| 1264 | 1338 |
'data' => $row_data['hsp_align_length'], |
| 1265 | 1339 |
), |
| 1266 |
// array( |
|
| 1267 |
// 'data' => $row_data['midline'], |
|
| 1268 |
// ), |
|
| 1269 | 1340 |
array( |
| 1270 |
'data' => $row_data['hsp_evalue'], |
|
| 1341 |
'data' => $row_data['hsp_identity'], |
|
| 1342 |
), |
|
| 1343 |
array( |
|
| 1344 |
'data' => $row_data['hsp_identity']/$row_data['hsp_align_length']*100, |
|
| 1271 | 1345 |
) |
| 1272 |
) |
|
| 1346 |
), |
|
| 1347 |
'id' => 'blast_summary' . $rowcount, // summary row id |
|
| 1348 |
'class' => array('summary_row'),
|
|
| 1349 |
); |
|
| 1350 |
$detail_html = ""; |
|
| 1351 |
|
|
| 1352 |
$detail_html .= create_label("Details") . $row_data["hsp_align_length"] . "<br>";
|
|
| 1353 |
|
|
| 1354 |
|
|
| 1355 |
$detail_html .= "<br>"; |
|
| 1356 |
$detail_html .= $row_data["hsp_midline"]; |
|
| 1357 |
|
|
| 1358 |
//$detail_html .= "<br>"; |
|
| 1359 |
|
|
| 1360 |
$rows[] = array( |
|
| 1361 |
'data' => array( |
|
| 1362 |
array( |
|
| 1363 |
'data' => "", //empty first column |
|
| 1364 |
'class' => array('expand_column')
|
|
| 1365 |
), |
|
| 1366 |
array( |
|
| 1367 |
'data' => $detail_html, |
|
| 1368 |
'colspan' => 5, |
|
| 1369 |
), |
|
| 1370 |
), |
|
| 1371 |
'id' => 'blast_detail' . $rowcount,//details row ID |
|
| 1372 |
'class' => array('detail_row'),
|
|
| 1273 | 1373 |
); |
| 1374 |
$rowcount++; |
|
| 1274 | 1375 |
} |
| 1376 |
|
|
| 1275 | 1377 |
$tableId = "blast_result_table"; |
| 1276 | 1378 |
$blast_result_table = array( |
| 1277 | 1379 |
"#theme" => "table", |
| 1278 | 1380 |
"#weight" => 2, |
| 1279 | 1381 |
"#header" => array( |
| 1280 |
"Name", "id", "Align Length", "e Value"), |
|
| 1382 |
array( |
|
| 1383 |
'data' => "", |
|
| 1384 |
'class' => array('expand_column')
|
|
| 1385 |
), |
|
| 1386 |
"Name", "Accession Number", "Align Length", "Identity", "% Identity"), |
|
| 1281 | 1387 |
"#rows" => $rows, |
| 1282 | 1388 |
"#attributes" => array( |
| 1283 | 1389 |
"id" => $tableId, |
| ... | ... | |
| 1287 | 1393 |
|
| 1288 | 1394 |
drupal_add_js_rowToggle("#".$tableId);
|
| 1289 | 1395 |
|
| 1290 |
$render_array['content'] = $blast_result_table;
|
|
| 1396 |
$render_array[$tableId] = $blast_result_table;
|
|
| 1291 | 1397 |
$out = drupal_render($render_array); |
| 1292 | 1398 |
//$blast_result_page-> content = drupal_render($render_array); |
| 1293 | 1399 |
return $out; |
| 1294 | 1400 |
} |
| 1295 | 1401 |
|
| 1296 |
|
|
| 1297 |
|
|
Also available in: Unified diff
ref #8182: specimen tree is collapsable, blast result table with clickable details