Merge branch 'develop' into issue#2592_shup_mass_import_bugfix

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/controler/DatasetApiController.java

@@ -165,13 +165,11 @@ public ResponseEntity<Void> deleteDataset(
 			if (ds == null) {
 				return new ResponseEntity<>(HttpStatus.NO_CONTENT);
 			}
+			LOG.info("Deletion of dataset with ID: " + ds.getId());
 			Long studyId = datasetService.getStudyId(ds);
-
-
 			datasetService.deleteById(datasetId);
 			solrService.deleteFromIndex(datasetId);
 			rabbitTemplate.convertAndSend(RabbitMQConfiguration.RELOAD_BIDS, objectMapper.writeValueAsString(studyId));
-
 			return new ResponseEntity<>(HttpStatus.NO_CONTENT);
 		} catch (EntityNotFoundException | RestServiceException e) {
 			throw e;
@@ -187,6 +185,10 @@ public ResponseEntity<Void> deleteDatasets(
 			@RequestBody List<Long> datasetIds)
 			throws RestServiceException {
 		try {
+			if (datasetIds.size() > DATASET_LIMIT) {
+				throw new RestServiceException(
+						new ErrorModel(HttpStatus.FORBIDDEN.value(), "This selection includes " + datasetIds.size() + " datasets. You can't delete more than " + DATASET_LIMIT + " datasets."));
+			}
 			datasetService.deleteByIdIn(datasetIds);
 			solrService.deleteFromIndex(datasetIds);
 			return new ResponseEntity<>(HttpStatus.NO_CONTENT);

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetService.java

@@ -144,7 +144,7 @@ public interface DatasetService {
 	List<Dataset> findByStudycard(Long studycardId);
 
 	@PreAuthorize("hasRole('ADMIN') or (hasRole('EXPERT') and @datasetSecurityService.hasRightOnDataset(#dataset.getId(), 'CAN_ADMINISTRATE'))")
-	void deleteDatasetFromPacs(Dataset dataset) throws ShanoirException;
+	void deleteDatasetFromDiskAndPacs(Dataset dataset) throws ShanoirException;
 
 	boolean existsById(Long id);
 

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/service/DatasetServiceImpl.java

@@ -142,7 +142,6 @@ private void delete(Dataset entity) throws ShanoirException, SolrServerException
 	public void deleteById(final Long id) throws ShanoirException, SolrServerException, IOException, RestServiceException {
 		final Dataset dataset = repository.findById(id)
 				.orElseThrow(() -> new EntityNotFoundException(Dataset.class, id));
-
 		// Do not delete entity if it is the source (or if it has copies). If getSourceId() is not null, it means it's a copy
 		if (!CollectionUtils.isEmpty(dataset.getCopies())) {
 			throw new RestServiceException(
@@ -151,10 +150,12 @@ public void deleteById(final Long id) throws ShanoirException, SolrServerExcepti
 							"This dataset is linked to another dataset that was copied."
 					));
 		}
-
+		long startTime = System.currentTimeMillis();
 		delete(dataset);
-
-		this.deleteDatasetFromPacs(dataset);
+		deleteDatasetFromDiskAndPacs(dataset);
+        long endTime = System.currentTimeMillis();
+        long elapsedTime = endTime - startTime;
+        LOG.info("Dataset deletion time: " + elapsedTime + " milliseconds");
 	}
 
 	/**
@@ -182,28 +183,27 @@ public void deleteByIdCascade(final Long id) throws ShanoirException, SolrServer
 	}
 
 	@Override
-	public void deleteDatasetFromPacs(Dataset dataset) throws ShanoirException {
+	public void deleteDatasetFromDiskAndPacs(Dataset dataset) throws ShanoirException {
         if (!dicomWeb) {
             return;
         }
-
 		for (DatasetExpression expression : dataset.getDatasetExpressions()) {
 			boolean isDicom = DatasetExpressionFormat.DICOM.equals(expression.getDatasetExpressionFormat());
-
 			for (DatasetFile file : expression.getDatasetFiles()) {
+				// DICOM
 				if (isDicom && file.isPacs()) {
 					dicomWebService.rejectDatasetFromPacs(file.getPath());
+				// NIfTI
 				} else if (!file.isPacs()) {
 					try {
 						URL url = new URL(file.getPath().replaceAll("%20", " "));
 						File srcFile = new File(UriUtils.decode(url.getPath(), "UTF-8"));
 						FileUtils.deleteQuietly(srcFile);
 					} catch (MalformedURLException e) {
-						throw new ShanoirException("Error while deleting dataset file", e);
+						throw new ShanoirException("Error while deleting dataset file.", e);
 					}
 				}
 			}
-			break;
 		}
 	}
 

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dicom/web/DICOMWebApiController.java

@@ -168,14 +168,16 @@ public ResponseEntity<String> findSeriesOfStudy(String examinationUID, Map<Strin
 			acquisitionUID = allParams.get(SERIES_INSTANCE_UID);
 			seriesInstanceUID = seriesInstanceUIDHandler.findSeriesInstanceUIDFromCacheOrDatabase(acquisitionUID);
 		}
-
 		if (studyInstanceUID != null) {
 			String response = dicomWebService.findSeriesOfStudy(studyInstanceUID, includefield, seriesInstanceUID);
-			JsonNode root = mapper.readTree(response);
-			root = sortSeriesBySeriesNumber(root);
-			studyInstanceUIDHandler.replaceStudyInstanceUIDsWithExaminationUIDs(root, examinationUID, false);
-
-			return new ResponseEntity<String>(mapper.writeValueAsString(root), HttpStatus.OK);
+			if (response != null) {
+				JsonNode root = mapper.readTree(response);
+				root = sortSeriesBySeriesNumber(root);
+				studyInstanceUIDHandler.replaceStudyInstanceUIDsWithExaminationUIDs(root, examinationUID, false);
+				return new ResponseEntity<String>(mapper.writeValueAsString(root), HttpStatus.OK);	
+			} else {
+				return new ResponseEntity<>(HttpStatus.NO_CONTENT);
+			}
 		}
 		else {
 			return new ResponseEntity<>(HttpStatus.NO_CONTENT);

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dicom/web/service/DICOMWebService.java

@@ -210,7 +210,9 @@ public ResponseEntity findInstance(String studyInstanceUID, String serieInstance
 				if (entity != null) {
 					ByteArrayResource byteArrayResource = new ByteArrayResource(EntityUtils.toByteArray(entity));
 					HttpHeaders responseHeaders = new HttpHeaders();
-					responseHeaders.setContentLength(entity.getContentLength());
+					if (!entity.isChunked() && entity.getContentLength() >= 0) {
+						responseHeaders.setContentLength(entity.getContentLength());
+					}
 					return new ResponseEntity(byteArrayResource, responseHeaders, HttpStatus.OK);
 				} else {
 					LOG.error("DICOMWeb: findInstance: empty response entity.");				
@@ -298,13 +300,11 @@ private void sendMultipartRequest(HttpEntity entity) throws ShanoirException {
 
 	public void rejectExaminationFromPacs(String studyInstanceUID) throws ShanoirException {
 		String rejectURL = this.serverURL + "/" + studyInstanceUID + REJECT_SUFFIX;
-
 		rejectURLFromPacs(rejectURL);
 	}
 
 	public void rejectAcquisitionFromPacs(String studyInstanceUID, String seriesInstanceUID) throws ShanoirException {
 		String rejectURL = this.serverURL + "/" + studyInstanceUID + "/series/" + seriesInstanceUID + REJECT_SUFFIX;
-
 		rejectURLFromPacs(rejectURL);
 	}
 
@@ -324,12 +324,12 @@ private void rejectURLFromPacs(String url) throws ShanoirException {
 		post.setHeader(HttpHeaders.CONTENT_TYPE, CONTENT_TYPE_JSON);
 		try (CloseableHttpResponse response = httpClient.execute(post)) {
 			if (HttpStatus.OK.value() == response.getCode()) {
-				LOG.info("Rejected from PACS: " + post);
+				LOG.debug("Rejected from PACS: " + post);
 			} else {
 				LOG.error(response.getCode() + ": Could not reject instance from PACS: " + response.getReasonPhrase()
 						+ " for rejectURL: " + url);
+				// in case one URL is Not Found (no DICOM instance present), we continue with deletion
 				if (response.getCode() == 404 && response.getReasonPhrase().startsWith("Not Found")) {
-					LOG.error("Could not delete from pacs: " + response.getCode() + " " + response.getReasonPhrase());
 					return;
 				} else {
 					throw new ShanoirException(response.getCode() + ": Could not reject instance from PACS: " + response.getReasonPhrase()
@@ -345,13 +345,13 @@ private void rejectURLFromPacs(String url) throws ShanoirException {
 	@Scheduled(cron = "0 */30 * * * *", zone="Europe/Paris")
 	public void deleteDicomFilesFromPacs() throws ShanoirException {
 		// Doc : https://smart-api.info/ui/be87344696148a41f577aca202ce84df#/IOCM-RS/deleteRejectedInstancesPermanently
-		LOG.error("Scheduled call to delete all rejected instances from pacs.");
+		LOG.info("Scheduled call to delete all rejected instances from pacs.");
 		String url = this.serverURL.substring(0, this.serverURL.indexOf("/aets/")) + REJECT_SUFFIX;
 		HttpDelete httpDelete = new HttpDelete(url);
 		httpDelete.setHeader(HttpHeaders.CONTENT_TYPE, CONTENT_TYPE_JSON);
 		try (CloseableHttpResponse response = httpClient.execute(httpDelete)) {
 			if (response.getCode() == HttpStatus.OK.value()) {
-				LOG.error("Deleted from PACS: " + url);
+				LOG.info("Deleted from PACS: " + url);
 			} else {
 				LOG.error(response.getCode() + ": Could not delete instance from PACS: " + response.getReasonPhrase()
 						+ "for deleteURL: " + url);

shanoir-ng-datasets/src/main/java/org/shanoir/ng/importer/service/DicomSEGAndSRImporterService.java

@@ -154,7 +154,7 @@ private Examination modifyDicom(Attributes datasetAttributes) {
 		Examination examination = examinationRepository.findById(examinationID).get();
 		// replace artificial examinationUID with real StudyInstanceUID in DICOM server
 		String studyInstanceUID = studyInstanceUIDHandler.findStudyInstanceUIDFromCacheOrDatabase(examinationUID);
-		datasetAttributes.setString(Tag.StudyInstanceUID, VR.UI, studyInstanceUID);		
+		datasetAttributes.setString(Tag.StudyInstanceUID, VR.UI, studyInstanceUID);
 		// replace subject name, that is sent by the viewer wrongly with P-0000001 etc.
 		Optional<Subject> subjectOpt = subjectRepository.findById(examination.getSubject().getId());
 		String subjectName = "error_subject_name_not_found_in_db";
@@ -163,7 +163,7 @@ private Examination modifyDicom(Attributes datasetAttributes) {
 		}
 		datasetAttributes.setString(Tag.PatientName, VR.PN, subjectName);
 		datasetAttributes.setString(Tag.PatientID, VR.LO, subjectName);
-		// set user name, as person, who created the measurement
+		// set user name, as person, who created the measurement/segmentation
 		final String userName = KeycloakUtil.getTokenUserName();
 		datasetAttributes.setString(Tag.PersonName, VR.PN, userName);
 		// set as well person observer name in content sequence

shanoir-ng-datasets/src/test/java/org/shanoir/ng/dataset/DatasetServiceSecurityTest.java

@@ -234,20 +234,20 @@ private void testDelete(String role) throws ShanoirException {
 		if ("ROLE_USER".equals(role)) {
 			given(rightsService.hasRightOnStudy(1L, "CAN_ADMINISTRATE")).willReturn(true);
 			given(rightsService.hasRightOnStudies(Utils.toSet(1L), "CAN_ADMINISTRATE")).willReturn(Utils.toSet(1L));
-			assertAccessDenied(service::deleteDatasetFromPacs, mockDataset(1L, 1L, 1L, 1L, 1L));
+			assertAccessDenied(service::deleteDatasetFromDiskAndPacs, mockDataset(1L, 1L, 1L, 1L, 1L));
 			assertAccessDenied(service::deleteById, 1L);
 			assertAccessDenied(service::deleteByIdIn, Utils.toList(1L, 2L, 3L, 4L));
 			assertAccessDenied(service::deleteByIdIn, Utils.toList(1L, 3L));
 		} else if ("ROLE_EXPERT".equals(role)) {
 			given(rightsService.hasRightOnStudy(1L, "CAN_ADMINISTRATE")).willReturn(false);
 			given(rightsService.hasRightOnStudies(Utils.toSet(1L), "CAN_ADMINISTRATE")).willReturn(Utils.toSet());
-			assertAccessDenied(service::deleteDatasetFromPacs, mockDataset(1L, 1L, 1L, 1L, 1L));
+			assertAccessDenied(service::deleteDatasetFromDiskAndPacs, mockDataset(1L, 1L, 1L, 1L, 1L));
 			assertAccessDenied(service::deleteById, 1L);
 			assertAccessDenied(service::deleteByIdIn, Utils.toList(1L, 2L, 3L, 4L));
 			assertAccessDenied(service::deleteByIdIn, Utils.toList(1L, 3L));
 			given(rightsService.hasRightOnStudy(1L, "CAN_ADMINISTRATE")).willReturn(true);
 			given(rightsService.hasRightOnStudies(Utils.toSet(1L), "CAN_ADMINISTRATE")).willReturn(Utils.toSet(1L));
-			assertAccessAuthorized(service::deleteDatasetFromPacs, mockDataset(1L, 1L, 1L, 1L, 1L));
+			assertAccessAuthorized(service::deleteDatasetFromDiskAndPacs, mockDataset(1L, 1L, 1L, 1L, 1L));
 			assertAccessAuthorized(service::deleteById, 1L);
 			assertAccessDenied(service::deleteByIdIn, Utils.toList(1L, 2L, 3L, 4L));
 			assertAccessDenied(service::deleteByIdIn, Utils.toList(1L, 3L));

shanoir-ng-front/src/app/quality-control/quality-control.component.html

@@ -42,7 +42,7 @@
                 </span>
             </td>
             <td>
-                <button type="button" *ngIf="!pagings.get(qualityCard.id)" class="alt right-icon apply" (click)="apply(qualityCard)" [disabled]="loading.get(qualityCard.id)">
+                <button type="button" *ngIf="!pagings.get(qualityCard.id)" class="alt right-icon apply" (click)="apply(qualityCard)" [disabled]="true || loading.get(qualityCard.id)">
                     Apply now
                     <i *ngIf="!loading.get(qualityCard.id)" class="fa-solid fa-play"></i>
                     <i *ngIf="loading.get(qualityCard.id)" class="fa fa-cog fa-spin"></i>