#2488 : API for in/out download from a list of processingIds

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

@@ -60,6 +60,7 @@
 import org.slf4j.LoggerFactory;
 import org.springframework.amqp.rabbit.core.RabbitTemplate;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.core.io.ByteArrayResource;
 import org.springframework.data.domain.Page;
@@ -139,8 +140,9 @@ public class DatasetApiController implements DatasetApi {
 	@Autowired
 	private SolrService solrService;
 
-	@Autowired
-	DatasetDownloaderServiceImpl datasetDownloaderService;
+    @Qualifier("datasetDownloaderServiceImpl")
+    @Autowired
+	protected DatasetDownloaderServiceImpl datasetDownloaderService;
 
 	@Autowired
 	private ObjectMapper objectMapper;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/repository/DatasetRepository.java

@@ -79,4 +79,9 @@ public interface DatasetRepository extends PagingAndSortingRepository<Dataset, L
     List<Dataset> deleteByDatasetProcessingId(Long id);
 
 	boolean existsByTagsContains(StudyTag tag);
+
+	@Query(value="SELECT ds.id FROM dataset as ds " +
+			"INNER JOIN input_of_dataset_processing as input ON ds.id=input.dataset_id " +
+			"WHERE input.processing_id = :processingId or ds.dataset_processing_id = :processingId", nativeQuery = true)
+	List<Dataset> findDatasetsByProcessingId(Long processingId);
 }

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/security/DatasetSecurityService.java

@@ -1103,5 +1103,60 @@ public boolean hasRightOnExamination(String examinationUID, String rightStr) thr
 		Long id = studyInstanceUIDHandler.extractExaminationId(examinationUID);
 		return hasRightOnExamination(id, rightStr);
     }
-
+
+	public boolean HasRightOnEveryDatasetOfProcessings(List<Long> processingIds, String rightStr) {
+		boolean hasRight = true;
+
+		for (Long processingId : processingIds) {
+			if (KeycloakUtil.getTokenRoles().contains("ROLE_ADMIN") || processingId == null) {
+				continue;
+			}
+			Iterable<Dataset> datasets = datasetRepository.findDatasetsByProcessingId(processingId);
+
+			for (Dataset dataset : datasets) {
+				if (dataset.getDatasetAcquisition() == null
+						|| dataset.getDatasetAcquisition().getExamination() == null
+						|| dataset.getDatasetAcquisition().getExamination().getStudyId() == null) {
+
+					if (dataset.getDatasetProcessing() != null && dataset.getDatasetProcessing().getInputDatasets() != null) {
+						for (Dataset inputDs : dataset.getDatasetProcessing().getInputDatasets()) {
+							hasRight &= hasRightOnTrustedDataset(inputDs, rightStr);
+						}
+					} else {
+						throw new IllegalStateException("Cannot check dataset n°" + dataset.getId() + " rights, this dataset has neither examination nor processing parent !");
+					}
+				} else {
+					hasRight &= this.hasRightOnStudyCenter(dataset.getDatasetAcquisition().getExamination().getCenterId(), dataset.getDatasetAcquisition().getExamination().getStudyId(), rightStr);
+				}
+			}
+		}
+		return hasRight;
+	}
+
+	/**
+	 * Check that the connected user has the given right for the given examination.
+	 *
+	 * @param examinationIds the examination ids
+	 * @param rightStr the right
+	 * @return true or false
+	 * @throws EntityNotFoundException
+	 */
+	public boolean hasRightOnExaminations(List<Long> examinationIds, String rightStr) throws EntityNotFoundException {
+		if (KeycloakUtil.getTokenRoles().contains(ROLE_ADMIN)) {
+			return true;
+		}
+		for (Long examinationId : examinationIds) {
+			Examination exam = examinationRepository.findById(examinationId).orElse(null);
+			if (exam == null) {
+				throw new EntityNotFoundException("Cannot find examination with id " + examinationId);
+			}
+			if (exam.getStudyId() == null) {
+				return false;
+			}
+			if(!this.hasRightOnStudyCenter(exam.getCenterId(), exam.getStudyId(), rightStr)){
+				return false;
+			}
+		}
+		return true;
+	}
 }

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

@@ -60,51 +60,49 @@
 @Service
 public class DatasetDownloaderServiceImpl {
 
-	private static final String FAILURES_TXT = "failures.txt";
+	protected static final String FAILURES_TXT = "failures.txt";
 
-	private static final String NII = "nii";
+	protected static final String NII = "nii";
 
-	private static final String DCM = "dcm";
+	protected static final String DCM = "dcm";
 
-	private static final String ZIP = ".zip";
+	protected static final String ZIP = ".zip";
 
-	private static final Logger LOG = LoggerFactory.getLogger(DatasetDownloaderServiceImpl.class);
+	protected static final Logger LOG = LoggerFactory.getLogger(DatasetDownloaderServiceImpl.class);
 
-	private static final String JSON_RESULT_FILENAME = "ERRORS.json";
+	protected static final String JSON_RESULT_FILENAME = "ERRORS.json";
 
-	private static final Long DEFAULT_NIFTI_CONVERTER_ID = 6L;
+	protected static final Long DEFAULT_NIFTI_CONVERTER_ID = 6L;
 
-	public static final String GZIP_EXTENSION = ".gz";
+	protected static final String GZIP_EXTENSION = ".gz";
 
-    public static final String NII_GZ = ".nii.gz";
-	
-	public static final String CONVERSION_FAILED_ERROR_MSG = "Nifti conversion failed, you may try to select another one.";
+	protected static final String NII_GZ = ".nii.gz";
+
+	protected static final String CONVERSION_FAILED_ERROR_MSG = "Nifti conversion failed, you may try to select another one.";
 
 	@Autowired
 	DatasetService datasetService;
 
 	@Autowired
-	private WADODownloaderService downloader;
+	protected WADODownloaderService downloader;
 
 	@Autowired
-	private SubjectRepository subjectRepository;
+	protected SubjectRepository subjectRepository;
 
 	@Autowired
-	private StudyRepository studyRepository;
+	protected StudyRepository studyRepository;
 
 	@Autowired
-	private RabbitTemplate rabbitTemplate;
+	protected RabbitTemplate rabbitTemplate;
 
 	@Autowired
-	ShanoirEventService eventService;
-
-	SimpleDateFormat fileDateformatter = new SimpleDateFormat("yyyyMMddHHmmss");
+	protected ShanoirEventService eventService;
 
 	@Autowired
-	private ObjectMapper objectMapper;
+	protected ObjectMapper objectMapper;
 
 	@PostConstruct
-	private void initialize() {
+	protected void initialize() {
 		// Set timeout to 5mn (consider nifti reconversion can take some time)
 		this.rabbitTemplate.setReplyTimeout(300000);
 	}
@@ -115,7 +113,6 @@ public void massiveDownload(String format, List<Dataset> datasets, HttpServletRe
 		response.setContentType("application/zip");
 		response.setHeader("Content-Disposition",
 				"attachment;filename=" + getFileName(datasets));
-		SimpleDateFormat formatter = new SimpleDateFormat("yyyyMMddHHmmssSSS");
 		Map<Long, DatasetDownloadError> downloadResults = new HashMap<Long, DatasetDownloadError>();
 
 		try (ZipOutputStream zipOutputStream = new ZipOutputStream(response.getOutputStream())) {
@@ -165,15 +162,15 @@ public void massiveDownload(String format, List<Dataset> datasets, HttpServletRe
 				} else if (NII.equals(format)) {
 					// Check if we have a specific converter -> nifti reconversion
 					if (converterId != null) {
-						reconvertToNifti(format, response, converterId, dataset, formatter, pathURLs, downloadResult, subjectName, zipOutputStream);
+						reconvertToNifti(format, converterId, dataset, pathURLs, downloadResult, subjectName, zipOutputStream);
 					} else {
 						// Check that we have existing nifti, otherwise reconvert using dcm2niix by default.
 						DatasetFileUtils.getDatasetFilePathURLs(dataset, pathURLs, DatasetExpressionFormat.NIFTI_SINGLE_FILE, downloadResult);
 						if (!pathURLs.isEmpty()) {
 							List<String> files = DatasetFileUtils.copyNiftiFilesForURLs(pathURLs, zipOutputStream, dataset, subjectName, false, datasetFilePath);
 						} else {
 							// Reconvert using dcm2niix by default.
-							reconvertToNifti(format, response, DEFAULT_NIFTI_CONVERTER_ID, dataset, formatter, pathURLs, downloadResult, subjectName, zipOutputStream);
+							reconvertToNifti(format, DEFAULT_NIFTI_CONVERTER_ID, dataset, pathURLs, downloadResult, subjectName, zipOutputStream);
 						}
 					}
 				} else {
@@ -211,7 +208,7 @@ public void massiveDownload(String format, List<Dataset> datasets, HttpServletRe
 		}
 	}
 
-	private void reconvertToNifti(String format, HttpServletResponse response, Long converterId, Dataset dataset, SimpleDateFormat formatter, List<URL> pathURLs, DatasetDownloadError downloadResult, String subjectName, ZipOutputStream zipOutputStream) throws RestServiceException, IOException {
+	protected void reconvertToNifti(String format, Long converterId, Dataset dataset, List<URL> pathURLs, DatasetDownloadError downloadResult, String subjectName, ZipOutputStream zipOutputStream) throws RestServiceException, IOException {
 		File userDir = DatasetFileUtils.getUserImportDir("/tmp");
 		String tmpFilePath = userDir + File.separator + dataset.getId() + "_" + format;
 
@@ -272,7 +269,7 @@ private void reconvertToNifti(String format, HttpServletResponse response, Long
 		}
 	}
 
-	private String getSubjectName(Dataset dataset) {
+	protected String getSubjectName(Dataset dataset) {
 		String subjectName = "unknownSubject";
 		if(dataset.getSubjectId() != null){
 			Optional<Subject> subjectOpt = subjectRepository.findById(dataset.getSubjectId());
@@ -283,7 +280,8 @@ private String getSubjectName(Dataset dataset) {
 		return subjectName;
 	}
 
-	private String getFileName(List<Dataset> datasets) {
+	protected String getFileName(List<Dataset> datasets) {
+		SimpleDateFormat fileDateformatter = new SimpleDateFormat("yyyyMMddHHmmss");
 		if (datasets != null && datasets.size() == 1) {
 			String datasetName = getDatasetFileName(datasets.get(0));
 			return "Dataset_" +  datasetName + "_" + fileDateformatter.format(new DateTime().toDate()) + ZIP;
@@ -292,7 +290,7 @@ private String getFileName(List<Dataset> datasets) {
 		}
 	}
 
-	private String getDatasetFileName(Dataset dataset) {
+	protected String getDatasetFileName(Dataset dataset) {
 		// Only one dataset -> the logic for one dataset is used
 		String subjectName = getSubjectName(dataset);
 
@@ -305,7 +303,7 @@ private String getDatasetFileName(Dataset dataset) {
 		return datasetName;
 	}
 
-	private String getDatasetFilepath(Dataset dataset, String studyName, String subjectName) {
+	protected String getDatasetFilepath(Dataset dataset, String studyName, String subjectName) {
 		Examination exam = datasetService.getExamination(dataset);
 
 		String datasetFilePath = studyName + "_" + subjectName + "_Exam-" + exam.getId();

shanoir-ng-datasets/src/main/java/org/shanoir/ng/processing/controler/DatasetProcessingApi.java

@@ -19,11 +19,13 @@
 import io.swagger.v3.oas.annotations.responses.ApiResponse;
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
 import io.swagger.v3.oas.annotations.tags.Tag;
+import jakarta.servlet.http.HttpServletResponse;
 import jakarta.validation.Valid;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.shanoir.ng.dataset.dto.DatasetDTO;
 import org.shanoir.ng.processing.dto.DatasetProcessingDTO;
 import org.shanoir.ng.processing.model.DatasetProcessing;
+import org.shanoir.ng.shared.exception.EntityNotFoundException;
 import org.shanoir.ng.shared.exception.RestServiceException;
 import org.shanoir.ng.shared.exception.ShanoirException;
 import org.springframework.http.ResponseEntity;
@@ -120,4 +122,34 @@ ResponseEntity<Void> updateDatasetProcessing(
 			@Parameter(description = "dataset processing to update", required = true) @Valid @RequestBody DatasetProcessing datasetProcessing, BindingResult result)
 			throws RestServiceException;
 
+	@Operation(summary = "massiveDownloadDatasetsByProcessingIds", description = "If exists, returns a zip file of the inputs/outputs per processing corresponding to the given processing IDs")
+	@ApiResponses(value = {
+			@ApiResponse(responseCode = "200", description = "zip file"),
+			@ApiResponse(responseCode = "401", description = "unauthorized"),
+			@ApiResponse(responseCode = "403", description = "forbidden"),
+			@ApiResponse(responseCode = "404", description = "no dataset found"),
+			@ApiResponse(responseCode = "500", description = "unexpected error") })
+	@GetMapping(value = "/massiveDownloadByProcessing")
+	@PreAuthorize("hasRole('ADMIN') or (hasAnyRole('EXPERT', 'USER') and @datasetSecurityService.HasRightOnEveryDatasetOfProcessings(#processingIds, 'CAN_DOWNLOAD'))")
+	void massiveDownloadByProcessingId(
+			@Parameter(description = "id of the processing", required=true) @Valid
+			@RequestParam(value = "processingIds") List<Long> processingIds,
+			@Parameter(description = "outputs to extract") @Valid
+			@RequestParam(value = "resultOnly") boolean resultOnly, HttpServletResponse response) throws RestServiceException;
+
+	@Operation(summary = "massiveDownloadProcessingDatasetsByExaminationIds", description = "If exists, returns a zip file of the inputs/outputs per processing corresponding to the given examination IDs")
+	@ApiResponses(value = {
+			@ApiResponse(responseCode = "200", description = "zip file"),
+			@ApiResponse(responseCode = "401", description = "unauthorized"),
+			@ApiResponse(responseCode = "403", description = "forbidden"),
+			@ApiResponse(responseCode = "404", description = "no dataset found"),
+			@ApiResponse(responseCode = "500", description = "unexpected error") })
+	@GetMapping(value = "/massiveDownloadProcessingByExamination")
+	@PreAuthorize("hasRole('ADMIN') or (hasAnyRole('EXPERT', 'USER') and @datasetSecurityService.hasRightOnExaminations(#examinationIds, 'CAN_DOWNLOAD'))")
+	void massiveDownloadProcessingByExaminationId(
+			@Parameter(description = "id of the examination", required=true) @Valid
+			@RequestParam(value = "examiantionIds") List<Long> examinationIds,
+			@Parameter(description = "outputs to extract") @Valid
+			@RequestParam(value = "resultOnly") boolean resultOnly, HttpServletResponse response) throws RestServiceException;
+
 }