shanoir-issue#2372: add endpoint to remove SR from viewer

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

@@ -16,6 +16,7 @@
 
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
+import jakarta.persistence.EntityManager;
 import jakarta.transaction.Transactional;
 import org.apache.commons.io.FileUtils;
 import org.apache.solr.client.solrj.SolrServerException;
@@ -107,6 +108,9 @@ public class DatasetServiceImpl implements DatasetService {
 	@Autowired
 	private ProcessingResourceService processingResourceService;
 
+	@Autowired
+	EntityManager entityManager;
+
 	private static final Logger LOG = LoggerFactory.getLogger(DatasetServiceImpl.class);
 
 	@Override
@@ -125,13 +129,18 @@ public void deleteById(final Long id) throws ShanoirException, SolrServerExcepti
 					));
 
 		}
-		// Remove parent processing to avoid errors
-		dataset.setDatasetProcessing(null);
-		processingService.removeDatasetFromAllProcessingInput(id);
-		processingResourceService.deleteByDatasetId(id);
-		propertyService.deleteByDatasetId(id);
-		repository.deleteById(id);
-
+		try {
+			// Remove parent processing to avoid errors
+			dataset.setDatasetProcessing(null);
+			processingService.removeDatasetFromAllProcessingInput(id);
+			processingResourceService.deleteByDatasetId(id);
+			propertyService.deleteByDatasetId(id);
+
+			repository.deleteById(id);
+			entityManager.flush();
+		} catch (Exception e) {
+			LOG.error("ERREUR e : " + e.getMessage());
+		}
 		if (dataset.getSourceId() == null) {
 			this.deleteDatasetFromPacs(dataset);
 		}

shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/validation/DatasetsModalityTypeCheckValidator.java

@@ -16,14 +16,16 @@
 
 import jakarta.validation.ConstraintValidator;
 import jakarta.validation.ConstraintValidatorContext;
-import org.shanoir.ng.dataset.modality.CtDataset;
-import org.shanoir.ng.dataset.modality.MrDataset;
-import org.shanoir.ng.dataset.modality.PetDataset;
+import org.shanoir.ng.dataset.modality.*;
 import org.shanoir.ng.dataset.model.Dataset;
 import org.shanoir.ng.datasetacquisition.model.DatasetAcquisition;
+import org.shanoir.ng.datasetacquisition.model.GenericDatasetAcquisition;
+import org.shanoir.ng.datasetacquisition.model.bids.BidsDatasetAcquisition;
 import org.shanoir.ng.datasetacquisition.model.ct.CtDatasetAcquisition;
+import org.shanoir.ng.datasetacquisition.model.eeg.EegDatasetAcquisition;
 import org.shanoir.ng.datasetacquisition.model.mr.MrDatasetAcquisition;
 import org.shanoir.ng.datasetacquisition.model.pet.PetDatasetAcquisition;
+import org.shanoir.ng.datasetacquisition.model.xa.XaDatasetAcquisition;
 
 /**
  * Validates if all datasets of an acquisition have same modality type than the
@@ -45,7 +47,7 @@ public boolean isValid(final DatasetAcquisition datasetAcquisition, final Constr
 		if (datasetAcquisition.getDatasets() != null && !datasetAcquisition.getDatasets().isEmpty()) {			
 			if (datasetAcquisition instanceof MrDatasetAcquisition) {
 				for (Dataset dataset : datasetAcquisition.getDatasets()) {
-					if (!(dataset instanceof MrDataset)) {
+					if (!(dataset instanceof MrDataset || dataset instanceof MeasurementDataset || dataset instanceof SegmentationDataset)) {
 						return false;
 					}
 				}
@@ -61,6 +63,30 @@ public boolean isValid(final DatasetAcquisition datasetAcquisition, final Constr
 						return false;
 					}
 				}
+			} else if (datasetAcquisition instanceof GenericDatasetAcquisition) {
+				for (Dataset dataset : datasetAcquisition.getDatasets()) {
+					if (!(dataset instanceof GenericDataset)) {
+						return false;
+					}
+				}
+			} else if (datasetAcquisition instanceof EegDatasetAcquisition) {
+				for (Dataset dataset : datasetAcquisition.getDatasets()) {
+					if (!(dataset instanceof EegDataset)) {
+						return false;
+					}
+				}
+			} else if (datasetAcquisition instanceof BidsDatasetAcquisition) {
+				for (Dataset dataset : datasetAcquisition.getDatasets()) {
+					if (!(dataset instanceof BidsDataset)) {
+						return false;
+					}
+				}
+			} else if (datasetAcquisition instanceof XaDatasetAcquisition) {
+				for (Dataset dataset : datasetAcquisition.getDatasets()) {
+					if (!(dataset instanceof XaDataset)) {
+						return false;
+					}
+				}
 			}
 		}
 		return true;

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

@@ -8,12 +8,15 @@
 import io.swagger.v3.oas.annotations.responses.ApiResponses;
 import io.swagger.v3.oas.annotations.tags.Tag;
 import jakarta.servlet.http.HttpServletRequest;
+import org.shanoir.ng.datasetacquisition.dto.DatasetAcquisitionDatasetsDTO;
 import org.shanoir.ng.shared.exception.RestServiceException;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PostAuthorize;
 import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.web.bind.annotation.*;
 
+import java.util.List;
 import java.util.Map;
 
 /**
@@ -170,6 +173,20 @@ ResponseEntity<String> findInstancesOfStudy(
 	@PreAuthorize("hasAnyRole('ADMIN', 'EXPERT', 'USER')")
 	ResponseEntity<Void> stow(HttpServletRequest request) throws RestServiceException;
 
+	@Operation(summary = "", description = "Delete the structured report")
+	@ApiResponses(value = {
+			@ApiResponse(responseCode = "200", description = "found series/acquisitions"),
+			@ApiResponse(responseCode = "204", description = "serie/acquisition deleted"),
+			@ApiResponse(responseCode = "401", description = "unauthorized"),
+			@ApiResponse(responseCode = "403", description = "forbidden"),
+			@ApiResponse(responseCode = "500", description = "unexpected error") })
+	@RequestMapping(value = "/studies/{examinationUID}/series/{seriesInstanceUID}/reject/{reject}", method=RequestMethod.POST)
+	@PreAuthorize("hasAnyRole('ADMIN', 'EXPERT', 'USER')")
+	ResponseEntity<Void> deleteSEGAndSR(
+			@Parameter(description = "examinationUID", required = true) @PathVariable("examinationUID") String examinationUID,
+			@Parameter(description = "seriesInstanceUID", required = true) @PathVariable("seriesInstanceUID") String seriesInstanceUID,
+			@Parameter(description = "reject", required = true) @PathVariable("reject") String reject
+	) throws RestServiceException;
 
 //    @GET
 //    @NoCache

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

@@ -10,7 +10,9 @@
 import org.shanoir.ng.dicom.web.service.DICOMWebService;
 import org.shanoir.ng.examination.model.Examination;
 import org.shanoir.ng.examination.service.ExaminationService;
+import org.shanoir.ng.importer.service.DicomSEGAndSRImporterService;
 import org.shanoir.ng.shared.exception.RestServiceException;
+import org.shanoir.ng.utils.SecurityContextUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -65,9 +67,12 @@ public class DICOMWebApiController implements DICOMWebApi {
 	@Autowired
 	private SeriesInstanceUIDHandler seriesInstanceUIDHandler;
 
+	@Autowired
+	private DicomSEGAndSRImporterService dicomSRImporterService;
+
 	@Autowired
 	private ObjectMapper mapper;
-	
+
 	@Override
 	public ResponseEntity<String> findPatients() throws RestServiceException {
 		return null;
@@ -264,5 +269,14 @@ public ResponseEntity<String> findInstancesOfStudy(String studyInstanceUID) thro
 	public ResponseEntity<Void> stow(HttpServletRequest request) throws RestServiceException {
 		return null;
 	}
-
-}
+
+	@Override
+	public ResponseEntity<Void> deleteSEGAndSR(String examinationIdStr, String seriesInstanceUid, String reject) {
+		Long examinationId = studyInstanceUIDHandler.extractExaminationId(examinationIdStr);
+		if (examinationId != null && seriesInstanceUid != null) {
+			dicomSRImporterService.deleteSR(examinationId, seriesInstanceUid);
+		}
+
+		return new ResponseEntity<Void>(HttpStatus.NO_CONTENT);
+	}
+}

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

@@ -71,7 +71,7 @@ public String findSeriesInstanceUIDFromCacheOrDatabase(String acquisitionUID) {
         return seriesInstanceUID;
     }
 
-    private String findSeriesInstanceUID(DatasetAcquisition acquisition) {
+    public String findSeriesInstanceUID(DatasetAcquisition acquisition) {
         if (acquisition instanceof MrDatasetAcquisition
                 || acquisition instanceof CtDatasetAcquisition
                 || acquisition instanceof PetDatasetAcquisition) {
@@ -99,6 +99,26 @@ private String findSeriesInstanceUID(DatasetAcquisition acquisition) {
         return null;
     }
 
+    public String findSeriesInstanceUID(Dataset ds) {
+        List<DatasetExpression> expressions = ds.getDatasetExpressions();
+        if (!expressions.isEmpty()) {
+            for (DatasetExpression expression : expressions) {
+                // only DICOM is of interest here
+                if (expression.getDatasetExpressionFormat().equals(DatasetExpressionFormat.DICOM)) {
+                    List<DatasetFile> files = expression.getDatasetFiles();
+                    if (!files.isEmpty()) {
+                        DatasetFile file = files.get(0);
+                        if (file.isPacs()) {
+                            String path = file.getPath();
+                            return findSeriesInstanceUID(path);
+                        }
+                    }
+                }
+            }
+        }
+        return null;
+    }
+
     private String findSeriesInstanceUID(String path) {
         Pattern p = Pattern.compile(WADO_URI_SERIES_UID_OBJECT_UID);
         Matcher m = p.matcher(path);

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

@@ -67,9 +67,11 @@ public void doFilter(
       ServletRequest request, 
       ServletResponse response,
       FilterChain chain) throws IOException, ServletException {
+
     	HttpServletRequest httpRequest = (HttpServletRequest) request;
     	if (httpRequest.getMethod().equals(HttpMethod.POST.toString())
     			&& httpRequest.getRequestURI().contains(DICOMWEB_STUDIES)
+				&& httpRequest.getContentType() != null
     			&& httpRequest.getContentType().contains(MediaType.MULTIPART_RELATED_VALUE)) {
     		try(ByteArrayInputStream bIS = new ByteArrayInputStream(httpRequest.getInputStream().readAllBytes())) {
     			ByteArrayDataSource datasource = new ByteArrayDataSource(bIS, MediaType.MULTIPART_RELATED_VALUE);
@@ -92,5 +94,4 @@ public void doFilter(
     	}
         chain.doFilter(request, response);
     }
-
 }

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

@@ -164,7 +164,7 @@ public String findStudyInstanceUIDFromCacheOrDatabase(String examinationUID) {
 	 * @param examination
 	 * @return
 	 */
-	private String findStudyInstanceUID(Examination examination) {
+	public String findStudyInstanceUID(Examination examination) {
 		List<DatasetAcquisition> acquisitions = examination.getDatasetAcquisitions();
 		for (DatasetAcquisition acquisition : acquisitions) {
 			if (acquisition instanceof MrDatasetAcquisition

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

@@ -13,13 +13,15 @@
 import java.util.List;
 import java.util.Optional;
 
+import jakarta.persistence.EntityManager;
 import org.apache.solr.client.solrj.SolrServerException;
 import org.dcm4che3.data.Attributes;
 import org.dcm4che3.data.Sequence;
 import org.dcm4che3.data.Tag;
 import org.dcm4che3.data.VR;
 import org.dcm4che3.io.DicomInputStream;
 import org.dcm4che3.io.DicomOutputStream;
+import org.hibernate.Hibernate;
 import org.shanoir.ng.dataset.modality.MeasurementDataset;
 import org.shanoir.ng.dataset.modality.SegmentationDataset;
 import org.shanoir.ng.dataset.model.CardinalityOfRelatedSubjects;
@@ -35,6 +37,7 @@
 import org.shanoir.ng.datasetacquisition.model.pet.PetDatasetAcquisition;
 import org.shanoir.ng.datasetacquisition.model.xa.XaDatasetAcquisition;
 import org.shanoir.ng.datasetfile.DatasetFile;
+import org.shanoir.ng.dicom.web.SeriesInstanceUIDHandler;
 import org.shanoir.ng.dicom.web.StudyInstanceUIDHandler;
 import org.shanoir.ng.dicom.web.service.DICOMWebService;
 import org.shanoir.ng.examination.model.Examination;
@@ -43,6 +46,7 @@
 import org.shanoir.ng.shared.repository.SubjectRepository;
 import org.shanoir.ng.solr.service.SolrService;
 import org.shanoir.ng.utils.KeycloakUtil;
+import org.shanoir.ng.utils.SecurityContextUtil;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -88,10 +92,12 @@ public class DicomSEGAndSRImporterService {
 
 	@Autowired
 	private DICOMWebService dicomWebService;
-	
+
 	@Autowired
 	private StudyInstanceUIDHandler studyInstanceUIDHandler;
-
+
+	@Autowired
+	private SeriesInstanceUIDHandler seriesInstanceUIDHandler;
 	@Value("${dcm4chee-arc.protocol}")
 	private String dcm4cheeProtocol;
 
@@ -103,7 +109,10 @@ public class DicomSEGAndSRImporterService {
 
 	@Value("${dcm4chee-arc.dicom.web.rs}")
 	private String dicomWebRS;
-
+
+	@Autowired
+	EntityManager entityManager;
+
 	@Transactional
 	public boolean importDicomSEGAndSR(InputStream inputStream) {
 		// DicomInputStream consumes the input stream to read the data
@@ -133,6 +142,30 @@ public boolean importDicomSEGAndSR(InputStream inputStream) {
 		return true;
 	}
 
+	@Transactional
+	public void deleteSR(Long examId, String seriesUid) {
+		try {
+			Examination exam = examinationRepository.findById(examId).orElse(null);
+			if (exam != null) {
+				for (DatasetAcquisition acq : exam.getDatasetAcquisitions()) {
+					for (Dataset ds : acq.getDatasets()) {
+						String dsSeriesInstanceUid = seriesInstanceUIDHandler.findSeriesInstanceUID(ds);
+						if (dsSeriesInstanceUid.equals(seriesUid)) {
+							entityManager.clear();
+							SecurityContextUtil.initAuthenticationContext("ROLE_ADMIN");
+							datasetService.deleteById(ds.getId());
+							dicomWebService.deleteDicomFilesFromPacs();
+							solrService.deleteFromIndex(ds.getId());
+							return;
+						}
+					}
+				}
+			}
+		} catch (Exception e) {
+			LOG.error(e.getMessage(), e);
+		}
+	}
+
 	/**
 	 * This method replaces values of dicom tags within the DICOM SR file
 	 * and searches the corresponding examination and returns it:

shanoir-ng-studies/src/main/java/org/shanoir/ng/configuration/amqp/RabbitMQStudiesService.java

@@ -109,7 +109,7 @@ public void deleteExaminationStudy(final String eventStr) {
 			ObjectMapper objectMapper = new ObjectMapper();
 			ShanoirEvent event =  objectMapper.readValue(eventStr, ShanoirEvent.class);
 			Long examinationId = Long.valueOf(event.getObjectId());
-			Long studyId = Long.valueOf(event.getMessage());
+			Long studyId = Long.valueOf(event.getStudyId());
 			this.studyService.deleteExamination(examinationId, studyId);
 		} catch (Exception e) {
 			LOG.error("Could not index examination on given study ", e);