[fli-iam#1864] Add NIRS type BIDS

shanoir-ng-datasets/src/main/java/org/shanoir/ng/bids/service/BIDSServiceImpl.java

@@ -21,12 +21,7 @@
 import org.apache.commons.io.FileUtils;
 import org.shanoir.ng.dataset.DatasetDescription;
 import org.shanoir.ng.dataset.controler.DatasetApiController.CoordinatesSystem;
-import org.shanoir.ng.dataset.modality.BidsDataset;
-import org.shanoir.ng.dataset.modality.EegDataSetDescription;
-import org.shanoir.ng.dataset.modality.EegDataset;
-import org.shanoir.ng.dataset.modality.MrDataset;
-import org.shanoir.ng.dataset.modality.MrDatasetNature;
-import org.shanoir.ng.dataset.modality.PetDataset;
+import org.shanoir.ng.dataset.modality.*;
 import org.shanoir.ng.dataset.model.Dataset;
 import org.shanoir.ng.dataset.model.DatasetExpression;
 import org.shanoir.ng.dataset.model.DatasetExpressionFormat;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/modality/BidsDataType.java

@@ -36,7 +36,10 @@ public enum BidsDataType {
 	PET("pet"),
 
 	/* Microscopy.*/
-	MICR("micr");	
+	MICR("micr"),
+
+	/* Near-Infrared Spectroscopy */
+	NIRS("nirs");
 
 	private String folderName;
 

shanoir-ng-datasets/src/main/java/org/shanoir/ng/dataset/model/DatasetModalityType.java

@@ -50,7 +50,10 @@ public enum DatasetModalityType {
 	MICR_DATASET(9),
 
 	// Behavioural Dataset
-	BEH_DATASET(10);
+	BEH_DATASET(10),
+
+	// Near-Infrared Spectroscopy dataset
+	NIRS_DATASET(11);
 
 	private int id;
 

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

@@ -574,36 +574,70 @@ public boolean hasUpdateRightOnDataset(Dataset dataset, String rightStr) throws
     	}
     }
 
+	/**
+	 * Check the connected user has the given right for the given dataset acquisition.
+	 * If the study is updated, check the user has the given right in both former and new studies.
+	 *
+	 * @param datasetAcq the dataset acquisition
+	 * @param rightStr the right
+	 * @return true or false
+	 * @throws EntityNotFoundException
+	 */
+	public boolean hasUpdateRightOnDatasetAcquisition(DatasetAcquisition datasetAcq, String rightStr) throws EntityNotFoundException {
+		if (KeycloakUtil.getTokenRoles().contains("ROLE_ADMIN")) {
+			return true;
+		}
+		if (datasetAcq == null) {
+			throw new IllegalArgumentException("Dataset acquisition cannot be null here.");
+		}
+		if (datasetAcq.getId() == null) {
+			throw new IllegalArgumentException("Dataset acquisition id cannot be null here.");
+		}
+		if (datasetAcq.getExamination() == null || datasetAcq.getExamination().getStudyId() == null) {
+			return false;
+		}
+		DatasetAcquisition dbDatasetAcq = datasetAcquisitionRepository.findById(datasetAcq.getId()).orElse(null);
+		if (dbDatasetAcq == null) {
+			throw new EntityNotFoundException("Cannot find dataset acquisition with id " + datasetAcq.getId());
+		}
+		if (datasetAcq.getExamination().getStudyId() == dbDatasetAcq.getExamination().getStudyId()) { // study hasn't changed
+			return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr);
+		} else { // study has changed : check user has right on both studies
+			return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr) &&
+					this.hasRightOnStudyCenter(dbDatasetAcq.getExamination().getCenterId(), dbDatasetAcq.getExamination().getStudyId(), rightStr);
+		}
+	}
+
     /**
-     * Check the connected user has the given right for the given dataset acquisition.
+     * Check the connected user has the given right for the given dataset acquisition DTO.
      * If the study is updated, check the user has the given right in both former and new studies.
      * 
-     * @param datasetAcq the dataset acquisition
+     * @param datasetAcqDto the dataset acquisition dto
      * @param rightStr the right
      * @return true or false
      * @throws EntityNotFoundException
      */
-    public boolean hasUpdateRightOnDatasetAcquisition(DatasetAcquisition datasetAcq, String rightStr) throws EntityNotFoundException {
+    public boolean hasUpdateRightOnDatasetAcquisitionDTO(DatasetAcquisitionDTO datasetAcqDto, String rightStr) throws EntityNotFoundException {
     	if (KeycloakUtil.getTokenRoles().contains("ROLE_ADMIN")) {
 			return true;
 		}
-    	if (datasetAcq == null) {
+    	if (datasetAcqDto == null) {
 			throw new IllegalArgumentException("Dataset acquisition cannot be null here.");
 		}
-    	if (datasetAcq.getId() == null) {
+    	if (datasetAcqDto.getId() == null) {
 			throw new IllegalArgumentException("Dataset acquisition id cannot be null here.");
 		}
-    	if (datasetAcq.getExamination() == null || datasetAcq.getExamination().getStudyId() == null) {
+    	if (datasetAcqDto.getExamination() == null || datasetAcqDto.getExamination().getStudyId() == null) {
 			return false;
 		}
-    	DatasetAcquisition dbDatasetAcq = datasetAcquisitionRepository.findById(datasetAcq.getId()).orElse(null);
+    	DatasetAcquisition dbDatasetAcq = datasetAcquisitionRepository.findById(datasetAcqDto.getId()).orElse(null);
     	if (dbDatasetAcq == null) {
-			throw new EntityNotFoundException("Cannot find dataset acquisition with id " + datasetAcq.getId());
+			throw new EntityNotFoundException("Cannot find dataset acquisition with id " + datasetAcqDto.getId());
 		}
-    	if (datasetAcq.getExamination().getStudyId() == dbDatasetAcq.getExamination().getStudyId()) { // study hasn't changed
-    		return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr);
-    	} else { // study has changed : check user has right on both studies
-    		return this.hasRightOnStudyCenter(datasetAcq.getExamination().getCenterId(), datasetAcq.getExamination().getStudyId(), rightStr) &&
+    	if (datasetAcqDto.getExamination().getStudyId() == dbDatasetAcq.getExamination().getStudyId()) { // study hasn't changed
+			return this.hasRightOnStudyCenter(datasetAcqDto.getExamination().getCenterId(), datasetAcqDto.getExamination().getStudyId(), rightStr);
+		} else { // study has changed : check user has right on both studies
+			return this.hasRightOnStudyCenter(datasetAcqDto.getExamination().getCenterId(), datasetAcqDto.getExamination().getStudyId(), rightStr) &&
     				this.hasRightOnStudyCenter(dbDatasetAcq.getExamination().getCenterId(), dbDatasetAcq.getExamination().getStudyId(), rightStr);
     	}
     }

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

@@ -5,21 +5,7 @@
 import java.util.Iterator;
 import java.util.List;
 
-import org.shanoir.ng.dataset.modality.BidsDataset;
-import org.shanoir.ng.dataset.modality.CalibrationDataset;
-import org.shanoir.ng.dataset.modality.CtDataset;
-import org.shanoir.ng.dataset.modality.EegDataset;
-import org.shanoir.ng.dataset.modality.GenericDataset;
-import org.shanoir.ng.dataset.modality.MegDataset;
-import org.shanoir.ng.dataset.modality.MeshDataset;
-import org.shanoir.ng.dataset.modality.MrDataset;
-import org.shanoir.ng.dataset.modality.ParameterQuantificationDataset;
-import org.shanoir.ng.dataset.modality.PetDataset;
-import org.shanoir.ng.dataset.modality.RegistrationDataset;
-import org.shanoir.ng.dataset.modality.SegmentationDataset;
-import org.shanoir.ng.dataset.modality.SpectDataset;
-import org.shanoir.ng.dataset.modality.StatisticalDataset;
-import org.shanoir.ng.dataset.modality.TemplateDataset;
+import org.shanoir.ng.dataset.modality.*;
 import org.shanoir.ng.dataset.model.Dataset;
 import org.shanoir.ng.dataset.model.DatasetExpression;
 import org.shanoir.ng.dataset.model.DatasetExpressionFormat;

shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/controler/DatasetAcquisitionApi.java

@@ -138,7 +138,7 @@ ResponseEntity<List<DatasetAcquisitionDatasetsDTO>> findDatasetAcquisitionByData
 			@ApiResponse(responseCode = "500", description = "unexpected error") })
 	@RequestMapping(value = "/datasetacquisition/{datasetAcquisitionId}", produces = { "application/json" }, consumes = {
 			"application/json" }, method = RequestMethod.PUT)
-	@PreAuthorize("hasAnyRole('ADMIN', 'EXPERT') and #datasetAcquisitionId == #datasetAcquisition.getId() and @datasetSecurityService.hasUpdateRightOnDatasetAcquisition(#datasetAcquisition, 'CAN_ADMINISTRATE')")
+	@PreAuthorize("hasAnyRole('ADMIN', 'EXPERT') and #datasetAcquisitionId == #datasetAcquisition.getId() and @datasetSecurityService.hasUpdateRightOnDatasetAcquisitionDTO(#datasetAcquisition, 'CAN_ADMINISTRATE')")
 	ResponseEntity<Void> updateDatasetAcquisition(
 			@Parameter(name = "id of the datasetAcquisition", required = true) @PathVariable("datasetAcquisitionId") Long datasetAcquisitionId,
 			@Parameter(name = "datasetAcquisition to update", required = true) @Valid @RequestBody DatasetAcquisitionDTO datasetAcquisition, BindingResult result)

shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/dto/mapper/DatasetAcquisitionDatasetsMapper.java

@@ -28,7 +28,10 @@
 import org.shanoir.ng.dataset.service.DatasetUtils;
 import org.shanoir.ng.datasetacquisition.dto.DatasetAcquisitionDatasetsDTO;
 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.examination.dto.mapper.ExaminationMapper;
@@ -54,8 +57,11 @@ DatasetAcquisitionDatasetsDTO datasetAcquisitionToDatasetAcquisitionDatasetsDTO(
 	default DatasetAcquisition createDatasetAcquisition(DatasetAcquisitionDatasetsDTO dto) {
 		if (dto.getType().equals("Mr")) return new MrDatasetAcquisition(); 
         else if (dto.getType().equals("Pet")) return new PetDatasetAcquisition(); 
-        else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition(); 
-        else throw new IllegalStateException("Cannot map from a dataset acquisition dto that don't provide a valid type. Given type = " + dto.getType());
+        else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition();
+		else if (dto.getType().equals("BIDS")) return new BidsDatasetAcquisition();
+		else if (dto.getType().equals("Eeg")) return new EegDatasetAcquisition();
+		else if (dto.getType().equals("Generic")) return new GenericDatasetAcquisition();
+		else throw new IllegalStateException("Cannot map from a dataset acquisition dto that don't provide a valid type. Given type = " + dto.getType());
     }
 
 	@ObjectFactory

shanoir-ng-datasets/src/main/java/org/shanoir/ng/datasetacquisition/dto/mapper/DatasetAcquisitionMapper.java

@@ -23,7 +23,10 @@
 import org.mapstruct.ObjectFactory;
 import org.shanoir.ng.datasetacquisition.dto.DatasetAcquisitionDTO;
 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.examination.dto.mapper.ExaminationMapper;
@@ -49,9 +52,12 @@ DatasetAcquisitionDTO datasetAcquisitionToDatasetAcquisitionDTO(
 
 	@ObjectFactory
 	default DatasetAcquisition createDatasetAcquisition(DatasetAcquisitionDTO dto) {
-        if (dto.getType().equals("Mr")) return new MrDatasetAcquisition(); 
-        else if (dto.getType().equals("Pet")) return new PetDatasetAcquisition(); 
-        else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition(); 
+		if (dto.getType().equals("Mr")) return new MrDatasetAcquisition();
+		else if (dto.getType().equals("Pet")) return new PetDatasetAcquisition();
+		else if (dto.getType().equals("Ct")) return new CtDatasetAcquisition();
+		else if (dto.getType().equals("BIDS")) return new BidsDatasetAcquisition();
+		else if (dto.getType().equals("Eeg")) return new EegDatasetAcquisition();
+		else if (dto.getType().equals("Generic")) return new GenericDatasetAcquisition();
         else throw new IllegalStateException("Cannot map from a dataset acquisition dto that don't provide a valid type. Given type = " + dto.getType());
     }
 

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

@@ -132,6 +132,9 @@ public void createAllBidsDatasetAcquisition(Message importJobStr) throws AmqpRej
 			case "micr":
 				importDataset(importJob, BidsDataType.MICR, DatasetModalityType.MICR_DATASET, event);
 				break;
+			case "nirs":
+				importDataset(importJob, BidsDataType.NIRS, DatasetModalityType.NIRS_DATASET, event);
+				break;
 			default:
 				if (event != null) {
 					LOG.error("The data type folder is not recognized. Please update your BIDS archive following the rules.");

shanoir-ng-datasets/src/test/java/org/shanoir/ng/datasetacquisition/DatasetAcquisitionApiSecurityTest.java

@@ -246,7 +246,8 @@ private void testAll(String role) throws ShanoirException, RestServiceException
 
 		// findDatasetAcquisitions(Pageable)
 		assertThat(api.findDatasetAcquisitions(PageRequest.of(0, 10)).getBody()).hasSize(1);
-
+
+		given(rightsService.hasRightOnStudy(1L, "CAN_ADMINISTRATE")).willReturn(true);
 		// updateDatasetAcquisition(Long, DatasetAcquisitionDTO, BindingResult)
 		if ("ROLE_USER".equals(role)) {
 			assertAccessDenied(api::updateDatasetAcquisition, 1L, mockDsAcqDTO(1L), mockBindingResult);			
@@ -291,6 +292,8 @@ private DatasetAcquisitionDTO mockDsAcqDTO(Long id) {
 		dto.setId(id);
 		dto.setAcquisitionEquipmentId(1L);
 		dto.setExamination(new ExaminationDTO());
+		dto.getExamination().setStudyId(1L);
+		dto.getExamination().setCenterId(1L);
 		dto.setRank(1);
 		dto.setSoftwareRelease("v1.0.0");
 		dto.setSortingIndex(1);

shanoir-ng-front/src/app/dataset-acquisitions/dataset-acquisition/dataset-acquisition.component.html

@@ -52,8 +52,8 @@ <h2 class="header command-zone">Create dataset acquisition</h2>
 							<ng-template [ngSwitchCase]="'view'">
 								<a [routerLink]="['/study/details/', datasetAcquisition.examination?.study?.id]">
 									{{datasetAcquisition.examination?.study?.name}}
-								</a> 
-							</ng-template> 
+								</a>
+							</ng-template>
 						</span>
 					</li>
 					<li>
@@ -62,8 +62,8 @@ <h2 class="header command-zone">Create dataset acquisition</h2>
                             <ng-template [ngSwitchCase]="'view'">
                                 <a [routerLink]="['/examination/details/', datasetAcquisition.examination?.id]">
                                     {{datasetAcquisition.examination?.comment}}
-                                </a> 
-                            </ng-template> 
+                                </a>
+                            </ng-template>
                         </span>
                     </li>
 					<li>
@@ -90,10 +90,10 @@ <h2 class="header command-zone">Create dataset acquisition</h2>
 						<label>Acquisition equipment</label>
 						<span class="right-col" [ngSwitch]="mode">
 							<ng-template [ngSwitchCase]="'view'">
-								<a [routerLink]="['/acquisition-equipment/details/', datasetAcquisition.acquisitionEquipment?.id]">
+								<a *ngIf="datasetAcquisition.acquisitionEquipment?.id" [routerLink]="['/acquisition-equipment/details/', datasetAcquisition.acquisitionEquipment.id]">
 									{{datasetAcquisition.acquisitionEquipment | acqEqptLabel}}
 								</a>
-							</ng-template> 
+							</ng-template>
 							<ng-template ngSwitchDefault>
 								<select-box formControlName="acq-eq" [(ngModel)]="datasetAcquisition.acquisitionEquipment" [optionArr]="acquisitionEquipments" [pipe]="acqEqPipe">
 								</select-box>
@@ -143,11 +143,11 @@ <h2 class="header command-zone">Create dataset acquisition</h2>
 
 			<fieldset *ngIf="mode=='view'">
 				<legend i18n="Examination data|Title@@examinationDetailDataTitle">Data</legend>
-				<dataset-acquisition-node 
-						[input]="acquisitionNode" 
+				<dataset-acquisition-node
+						[input]="acquisitionNode"
 						(nodeInit)="onNodeInit($event)"></dataset-acquisition-node >
 			</fieldset>
-			
+
 			<form-footer
 				[state]="footerState"
 				(save)="save()"
@@ -158,4 +158,4 @@ <h2 class="header command-zone">Create dataset acquisition</h2>
 			></form-footer>
 		</div>
 	</form>
-</div>
+</div>

shanoir-ng-front/src/app/dataset-acquisitions/shared/dataset-acquisition.dto.ts

@@ -2,12 +2,12 @@
  * Shanoir NG - Import, manage and share neuroimaging data
  * Copyright (C) 2009-2019 Inria - https://www.inria.fr/
  * Contact us on https://project.inria.fr/shanoir/
- * 
+ *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
- * 
+ *
  * You should have received a copy of the GNU General Public License
  * along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html
  */
@@ -46,13 +46,17 @@ export class DatasetAcquisitionDTOService {
      * Warning : DO NOT USE THIS IN A LOOP, use toDatasetAcquisitions instead
      * @param result can be used to get an immediate temporary result without async data
      */
-    public toDatasetAcquisition(dto: DatasetAcquisitionDTO, result?: DatasetAcquisition): Promise<DatasetAcquisition> {   
+    public toDatasetAcquisition(dto: DatasetAcquisitionDTO, result?: DatasetAcquisition): Promise<DatasetAcquisition> {
         if (!result) result = DatasetAcquisitionUtils.getNewDAInstance(dto.type);
         DatasetAcquisitionDTOService.mapSyncFields(dto, result);
-        return Promise.all([
-            this.acqEqService.get(dto.acquisitionEquipmentId).then(acqEq => result.acquisitionEquipment = acqEq), // TODO dto
-            this.studyService.get(dto.examination.studyId).then(study => result.examination.study = study) // TODO dto
-        ]).then(([]) => {
+        let promises = [];
+        if(dto.acquisitionEquipmentId > 0){
+            promises.push(this.acqEqService.get(dto.acquisitionEquipmentId).then(acqEq => result.acquisitionEquipment = acqEq));
+        }else{
+            result.acquisitionEquipment = new AcquisitionEquipment();
+        }
+        promises.push( this.studyService.get(dto.examination.studyId).then(study => result.examination.study = study));
+        return Promise.all(promises).then(([]) => {
             return result;
         });
     }
@@ -66,10 +70,6 @@ export class DatasetAcquisitionDTOService {
         for (let dto of dtos ? dtos : []) {
             let entity = DatasetAcquisitionUtils.getNewDAInstance(dto.type);
             DatasetAcquisitionDTOService.mapSyncFields(dto, entity);
-            if (dto.acquisitionEquipmentId) {
-                entity.acquisitionEquipment = new AcquisitionEquipment();
-                entity.acquisitionEquipment.id = dto.acquisitionEquipmentId;
-            }
             if ((dto as DatasetAcquisitionDatasetsDTO).datasets) {
                 entity.datasets = (dto as DatasetAcquisitionDatasetsDTO).datasets.map(dsdto => {
                     let simpleDataset: Dataset = DatasetUtils.getDatasetInstance(dsdto.type);
@@ -102,6 +102,10 @@ export class DatasetAcquisitionDTOService {
         entity.sortingIndex = dto.sortingIndex;
         entity.type = dto.type;
         entity.creationDate = dto.creationDate;
+        if (dto.acquisitionEquipmentId) {
+            entity.acquisitionEquipment = new AcquisitionEquipment();
+            entity.acquisitionEquipment.id = dto.acquisitionEquipmentId;
+        }
         if (dto.examination) {
             entity.examination = new Examination();
             ExaminationDTOService.mapSyncFields(dto.examination, entity.examination);
@@ -136,7 +140,7 @@ export class DatasetAcquisitionDTO {
         }
         this.acquisitionEquipmentId = dsAcq.acquisitionEquipment ? dsAcq.acquisitionEquipment.id : null;
         if (dsAcq.examination) {
-            this.examination = new ExaminationDTO(); 
+            this.examination = new ExaminationDTO();
             this.examination.id = dsAcq.examination.id;
         }
         this.rank = dsAcq.rank;

shanoir-ng-front/src/app/datasets/shared/dataset-type.model.ts

@@ -2,12 +2,12 @@
  * Shanoir NG - Import, manage and share neuroimaging data
  * Copyright (C) 2009-2019 Inria - https://www.inria.fr/
  * Contact us on https://project.inria.fr/shanoir/
- * 
+ *
  * This program is free software: you can redistribute it and/or modify
  * it under the terms of the GNU General Public License as published by
  * the Free Software Foundation, either version 3 of the License, or
  * (at your option) any later version.
- * 
+ *
  * You should have received a copy of the GNU General Public License
  * along with this program. If not, see https://www.gnu.org/licenses/gpl-3.0.html
  */
@@ -31,9 +31,10 @@ export enum DatasetType {
   Statistical = 'Statistical',
   Template = 'Template',
   BIDS = 'BIDS',
+  NIRS = 'NIRS',
   Measurement = 'Measurement'
 } export namespace DatasetType {
-  
+
   export function all(): Array<DatasetType> {
       return allOfEnum<DatasetType>(DatasetType);
   }