#2506 : dataset tag API created (add/remove tags to a dataset only)

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

@@ -351,20 +351,4 @@ ResponseEntity<ByteArrayResource> downloadStatisticsByEventId(
 	@PreAuthorize("hasRole('ADMIN') or (hasAnyRole('EXPERT', 'USER') and @datasetSecurityService.hasRightOnEveryDataset(#datasetIds, 'CAN_SEE_ALL'))")
 	ResponseEntity<List<DatasetWithDependenciesDTOInterface>> findDatasetsByIds(
 			@RequestParam(value = "datasetIds", required = true) List<Long> datasetIds);
-
-	@Operation(summary = "", description = "Updates the study tags of a dataset")
-	@ApiResponses(value = { @ApiResponse(responseCode = "200", description = "dataset study tags updated"),
-			@ApiResponse(responseCode = "401", description = "unauthorized"),
-			@ApiResponse(responseCode = "403", description = "forbidden"),
-			@ApiResponse(responseCode = "404", description = "dataset does not exists"),
-			@ApiResponse(responseCode = "422", description = "bad parameters"),
-			@ApiResponse(responseCode = "500", description = "unexpected error") })
-	@PutMapping(value = "/{datasetId}/tags", produces = { "application/json" }, consumes = {
-			"application/json" })
-	@PreAuthorize("hasRole('ADMIN') or (hasRole('EXPERT') and @datasetSecurityService.hasRightOnDataset(#datasetId, 'CAN_ADMINISTRATE'))")
-	ResponseEntity<Void> updateDatasetTags(
-			@Parameter(description = "id of the dataset", required = true) @PathVariable("datasetId") Long datasetId,
-			@io.swagger.v3.oas.annotations.parameters.RequestBody(description = "array of study tag ids", required = true) @RequestBody List<Long> studyTagIds,
-			BindingResult result) throws RestServiceException, EntityNotFoundException, SolrServerException, IOException;
-
 }

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

@@ -52,8 +52,6 @@
 import org.shanoir.ng.shared.exception.ErrorModel;
 import org.shanoir.ng.shared.exception.RestServiceException;
 import org.shanoir.ng.solr.service.SolrService;
-import org.shanoir.ng.tag.model.StudyTag;
-import org.shanoir.ng.tag.service.StudyTagService;
 import org.shanoir.ng.utils.DatasetFileUtils;
 import org.shanoir.ng.utils.KeycloakUtil;
 import org.slf4j.Logger;
@@ -147,9 +145,6 @@ public class DatasetApiController implements DatasetApi {
 	@Autowired
 	private ObjectMapper objectMapper;
 
-	@Autowired
-	private StudyTagService studyTagService;
-
 	@Autowired
 	private DatasetRepository datasetRepository;
 
@@ -272,30 +267,6 @@ public ResponseEntity<List<DatasetWithDependenciesDTOInterface>> findDatasetsByI
 		return new ResponseEntity<>(dtos, HttpStatus.OK);
 	}
 
-	@Override
-	public ResponseEntity<Void> updateDatasetTags(Long datasetId, List<Long> studyTagIds, BindingResult result) throws EntityNotFoundException, SolrServerException, IOException {
-		Dataset ds = datasetService.findById(datasetId);
-		if (ds == null) {
-			throw new EntityNotFoundException(Dataset.class, datasetId);
-		}
-
-		List<StudyTag> tags = studyTagService.findByIds(studyTagIds);
-
-		ds.setTags(new ArrayList<>());
-
-		for(StudyTag tag : tags){
-			if(tag.getStudy().getId().equals(ds.getStudyId())){
-				ds.getTags().add(tag);
-			}
-		}
-
-		datasetRepository.save(ds);
-
-		solrService.indexDataset(datasetId);
-
-		return new ResponseEntity<>(HttpStatus.OK);
-	}
-
   @Override
 	public ResponseEntity<List<DatasetDTO>> findDatasetsByExaminationId(Long examinationId) {
 		List<Dataset> datasets = datasetService.findByExaminationId(examinationId);

shanoir-ng-datasets/src/main/java/org/shanoir/ng/tag/controller/StudyTagApi.java

@@ -0,0 +1,64 @@
+/**
+ * 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
+ */
+
+package org.shanoir.ng.tag.controller;
+
+import io.swagger.v3.oas.annotations.Operation;
+import io.swagger.v3.oas.annotations.Parameter;
+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 org.apache.solr.client.solrj.SolrServerException;
+import org.shanoir.ng.shared.exception.EntityNotFoundException;
+import org.shanoir.ng.shared.exception.RestServiceException;
+import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.validation.BindingResult;
+import org.springframework.web.bind.annotation.*;
+
+import java.io.IOException;
+import java.util.List;
+
+@Tag(name = "studytag")
+@RequestMapping("/studytag")
+public interface StudyTagApi {
+
+	@Operation(summary = "addStudyTagsToDataset", description = "Add study tags to a dataset")
+	@ApiResponses(value = { @ApiResponse(responseCode = "200", description = "dataset associated to study tags"),
+			@ApiResponse(responseCode = "401", description = "unauthorized"),
+			@ApiResponse(responseCode = "403", description = "forbidden"),
+			@ApiResponse(responseCode = "404", description = "dataset does not exists"),
+			@ApiResponse(responseCode = "422", description = "bad parameters"),
+			@ApiResponse(responseCode = "500", description = "unexpected error") })
+	@PutMapping(value = "/addStudyTagsToDataset")
+	@PreAuthorize("hasRole('ADMIN') or (hasRole('EXPERT') and @datasetSecurityService.hasRightOnDataset(#datasetId, 'CAN_IMPORT'))")
+	ResponseEntity<Void> addStudyTagsToDataset(
+			@Parameter(description = "id of the dataset", required = true) @RequestParam(value = "datasetId") Long datasetId,
+			@Parameter(description = "study tag ids", required = true) @RequestParam(value = "studyTagIds") List<Long> studyTagIds)
+			throws RestServiceException, EntityNotFoundException, SolrServerException, IOException;
+
+	@Operation(summary = "removeStudyTagsFromDataset", description = "Add study tags to a dataset")
+	@ApiResponses(value = { @ApiResponse(responseCode = "200", description = "dataset associated to study tags"),
+			@ApiResponse(responseCode = "401", description = "unauthorized"),
+			@ApiResponse(responseCode = "403", description = "forbidden"),
+			@ApiResponse(responseCode = "404", description = "dataset does not exists"),
+			@ApiResponse(responseCode = "422", description = "bad parameters"),
+			@ApiResponse(responseCode = "500", description = "unexpected error") })
+	@PutMapping(value = "/removeStudyTagsFromDataset")
+	@PreAuthorize("hasRole('ADMIN') or (hasRole('EXPERT') and @datasetSecurityService.hasRightOnDataset(#datasetId, 'CAN_IMPORT'))")
+	ResponseEntity<Void> removeStudyTagsFromDataset(
+			@Parameter(description = "id of the dataset", required = true) @RequestParam(value = "datasetId") Long datasetId,
+			@Parameter(description = "study tag ids", required = true) @RequestParam(value = "studyTagIds") List<Long> studyTagIds)
+			throws RestServiceException, EntityNotFoundException, SolrServerException, IOException;
+}

shanoir-ng-datasets/src/main/java/org/shanoir/ng/tag/controller/StudyTagApiController.java

@@ -0,0 +1,123 @@
+/**
+
+ * 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
+ */
+
+package org.shanoir.ng.tag.controller;
+
+import com.fasterxml.jackson.databind.ObjectMapper;
+import io.swagger.v3.oas.annotations.Parameter;
+import jakarta.mail.MessagingException;
+import jakarta.servlet.http.HttpServletResponse;
+import jakarta.validation.Valid;
+import org.apache.commons.lang3.StringUtils;
+import org.apache.solr.client.solrj.SolrServerException;
+import org.shanoir.ng.dataset.dto.DatasetDTO;
+import org.shanoir.ng.dataset.dto.DatasetWithDependenciesDTOInterface;
+import org.shanoir.ng.dataset.dto.mapper.DatasetMapper;
+import org.shanoir.ng.dataset.modality.EegDataset;
+import org.shanoir.ng.dataset.modality.EegDatasetMapper;
+import org.shanoir.ng.dataset.modality.MrDataset;
+import org.shanoir.ng.dataset.modality.MrDatasetMapper;
+import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.model.DatasetExpressionFormat;
+import org.shanoir.ng.dataset.repository.DatasetRepository;
+import org.shanoir.ng.dataset.service.CreateStatisticsService;
+import org.shanoir.ng.dataset.service.DatasetDownloaderServiceImpl;
+import org.shanoir.ng.dataset.service.DatasetService;
+import org.shanoir.ng.datasetacquisition.model.DatasetAcquisition;
+import org.shanoir.ng.download.DatasetDownloadError;
+import org.shanoir.ng.download.WADODownloaderService;
+import org.shanoir.ng.examination.model.Examination;
+import org.shanoir.ng.examination.service.ExaminationService;
+import org.shanoir.ng.importer.dto.ProcessedDatasetImportJob;
+import org.shanoir.ng.importer.service.ImporterService;
+import org.shanoir.ng.shared.configuration.RabbitMQConfiguration;
+import org.shanoir.ng.shared.error.FieldErrorMap;
+import org.shanoir.ng.shared.event.ShanoirEvent;
+import org.shanoir.ng.shared.event.ShanoirEventService;
+import org.shanoir.ng.shared.event.ShanoirEventType;
+import org.shanoir.ng.shared.exception.EntityNotFoundException;
+import org.shanoir.ng.shared.exception.ErrorDetails;
+import org.shanoir.ng.shared.exception.ErrorModel;
+import org.shanoir.ng.shared.exception.RestServiceException;
+import org.shanoir.ng.solr.service.SolrService;
+import org.shanoir.ng.tag.model.StudyTag;
+import org.shanoir.ng.tag.service.StudyTagService;
+import org.shanoir.ng.utils.DatasetFileUtils;
+import org.shanoir.ng.utils.KeycloakUtil;
+import org.slf4j.Logger;
+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;
+import org.springframework.data.domain.Pageable;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.stereotype.Controller;
+import org.springframework.validation.BindingResult;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestParam;
+
+import java.io.File;
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.nio.file.DirectoryStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.attribute.BasicFileAttributes;
+import java.nio.file.attribute.FileTime;
+import java.util.*;
+import java.util.concurrent.TimeUnit;
+import java.util.stream.Collectors;
+
+
+@Controller
+public class StudyTagApiController implements StudyTagApi {
+
+	private static final Logger LOG = LoggerFactory.getLogger(StudyTagApiController.class);
+
+	@Autowired
+	private DatasetService datasetService;
+
+	@Autowired
+	private StudyTagService studyTagService;
+
+	@Override
+	public ResponseEntity<Void> addStudyTagsToDataset(Long datasetId, List<Long> studyTagIds) throws EntityNotFoundException, SolrServerException, IOException {
+		Dataset ds = datasetService.findById(datasetId);
+		if (Objects.isNull(ds)) {throw new EntityNotFoundException(Dataset.class, datasetId);}
+
+		studyTagService.addStudyTagsToDataset(ds, studyTagIds);
+
+		return new ResponseEntity<>(HttpStatus.OK);
+	}
+
+	@Override
+	public ResponseEntity<Void> removeStudyTagsFromDataset(Long datasetId, List<Long> studyTagIds) throws EntityNotFoundException, SolrServerException, IOException {
+		Dataset ds = datasetService.findById(datasetId);
+		if (Objects.isNull(ds)) {throw new EntityNotFoundException(Dataset.class, datasetId);}
+
+		studyTagService.removeStudyTagsFromDataset(ds, studyTagIds);
+
+		return new ResponseEntity<>(HttpStatus.OK);
+	}
+}

shanoir-ng-datasets/src/main/java/org/shanoir/ng/tag/service/StudyTagService.java

@@ -1,25 +1,65 @@
 package org.shanoir.ng.tag.service;
 
 import org.apache.commons.collections4.IterableUtils;
+import org.apache.solr.client.solrj.SolrServerException;
+import org.shanoir.ng.dataset.model.Dataset;
+import org.shanoir.ng.dataset.repository.DatasetRepository;
+import org.shanoir.ng.shared.exception.EntityNotFoundException;
+import org.shanoir.ng.solr.service.SolrService;
 import org.shanoir.ng.tag.model.StudyTag;
 import org.shanoir.ng.tag.repository.StudyTagRepository;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Service;
+import org.springframework.transaction.annotation.Transactional;
+import org.springframework.validation.BindingResult;
 
-import java.util.List;
+import java.io.IOException;
+import java.util.*;
 
 @Service
 public class StudyTagService {
 
     @Autowired
     private StudyTagRepository repository;
 
+    @Autowired
+    private DatasetRepository datasetRepository;
+
+    @Autowired
+    private SolrService solrService;
+
     public List<StudyTag> findByIds(List<Long> ids){
         return IterableUtils.toList(repository.findAllById(ids));
     }
 
-    public boolean existsById(Long id){
-        return repository.existsById(id);
+    @Transactional
+    public void addStudyTagsToDataset(Dataset dataset, List<Long> studyTagIds) throws SolrServerException, IOException {
+        Set<StudyTag> datasetTags = new HashSet<>(dataset.getTags());
+
+        for (StudyTag tag : findByIds(studyTagIds)) {
+            if (tag.getStudy().getId().equals(dataset.getStudyId())) {
+                datasetTags.add(tag);
+            }
+        }
+        dataset.setTags(new ArrayList<>(datasetTags));
+        datasetRepository.save(dataset);
+        solrService.indexDataset(dataset.getId());
     }
 
+    @Transactional
+    public void removeStudyTagsFromDataset(Dataset dataset, List<Long> studyTagIds) throws SolrServerException, IOException {
+        Set<StudyTag> datasetTags = new HashSet<>(dataset.getTags());
+
+        for (StudyTag tag : findByIds(studyTagIds)) {
+            if (tag.getStudy().getId().equals(dataset.getStudyId())) {
+                datasetTags.remove(tag);
+            }
+        }
+
+        dataset.setTags(new ArrayList<>(datasetTags));
+        datasetRepository.save(dataset);
+        solrService.indexDataset(dataset.getId());
+    }
 }

shanoir-ng-datasets/src/test/java/org/shanoir/ng/dataset/DatasetApiControllerTest.java → shanoir-ng-datasets/src/test/java/org/shanoir/ng/dataset/StudyTagApiControllerTest.java

@@ -86,7 +86,7 @@
 @WebMvcTest(controllers = DatasetApiController.class)
 @AutoConfigureMockMvc(addFilters = false)
 @ActiveProfiles("test")
-public class DatasetApiControllerTest {
+public class StudyTagApiControllerTest {
 
 	private static final String REQUEST_PATH = "/datasets";
 	private static final String REQUEST_PATH_WITH_ID = REQUEST_PATH + "/1";