Merge pull request #2493 from pierrehenri-dauvergne/shanoir-issue#2482

shanoir-issue#2482: call subject delete in preclinical and datasets at the same time

shanoir-ng-datasets/src/main/java/org/shanoir/ng/configuration/amqp/RabbitMQDatasetsService.java

@@ -312,21 +312,15 @@ public void createDatasetAcquisition(final String studyStr) {
 
 
 	/**
-         * Receives a shanoirEvent as a json object, concerning a subject deletion
-         * @param eventAsString the task as a json string.
-         */
-	@RabbitListener(bindings = @QueueBinding(
-			key = ShanoirEventType.DELETE_SUBJECT_EVENT,
-			value = @Queue(value = RabbitMQConfiguration.DELETE_SUBJECT_QUEUE, durable = "true"),
-			exchange = @Exchange(value = RabbitMQConfiguration.EVENTS_EXCHANGE, ignoreDeclarationExceptions = "true",
-			autoDelete = "false", durable = "true", type=ExchangeTypes.TOPIC)), containerFactory = "singleConsumerFactory"
-			)
+	 * Receives a shanoirEvent as a json object, concerning a subject deletion
+	 * @param subjectIdAsString a string of the subject's id
+	 */
+	@RabbitListener(queues = RabbitMQConfiguration.DELETE_SUBJECT_QUEUE, containerFactory = "singleConsumerFactory")
 	@Transactional
-	public void deleteSubject(String eventAsString) throws AmqpRejectAndDontRequeueException {
+	public void deleteSubject(String subjectIdAsString) throws AmqpRejectAndDontRequeueException {
 		SecurityContextUtil.initAuthenticationContext("ROLE_ADMIN");
 		try {
-			ShanoirEvent event = objectMapper.readValue(eventAsString, ShanoirEvent.class);
-			Long subjectId = Long.valueOf(event.getObjectId());
+			Long subjectId = Long.valueOf(subjectIdAsString);
 			Set<Long> studyIds = new HashSet<>();
 
 			// Inverse order to remove copied examination before its source (if copied)

shanoir-ng-datasets/src/main/java/org/shanoir/ng/examination/service/ExaminationServiceImpl.java

@@ -131,8 +131,10 @@ public void deleteById(final Long id, ShanoirEvent event) throws ShanoirExceptio
 					}
 				}
 				for (DatasetAcquisition dsAcq : dsAcqs) {
-					event.setMessage("Delete examination - acquisition with id : " + dsAcq.getId());
-					eventService.publishEvent(event);
+					if (event != null) {
+						event.setMessage("Delete examination - acquisition with id : " + dsAcq.getId());
+						eventService.publishEvent(event);
+					}
 					this.datasetAcquisitionService.deleteById(dsAcq.getId(), event);
 				}
 				if (event != null) {

shanoir-ng-datasets/src/main/java/org/shanoir/ng/shared/service/StudyServiceImpl.java

@@ -36,7 +36,7 @@ public class StudyServiceImpl implements StudyService {
 
 	@Autowired
 	private DatasetRepository dsRepository;
-	
+
 	@Override
 	public Study findById(final Long id) {
 		return repository.findById(id).orElse(null);

shanoir-ng-front/src/app/shared/components/subject-study-list/subject-study-list.component.ts

@@ -240,7 +240,7 @@ export class SubjectStudyListComponent extends AbstractInput<SubjectStudy[]> imp
     removeSubjectStudy(subjectStudy: SubjectStudy):void {
         if (!this.warningDisplayed) {
             this.confirmDialogService.confirm('Deleting subject',
-            'Warning: If this subject is only linked to this study, it will be completely deleted from the database.')
+            'Warning: If this subject is only linked to this study, it will be completely deleted from the database. This means each examination, acquisition and dataset of this subject will be deleted. Are you sure ?')
             .then(userChoice => {
                 if (userChoice) {
                     this.removeSubjectStudyOk(subjectStudy);

shanoir-ng-ms-common/src/main/java/org/shanoir/ng/shared/configuration/RabbitMQConfiguration.java

@@ -313,24 +313,26 @@ public static Queue studiesSubjectStudyStudyCardTagQueue() {
 		return new Queue(STUDIES_SUBJECT_STUDY_STUDY_CARD_TAG, true);
 	}
 
+	@Bean
+	public static Queue deleteSubjectQueue() { return new Queue(DELETE_SUBJECT_QUEUE, true); }
+
 	@Bean
 	public static Queue importerQueue() {
 		return new Queue(IMPORTER_QUEUE_DATASET, true);
 	}
 
 	@Bean
 	public FanoutExchange fanout() {
-	    return new FanoutExchange(STUDY_USER_EXCHANGE, true, false);
+		return new FanoutExchange(STUDY_USER_EXCHANGE, true, false);
 	}
-
 	@Bean
 	public TopicExchange topicExchange() {
 	    return new TopicExchange(EVENTS_EXCHANGE);
 	}
 
 	@Bean
 	public FanoutExchange fanoutSubjectExchange() {
-	    return new FanoutExchange(STUDY_USER_EXCHANGE, true, false);
+		return new FanoutExchange(STUDY_USER_EXCHANGE, true, false);
 	}
 
 	@Bean

shanoir-ng-preclinical/src/main/java/org/shanoir/ng/configuration/amqp/RabbitMQPreclinicalService.java

@@ -3,7 +3,6 @@
 import com.fasterxml.jackson.databind.ObjectMapper;
 import org.shanoir.ng.preclinical.pathologies.subject_pathologies.SubjectPathologyService;
 import org.shanoir.ng.preclinical.subjects.model.AnimalSubject;
-import org.shanoir.ng.preclinical.subjects.repository.AnimalSubjectRepository;
 import org.shanoir.ng.preclinical.subjects.service.AnimalSubjectService;
 import org.shanoir.ng.preclinical.therapies.subject_therapies.SubjectTherapyService;
 import org.shanoir.ng.shared.configuration.RabbitMQConfiguration;
@@ -21,13 +20,9 @@
 import org.springframework.amqp.rabbit.annotation.QueueBinding;
 import org.springframework.amqp.rabbit.annotation.RabbitListener;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Component;
 import org.springframework.transaction.annotation.Transactional;
 
-import java.util.*;
-
 @Component
 public class RabbitMQPreclinicalService {
 
@@ -36,7 +31,7 @@ public class RabbitMQPreclinicalService {
     private ObjectMapper objectMapper;
 
     @Autowired
-    private AnimalSubjectService subjectService;
+    private AnimalSubjectService animalSubjectService;
 
     @Autowired
     private SubjectPathologyService subjectPathologyService;
@@ -51,23 +46,16 @@ public class RabbitMQPreclinicalService {
 
     /**
      * Receives a shanoirEvent as a json object, concerning a subject deletion
-     * @param eventAsString the task as a json string.
+     * @param subjectIdAsStr the subject's id to delete, as string
      */
-    @RabbitListener(bindings = @QueueBinding(
-            key = ShanoirEventType.DELETE_SUBJECT_EVENT,
-            value = @Queue(value = RabbitMQConfiguration.DELETE_SUBJECT_QUEUE, durable = "true"),
-            exchange = @Exchange(value = RabbitMQConfiguration.EVENTS_EXCHANGE, ignoreDeclarationExceptions = "true",
-                    autoDelete = "false", durable = "true", type= ExchangeTypes.TOPIC))
-    )
+    @RabbitListener(queues = RabbitMQConfiguration.DELETE_ANIMAL_SUBJECT_QUEUE)
     @Transactional
-    public void deleteAnimalSubject(String eventAsString) throws AmqpRejectAndDontRequeueException {
+    public void deleteAnimalSubject(String subjectIdAsStr) throws AmqpRejectAndDontRequeueException {
         SecurityContextUtil.initAuthenticationContext("ADMIN_ROLE");
         try {
+            Long subjectId = Long.valueOf(subjectIdAsStr);
 
-            ShanoirEvent event = objectMapper.readValue(eventAsString, ShanoirEvent.class);
-            Long subjectId = Long.valueOf(event.getObjectId());
-
-            AnimalSubject animalSubject = subjectService.getBySubjectId(subjectId);
+            AnimalSubject animalSubject = animalSubjectService.getBySubjectId(subjectId);
 
             if(animalSubject == null){
                 return;
@@ -76,12 +64,10 @@ public void deleteAnimalSubject(String eventAsString) throws AmqpRejectAndDontRe
 
             subjectPathologyService.deleteByAnimalSubject(animalSubject);
             subjectTherapyService.deleteByAnimalSubject(animalSubject);
-            subjectService.deleteBySubjectId(subjectId);
+            animalSubjectService.deleteBySubjectId(subjectId);
 
             LOG.info("Animal subject [{}] has been deleted following deletion of subject [{}]", id, subjectId);
 
-            eventService.publishEvent(new ShanoirEvent(ShanoirEventType.DELETE_PRECLINICAL_SUBJECT_EVENT, subjectId.toString(), KeycloakUtil.getTokenUserId(), "", ShanoirEvent.SUCCESS));
-
         } catch (Exception e) {
             LOG.error("Something went wrong deserializing the event. {}", e.getMessage());
             throw new AmqpRejectAndDontRequeueException(RABBIT_MQ_ERROR + e.getMessage(), e);

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

@@ -190,41 +190,6 @@ public Long createOrUpdateSubject(String subjectAsString) {
 		}
 	}
 
-	/**
-	 * Receives a shanoirEvent as a json object, concerning a preclinical subject deletion
-	 * @param eventAsString the task as a json string.
-	 */
-	@RabbitListener(bindings = @QueueBinding(
-			key = ShanoirEventType.DELETE_PRECLINICAL_SUBJECT_EVENT,
-			value = @Queue(value = RabbitMQConfiguration.DELETE_ANIMAL_SUBJECT_QUEUE, durable = "true"),
-			exchange = @Exchange(value = RabbitMQConfiguration.EVENTS_EXCHANGE, ignoreDeclarationExceptions = "true",
-					autoDelete = "false", durable = "true", type= ExchangeTypes.TOPIC)), containerFactory = "multipleConsumersFactory"
-	)
-
-	@Transactional
-	public void deletePreclinicalSubject(String eventAsString) throws AmqpRejectAndDontRequeueException {
-		SecurityContextUtil.initAuthenticationContext("ADMIN_ROLE");
-		try {
-
-			ShanoirEvent event = mapper.readValue(eventAsString, ShanoirEvent.class);
-
-			Long id = Long.valueOf(event.getObjectId());
-
-			Optional<Subject> subject = subjectRepository.findById(id);
-
-			if(subject.isEmpty() || !subject.get().isPreclinical()){
-				return;
-			}
-
-			subjectService.deleteById(subject.get().getId());
-			LOG.info("Subject [{}] has been deleted following deletion of preclinical subject [{}]", subject.get().getId(), id);
-
-
-		} catch (Exception e) {
-			LOG.error("Something went wrong deserializing the event", e);
-			throw new AmqpRejectAndDontRequeueException(e);
-		}
-	}
 
 	private boolean studyListContains(List<SubjectStudy> subjectStudyList, Long studyId) {
 		for (SubjectStudy sustu : subjectStudyList) {

shanoir-ng-studies/src/main/java/org/shanoir/ng/study/service/StudyServiceImpl.java

@@ -366,11 +366,6 @@ public Study update(Study study) throws ShanoirException {
 			studyDb = studyRepository.save(studyDb);
 		}
 
-		// Actually delete subjects
-		for (Subject subjectToDelete : toBeDeleted) {
-			subjectService.deleteById(subjectToDelete.getId());
-		}
-
 		if (studyDb.getTags() != null) {
 			studyDb.getTags().removeIf(tag -> tagsToDelete.contains(tag.getId()));
 			studyDb = studyRepository.save(studyDb);
@@ -382,7 +377,12 @@ public Study update(Study study) throws ShanoirException {
 
 		String error = this.updateStudyName(studyMapper.studyToStudyDTODetailed(studyDb));
 
-		if(error != null && !error.isEmpty()){
+		// Actually delete subjects
+		for (Subject subjectToDelete : toBeDeleted) {
+			subjectService.deleteById(subjectToDelete.getId());
+		}
+
+		if (error != null && !error.isEmpty()) {
 			LOG.error("Study [" + studyDb.getId() + "] couldn't be sync with datasets microservice : {}", error);
 			throw new ShanoirException(error);
 		}

shanoir-ng-studies/src/main/java/org/shanoir/ng/studyexamination/StudyExaminationRepository.java

@@ -17,6 +17,7 @@
 import java.util.List;
 
 import org.shanoir.ng.subject.model.Subject;
+import org.springframework.data.jpa.repository.Modifying;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.CrudRepository;
 import org.springframework.data.repository.query.Param;
@@ -30,7 +31,11 @@ public interface StudyExaminationRepository extends CrudRepository<StudyExaminat
 
 	public Iterable<StudyExamination> findByCenterId(Long centerId);
 
-	public void deleteBySubject(Subject subject);
+    public void deleteBySubject(Subject subject);
+
+    @Modifying
+    @Query("DELETE FROM StudyExamination se WHERE se.subject.id = :subjectId")
+    public void deleteBySubjectId(Long subjectId);
 
     int countByStudyId(@Param("studyId") Long studyId);
 

shanoir-ng-studies/src/main/java/org/shanoir/ng/subject/controler/SubjectApiController.java

@@ -14,6 +14,8 @@
 
 package org.shanoir.ng.subject.controler;
 
+
+import org.shanoir.ng.shared.configuration.RabbitMQConfiguration;
 import io.swagger.v3.oas.annotations.Parameter;
 import org.shanoir.ng.shared.core.model.IdName;
 import org.shanoir.ng.shared.error.FieldErrorMap;
@@ -30,6 +32,7 @@
 import org.shanoir.ng.subject.service.SubjectService;
 import org.shanoir.ng.subject.service.SubjectUniqueConstraintManager;
 import org.shanoir.ng.utils.KeycloakUtil;
+import org.springframework.amqp.rabbit.core.RabbitTemplate;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
@@ -63,13 +66,17 @@ public class SubjectApiController implements SubjectApi {
 	@Autowired
 	private StudyService studyService;
 
+	@Autowired
+	private RabbitTemplate rabbitTemplate;
+
 	@Override
 	public ResponseEntity<Void> deleteSubject(
 			@Parameter(description = "id of the subject", required = true) @PathVariable("subjectId") Long subjectId) {
 		try {
 			// Delete all associated bids folders
 			subjectService.deleteById(subjectId);
 			eventService.publishEvent(new ShanoirEvent(ShanoirEventType.DELETE_SUBJECT_EVENT, subjectId.toString(), KeycloakUtil.getTokenUserId(), "", ShanoirEvent.SUCCESS));
+			rabbitTemplate.convertAndSend(RabbitMQConfiguration.DELETE_SUBJECT_QUEUE, subjectId.toString());
 
 			return new ResponseEntity<>(HttpStatus.NO_CONTENT);
 		} catch (EntityNotFoundException e) {

shanoir-ng-studies/src/main/java/org/shanoir/ng/subject/service/SubjectServiceImpl.java

@@ -110,11 +110,15 @@ public void deleteById(final Long id) throws EntityNotFoundException {
 		if (subject.isEmpty()) {
 			throw new EntityNotFoundException(Subject.class, id);
 		}
+
 		// Delete all associated study_examination
-		studyExaminationRepository.deleteBySubject(subject.get());
+		studyExaminationRepository.deleteBySubjectId(id);
 		subjectRepository.deleteById(id);
-		// Propagate deletion
-		eventService.publishEvent(new ShanoirEvent(ShanoirEventType.DELETE_SUBJECT_EVENT, id.toString(), KeycloakUtil.getTokenUserId(), "", ShanoirEvent.SUCCESS));
+		if (subject.get().isPreclinical())
+			rabbitTemplate.convertAndSend(RabbitMQConfiguration.DELETE_ANIMAL_SUBJECT_QUEUE, id.toString());
+
+		rabbitTemplate.convertAndSend(RabbitMQConfiguration.DELETE_SUBJECT_QUEUE, id.toString());
+
 	}
 
 	@Override

shanoir-ng-studies/src/test/java/org/shanoir/ng/subject/SubjectApiControllerTest.java

@@ -25,6 +25,7 @@
 
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Test;
+import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.shanoir.ng.shared.error.FieldErrorMap;
 import org.shanoir.ng.shared.event.ShanoirEventService;
@@ -43,6 +44,7 @@
 import org.shanoir.ng.subjectstudy.dto.SubjectStudyDTO;
 import org.shanoir.ng.utils.ModelsUtil;
 import org.shanoir.ng.utils.usermock.WithMockKeycloakUser;
+import org.springframework.amqp.rabbit.core.RabbitTemplate;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc;
 import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest;
@@ -79,10 +81,13 @@ public class SubjectApiControllerTest {
 
 	@MockBean
 	private SubjectMapper subjectMapperMock;
-
+
+	@MockBean
+	private RabbitTemplate rabbitTemplate;
+
 	@MockBean
 	private SubjectUniqueConstraintManager uniqueConstraintManager;
-	
+
 	@MockBean
 	private ShanoirEventService eventService;
 

shanoir-ng-studies/src/test/java/org/shanoir/ng/subject/service/SubjectServiceTest.java

@@ -84,9 +84,7 @@ public class SubjectServiceTest {
 
 	@Mock
 	private ObjectMapper objectMapper;
-
-	@Mock
-	private ShanoirEventService eventService;
+
 
 	@Mock
 	private StudyExaminationRepository studyExaminationRepository;
@@ -105,7 +103,6 @@ public void deleteByIdTest() throws EntityNotFoundException {
 		subjectService.deleteById(SUBJECT_ID);
 
 		Mockito.verify(subjectRepository, Mockito.times(1)).deleteById(Mockito.anyLong());
-		Mockito.verify(eventService, Mockito.times(1)).publishEvent(Mockito.any(ShanoirEvent.class));
 	}
 
 	@Test