Merge pull request #1466 from deepsidhu85/fix-set-default-object-null

Set Default Sequencing Object/Genome Assembly to null when deleted

CHANGELOG.md

@@ -15,6 +15,7 @@
 * [Developer]: Added support for cloud based storage. Currently, Microsoft Azure Blob and Amazon AWS S3 are supported. [See PR 1194](https://github.com/phac-nml/irida/pull/1194)
 * [Developer]: Updated metadata uploader to use react-router-dom Outlet. [See PR 1464](https://github.com/phac-nml/irida/pull/1464)
 * [Developer]: Deprecated "/api/projects/{projectId}/samples/bySequencerId/{seqeuncerId}" in favour of "/api/projects/{projectId}/samples/bySampleName", which accepts a json property "sampleName"
+* [Developer]: Fixed bug in setting a `default_sequencing_object and default_genome_assembly to `NULL` for a sample when the default sequencing object or genome assembly were removed. [See PR 1466](https://github.com/phac-nml/irida/pull/1466)
 
 ## [22.09.7] - 2022/01/24
 * [UI]: Fixed bugs on NCBI Export page preventing the NCBI `submission.xml` file from being properly written. See [PR 1451](https://github.com/phac-nml/irida/pull/1451)

src/main/java/ca/corefacility/bioinformatics/irida/repositories/sample/SampleRepositoryCustom.java

@@ -16,4 +16,18 @@ public interface SampleRepositoryCustom {
 	 * @param modifiedDate The new {@link Date}
 	 */
 	void updateSampleModifiedDate(Sample sample, Date modifiedDate);
+
+	/**
+	 * Update the default sequencing object in a {@link Sample} to NULL.
+	 *
+	 * @param sample The {@link Sample} to update
+	 */
+	void removeDefaultSequencingObject(Sample sample);
+
+	/**
+	 * Update the default genome assembly in a {@link Sample} to NULL.
+	 *
+	 * @param sample The {@link Sample} to update
+	 */
+	void removeDefaultGenomeAssembly(Sample sample);
 }

src/main/java/ca/corefacility/bioinformatics/irida/repositories/sample/SampleRepositoryImpl.java

@@ -31,4 +31,19 @@ public void updateSampleModifiedDate(Sample sample, Date modifiedDate) {
 		query.setParameter(2, sample.getId());
 		query.executeUpdate();
 	}
+
+	@Transactional
+	public void removeDefaultSequencingObject(Sample sample) {
+		Query query = entityManager.createNativeQuery("UPDATE sample SET default_sequencing_object = NULL where id = ?");
+		query.setParameter(1, sample.getId());
+		query.executeUpdate();
+	}
+
+
+	@Transactional
+	public void removeDefaultGenomeAssembly(Sample sample) {
+		Query query = entityManager.createNativeQuery("UPDATE sample SET default_genome_assembly = NULL where id = ?");
+		query.setParameter(1, sample.getId());
+		query.executeUpdate();
+	}
 }

src/main/java/ca/corefacility/bioinformatics/irida/ria/web/services/UISampleService.java

@@ -617,11 +617,6 @@ public String deleteSequencingObjectFromSample(Long sampleId, Long sequencingObj
 		SequencingObject sequencingObject = sequencingObjectService.read(sequencingObjectId);
 
 		try {
-			if (sample.getDefaultSequencingObject() != null
-					&& sample.getDefaultSequencingObject().getId() == sequencingObjectId) {
-				sample.setDefaultSequencingObject(null);
-				sampleService.update(sample);
-			}
 			sampleService.removeSequencingObjectFromSample(sample, sequencingObject);
 			return messageSource.getMessage("server.SampleFiles.removeSequencingObjectSuccess", new Object[] {},
 					locale);
@@ -644,11 +639,6 @@ public String deleteGenomeAssemblyFromSample(Long sampleId, Long genomeAssemblyI
 		GenomeAssembly genomeAssembly = genomeAssemblyService.getGenomeAssemblyForSample(sample, genomeAssemblyId);
 
 		try {
-			if (sample.getDefaultGenomeAssembly() != null
-					&& sample.getDefaultGenomeAssembly().getId() == genomeAssemblyId) {
-				sample.setDefaultGenomeAssembly(null);
-				sampleService.update(sample);
-			}
 			genomeAssemblyService.removeGenomeAssemblyFromSample(sample, genomeAssemblyId);
 			return messageSource.getMessage("server.SampleFiles.removeGenomeAssemblySuccess", new Object[] {}, locale);
 		} catch (Exception e) {

src/main/java/ca/corefacility/bioinformatics/irida/service/impl/GenomeAssemblyServiceImpl.java

@@ -17,7 +17,9 @@
 import ca.corefacility.bioinformatics.irida.model.sample.Sample;
 import ca.corefacility.bioinformatics.irida.repositories.assembly.GenomeAssemblyRepository;
 import ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleGenomeAssemblyJoinRepository;
+import ca.corefacility.bioinformatics.irida.repositories.sample.SampleRepository;
 import ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService;
+import ca.corefacility.bioinformatics.irida.service.sample.SampleService;
 
 /**
  * Service implementation for storing and retrieving {@link GenomeAssembly}
@@ -27,11 +29,18 @@ public class GenomeAssemblyServiceImpl extends CRUDServiceImpl<Long, GenomeAssem
 	private static final Logger logger = LoggerFactory.getLogger(GenomeAssemblyServiceImpl.class);
 	private final SampleGenomeAssemblyJoinRepository sampleGenomeAssemblyJoinRepository;
 
+	private final SampleService sampleService;
+
+	private SampleRepository sampleRepository;
+
 	@Autowired
 	public GenomeAssemblyServiceImpl(GenomeAssemblyRepository repository,
-			SampleGenomeAssemblyJoinRepository sampleGenomeAssemblyJoinRepository, Validator validator) {
+			SampleGenomeAssemblyJoinRepository sampleGenomeAssemblyJoinRepository, Validator validator,
+			SampleService sampleService, SampleRepository sampleRepository) {
 		super(repository, validator, GenomeAssembly.class);
 		this.sampleGenomeAssemblyJoinRepository = sampleGenomeAssemblyJoinRepository;
+		this.sampleService = sampleService;
+		this.sampleRepository = sampleRepository;
 	}
 
 	/**
@@ -85,7 +94,11 @@ public void removeGenomeAssemblyFromSample(Sample sample, Long genomeAssemblyId)
 				genomeAssemblyId);
 		if (join != null) {
 			logger.debug("Removing genome assembly [" + genomeAssemblyId + "] from sample [" + sample.getId() + "]");
-			sampleGenomeAssemblyJoinRepository.deleteById(join.getId());
+			sampleGenomeAssemblyJoinRepository.delete(join);
+			if (sample.getDefaultGenomeAssembly() != null
+					&& sample.getDefaultGenomeAssembly().getId().equals(genomeAssemblyId)) {
+				sampleRepository.removeDefaultGenomeAssembly(sample);
+			}
 		} else {
 			logger.trace("Genome assembly [" + genomeAssemblyId + "] is not associated with sample [" + sample.getId()
 					+ "]. Ignoring.");

src/main/java/ca/corefacility/bioinformatics/irida/service/impl/sample/SampleServiceImpl.java

@@ -363,6 +363,10 @@ public Map<String, List<Long>> getSampleIdsBySampleNameForProjects(List<Long> pr
 	public void removeSequencingObjectFromSample(Sample sample, SequencingObject object) {
 		SampleSequencingObjectJoin readObjectForSample = ssoRepository.readObjectForSample(sample, object.getId());
 		ssoRepository.delete(readObjectForSample);
+		if (sample.getDefaultSequencingObject() != null
+				&& sample.getDefaultSequencingObject().getId().equals(object.getId())) {
+			sampleRepository.removeDefaultSequencingObject(sample);
+		}
 	}
 
 	/**

src/main/java/ca/corefacility/bioinformatics/irida/service/remote/ProjectSynchronizationService.java

@@ -186,7 +186,7 @@ public synchronized void findMarkedProjectsToSync() {
 	 * 
 	 * @param project the {@link Project} to synchronize. This should have been read from a remote api.
 	 */
-	private void syncProject(Project project) {
+	private void syncProject(Project project) throws Exception {
 		SyncStatus syncType = project.getRemoteStatus().getSyncStatus();
 
 		project.getRemoteStatus().setSyncStatus(SyncStatus.UPDATING);
@@ -305,7 +305,7 @@ private void syncProject(Project project) {
 	 * @return A list of {@link ProjectSynchronizationException}s, empty if no errors.
 	 */
 	public List<ProjectSynchronizationException> syncSample(Sample sample, Project project,
-			Map<String, Sample> existingSamples) {
+			Map<String, Sample> existingSamples) throws Exception {
 		Sample localSample;
 
 		if (existingSamples.containsKey(sample.getRemoteStatus().getURL())) {

src/main/java/ca/corefacility/bioinformatics/irida/service/sample/SampleService.java

@@ -181,7 +181,7 @@ public Page<ProjectSampleJoin> getSamplesForProjectWithName(Project project, Str
 	 * @param sample {@link Sample} to remove sequences from
 	 * @param object {@link SequencingObject} to remove
 	 */
-	public void removeSequencingObjectFromSample(Sample sample, SequencingObject object);
+	public void removeSequencingObjectFromSample(Sample sample, SequencingObject object) throws Exception;
 
 	/**
 	 * Merge multiple samples into one. Merging samples copies the {@link SequenceFile} references from the set of

src/main/java/ca/corefacility/bioinformatics/irida/web/controller/api/samples/RESTSampleSequenceFilesController.java

@@ -695,7 +695,7 @@ public ResponseResource<SequencingObject> addNewSequenceFilePairToSample(@PathVa
 			description = "Delete the sequencing object from a given sample.", tags = "samples")
 	@RequestMapping(value = "/api/samples/{sampleId}/{objectType}/{objectId}", method = RequestMethod.DELETE)
 	public ResponseResource<RootResource> removeSequenceFileFromSample(@PathVariable Long sampleId,
-			@PathVariable String objectType, @PathVariable Long objectId) {
+			@PathVariable String objectType, @PathVariable Long objectId) throws Exception {
 		// load the project, sample and sequence file from the database
 		Sample s = sampleService.read(sampleId);
 		SequencingObject seqObject = sequencingObjectService.readSequencingObjectForSample(s, objectId);

src/test/java/ca/corefacility/bioinformatics/irida/service/ProjectHashingServiceIT.java

@@ -103,7 +103,7 @@ public void hashChangesWithRemovedSample() {
 
 	@WithMockUser(username = "admin", roles = "ADMIN")
 	@Test
-	public void hashChangesWithRemovedSequencingObject() {
+	public void hashChangesWithRemovedSequencingObject() throws Exception {
 		Project project = projectService.read(2L);
 
 		Integer originalHash = hashingService.getProjectHash(project);

src/test/java/ca/corefacility/bioinformatics/irida/service/ProjectSynchronizationServiceTest.java

@@ -199,7 +199,7 @@ public void testSyncProjectsUnauthorized() {
 	}
 
 	@Test
-	public void testSyncNewSample() {
+	public void testSyncNewSample() throws Exception {
 		Sample sample = new Sample();
 		RemoteStatus sampleStatus = new RemoteStatus("http://sample", api);
 		sample.setRemoteStatus(sampleStatus);
@@ -215,7 +215,7 @@ public void testSyncNewSample() {
 	}
 
 	@Test
-	public void testExistingSample() {
+	public void testExistingSample() throws Exception {
 		Sample sample = new Sample();
 		RemoteStatus sampleStatus = new RemoteStatus("http://sample", api);
 		sample.setRemoteStatus(sampleStatus);
@@ -233,7 +233,7 @@ public void testExistingSample() {
 	}
 
 	@Test
-	public void testSyncSampleNoAssemblies() {
+	public void testSyncSampleNoAssemblies() throws Exception {
 		Sample sample = new Sample();
 		RemoteStatus sampleStatus = new RemoteStatus("http://sample", api);
 		sample.setRemoteStatus(sampleStatus);
@@ -253,7 +253,7 @@ public void testSyncSampleNoAssemblies() {
 	}
 
 	@Test
-	public void testSyncExistingSampleWithDeletedFiles() {
+	public void testSyncExistingSampleWithDeletedFiles() throws Exception {
 		Sample sample = new Sample();
 		RemoteStatus sampleStatus = new RemoteStatus("http://sample", api);
 		sample.setRemoteStatus(sampleStatus);
@@ -278,7 +278,7 @@ public void testSyncExistingSampleWithDeletedFiles() {
 	}
 
 	@Test
-	public void testSyncExistingSampleWithDeletedAssemblies() {
+	public void testSyncExistingSampleWithDeletedAssemblies() throws Exception {
 		Sample sample = new Sample();
 		RemoteStatus sampleStatus = new RemoteStatus("http://sample", api);
 		sample.setRemoteStatus(sampleStatus);
@@ -321,7 +321,7 @@ public void testSyncFiles() {
 	}
 
 	@Test
-	public void testSyncSampleNoFast5() {
+	public void testSyncSampleNoFast5() throws Exception {
 		Sample sample = new Sample();
 		RemoteStatus sampleStatus = new RemoteStatus("http://sample", api);
 		sample.setRemoteStatus(sampleStatus);

src/test/java/ca/corefacility/bioinformatics/irida/service/impl/integration/sample/SampleServiceImplIT.java

@@ -18,6 +18,7 @@
 import ca.corefacility.bioinformatics.irida.annotation.ServiceIntegrationTest;
 import ca.corefacility.bioinformatics.irida.exceptions.EntityNotFoundException;
 import ca.corefacility.bioinformatics.irida.exceptions.SequenceFileAnalysisException;
+import ca.corefacility.bioinformatics.irida.model.assembly.GenomeAssembly;
 import ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin;
 import ca.corefacility.bioinformatics.irida.model.project.Project;
 import ca.corefacility.bioinformatics.irida.model.project.ReferenceFile;
@@ -26,9 +27,11 @@
 import ca.corefacility.bioinformatics.irida.model.sample.Sample;
 import ca.corefacility.bioinformatics.irida.model.sample.metadata.MetadataEntry;
 import ca.corefacility.bioinformatics.irida.model.sample.metadata.ProjectMetadataResponse;
+import ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject;
 import ca.corefacility.bioinformatics.irida.model.workflow.submission.AnalysisSubmission;
 import ca.corefacility.bioinformatics.irida.repositories.joins.sample.SampleGenomeAssemblyJoinRepository;
 import ca.corefacility.bioinformatics.irida.service.AnalysisSubmissionService;
+import ca.corefacility.bioinformatics.irida.service.GenomeAssemblyService;
 import ca.corefacility.bioinformatics.irida.service.ProjectService;
 import ca.corefacility.bioinformatics.irida.service.SequencingObjectService;
 import ca.corefacility.bioinformatics.irida.service.sample.MetadataTemplateService;
@@ -63,6 +66,9 @@ public class SampleServiceImplIT {
 	@Autowired
 	private MetadataTemplateService metadataTemplateService;
 
+	@Autowired
+	private GenomeAssemblyService genomeAssemblyService;
+
 	/**
 	 * Variation in a floating point number to be considered equal.
 	 */
@@ -80,6 +86,37 @@ public void testCreateSample() {
 		assertEquals(sampleName, saved.getSampleName(), "Wrong name was saved.");
 	}
 
+	@Test
+	@WithMockUser(username = "fbristow", roles = "ADMIN")
+	public void removeSampleDefaultSequencingObject() throws Exception {
+		Sample sample = sampleService.read(9L);
+		SequencingObject sequencingObject = objectService.read(2L);
+		sample.setDefaultSequencingObject(sequencingObject);
+		sampleService.update(sample);
+
+		assertNotNull(sample.getDefaultSequencingObject());
+		sampleService.removeSequencingObjectFromSample(sample, sequencingObject);
+
+		Sample sampleAfterDelete = sampleService.read(9L);
+		assertNull(sampleAfterDelete.getDefaultSequencingObject());
+	}
+
+	@Test
+	@WithMockUser(username = "fbristow", roles = "ADMIN")
+	public void removeSampleDefaultGenomeAssembly() {
+		Sample sample = sampleService.read(2L);
+		GenomeAssembly genomeAssembly = sampleGenomeAssemblyJoinRepository.findBySampleAndAssemblyId(sample.getId(), 2L)
+				.getObject();
+		sample.setDefaultGenomeAssembly(genomeAssembly);
+		sampleService.update(sample);
+
+		assertNotNull(sample.getDefaultGenomeAssembly());
+		genomeAssemblyService.removeGenomeAssemblyFromSample(sample, genomeAssembly.getId());
+
+		Sample sampleAfterDelete = sampleService.read(2L);
+		assertNull(sampleAfterDelete.getDefaultGenomeAssembly());
+	}
+
 	/**
 	 * Straightforward merging of samples all belonging to the same project.
 	 */