Examples with SingleEndSequenceFile ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile used on opensource projects

Example 51 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class ProjectEventHandlerTest method testHandleSequenceFileAddedEventSingle.

@SuppressWarnings("unchecked")
@Test
public void testHandleSequenceFileAddedEventSingle() {
    Class<? extends ProjectEvent> clazz = DataAddedToSampleProjectEvent.class;
    Project project = new Project();
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile();
    SingleEndSequenceFile seqObj = new SingleEndSequenceFile(file);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(sample, seqObj);
    when(psjRepository.getProjectForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true)));
    when(eventRepository.save(any(ProjectEvent.class))).thenReturn(new DataAddedToSampleProjectEvent(project, sample));
    Object[] args = {};
    MethodEvent methodEvent = new MethodEvent(clazz, join, args);
    handler.delegate(methodEvent);
    ArgumentCaptor<ProjectEvent> captor = ArgumentCaptor.forClass(ProjectEvent.class);
    verify(eventRepository).save(captor.capture());
    ProjectEvent event = captor.getValue();
    assertTrue(event instanceof DataAddedToSampleProjectEvent);
    verify(projectRepository).save(any(Project.class));
    verify(sampleRepository).save(any(Sample.class));
}

Example 52 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class AnalysisCollectionServiceGalaxyIT method testUploadSequenceFilesSingleSuccess.

/**
 * Tests successfully uploading a single end sequence file to Galaxy and
 * constructing a collection.
 *
 * @throws ExecutionManagerException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testUploadSequenceFilesSingleSuccess() throws ExecutionManagerException {
    History history = new History();
    history.setName("testUploadSequenceFilesSingleSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
    History createdHistory = historiesClient.create(history);
    Library library = new Library();
    library.setName("testUploadSequenceFilesSingleSuccess");
    Library createdLibrary = librariesClient.createLibrary(library);
    Set<SingleEndSequenceFile> sequenceFiles = Sets.newHashSet(databaseSetupGalaxyITService.setupSequencingObjectInDatabase(1L, sequenceFilePathA));
    Map<Sample, IridaSingleEndSequenceFile> sampleSequenceFiles = new HashMap<>(sequencingObjectService.getUniqueSamplesForSequencingObjects(sequenceFiles));
    Sample sample1 = sampleRepository.findOne(1L);
    CollectionResponse collectionResponse = analysisCollectionServiceGalaxy.uploadSequenceFilesSingleEnd(sampleSequenceFiles, createdHistory, createdLibrary);
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("historyContents should have size 2", 2, historyContents.size());
    Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
    assertTrue("sequenceFile should have been uploaded to history", contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
    assertTrue("dataset collection with name " + INPUTS_SINGLE_NAME + " should have been created in history", contentsMap.containsKey(INPUTS_SINGLE_NAME));
    // verify correct collection has been created
    assertEquals("constructed dataset collection should have been " + DatasetCollectionType.LIST + " but is instead " + collectionResponse.getCollectionType(), DatasetCollectionType.LIST.toString(), collectionResponse.getCollectionType());
    List<CollectionElementResponse> collectionElements = collectionResponse.getElements();
    assertEquals("dataset collection should have only 1 element", 1, collectionElements.size());
    Map<String, CollectionElementResponse> collectionElementsMap = collectionElementsAsMap(collectionElements);
    assertTrue("dataset collection should have an element with the name " + sample1.getSampleName(), collectionElementsMap.containsKey(sample1.getSampleName()));
    CollectionElementResponse sample1Response = collectionElementsMap.get(sample1.getSampleName());
    assertEquals("invalid type for dataset element", HISTORY_DATASET_NAME, sample1Response.getElementType());
}

Example 53 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method setup.

/**
 * Sets up variables for testing.
 *
 * @throws URISyntaxException
 * @throws IOException
 * @throws IridaWorkflowLoadException
 */
@Before
public void setup() throws URISyntaxException, IOException, IridaWorkflowLoadException {
    Assume.assumeFalse(WindowsPlatformCondition.isWindows());
    Path sequenceFilePathReal = Paths.get(DatabaseSetupGalaxyITService.class.getResource("testData1.fastq").toURI());
    Path referenceFilePathReal = Paths.get(DatabaseSetupGalaxyITService.class.getResource("testReference.fasta").toURI());
    Path tempDir = Files.createTempDirectory(rootTempDirectory, "workspaceServiceGalaxyTest");
    sequenceFilePathA = tempDir.resolve("testDataA_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePathA, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath2A = tempDir.resolve("testDataA_R2_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath2A, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePathB = tempDir.resolve("testDataB_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePathB, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath2B = tempDir.resolve("testDataB_R2_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath2B, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath3 = tempDir.resolve("testData3_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath3, StandardCopyOption.REPLACE_EXISTING);
    referenceFilePath = Files.createTempFile("testReference", ".fasta");
    Files.delete(referenceFilePath);
    Files.copy(referenceFilePathReal, referenceFilePath);
    singleFileSet = Sets.newHashSet(new SingleEndSequenceFile(new SequenceFile(sequenceFilePathA)));
    GalaxyInstance galaxyInstanceAdmin = localGalaxy.getGalaxyInstanceAdmin();
    HistoriesClient historiesClient = galaxyInstanceAdmin.getHistoriesClient();
    ToolsClient toolsClient = galaxyInstanceAdmin.getToolsClient();
    LibrariesClient librariesClient = galaxyInstanceAdmin.getLibrariesClient();
    GalaxyLibrariesService galaxyLibrariesService = new GalaxyLibrariesService(librariesClient, LIBRARY_POLLING_TIME, LIBRARY_TIMEOUT, 1);
    galaxyHistoriesService = new GalaxyHistoriesService(historiesClient, toolsClient, galaxyLibrariesService);
    pairSequenceFiles1A = new ArrayList<>();
    pairSequenceFiles1A.add(sequenceFilePathA);
    pairSequenceFiles2A = new ArrayList<>();
    pairSequenceFiles2A.add(sequenceFilePath2A);
    pairSequenceFiles1AB = new ArrayList<>();
    pairSequenceFiles1AB.add(sequenceFilePathA);
    pairSequenceFiles1AB.add(sequenceFilePathB);
    pairSequenceFiles2AB = new ArrayList<>();
    pairSequenceFiles2AB.add(sequenceFilePath2A);
    pairSequenceFiles2AB.add(sequenceFilePath2B);
}

Example 54 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisSinglePairedSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting of both single and paired sequence reads.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisSinglePairedSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisSinglePairedSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    ToolsClient toolsClient = localGalaxy.getGalaxyInstanceAdmin().getToolsClient();
    History createdHistory = historiesClient.create(history);
    // upload test outputs
    uploadFileToHistory(sequenceFilePathA, OUTPUT1_NAME, createdHistory.getId(), toolsClient);
    uploadFileToHistory(sequenceFilePathA, OUTPUT2_NAME, createdHistory.getId(), toolsClient);
    // wait for history
    Util.waitUntilHistoryComplete(createdHistory.getId(), galaxyHistoriesService, 60);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdSinglePaired);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    List<Path> paths1 = new ArrayList<>();
    paths1.add(sequenceFilePathA);
    List<Path> paths2 = new ArrayList<>();
    paths2.add(sequenceFilePath2A);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSinglePairSubmissionInDatabaseSameSample(1L, paths1, paths2, sequenceFilePath3, referenceFilePath, validWorkflowIdSinglePaired);
    Set<SingleEndSequenceFile> singleFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("invalid number of single end input files", 1, singleFiles.size());
    assertEquals("invalid number of paired end inputs", 1, pairedFiles.size());
    SequenceFilePair submittedSp = pairedFiles.iterator().next();
    Set<SequenceFile> submittedSf = submittedSp.getFiles();
    assertEquals("invalid number of files for paired input", 2, submittedSf.size());
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    analysisSubmission.setAnalysisState(AnalysisState.COMPLETING);
    analysisSubmissionRepository.save(analysisSubmission);
    Analysis analysis = analysisWorkspaceService.getAnalysisResults(analysisSubmission);
    assertNotNull("the analysis results were not properly created", analysis);
    assertEquals("the Analysis results class is invalid", Analysis.class, analysis.getClass());
    assertEquals("the analysis results has an invalid number of output files", 2, analysis.getAnalysisOutputFiles().size());
    assertEquals("the analysis results output file has an invalid name", Paths.get(OUTPUT1_NAME), analysis.getAnalysisOutputFile(OUTPUT1_KEY).getFile().getFileName());
    assertEquals("the analysis results output file has an invalid label", OUTPUT1_NAME, analysis.getAnalysisOutputFile(OUTPUT1_KEY).getLabel());
    assertEquals("the analysis results output file has an invalid name", Paths.get(OUTPUT2_NAME), analysis.getAnalysisOutputFile(OUTPUT2_KEY).getFile().getFileName());
    assertEquals("the analysis results output file has an invalid label", OUTPUT2_NAME, analysis.getAnalysisOutputFile(OUTPUT2_KEY).getLabel());
}

Example 55 with SingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SingleEndSequenceFile in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyTest method testPrepareAnalysisFilesSinglePairedSuccess.

/**
 * Tests out successfully to preparing an analysis with both single and
 * paired files
 *
 * @throws ExecutionManagerException
 * @throws IridaWorkflowException
 */
@SuppressWarnings("unchecked")
@Test
public void testPrepareAnalysisFilesSinglePairedSuccess() throws ExecutionManagerException, IridaWorkflowException {
    Set<SingleEndSequenceFile> singleFiles = Sets.newHashSet(sampleSingleSequenceFileMap.values());
    Set<SequenceFilePair> pairedFiles = Sets.newHashSet(sampleSequenceFilePairMap.values());
    Set<SequencingObject> joinedInput = Sets.newHashSet(singleFiles);
    joinedInput.addAll(pairedFiles);
    submission = AnalysisSubmission.builder(workflowId).name("my analysis").inputFiles(joinedInput).referenceFile(referenceFile).build();
    submission.setRemoteAnalysisId(HISTORY_ID);
    submission.setRemoteWorkflowId(WORKFLOW_ID);
    when(sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(submission, SingleEndSequenceFile.class)).thenReturn(singleFiles);
    when(sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(submission, SequenceFilePair.class)).thenReturn(pairedFiles);
    when(iridaWorkflowsService.getIridaWorkflow(workflowId)).thenReturn(iridaWorkflowSinglePaired);
    when(galaxyHistoriesService.findById(HISTORY_ID)).thenReturn(workflowHistory);
    when(galaxyLibrariesService.buildEmptyLibrary(any(GalaxyProjectName.class))).thenReturn(workflowLibrary);
    when(sequencingObjectService.getUniqueSamplesForSequencingObjects(singleFiles)).thenReturn(sampleSingleSequenceFileMap);
    when(sequencingObjectService.getUniqueSamplesForSequencingObjects(pairedFiles)).thenReturn(sampleSequenceFilePairMap);
    when(galaxyHistoriesService.fileToHistory(refFile, InputFileType.FASTA, workflowHistory)).thenReturn(refDataset);
    when(galaxyWorkflowService.getWorkflowDetails(WORKFLOW_ID)).thenReturn(workflowDetails);
    when(analysisParameterServiceGalaxy.prepareAnalysisParameters(any(Map.class), any(IridaWorkflow.class))).thenReturn(new WorkflowInputsGalaxy(new WorkflowInputs()));
    when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, SEQUENCE_FILE_SINGLE_LABEL)).thenReturn(SEQUENCE_FILE_SINGLE_ID);
    when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, SEQUENCE_FILE_PAIRED_LABEL)).thenReturn(SEQUENCE_FILE_PAIRED_ID);
    when(galaxyWorkflowService.getWorkflowInputId(workflowDetails, REFERENCE_FILE_LABEL)).thenReturn(REFERENCE_FILE_ID);
    when(analysisCollectionServiceGalaxy.uploadSequenceFilesSingleEnd(any(Map.class), eq(workflowHistory), eq(workflowLibrary))).thenReturn(collectionResponseSingle);
    when(analysisCollectionServiceGalaxy.uploadSequenceFilesPaired(any(Map.class), eq(workflowHistory), eq(workflowLibrary))).thenReturn(collectionResponsePaired);
    PreparedWorkflowGalaxy preparedWorkflow = workflowPreparation.prepareAnalysisFiles(submission);
    assertEquals("preparedWorflow history id not equal to " + HISTORY_ID, HISTORY_ID, preparedWorkflow.getRemoteAnalysisId());
    assertEquals("preparedWorkflow library is invalid", LIBRARY_ID, preparedWorkflow.getRemoteDataId());
    assertNotNull("workflowInputs in preparedWorkflow is null", preparedWorkflow.getWorkflowInputs());
    Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
    assertEquals("invalid number of workflow inputs", 3, workflowInputsMap.size());
    assertTrue("workflow inputs should contain reference entry", workflowInputsMap.containsKey(REFERENCE_FILE_ID));
    assertTrue("workflow inputs should contain sequence file single entry", workflowInputsMap.containsKey(SEQUENCE_FILE_SINGLE_ID));
    assertTrue("workflow inputs should contain sequence file paired entry", workflowInputsMap.containsKey(SEQUENCE_FILE_PAIRED_ID));
    verify(analysisCollectionServiceGalaxy).uploadSequenceFilesSingleEnd(any(Map.class), any(History.class), any(Library.class));
    verify(analysisCollectionServiceGalaxy).uploadSequenceFilesPaired(any(Map.class), any(History.class), any(Library.class));
}