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

Example 36 with SequenceFilePair

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequenceFilePair 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));
}

Example 37 with SequenceFilePair

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

the class SamplesControllerTest method testUploadSequenceFilePairs.

@Test
public void testUploadSequenceFilePairs() throws IOException {
    Sample sample = TestDataFactory.constructSample();
    when(sampleService.read(sample.getId())).thenReturn(sample);
    List<MultipartFile> fileList = createMultipartFileList(MULTIPARTFILE_PAIR_PATHS);
    ArgumentCaptor<SequenceFilePair> sequenceFileArgumentCaptor = ArgumentCaptor.forClass(SequenceFilePair.class);
    HttpServletResponse response = new MockHttpServletResponse();
    controller.uploadSequenceFiles(sample.getId(), fileList, response);
    assertEquals("Response is ok", HttpServletResponse.SC_OK, response.getStatus());
    verify(sequencingObjectService).createSequencingObjectInSample(sequenceFileArgumentCaptor.capture(), eq(sample));
    assertEquals("Should have the correct file name", "pair_test_R1_001.fastq", sequenceFileArgumentCaptor.getValue().getForwardSequenceFile().getLabel());
    assertEquals("Should have the correct file name", "pair_test_R2_001.fastq", sequenceFileArgumentCaptor.getValue().getReverseSequenceFile().getLabel());
}

Example 38 with SequenceFilePair

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

the class SamplesControllerTest method testUploadSequenceFilePairsAndSingle.

@Test
public void testUploadSequenceFilePairsAndSingle() throws IOException {
    Sample sample = TestDataFactory.constructSample();
    when(sampleService.read(sample.getId())).thenReturn(sample);
    List<MultipartFile> fileList = createMultipartFileList(ArrayUtils.addAll(MULTIPARTFILE_PATHS, MULTIPARTFILE_PAIR_PATHS));
    ArgumentCaptor<SequencingObject> sequenceFileArgumentCaptor = ArgumentCaptor.forClass(SequencingObject.class);
    HttpServletResponse response = new MockHttpServletResponse();
    controller.uploadSequenceFiles(sample.getId(), fileList, response);
    assertEquals("Response is ok", HttpServletResponse.SC_OK, response.getStatus());
    verify(sequencingObjectService, times(3)).createSequencingObjectInSample(sequenceFileArgumentCaptor.capture(), eq(sample));
    List<SequencingObject> allValues = sequenceFileArgumentCaptor.getAllValues();
    assertEquals("Should have created 2 single end sequence files", 2, allValues.stream().filter(o -> o instanceof SingleEndSequenceFile).count());
    assertEquals("Should have created 1 file pair", 1, allValues.stream().filter(o -> o instanceof SequenceFilePair).count());
}

Example 39 with SequenceFilePair

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

the class ReadAnalysisSubmissionPermissionTest method testPermitSISTR.

@Test
public void testPermitSISTR() {
    String username = "aaron";
    User u = new User();
    u.setUsername(username);
    Authentication auth = new UsernamePasswordAuthenticationToken("aaron", "password1");
    Project p = new Project();
    SequenceFilePair pair = new SequenceFilePair();
    AnalysisSubmission analysisSubmission = AnalysisSubmission.builder(workflowId).name("test").inputFiles(ImmutableSet.of(pair)).referenceFile(referenceFile).build();
    analysisSubmission.setSubmitter(new User());
    pair.setSistrTyping(analysisSubmission);
    /*
		 * testing that analysis is shared with a project that user isn't a part
		 * of
		 */
    when(pasRepository.getProjectsForSubmission(analysisSubmission)).thenReturn(ImmutableList.of(new ProjectAnalysisSubmissionJoin(p, analysisSubmission)));
    when(readProjectPermission.customPermissionAllowed(auth, p)).thenReturn(false);
    when(userRepository.loadUserByUsername(username)).thenReturn(u);
    when(analysisSubmissionRepository.findOne(1L)).thenReturn(analysisSubmission);
    when(seqObjectPermission.customPermissionAllowed(auth, pair)).thenReturn(true);
    when(sequencingObjectRepository.findSequencingObjectsForAnalysisSubmission(analysisSubmission)).thenReturn(ImmutableSet.of(pair));
    assertTrue("permission should be granted.", readAnalysisSubmissionPermission.isAllowed(auth, 1L));
    verify(userRepository).loadUserByUsername(username);
    verify(analysisSubmissionRepository).findOne(1L);
    verify(seqObjectPermission).customPermissionAllowed(auth, pair);
}

Example 40 with SequenceFilePair

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

the class DatabaseSetupGalaxyITService method setupPairSubmissionInDatabase.

/**
 * Sets up an {@link AnalysisSubmission} with a list of paired sequence
 * files and saves all dependencies in database.
 *
 * @param sampleId
 *            The id of the sample to associate with the given sequence
 *            file.
 * @param sequenceFilePaths1
 *            A list of paths for the first part of the pair.
 * @param sequenceFilePaths2
 *            A list of paths for the second part of the pair. The path to
 *            an input sequence file for this test.
 * @param referenceFilePath
 *            The path to an input reference file for this test.
 * @param parameters
 *            The input parameters.
 * @param iridaWorkflowId
 *            The id of an irida workflow.
 * @param state
 *            {@link AnalysisState} of the submission
 * @return An {@link AnalysisSubmission} which has been saved to the
 *         database.
 */
public AnalysisSubmission setupPairSubmissionInDatabase(long sampleId, List<Path> sequenceFilePaths1, List<Path> sequenceFilePaths2, Path referenceFilePath, Map<String, String> parameters, UUID iridaWorkflowId, AnalysisState state) {
    List<SequenceFilePair> sequenceFilePairs = setupSampleSequenceFileInDatabase(sampleId, sequenceFilePaths1, sequenceFilePaths2);
    ReferenceFile referenceFile = referenceFileRepository.save(new ReferenceFile(referenceFilePath));
    AnalysisSubmission submission = AnalysisSubmission.builder(iridaWorkflowId).name("paired analysis").inputFiles(Sets.newHashSet(sequenceFilePairs)).referenceFile(referenceFile).inputParameters(parameters).build();
    submission.setAnalysisState(state);
    analysisSubmissionService.create(submission);
    return analysisSubmissionRepository.findOne(submission.getId());
}