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

Example 81 with SingleEndSequenceFile

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

the class SampleSequenceFilesControllerTest method testRemoveSequenceFileFromSample.

@Test
public void testRemoveSequenceFileFromSample() throws IOException {
    Sample s = TestDataFactory.constructSample();
    SingleEndSequenceFile so = TestDataFactory.constructSingleEndSequenceFile();
    when(sampleService.read(s.getId())).thenReturn(s);
    when(sequencingObjectService.readSequencingObjectForSample(s, so.getId())).thenReturn(so);
    ModelMap modelMap = controller.removeSequenceFileFromSample(s.getId(), "unpaired", so.getId());
    verify(sampleService, times(1)).read(s.getId());
    verify(sequencingObjectService).readSequencingObjectForSample(s, so.getId());
    verify(sampleService, times(1)).removeSequencingObjectFromSample(s, so);
    Object o = modelMap.get(RESTGenericController.RESOURCE_NAME);
    assertNotNull(o);
    assertTrue(o instanceof RootResource);
    RootResource resource = (RootResource) o;
    Link sample = resource.getLink(RESTSampleSequenceFilesController.REL_SAMPLE);
    Link sequenceFiles = resource.getLink(RESTSampleSequenceFilesController.REL_SAMPLE_SEQUENCE_FILES);
    String sampleLocation = "http://localhost/api/samples/" + s.getId();
    assertNotNull(sample);
    assertEquals(sampleLocation, sample.getHref());
    assertNotNull(sequenceFiles);
    assertEquals(sampleLocation + "/sequenceFiles", sequenceFiles.getHref());
}

Example 82 with SingleEndSequenceFile

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

the class SampleSequenceFilesControllerTest method testGetQcForFile.

@Test
public void testGetQcForFile() throws IOException {
    Sample s = TestDataFactory.constructSample();
    SingleEndSequenceFile so = TestDataFactory.constructSingleEndSequenceFile();
    AnalysisFastQC analysisFastQC = new AnalysisFastQC(AnalysisFastQC.builder());
    when(sampleService.read(s.getId())).thenReturn(s);
    when(sequencingObjectService.readSequencingObjectForSample(s, so.getId())).thenReturn(so);
    when(analysisService.getFastQCAnalysisForSequenceFile(so, so.getSequenceFile().getId())).thenReturn(analysisFastQC);
    ModelMap readQCForSequenceFile = controller.readQCForSequenceFile(s.getId(), RESTSampleSequenceFilesController.objectLabels.get(so.getClass()), so.getId(), so.getSequenceFile().getId());
    verify(sampleService).read(s.getId());
    verify(sequencingObjectService).readSequencingObjectForSample(s, so.getId());
    verify(analysisService).getFastQCAnalysisForSequenceFile(so, so.getSequenceFile().getId());
    assertTrue(readQCForSequenceFile.containsKey(RESTGenericController.RESOURCE_NAME));
    Object object = readQCForSequenceFile.get(RESTGenericController.RESOURCE_NAME);
    assertTrue(object instanceof AnalysisFastQC);
    AnalysisFastQC qc = (AnalysisFastQC) object;
    assertNotNull(qc.getLink(RESTSampleSequenceFilesController.REL_QC_SEQFILE));
}

Example 83 with SingleEndSequenceFile

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

the class SampleServiceImplTest method testGetTotalBasesForSampleFailNoFastQC.

/**
 * Tests out failing to get the total bases from a sample with one sequence
 * file due to missing FastQC
 *
 * @throws SequenceFileAnalysisException
 */
@Test(expected = SequenceFileAnalysisException.class)
public void testGetTotalBasesForSampleFailNoFastQC() throws SequenceFileAnalysisException {
    Sample s1 = new Sample();
    s1.setId(1L);
    SequenceFile sf1 = new SequenceFile();
    sf1.setId(2222L);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(s1, new SingleEndSequenceFile(sf1));
    when(ssoRepository.getSequencesForSample(s1)).thenReturn(Arrays.asList(join));
    sampleService.getTotalBasesForSample(s1);
}

Example 84 with SingleEndSequenceFile

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

the class SampleServiceImplTest method so.

private SequencingObject so(Long id) {
    SequencingObject so = new SingleEndSequenceFile(sf(id));
    so.setId(id);
    return so;
}

Example 85 with SingleEndSequenceFile

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

the class AnalysisWorkspaceServiceGalaxy method prepareAnalysisFiles.

/**
 * {@inheritDoc}
 */
@Override
public PreparedWorkflowGalaxy prepareAnalysisFiles(AnalysisSubmission analysisSubmission) throws ExecutionManagerException, IridaWorkflowException {
    checkNotNull(analysisSubmission, "analysisSubmission is null");
    checkNotNull(analysisSubmission.getRemoteAnalysisId(), "analysisId is null");
    checkNotNull(analysisSubmission.getWorkflowId(), "workflowId is null");
    checkNotNull(analysisSubmission.getRemoteWorkflowId(), "remoteWorkflowId is null");
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(analysisSubmission.getWorkflowId());
    IridaWorkflowInput workflowInput = iridaWorkflow.getWorkflowDescription().getInputs();
    Set<SingleEndSequenceFile> singleEndFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedEndFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    if (iridaWorkflow.getWorkflowDescription().requiresReference()) {
        checkArgument(analysisSubmission.getReferenceFile().isPresent(), "workflow requires reference but none defined in submission");
    } else {
        checkArgument(!analysisSubmission.getReferenceFile().isPresent(), "workflow does not require a reference and a reference file is set in the submission");
    }
    if (!iridaWorkflow.getWorkflowDescription().acceptsSingleSequenceFiles()) {
        checkArgument(singleEndFiles.isEmpty(), "workflow does not accept single sequence files, but single sequence files are passed as input to " + analysisSubmission);
    }
    if (!iridaWorkflow.getWorkflowDescription().acceptsPairedSequenceFiles()) {
        checkArgument(pairedEndFiles.isEmpty(), "workflow does not accept paired sequence files, but paired sequence files are passed as input to " + analysisSubmission);
    }
    String temporaryLibraryName = AnalysisSubmission.class.getSimpleName() + "-" + UUID.randomUUID().toString();
    History workflowHistory = galaxyHistoriesService.findById(analysisSubmission.getRemoteAnalysisId());
    Library workflowLibrary = galaxyLibrariesService.buildEmptyLibrary(new GalaxyProjectName(temporaryLibraryName));
    // get unique files for pairs and single files
    Map<Sample, SingleEndSequenceFile> singleFiles = sequencingObjectService.getUniqueSamplesForSequencingObjects(singleEndFiles);
    Map<Sample, SequenceFilePair> pairedFiles = sequencingObjectService.getUniqueSamplesForSequencingObjects(pairedEndFiles);
    // check that there aren't common sample names between single and paired
    if (samplesInCommon(singleFiles, pairedFiles)) {
        throw new SampleAnalysisDuplicateException("Single and paired input files share a common sample for submission " + analysisSubmission);
    }
    String workflowId = analysisSubmission.getRemoteWorkflowId();
    WorkflowDetails workflowDetails = galaxyWorkflowService.getWorkflowDetails(workflowId);
    WorkflowInputsGalaxy workflowInputsGalaxy = analysisParameterServiceGalaxy.prepareAnalysisParameters(analysisSubmission.getInputParameters(), iridaWorkflow);
    WorkflowInputs inputs = workflowInputsGalaxy.getInputsObject();
    inputs.setDestination(new WorkflowInputs.ExistingHistory(workflowHistory.getId()));
    inputs.setWorkflowId(workflowDetails.getId());
    if (!singleFiles.isEmpty()) {
        String sequenceFilesLabelSingle = workflowInput.getSequenceReadsSingle().get();
        String workflowSequenceFileSingleInputId = galaxyWorkflowService.getWorkflowInputId(workflowDetails, sequenceFilesLabelSingle);
        CollectionResponse collectionResponseSingle = analysisCollectionServiceGalaxy.uploadSequenceFilesSingleEnd(singleFiles, workflowHistory, workflowLibrary);
        inputs.setInput(workflowSequenceFileSingleInputId, new WorkflowInputs.WorkflowInput(collectionResponseSingle.getId(), WorkflowInputs.InputSourceType.HDCA));
    }
    if (!pairedFiles.isEmpty()) {
        String sequenceFilesLabelPaired = workflowInput.getSequenceReadsPaired().get();
        String workflowSequenceFilePairedInputId = galaxyWorkflowService.getWorkflowInputId(workflowDetails, sequenceFilesLabelPaired);
        CollectionResponse collectionResponsePaired = analysisCollectionServiceGalaxy.uploadSequenceFilesPaired(pairedFiles, workflowHistory, workflowLibrary);
        inputs.setInput(workflowSequenceFilePairedInputId, new WorkflowInputs.WorkflowInput(collectionResponsePaired.getId(), WorkflowInputs.InputSourceType.HDCA));
    }
    String analysisId = workflowHistory.getId();
    if (iridaWorkflow.getWorkflowDescription().requiresReference()) {
        String referenceFileLabel = workflowInput.getReference().get();
        prepareReferenceFile(analysisSubmission.getReferenceFile().get(), workflowHistory, referenceFileLabel, workflowDetails, inputs);
    }
    return new PreparedWorkflowGalaxy(analysisId, workflowLibrary.getId(), new WorkflowInputsGalaxy(inputs));
}