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

Example 36 with SequencingObject

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

the class RESTSequencingRunSequenceFilesController method addSequenceFileToMiseqRun.

/**
 * Add a relationship between a {@link MiseqRun} and a {@link SequenceFile}.
 *
 * @param sequencingrunId
 *            the id of the run to add sequence file to.
 * @param representation
 *            the JSON key-value pair that contains the identifier for the
 *            sequenceFile
 * @param response
 *            a reference to the response.
 * @return a response indicating that the collection was modified.
 */
@RequestMapping(value = "/api/sequencingrun/{sequencingrunId}/sequenceFiles", method = RequestMethod.POST)
public ModelMap addSequenceFileToMiseqRun(@PathVariable Long sequencingrunId, @RequestBody Map<String, String> representation, HttpServletResponse response) {
    ModelMap modelMap = new ModelMap();
    String stringId = representation.get(SEQUENCEFILE_ID_KEY);
    long seqId = Long.parseLong(stringId);
    // first, get the SequenceFile
    SequencingObject sequencingObject = sequencingObjectService.read(seqId);
    // then, get the miseq run
    SequencingRun run = miseqRunService.read(sequencingrunId);
    // then add the user to the project with the specified role.
    miseqRunService.addSequencingObjectToSequencingRun(run, sequencingObject);
    MiseqRun miseqRun;
    if (run instanceof MiseqRun) {
        miseqRun = (MiseqRun) run;
    } else {
        throw new IllegalArgumentException("The sequencing run ID must correspond to a a valid MiSeq sequence");
    }
    Link seqFileLocation = linkTo(RESTSequencingRunController.class).slash(sequencingrunId).slash("sequenceFiles").slash(seqId).withSelfRel();
    miseqRun.add(seqFileLocation);
    modelMap.addAttribute(RESTGenericController.RESOURCE_NAME, miseqRun);
    response.addHeader(HttpHeaders.LOCATION, seqFileLocation.getHref());
    response.setStatus(HttpStatus.CREATED.value());
    return modelMap;
}

Example 37 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject 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 38 with SequencingObject

use of ca.corefacility.bioinformatics.irida.model.sequenceFile.SequencingObject 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 SequencingObject

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

the class DatabaseSetupGalaxyITService method setupSinglePairSubmissionInDatabaseDifferentSample.

/**
 * Sets up an {@link AnalysisSubmission} with a list of paired sequence
 * files and a single sequence file under a different sample and saves all
 * dependencies in database.
 *
 * @param sampleIdPaired
 *            The id of the sample to associate with the paired sequence
 *            files.
 * @param sampleIdSingle
 *            The id of the sample to associate with the single 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 singleSequenceFile
 *            A single sequence file to add.
 * @param referenceFilePath
 *            The path to an input reference file for this test.
 * @param iridaWorkflowId
 *            The id of an irida workflow.
 * @return An {@link AnalysisSubmission} which has been saved to the
 *         database.
 */
public AnalysisSubmission setupSinglePairSubmissionInDatabaseDifferentSample(long sampleIdPaired, long sampleIdSingle, List<Path> sequenceFilePaths1, List<Path> sequenceFilePaths2, Path singleSequenceFile, Path referenceFilePath, UUID iridaWorkflowId) {
    SingleEndSequenceFile singleEndFile = (SingleEndSequenceFile) setupSequencingObjectInDatabase(sampleIdSingle, singleSequenceFile).get(0);
    List<SequenceFilePair> sequenceFilePairs = setupSampleSequenceFileInDatabase(sampleIdPaired, sequenceFilePaths1, sequenceFilePaths2);
    Set<SequencingObject> inputs = Sets.newHashSet(sequenceFilePairs);
    inputs.add(singleEndFile);
    ReferenceFile referenceFile = referenceFileRepository.save(new ReferenceFile(referenceFilePath));
    AnalysisSubmission submission = AnalysisSubmission.builder(iridaWorkflowId).name("paired analysis").inputFiles(inputs).referenceFile(referenceFile).build();
    analysisSubmissionService.create(submission);
    return analysisSubmissionRepository.findOne(submission.getId());
}

Example 40 with SequencingObject

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

the class SequencingRunControllerTest method testGetFilesPage.

@SuppressWarnings("rawtypes")
@Test
public void testGetFilesPage() throws IOException {
    Long runId = 1L;
    ExtendedModelMap model = new ExtendedModelMap();
    SequencingRun sequencingRunEntity = new MiseqRun(SequencingRun.LayoutType.PAIRED_END, "");
    ImmutableSet<SequencingObject> files = ImmutableSet.of(new SingleEndSequenceFile(new SequenceFile()));
    when(sequencingRunService.read(runId)).thenReturn(sequencingRunEntity);
    when(objectService.getSequencingObjectsForSequencingRun(sequencingRunEntity)).thenReturn(files);
    String filesPage = controller.getFilesPage(runId, model);
    assertEquals(SequencingRunController.FILES_VIEW, filesPage);
    assertFalse(((Collection) model.get("sequencingObjects")).isEmpty());
    assertEquals(sequencingRunEntity, model.get("run"));
    assertTrue(model.containsKey("fileCount"));
    verify(sequencingRunService).read(runId);
    verify(objectService).getSequencingObjectsForSequencingRun(sequencingRunEntity);
}