Examples with IridaWorkflow ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow used on opensource projects

Example 16 with IridaWorkflow

use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisPairedSingleSampleSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting only of paired sequence reads.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisPairedSingleSampleSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisPairedSingleSampleSuccess");
    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(validWorkflowIdPairedSingleSample);
    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.setupPairSubmissionInDatabase(1L, paths1, paths2, referenceFilePath, validWorkflowIdPairedSingleSample, false);
    Set<SingleEndSequenceFile> submittedSingleFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("the created submission should have no single input files", 0, submittedSingleFiles.size());
    assertEquals("the created submission has an invalid number of paired input files", 1, pairedFiles.size());
    SequenceFilePair submittedSp = pairedFiles.iterator().next();
    Set<SequenceFile> submittedSf = submittedSp.getFiles();
    assertEquals("the paired input should have 2 files", 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", SAMPLE1_NAME + "-" + 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", SAMPLE1_NAME + "-" + OUTPUT2_NAME, analysis.getAnalysisOutputFile(OUTPUT2_KEY).getLabel());
}

Example 17 with IridaWorkflow

use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesSingleFail.

/**
 * Tests out failing to prepare single workflow input files for execution
 * (duplicate samples).
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test(expected = DuplicateSampleException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesSingleFail() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesSingleFail");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    History createdHistory = historiesClient.create(history);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdSingle);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    List<SingleEndSequenceFile> sequenceFiles = analysisExecutionGalaxyITService.setupSequencingObjectInDatabase(1L, sequenceFilePathA, sequenceFilePath2A);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, Sets.newHashSet(sequenceFiles), referenceFilePath, validWorkflowIdSingle);
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
}

Example 18 with IridaWorkflow

use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisPairedSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting only of paired sequence reads.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisPairedSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisPairedSuccess");
    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(validWorkflowIdPaired);
    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.setupPairSubmissionInDatabase(1L, paths1, paths2, referenceFilePath, validWorkflowIdPaired, false);
    Set<SingleEndSequenceFile> submittedSingleFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("the created submission should have no single input files", 0, submittedSingleFiles.size());
    assertEquals("the created submission has an invalid number of paired input files", 1, pairedFiles.size());
    SequenceFilePair submittedSp = pairedFiles.iterator().next();
    Set<SequenceFile> submittedSf = submittedSp.getFiles();
    assertEquals("the paired input should have 2 files", 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 19 with IridaWorkflow

use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.

the class AnalysisControllerTest method testGetAnalysisDetailsTree.

@Test
public void testGetAnalysisDetailsTree() throws IOException, IridaWorkflowNotFoundException {
    Long submissionId = 1L;
    ExtendedModelMap model = new ExtendedModelMap();
    Locale locale = Locale.ENGLISH;
    final IridaWorkflowInput input = new IridaWorkflowInput("single", "paired", "reference", true);
    AnalysisSubmission submission = TestDataFactory.constructAnalysisSubmission();
    IridaWorkflowDescription description = new IridaWorkflowDescription(submission.getWorkflowId(), "My Workflow", "V1", AnalysisType.PHYLOGENOMICS, input, Lists.newArrayList(), Lists.newArrayList(), Lists.newArrayList());
    IridaWorkflow iridaWorkflow = new IridaWorkflow(description, null);
    submission.setAnalysisState(AnalysisState.COMPLETED);
    when(analysisSubmissionServiceMock.read(submissionId)).thenReturn(submission);
    when(iridaWorkflowsServiceMock.getIridaWorkflow(submission.getWorkflowId())).thenReturn(iridaWorkflow);
    String detailsPage = analysisController.getDetailsPage(submissionId, model, locale);
    assertEquals("should be details page", AnalysisController.PAGE_DETAILS_DIRECTORY + "tree", detailsPage);
    assertEquals("Tree preview should be set", "tree", model.get("preview"));
    assertEquals("submission should be in model", submission, model.get("analysisSubmission"));
    assertEquals("submission reference file should be in model.", submission.getReferenceFile().get(), model.get("referenceFile"));
}

Example 20 with IridaWorkflow

use of ca.corefacility.bioinformatics.irida.model.workflow.IridaWorkflow in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxy method getAnalysisResults.

/**
 * {@inheritDoc}
 */
@Override
public Analysis getAnalysisResults(AnalysisSubmission analysisSubmission) throws ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException {
    checkNotNull(analysisSubmission, "analysisSubmission is null");
    checkNotNull(analysisSubmission.getWorkflowId(), "workflowId is null");
    checkNotNull(analysisSubmission.getRemoteWorkflowId(), "remoteWorkflowId is null");
    Path outputDirectory = Files.createTempDirectory("analysis-output");
    logger.trace("Created temporary directory " + outputDirectory + " for analysis output files");
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(analysisSubmission.getWorkflowId());
    String analysisId = analysisSubmission.getRemoteAnalysisId();
    Map<String, IridaWorkflowOutput> outputsMap = iridaWorkflow.getWorkflowDescription().getOutputsMap();
    String labelPrefix = getLabelPrefix(analysisSubmission, iridaWorkflow);
    Map<String, AnalysisOutputFile> analysisOutputFiles = Maps.newHashMap();
    for (String analysisOutputName : outputsMap.keySet()) {
        String outputFileName = outputsMap.get(analysisOutputName).getFileName();
        Dataset outputDataset = galaxyHistoriesService.getDatasetForFileInHistory(outputFileName, analysisId);
        AnalysisOutputFile analysisOutput = buildOutputFile(analysisId, labelPrefix, outputDataset, outputDirectory);
        analysisOutputFiles.put(analysisOutputName, analysisOutput);
    }
    AnalysisType analysisType = iridaWorkflow.getWorkflowDescription().getAnalysisType();
    return new Analysis(analysisId, analysisOutputFiles, analysisType);
}