Examples with History com.github.jmchilton.blend4j.galaxy.beans.History used on opensource projects

Example 21 with History

use of com.github.jmchilton.blend4j.galaxy.beans.History in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesParametersSuccess.

/**
 * Tests out successfully preparing paired workflow input files for
 * execution with parameters.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesParametersSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesParametersSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    History createdHistory = historiesClient.create(history);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdPairedWithParameters);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    Map<String, String> parameters = ImmutableMap.of("coverage", "20");
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A, referenceFilePath, parameters, validWorkflowIdPairedWithParameters);
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    PreparedWorkflowGalaxy preparedWorkflow = analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
    assertEquals("the response history id should match the input history id", createdHistory.getId(), preparedWorkflow.getRemoteAnalysisId());
    WorkflowInputsGalaxy workflowInputsGalaxy = preparedWorkflow.getWorkflowInputs();
    assertNotNull("the returned workflow inputs should not be null", workflowInputsGalaxy);
    assertNotNull("the returned library id should not be null", preparedWorkflow.getRemoteDataId());
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("the created history has an invalid number of elements", 4, historyContents.size());
    WorkflowInputs workflowInputs = preparedWorkflow.getWorkflowInputs().getInputsObject();
    assertNotNull("created workflowInputs is null", workflowInputs);
    Map<String, Object> toolParameters = workflowInputs.getParameters().get("core_pipeline_outputs_paired_with_parameters");
    assertNotNull("toolParameters is null", toolParameters);
    String coverageMinValue = (String) toolParameters.get("coverageMin");
    assertEquals("coverageMinValue should have been changed", "20", coverageMinValue);
    assertEquals("coverageMidValue should have been changed", ImmutableMap.of("coverageMid", "20"), toolParameters.get("conditional"));
    String coverageMaxValue = (String) toolParameters.get("coverageMin");
    assertEquals("coverageMaxValue should have been changed", "20", coverageMaxValue);
}

Example 22 with History

use of com.github.jmchilton.blend4j.galaxy.beans.History in project irida by phac-nml.

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisSingleSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting only of single end sequence reads.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 * @throws IridaWorkflowAnalysisLabelException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisSingleSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisSingleSuccess");
    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(validWorkflowIdSingle);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePathA, referenceFilePath, validWorkflowIdSingle, false);
    Set<SingleEndSequenceFile> submittedSf = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("the created submission should have no paired input files", 0, pairedFiles.size());
    assertEquals("the created submission should have 1 single input file", 1, 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 23 with History

use of com.github.jmchilton.blend4j.galaxy.beans.History 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 24 with History

use of com.github.jmchilton.blend4j.galaxy.beans.History 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 25 with History

use of com.github.jmchilton.blend4j.galaxy.beans.History 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());
}