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

Example 16 with Workflow

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

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesPairSuccess.

/**
 * Tests out successfully preparing paired workflow input files for
 * execution.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesPairSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesPairSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
    History createdHistory = historiesClient.create(history);
    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);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A, referenceFilePath, validWorkflowIdPaired, false);
    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 library is created
    List<LibraryContent> libraryContents = librariesClient.getLibraryContents(preparedWorkflow.getRemoteDataId());
    Map<String, List<LibraryContent>> libraryContentsMap = libraryContents.stream().collect(Collectors.groupingBy(LibraryContent::getName));
    assertFalse("the returned library should exist in Galaxy", libraryContentsMap.isEmpty());
    String sequenceFile1ALibraryName = "/" + sequenceFilePathA.getFileName().toString();
    String sequenceFile2ALibraryName = "/" + sequenceFilePath2A.getFileName().toString();
    assertEquals("the returned library does not contain the correct number of elements", 3, libraryContentsMap.size());
    assertTrue("the returned library does not contain a root folder", libraryContentsMap.containsKey("/"));
    assertTrue("the returned library does not contain the correct sequence file", libraryContentsMap.containsKey(sequenceFile1ALibraryName));
    assertEquals("the returned library does not contain the correct sequence file", 1, libraryContentsMap.get(sequenceFile1ALibraryName).size());
    assertTrue("the returned library does not contain the correct sequence file", libraryContentsMap.containsKey(sequenceFile2ALibraryName));
    assertEquals("the returned library does not contain the correct sequence file", 1, libraryContentsMap.get(sequenceFile2ALibraryName).size());
    // 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());
    Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
    assertTrue("the created history should contain the file " + sequenceFilePathA.toFile().getName(), contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
    assertTrue("the created history should contain the file " + sequenceFilePath2A.toFile().getName(), contentsMap.containsKey(sequenceFilePath2A.toFile().getName()));
    assertTrue("the created history should contain the file " + referenceFilePath.toFile().getName(), contentsMap.containsKey(referenceFilePath.toFile().getName()));
    assertTrue("the created history should contain the collection with name " + INPUTS_PAIRED_NAME, contentsMap.containsKey(INPUTS_PAIRED_NAME));
    // make sure workflow inputs contains correct information
    Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
    assertEquals("the created workflow inputs has an invalid number of elements", 2, workflowInputsMap.size());
}

Example 17 with Workflow

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

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesParametersSuccessIgnoreDefaultParameters.

/**
 * Tests out successfully preparing paired workflow input files for
 * execution and ignoring default parameters.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesParametersSuccessIgnoreDefaultParameters() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesParametersSuccessIgnoreDefaultParameters");
    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", IridaWorkflowParameter.IGNORE_DEFAULT_VALUE);
    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");
    assertNull("toolParameters is not null", toolParameters);
}

Example 18 with Workflow

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

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesSingleSuccess.

/**
 * Tests out successfully preparing single workflow input files for
 * execution.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesSingleSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesSingleSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
    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);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePathA, referenceFilePath, validWorkflowIdSingle, false);
    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());
    assertNotNull("the returned workflow inputs should not be null", preparedWorkflow.getWorkflowInputs());
    assertNotNull("the returned library id should not be null", preparedWorkflow.getRemoteDataId());
    // verify correct library is created
    List<LibraryContent> libraryContents = librariesClient.getLibraryContents(preparedWorkflow.getRemoteDataId());
    Map<String, List<LibraryContent>> libraryContentsMap = libraryContents.stream().collect(Collectors.groupingBy(LibraryContent::getName));
    assertFalse("the returned library should exist in Galaxy", libraryContentsMap.isEmpty());
    String sequenceFileALibraryName = "/" + sequenceFilePathA.getFileName().toString();
    assertEquals("the returned library does not contain the correct number of elements", 2, libraryContentsMap.size());
    assertTrue("the returned library does not contain a root folder", libraryContentsMap.containsKey("/"));
    assertTrue("the returned library does not contain the correct sequence file", libraryContentsMap.containsKey(sequenceFileALibraryName));
    assertEquals("the returned library does not contain the correct sequence file", 1, libraryContentsMap.get(sequenceFileALibraryName).size());
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("the created history should contain 3 entries", 3, historyContents.size());
    Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
    assertTrue("the created history should contain the file " + sequenceFilePathA.toFile().getName(), contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
    assertTrue("the created history should contain the file " + referenceFilePath.toFile().getName(), contentsMap.containsKey(referenceFilePath.toFile().getName()));
    assertTrue("the created history should contain the collection with name " + INPUTS_SINGLE_NAME, contentsMap.containsKey(INPUTS_SINGLE_NAME));
    // make sure workflow inputs contains correct information
    Map<String, WorkflowInput> workflowInputsMap = preparedWorkflow.getWorkflowInputs().getInputsObject().getInputs();
    assertEquals("the created workflow inputs has an invalid number of elements", 2, workflowInputsMap.size());
}

Example 19 with Workflow

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

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesSinglePairFail.

/**
 * Tests out failing to prepare paired and single workflow input files for
 * execution (duplicate samples among single and paired input files).
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test(expected = SampleAnalysisDuplicateException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesSinglePairFail() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesSinglePairFail");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    WorkflowsClient workflowsClient = localGalaxy.getGalaxyInstanceAdmin().getWorkflowsClient();
    History createdHistory = historiesClient.create(history);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(validWorkflowIdSinglePaired);
    Path workflowPath = iridaWorkflow.getWorkflowStructure().getWorkflowFile();
    String workflowString = new String(Files.readAllBytes(workflowPath), StandardCharsets.UTF_8);
    Workflow galaxyWorkflow = workflowsClient.importWorkflow(workflowString);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSinglePairSubmissionInDatabaseSameSample(1L, pairSequenceFiles1A, pairSequenceFiles2A, sequenceFilePath3, referenceFilePath, validWorkflowIdSinglePaired);
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    analysisWorkspaceService.prepareAnalysisFiles(analysisSubmission);
}

Example 20 with Workflow

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

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisSinglePairedSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * consisting of both single and paired sequence reads.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisSinglePairedSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisSinglePairedSuccess");
    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(validWorkflowIdSinglePaired);
    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.setupSinglePairSubmissionInDatabaseSameSample(1L, paths1, paths2, sequenceFilePath3, referenceFilePath, validWorkflowIdSinglePaired);
    Set<SingleEndSequenceFile> singleFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SingleEndSequenceFile.class);
    Set<SequenceFilePair> pairedFiles = sequencingObjectService.getSequencingObjectsOfTypeForAnalysisSubmission(analysisSubmission, SequenceFilePair.class);
    assertEquals("invalid number of single end input files", 1, singleFiles.size());
    assertEquals("invalid number of paired end inputs", 1, pairedFiles.size());
    SequenceFilePair submittedSp = pairedFiles.iterator().next();
    Set<SequenceFile> submittedSf = submittedSp.getFiles();
    assertEquals("invalid number of files for paired input", 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());
}