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

Example 16 with HistoriesClient

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

the class AnalysisWorkspaceServiceGalaxyIT method setup.

/**
 * Sets up variables for testing.
 *
 * @throws URISyntaxException
 * @throws IOException
 * @throws IridaWorkflowLoadException
 */
@Before
public void setup() throws URISyntaxException, IOException, IridaWorkflowLoadException {
    Assume.assumeFalse(WindowsPlatformCondition.isWindows());
    Path sequenceFilePathReal = Paths.get(DatabaseSetupGalaxyITService.class.getResource("testData1.fastq").toURI());
    Path referenceFilePathReal = Paths.get(DatabaseSetupGalaxyITService.class.getResource("testReference.fasta").toURI());
    Path tempDir = Files.createTempDirectory(rootTempDirectory, "workspaceServiceGalaxyTest");
    sequenceFilePathA = tempDir.resolve("testDataA_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePathA, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath2A = tempDir.resolve("testDataA_R2_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath2A, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePathB = tempDir.resolve("testDataB_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePathB, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath2B = tempDir.resolve("testDataB_R2_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath2B, StandardCopyOption.REPLACE_EXISTING);
    sequenceFilePath3 = tempDir.resolve("testData3_R1_001.fastq");
    Files.copy(sequenceFilePathReal, sequenceFilePath3, StandardCopyOption.REPLACE_EXISTING);
    referenceFilePath = Files.createTempFile("testReference", ".fasta");
    Files.delete(referenceFilePath);
    Files.copy(referenceFilePathReal, referenceFilePath);
    singleFileSet = Sets.newHashSet(new SingleEndSequenceFile(new SequenceFile(sequenceFilePathA)));
    GalaxyInstance galaxyInstanceAdmin = localGalaxy.getGalaxyInstanceAdmin();
    HistoriesClient historiesClient = galaxyInstanceAdmin.getHistoriesClient();
    ToolsClient toolsClient = galaxyInstanceAdmin.getToolsClient();
    LibrariesClient librariesClient = galaxyInstanceAdmin.getLibrariesClient();
    GalaxyLibrariesService galaxyLibrariesService = new GalaxyLibrariesService(librariesClient, LIBRARY_POLLING_TIME, LIBRARY_TIMEOUT, 1);
    galaxyHistoriesService = new GalaxyHistoriesService(historiesClient, toolsClient, galaxyLibrariesService);
    pairSequenceFiles1A = new ArrayList<>();
    pairSequenceFiles1A.add(sequenceFilePathA);
    pairSequenceFiles2A = new ArrayList<>();
    pairSequenceFiles2A.add(sequenceFilePath2A);
    pairSequenceFiles1AB = new ArrayList<>();
    pairSequenceFiles1AB.add(sequenceFilePathA);
    pairSequenceFiles1AB.add(sequenceFilePathB);
    pairSequenceFiles2AB = new ArrayList<>();
    pairSequenceFiles2AB.add(sequenceFilePath2A);
    pairSequenceFiles2AB.add(sequenceFilePath2B);
}

Example 17 with HistoriesClient

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

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesParametersSuccessWithNoParameters.

/**
 * Tests out successfully preparing paired workflow input files for
 * execution, no parameters set.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesParametersSuccessWithNoParameters() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesParametersSuccessWithNoParameters");
    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);
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupPairSubmissionInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A, referenceFilePath, validWorkflowIdPairedWithParameters, 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 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 to default", "10", coverageMinValue);
    assertEquals("coverageMidValue should have been changed to default", ImmutableMap.of("coverageMid", "10"), toolParameters.get("conditional"));
    String coverageMaxValue = (String) toolParameters.get("coverageMin");
    assertEquals("coverageMaxValue should have been changed to default", "10", coverageMaxValue);
}

Example 18 with HistoriesClient

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

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsPhylogenomicsSuccess.

/**
 * Tests out successfully getting results for an analysis (phylogenomics).
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsPhylogenomicsSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsPhylogenomicsSuccess");
    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, TABLE_NAME, createdHistory.getId(), toolsClient);
    uploadFileToHistory(sequenceFilePathA, MATRIX_NAME, createdHistory.getId(), toolsClient);
    uploadFileToHistory(sequenceFilePathA, TREE_NAME, createdHistory.getId(), toolsClient);
    // wait for history
    Util.waitUntilHistoryComplete(createdHistory.getId(), galaxyHistoriesService, 60);
    IridaWorkflow iridaWorkflow = iridaWorkflowsService.getIridaWorkflow(phylogenomicsWorkflowId);
    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, phylogenomicsWorkflowId, false);
    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", AnalysisType.PHYLOGENOMICS, analysis.getAnalysisType());
    assertEquals("the analysis results has an invalid number of output files", 3, analysis.getAnalysisOutputFiles().size());
    assertEquals("the analysis results output file has an invalid name", Paths.get(TABLE_NAME), analysis.getAnalysisOutputFile(TABLE_KEY).getFile().getFileName());
    assertEquals("the analysis results output file has an invalid label", TABLE_NAME, analysis.getAnalysisOutputFile(TABLE_KEY).getLabel());
    assertEquals("the analysis results output file has an invalid name", Paths.get(MATRIX_NAME), analysis.getAnalysisOutputFile(MATRIX_KEY).getFile().getFileName());
    assertEquals("the analysis results output file has an invalid label", MATRIX_NAME, analysis.getAnalysisOutputFile(MATRIX_KEY).getLabel());
    assertEquals("the analysis results output file has an invalid name", Paths.get(TREE_NAME), analysis.getAnalysisOutputFile(TREE_KEY).getFile().getFileName());
    assertEquals("the analysis results output file has an invalid label", TREE_NAME, analysis.getAnalysisOutputFile(TREE_KEY).getLabel());
}

Example 19 with HistoriesClient

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

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisFail.

/**
 * Tests out failing to get results for an analysis (missing output file).
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test(expected = GalaxyDatasetNotFoundException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisFail() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisFail");
    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);
    // 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);
    analysisSubmission.setRemoteAnalysisId(createdHistory.getId());
    analysisSubmission.setRemoteWorkflowId(galaxyWorkflow.getId());
    analysisSubmission.setAnalysisState(AnalysisState.COMPLETING);
    analysisSubmissionRepository.save(analysisSubmission);
    analysisWorkspaceService.getAnalysisResults(analysisSubmission);
}

Example 20 with HistoriesClient

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

the class AnalysisWorkspaceServiceGalaxyIT method testGetAnalysisResultsTestAnalysisDeleteSampleRunningSuccess.

/**
 * Tests out successfully getting results for an analysis (TestAnalysis)
 * when sequencing objects are present, but the sample was deleted while pipeline was running.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IridaWorkflowNotFoundException
 * @throws IOException
 * @throws IridaWorkflowAnalysisTypeException
 * @throws TimeoutException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetAnalysisResultsTestAnalysisDeleteSampleRunningSuccess() throws InterruptedException, ExecutionManagerException, IridaWorkflowNotFoundException, IOException, IridaWorkflowAnalysisTypeException, TimeoutException {
    History history = new History();
    history.setName("testGetAnalysisResultsTestAnalysisDeleteSampleRunningSuccess");
    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);
    sampleRepository.delete(1L);
    assertTrue(!sampleService.exists(1L));
    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());
}