Examples with PreparedWorkflowGalaxy ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy used on opensource projects

Example 6 with PreparedWorkflowGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy 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 7 with PreparedWorkflowGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy 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 8 with PreparedWorkflowGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy 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 9 with PreparedWorkflowGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy 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 10 with PreparedWorkflowGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.PreparedWorkflowGalaxy 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));
}