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

Example 11 with WorkflowInputsGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy 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 12 with WorkflowInputsGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy 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 13 with WorkflowInputsGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy in project irida by phac-nml.

the class AnalysisParameterServiceGalaxyTest method testPrepareParametersOverrideSuccess.

/**
 * Tests preparing workflow parameters and overriding with custom value
 * successfully.
 *
 * @throws IridaWorkflowParameterException
 */
@Test
public void testPrepareParametersOverrideSuccess() throws IridaWorkflowParameterException {
    Map<String, String> parameters = Maps.newHashMap();
    parameters.put("parameter1", "1");
    WorkflowInputsGalaxy workflowInputsGalaxy = analysisParameterService.prepareAnalysisParameters(parameters, iridaWorkflow);
    assertNotNull("workflowInputsGalaxy is null", workflowInputsGalaxy);
    WorkflowInputs workflowInputs = workflowInputsGalaxy.getInputsObject();
    Map<Object, Map<String, Object>> workflowParameters = workflowInputs.getParameters();
    Map<String, Object> tool1Parameters = workflowParameters.get("galaxy-tool1");
    assertNotNull("parameters for galaxy-tool1 should not be null", tool1Parameters);
    assertEquals("galaxy-tool1,parameter1 is not valid", "1", tool1Parameters.get("parameter1"));
}

Example 14 with WorkflowInputsGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy in project irida by phac-nml.

the class AnalysisParameterServiceGalaxyTest method testPrepareParametersOverrideThreeLevelMultipleParameterSuccess.

/**
 * Tests preparing workflow parameters with three levels, multiple
 * parameters and overriding with custom value successfully.
 *
 * @throws IridaWorkflowParameterException
 */
@Test
public void testPrepareParametersOverrideThreeLevelMultipleParameterSuccess() throws IridaWorkflowParameterException {
    IridaToolParameter iridaToolParameter = new IridaToolParameter("galaxy-tool1", "level1.level2.parameter1");
    IridaToolParameter iridaToolParameter2 = new IridaToolParameter("galaxy-tool1", "level1.level2.parameter2");
    IridaToolParameter iridaToolParameter3 = new IridaToolParameter("galaxy-tool1", "level1.parameter3");
    IridaWorkflowParameter parameter1 = new IridaWorkflowParameter("parameter1", "0", Lists.newArrayList(iridaToolParameter, iridaToolParameter2, iridaToolParameter3));
    List<IridaWorkflowParameter> iridaWorkflowParameters = Lists.newArrayList(parameter1);
    when(iridaWorkflowDescription.getParameters()).thenReturn(iridaWorkflowParameters);
    Map<String, String> parameters = Maps.newHashMap();
    parameters.put("parameter1", "1");
    WorkflowInputsGalaxy workflowInputsGalaxy = analysisParameterService.prepareAnalysisParameters(parameters, iridaWorkflow);
    assertNotNull("workflowInputsGalaxy is null", workflowInputsGalaxy);
    WorkflowInputs workflowInputs = workflowInputsGalaxy.getInputsObject();
    Map<Object, Map<String, Object>> workflowParameters = workflowInputs.getParameters();
    Map<String, Object> tool1Parameters = workflowParameters.get("galaxy-tool1");
    assertNotNull("parameters for galaxy-tool1 should not be null", tool1Parameters);
    assertEquals("parameter not properly defined", ImmutableMap.of("level1", ImmutableMap.of("parameter3", "1", "level2", ImmutableMap.of("parameter1", "1", "parameter2", "1"))), tool1Parameters);
}

Example 15 with WorkflowInputsGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy in project irida by phac-nml.

the class AnalysisParameterServiceGalaxyTest method testPrepareParametersOverrideMultipleLevelMultipleParameterSuccess.

/**
 * Tests preparing workflow parameters with multiple levels, multiple
 * parameters and overriding with custom value successfully.
 *
 * @throws IridaWorkflowParameterException
 */
@Test
public void testPrepareParametersOverrideMultipleLevelMultipleParameterSuccess() throws IridaWorkflowParameterException {
    IridaToolParameter iridaToolParameter = new IridaToolParameter("galaxy-tool1", "level1.parameter1");
    IridaToolParameter iridaToolParameter2 = new IridaToolParameter("galaxy-tool1", "level1.parameter2");
    IridaWorkflowParameter parameter1 = new IridaWorkflowParameter("parameter1", "0", Lists.newArrayList(iridaToolParameter, iridaToolParameter2));
    List<IridaWorkflowParameter> iridaWorkflowParameters = Lists.newArrayList(parameter1);
    when(iridaWorkflowDescription.getParameters()).thenReturn(iridaWorkflowParameters);
    Map<String, String> parameters = Maps.newHashMap();
    parameters.put("parameter1", "1");
    WorkflowInputsGalaxy workflowInputsGalaxy = analysisParameterService.prepareAnalysisParameters(parameters, iridaWorkflow);
    assertNotNull("workflowInputsGalaxy is null", workflowInputsGalaxy);
    WorkflowInputs workflowInputs = workflowInputsGalaxy.getInputsObject();
    Map<Object, Map<String, Object>> workflowParameters = workflowInputs.getParameters();
    Map<String, Object> tool1Parameters = workflowParameters.get("galaxy-tool1");
    assertNotNull("parameters for galaxy-tool1 should not be null", tool1Parameters);
    assertEquals("parameter not properly defined", ImmutableMap.of("level1", ImmutableMap.of("parameter1", "1", "parameter2", "1")), tool1Parameters);
}