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

Example 1 with WorkflowInputsGalaxy

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

the class AnalysisWorkspaceServiceGalaxyIT method testPrepareAnalysisFilesSinglePairSuccess.

/**
 * Tests out successfully preparing paired and single workflow input files
 * for execution.
 *
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws IOException
 * @throws IridaWorkflowException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testPrepareAnalysisFilesSinglePairSuccess() throws InterruptedException, ExecutionManagerException, IOException, IridaWorkflowException {
    History history = new History();
    history.setName("testPrepareAnalysisFilesPairSuccess");
    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.setupSinglePairSubmissionInDatabaseDifferentSample(1L, 2L, pairSequenceFiles1A, pairSequenceFiles2A, sequenceFilePath3, referenceFilePath, validWorkflowIdSinglePaired);
    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);
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("the created history has an invalid number of elements", 6, 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 " + sequenceFilePath3.toFile().getName(), contentsMap.containsKey(sequenceFilePath3.toFile().getName()));
    assertTrue("the created history should contain the file " + referenceFilePath.toFile().getName(), contentsMap.containsKey(referenceFilePath.toFile().getName()));
    assertTrue("the created history should contain a dataset collection with the name " + INPUTS_SINGLE_NAME, contentsMap.containsKey(INPUTS_SINGLE_NAME));
    assertTrue("the created history should contain a dataset collection with the 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", 3, workflowInputsMap.size());
}

Example 2 with WorkflowInputsGalaxy

use of ca.corefacility.bioinformatics.irida.model.workflow.execution.galaxy.WorkflowInputsGalaxy 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 3 with WorkflowInputsGalaxy

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

the class AnalysisParameterServiceGalaxyTest method testPrepareParametersOverrideMultipleLevelSuccess.

/**
 * Tests preparing workflow parameters with multiple levels and overriding
 * with custom value successfully.
 *
 * @throws IridaWorkflowParameterException
 */
@Test
public void testPrepareParametersOverrideMultipleLevelSuccess() throws IridaWorkflowParameterException {
    IridaToolParameter iridaToolParameter = new IridaToolParameter("galaxy-tool1", "level1.parameter1");
    IridaWorkflowParameter parameter1 = new IridaWorkflowParameter("parameter1", "0", Lists.newArrayList(iridaToolParameter));
    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")), tool1Parameters);
}

Example 4 with WorkflowInputsGalaxy

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

the class AnalysisParameterServiceGalaxyTest method testPrepareParametersOverrideSuccessTwoTools.

/**
 * Tests preparing workflow parameters and overriding with custom value
 * successfully in two tools.
 *
 * @throws IridaWorkflowParameterException
 */
@Test
public void testPrepareParametersOverrideSuccessTwoTools() throws IridaWorkflowParameterException {
    Map<String, String> parameters = Maps.newHashMap();
    parameters.put("parameter1", "1");
    IridaToolParameter iridaToolParameter = new IridaToolParameter("galaxy-tool1", "parameter1");
    IridaToolParameter iridaToolParameter2 = new IridaToolParameter("galaxy-tool1", "parameter2");
    IridaWorkflowParameter parameter1 = new IridaWorkflowParameter("parameter1", "0", Lists.newArrayList(iridaToolParameter, iridaToolParameter2));
    List<IridaWorkflowParameter> iridaWorkflowParameters = Lists.newArrayList(parameter1);
    when(iridaWorkflowDescription.getParameters()).thenReturn(iridaWorkflowParameters);
    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"));
    assertEquals("galaxy-tool1,parameter2 is not valid", "1", tool1Parameters.get("parameter2"));
}

Example 5 with WorkflowInputsGalaxy

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

the class AnalysisParameterServiceGalaxyTest method testPrepareParametersSuccessNoParameters.

/**
 * Tests preparing workflow parameters when there are no parameters to prepare.
 *
 * @throws IridaWorkflowParameterException
 */
@Test
public void testPrepareParametersSuccessNoParameters() throws IridaWorkflowParameterException {
    when(iridaWorkflowDescription.acceptsParameters()).thenReturn(false);
    WorkflowInputsGalaxy workflowInputsGalaxy = analysisParameterService.prepareAnalysisParameters(ImmutableMap.of(), iridaWorkflow);
    assertNotNull("workflowInputsGalaxy is null", workflowInputsGalaxy);
    WorkflowInputs workflowInputs = workflowInputsGalaxy.getInputsObject();
    assertNotNull("workflowInputs is null", workflowInputs);
    verify(iridaWorkflowDescription).acceptsParameters();
}