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

Example 1 with WorkflowDetails

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

the class GalaxyWorkflowsIT method runSingleCollectionWorkflow.

/**
 * Starts the execution of a workflow with a list of fastq files and the given workflow id.
 * @param inputFilesForward  A list of forward read fastq files start the workflow.
 * @param inputFilesReverse  A list of reverse read fastq files start the workflow.
 * @param inputFileType The file type of the input files.
 * @param workflowId  The id of the workflow to start.
 * @param workflowInputLabel The label of a workflow input in Galaxy.
 * @throws ExecutionManagerException If there was an error executing the workflow.
 */
private WorkflowOutputs runSingleCollectionWorkflow(List<Path> inputFilesForward, List<Path> inputFilesReverse, InputFileType inputFileType, String workflowId, String workflowInputLabel) throws ExecutionManagerException {
    checkNotNull(inputFilesForward, "inputFilesForward is null");
    checkNotNull(inputFilesReverse, "inputFilesReverse is null");
    checkArgument(inputFilesForward.size() == inputFilesReverse.size(), "inputFiles have different number of elements");
    checkNotNull(inputFileType, "inputFileType is null");
    checkNotNull(workflowInputLabel, "workflowInputLabel is null");
    for (Path file : inputFilesForward) {
        checkArgument(Files.exists(file), "inputFileForward " + file + " does not exist");
    }
    for (Path file : inputFilesReverse) {
        checkArgument(Files.exists(file), "inputFilesReverse " + file + " does not exist");
    }
    History workflowHistory = galaxyHistory.newHistoryForWorkflow();
    WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflowId);
    // upload dataset to history
    List<Dataset> inputDatasetsForward = uploadFilesListToHistory(inputFilesForward, inputFileType, workflowHistory);
    List<Dataset> inputDatasetsReverse = uploadFilesListToHistory(inputFilesReverse, inputFileType, workflowHistory);
    assertEquals(inputFilesForward.size(), inputDatasetsForward.size());
    assertEquals(inputDatasetsForward.size(), inputDatasetsReverse.size());
    // construct list of datasets
    CollectionResponse collection = constructPairedFileCollection(inputDatasetsForward, inputDatasetsReverse, workflowHistory);
    logger.debug("Constructed dataset collection: id=" + collection.getId() + ", " + collection.getName());
    String workflowInputId = galaxyWorkflowService.getWorkflowInputId(workflowDetails, workflowInputLabel);
    WorkflowInputs inputs = new WorkflowInputs();
    inputs.setDestination(new WorkflowInputs.ExistingHistory(workflowHistory.getId()));
    inputs.setWorkflowId(workflowDetails.getId());
    inputs.setInput(workflowInputId, new WorkflowInputs.WorkflowInput(collection.getId(), WorkflowInputs.InputSourceType.HDCA));
    // execute workflow
    WorkflowOutputs output = workflowsClient.runWorkflow(inputs);
    logger.debug("Running workflow in history " + output.getHistoryId());
    return output;
}

Example 2 with WorkflowDetails

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

the class GalaxyWorkflowsIT method testDeleteWorkflowSuccess.

/**
 * Tests deleting a workflow and succeeding.
 *
 * @throws WorkflowUploadException
 * @throws IOException
 * @throws WorkflowException
 * @throws DeleteGalaxyObjectFailedException
 */
@Test
public void testDeleteWorkflowSuccess() throws WorkflowUploadException, IOException, WorkflowException, DeleteGalaxyObjectFailedException {
    String workflowId = galaxyWorkflowService.uploadGalaxyWorkflow(workflowPath);
    WorkflowDetails details = galaxyWorkflowService.getWorkflowDetails(workflowId);
    assertFalse(details.isDeleted());
    galaxyWorkflowService.deleteWorkflow(workflowId);
    details = galaxyWorkflowService.getWorkflowDetails(workflowId);
    assertTrue(details.isDeleted());
}

Example 3 with WorkflowDetails

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

the class GalaxyWorkflowsIT method runSingleFileTabularWorkflow.

/**
 * Runs a test workflow with the given parameters and input file.
 *
 * @param workflowId
 *            The id of the workflow to run.
 * @param workflowInputLabel
 *            The lable of the input for the workflow.
 * @param history
 *            The history to run the workflow in.
 * @param inputFile
 *            The file to run the workflow on.
 * @param toolName
 *            The toolName of a parameter to override.
 * @param toolParameter
 *            The overridden tool parameter.
 * @return A {@link WorkflowOutputs} for this workflow.
 * @throws ExecutionManagerException
 */
private WorkflowOutputs runSingleFileTabularWorkflow(String workflowId, String workflowInputLabel, History history, Path inputFile, String toolName, ToolParameter toolParameter) throws ExecutionManagerException {
    checkArgument(Files.exists(inputFile), "inputFile " + inputFile + " does not exist");
    WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflowId);
    // upload dataset to history
    Dataset inputDataset = fileToHistory(inputFile, "tabular", history.getId());
    assertNotNull(inputDataset);
    String workflowInputId = galaxyWorkflowService.getWorkflowInputId(workflowDetails, workflowInputLabel);
    WorkflowInputs inputs = new WorkflowInputs();
    inputs.setDestination(new WorkflowInputs.ExistingHistory(history.getId()));
    inputs.setWorkflowId(workflowDetails.getId());
    inputs.setInput(workflowInputId, new WorkflowInputs.WorkflowInput(inputDataset.getId(), WorkflowInputs.InputSourceType.HDA));
    inputs.setToolParameter(toolName, toolParameter);
    // execute workflow
    WorkflowOutputs output = workflowsClient.runWorkflow(inputs);
    logger.debug("Running workflow in history " + output.getHistoryId());
    return output;
}

Example 4 with WorkflowDetails

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

the class GalaxyWorkflowsIT method runSingleFileWorkflow.

/**
 * Starts the execution of a workflow with a single fastq file and the given workflow id.
 * @param inputFile  An input file to start the workflow.
 * @param inputFileType The file type of the input file.
 * @param workflowId  The id of the workflow to start.
 * @param workflowInputLabel The label of a workflow input in Galaxy.
 * @param toolParameters  A map of tool parameters to set.
 * @throws ExecutionManagerException If there was an error executing the workflow.
 */
private WorkflowOutputs runSingleFileWorkflow(Path inputFile, InputFileType inputFileType, String workflowId, String workflowInputLabel, Map<String, ToolParameter> toolParameters) throws ExecutionManagerException {
    checkNotNull(inputFile, "file is null");
    checkNotNull(inputFileType, "inputFileType is null");
    checkNotNull(workflowInputLabel, "workflowInputLabel is null");
    checkArgument(Files.exists(inputFile), "inputFile " + inputFile + " does not exist");
    History workflowHistory = galaxyHistory.newHistoryForWorkflow();
    WorkflowDetails workflowDetails = workflowsClient.showWorkflow(workflowId);
    // upload dataset to history
    Dataset inputDataset = galaxyHistory.fileToHistory(inputFile, inputFileType, workflowHistory);
    assertNotNull(inputDataset);
    String workflowInputId = galaxyWorkflowService.getWorkflowInputId(workflowDetails, workflowInputLabel);
    WorkflowInputs inputs = new WorkflowInputs();
    inputs.setDestination(new WorkflowInputs.ExistingHistory(workflowHistory.getId()));
    inputs.setWorkflowId(workflowDetails.getId());
    inputs.setInput(workflowInputId, new WorkflowInputs.WorkflowInput(inputDataset.getId(), WorkflowInputs.InputSourceType.HDA));
    if (toolParameters != null) {
        for (String toolId : toolParameters.keySet()) {
            ToolParameter toolParameter = toolParameters.get(toolId);
            inputs.setToolParameter(toolId, toolParameter);
        }
    }
    // execute workflow
    WorkflowOutputs output = workflowsClient.runWorkflow(inputs);
    logger.debug("Running workflow in history " + output.getHistoryId());
    return output;
}

Example 5 with WorkflowDetails

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

the class AnalysisExecutionServiceGalaxyIT method testCleanupErrorAnalysisSuccess.

/**
 * Tests out cleaning up an analysis in error successfully.
 *
 * @throws Exception
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testCleanupErrorAnalysisSuccess() throws Exception {
    AnalysisSubmission analysisSubmission = analysisExecutionGalaxyITService.setupSubmissionInDatabase(1L, sequenceFilePath, referenceFilePath, iridaTestAnalysisWorkflowId, false);
    Future<AnalysisSubmission> analysisSubmittedFuture = analysisExecutionService.prepareSubmission(analysisSubmission);
    AnalysisSubmission analysisSubmitted = analysisSubmittedFuture.get();
    analysisSubmitted.setAnalysisState(AnalysisState.ERROR);
    analysisSubmissionRepository.save(analysisSubmitted);
    WorkflowDetails workflowDetails = workflowsClient.showWorkflow(analysisSubmitted.getRemoteWorkflowId());
    assertFalse("Workflow is already deleted", workflowDetails.isDeleted());
    // Once analysis is complete, attempt to clean up
    Future<AnalysisSubmission> analysisSubmissionCleanedFuture = analysisExecutionService.cleanupSubmission(analysisSubmitted);
    AnalysisSubmission analysisSubmissionCleaned = analysisSubmissionCleanedFuture.get();
    assertEquals("Analysis submission not properly cleaned", AnalysisCleanedState.CLEANED, analysisSubmissionCleaned.getAnalysisCleanedState());
    workflowDetails = workflowsClient.showWorkflow(analysisSubmitted.getRemoteWorkflowId());
    assertTrue("Workflow is not deleted", workflowDetails.isDeleted());
}