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

Example 1 with WorkflowOutputs

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

the class GalaxyWorkflowsIT method testExecuteCollectionsPairedList.

/**
 * Tests executing a collections paired list workflow.
 * @throws ExecutionManagerException
 */
@Test
public void testExecuteCollectionsPairedList() throws ExecutionManagerException {
    String workflowId = localGalaxy.getWorklowCollectionListId();
    String workflowInputLabel = localGalaxy.getWorkflowCollectionListLabel();
    List<Path> dataFilesForward = new LinkedList<Path>();
    dataFilesForward.add(dataFile1);
    dataFilesForward.add(dataFile2);
    List<Path> dataFilesReverse = new LinkedList<Path>();
    dataFilesReverse.add(dataFile3);
    dataFilesReverse.add(dataFile4);
    WorkflowOutputs workflowOutput = runSingleCollectionWorkflow(dataFilesForward, dataFilesReverse, FILE_TYPE, workflowId, workflowInputLabel);
    assertNotNull(workflowOutput);
    assertNotNull(workflowOutput.getHistoryId());
    // history should exist
    HistoryDetails historyDetails = historiesClient.showHistory(workflowOutput.getHistoryId());
    assertNotNull(historyDetails);
    // outputs should exist
    assertNotNull(workflowOutput.getOutputIds());
    assertEquals(1, workflowOutput.getOutputIds().size());
    String outputId = workflowOutput.getOutputIds().get(0);
    // output dataset should exist
    Dataset outputDataset = historiesClient.showDataset(workflowOutput.getHistoryId(), outputId);
    assertNotNull(outputDataset);
    // test get workflow status
    GalaxyWorkflowStatus workflowStatus = galaxyHistory.getStatusForHistory(workflowOutput.getHistoryId());
    float percentComplete = workflowStatus.getProportionComplete();
    assertTrue(0.0f <= percentComplete && percentComplete <= 1.0f);
}

Example 2 with WorkflowOutputs

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

the class GalaxyWorkflowsIT method testExecuteWorkflowChangeToolParameter.

/**
 * Tests executing a single workflow in Galaxy and changing a single tool
 * parameter.
 *
 * @throws ExecutionManagerException
 */
@Test
public void testExecuteWorkflowChangeToolParameter() throws ExecutionManagerException {
    String toolId = "Grep1";
    String workflowId = localGalaxy.getSingleInputWorkflowId();
    String workflowInputLabel = localGalaxy.getSingleInputWorkflowLabel();
    Map<String, ToolParameter> toolParameters = ImmutableMap.of(toolId, new ToolParameter("pattern", "^#"));
    WorkflowOutputs workflowOutput = runSingleFileWorkflow(dataFile1, FILE_TYPE, workflowId, workflowInputLabel, toolParameters);
    assertNotNull("workflowOutput should not be null", workflowOutput);
    assertNotNull("workflowOutput history id should not be null", workflowOutput.getHistoryId());
    // history should exist
    HistoryDetails historyDetails = historiesClient.showHistory(workflowOutput.getHistoryId());
    assertNotNull("historyDetails for the history for the workflow should not be null", historyDetails);
    // outputs should exist
    assertNotNull("outputIds for the workflow should not be null", workflowOutput.getOutputIds());
    assertTrue("there should exist output dataset ids for the workflow", workflowOutput.getOutputIds().size() > 0);
    // each output dataset should exist
    for (String outputId : workflowOutput.getOutputIds()) {
        Dataset dataset = historiesClient.showDataset(workflowOutput.getHistoryId(), outputId);
        assertNotNull("the output dataset should exist", dataset);
        HistoryContentsProvenance provenance = historiesClient.showProvenance(workflowOutput.getHistoryId(), dataset.getId());
        if (toolId.equals(provenance.getToolId())) {
            Map<String, Object> parametersMap = provenance.getParameters();
            assertEquals("pattern parameter is correct", "\"^#\"", parametersMap.get("pattern"));
        }
    }
    // test get workflow status
    GalaxyWorkflowStatus workflowStatus = galaxyHistory.getStatusForHistory(workflowOutput.getHistoryId());
    float proportionComplete = workflowStatus.getProportionComplete();
    assertTrue("the workflow proportion complete should be between 0 and 1", 0.0f <= proportionComplete && proportionComplete <= 1.0f);
}

Example 3 with WorkflowOutputs

use of com.github.jmchilton.blend4j.galaxy.beans.WorkflowOutputs 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 4 with WorkflowOutputs

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

the class GalaxyWorkflowsIT method testGetWorkflowStatusComplete.

/**
 * Tests executing a single workflow in Galaxy and getting the status after completion.
 * @throws ExecutionManagerException
 * @throws InterruptedException
 * @throws TimeoutException
 */
@Test
public void testGetWorkflowStatusComplete() throws ExecutionManagerException, TimeoutException, InterruptedException {
    History history = galaxyHistory.newHistoryForWorkflow();
    WorkflowOutputs workflowOutput = runSingleFileTabularWorkflowFilterTool(history, dataFile1, VALID_FILTER_PARAMETER);
    Util.waitUntilHistoryComplete(workflowOutput.getHistoryId(), galaxyHistory, 60);
    // test get workflow status
    GalaxyWorkflowStatus workflowStatus = galaxyHistory.getStatusForHistory(workflowOutput.getHistoryId());
    assertEquals("final workflow state is invalid", GalaxyWorkflowState.OK, workflowStatus.getState());
    assertTrue("final workflow state is invalid", workflowStatus.completedSuccessfully());
}

Example 5 with WorkflowOutputs

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

the class GalaxyWorkflowsIT method testGetWorkflowStatusError.

/**
 * Tests executing a single workflow in Galaxy and getting an error status after completion.
 * @throws ExecutionManagerException
 * @throws InterruptedException
 * @throws TimeoutException
 */
@Test
public void testGetWorkflowStatusError() throws ExecutionManagerException, TimeoutException, InterruptedException {
    History history = galaxyHistory.newHistoryForWorkflow();
    // no column c2 for this input file, so should give an error
    WorkflowOutputs workflowOutput = runSingleFileTabularWorkflowFilterTool(history, dataFile1, INVALID_FILTER_PARAMETER);
    Util.waitUntilHistoryComplete(workflowOutput.getHistoryId(), galaxyHistory, 60);
    // test get workflow status
    GalaxyWorkflowStatus workflowStatus = galaxyHistory.getStatusForHistory(workflowOutput.getHistoryId());
    assertEquals("final workflow state is invalid", GalaxyWorkflowState.ERROR, workflowStatus.getState());
    assertTrue("final workflow state is invalid", workflowStatus.errorOccurred());
}