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

Example 16 with Dataset

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

the class GalaxyHistoriesServiceIT method testGetDatasetForFileInHistoryFail.

/**
 * Tests getting a dataset for a file in the history and failing.
 * @throws UploadException
 * @throws GalaxyDatasetException
 */
@Test(expected = GalaxyDatasetNotFoundException.class)
public void testGetDatasetForFileInHistoryFail() throws UploadException, GalaxyDatasetException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Dataset dataset = galaxyHistory.fileToHistory(dataFile, InputFileType.FASTQ_SANGER, history);
    String datasetName = dataset.getName() + "invalid";
    galaxyHistory.getDatasetForFileInHistory(datasetName, history.getId());
}

Example 17 with Dataset

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

the class GalaxyHistoriesServiceIT method testDownloadDatasetFailHistoryId.

/**
 * Tests failing to download a dataset (invalid history id)
 * @throws IOException
 * @throws InterruptedException
 * @throws ExecutionManagerException
 * @throws TimeoutException
 */
@Test(expected = ExecutionManagerDownloadException.class)
@Ignore("Ignored because if inconsistent behaviour between Galaxy revisions.")
public void testDownloadDatasetFailHistoryId() throws IOException, TimeoutException, ExecutionManagerException, InterruptedException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Dataset dataset = galaxyHistory.fileToHistory(dataFile, InputFileType.FASTQ_SANGER, history);
    Util.waitUntilHistoryComplete(history.getId(), galaxyHistory, 60);
    String invalidHistoryId = history.getId() + "a";
    Path datasetPath = Files.createTempFile("data", "fastq");
    galaxyHistory.downloadDatasetTo(invalidHistoryId, dataset.getId(), datasetPath);
}

Example 18 with Dataset

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

the class GalaxyWorkflowsIT method constructPairedFileCollection.

/**
 * Constructs a collection containing a list of files from the given datasets.
 * @param inputDatasetsForward  The forward datasets to construct a collection from.
 * @param inputDatasetsReverse  The reverse datasets to construct a collection from.
 * @param history  The history to construct the collection within.
 * @return  A CollectionResponse describing the dataset collection.
 * @throws ExecutionManagerException  If an exception occured constructing the collection.
 */
public CollectionResponse constructPairedFileCollection(List<Dataset> inputDatasetsForward, List<Dataset> inputDatasetsReverse, History history) throws ExecutionManagerException {
    checkNotNull(inputDatasetsForward, "inputDatasetsForward is null");
    checkNotNull(inputDatasetsReverse, "inputDatasetsReverse is null");
    checkNotNull(history, "history is null");
    checkNotNull(history.getId(), "history does not have an associated id");
    checkArgument(inputDatasetsForward.size() == inputDatasetsReverse.size(), "inputDatasets do not have equal sizes");
    CollectionDescription collectionDescription = new CollectionDescription();
    collectionDescription.setCollectionType(DatasetCollectionType.LIST_PAIRED.toString());
    collectionDescription.setName(COLLECTION_NAME);
    for (int i = 0; i < inputDatasetsForward.size(); i++) {
        Dataset datasetForward = inputDatasetsForward.get(i);
        Dataset datasetReverse = inputDatasetsReverse.get(i);
        HistoryDatasetElement elementForward = new HistoryDatasetElement();
        elementForward.setId(datasetForward.getId());
        elementForward.setName(FORWARD_PAIR_NAME);
        HistoryDatasetElement elementReverse = new HistoryDatasetElement();
        elementReverse.setId(datasetReverse.getId());
        elementReverse.setName(REVERSE_PAIR_NAME);
        // Create an object to link together the forward and reverse reads for file2
        CollectionElement element = new CollectionElement();
        element.setName(BASE_NAME + i);
        element.setCollectionType(DatasetCollectionType.PAIRED.toString());
        element.addCollectionElement(elementForward);
        element.addCollectionElement(elementReverse);
        collectionDescription.addDatasetElement(element);
    }
    try {
        return historiesClient.createDatasetCollection(history.getId(), collectionDescription);
    } catch (RuntimeException e) {
        throw new ExecutionManagerException("Could not construct dataset collection", e);
    }
}

Example 19 with Dataset

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

the class GalaxyWorkflowsIT method testExecuteWorkflow.

/**
 * Tests executing a single workflow in Galaxy.
 * @throws ExecutionManagerException
 */
@Test
public void testExecuteWorkflow() throws ExecutionManagerException {
    String workflowId = localGalaxy.getSingleInputWorkflowId();
    String workflowInputLabel = localGalaxy.getSingleInputWorkflowLabel();
    WorkflowOutputs workflowOutput = runSingleFileWorkflow(dataFile1, 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());
    assertTrue(workflowOutput.getOutputIds().size() > 0);
    // each output dataset should exist
    for (String outputId : workflowOutput.getOutputIds()) {
        Dataset dataset = historiesClient.showDataset(workflowOutput.getHistoryId(), outputId);
        assertNotNull(dataset);
    }
    // test get workflow status
    GalaxyWorkflowStatus workflowStatus = galaxyHistory.getStatusForHistory(workflowOutput.getHistoryId());
    float percentComplete = workflowStatus.getProportionComplete();
    assertTrue(0.0f <= percentComplete && percentComplete <= 1.0f);
}

Example 20 with Dataset

use of com.github.jmchilton.blend4j.galaxy.beans.Dataset 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;
}