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

Example 11 with History

use of com.github.jmchilton.blend4j.galaxy.beans.History 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 12 with History

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

the class GalaxyHistoriesServiceTest method setup.

/**
 * Sets up objects for history tests.
 * @throws URISyntaxException
 */
@Before
public void setup() throws URISyntaxException {
    MockitoAnnotations.initMocks(this);
    when(okayResponse.getClientResponseStatus()).thenReturn(ClientResponse.Status.OK);
    when(invalidResponse.getClientResponseStatus()).thenReturn(ClientResponse.Status.FORBIDDEN);
    galaxyHistory = new GalaxyHistoriesService(historiesClient, toolsClient, galaxyLibrariesService);
    dataFile = Paths.get(this.getClass().getResource("testData1.fastq").toURI());
    history = new History();
    history.setId(HISTORY_ID);
    datasetHistoryContents = buildHistoryContentsList(FILENAME, DATA_ID);
    datasetForFile = new Dataset();
    datasetForFile.setName(FILENAME);
    datasetForFile.setId(DATA_ID);
    datasetForFile.setUrl("datasets/" + DATA_ID + "/display");
    datasetForFile.setGalaxyUrl("http://fakehost");
    datasetForFile.setApiKey("1");
}

Example 13 with History

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

the class GalaxyHistoriesServiceTest method testLibraryDatasetToHistory.

/**
 * Tests moving a library dataset to a history.
 */
@Test
public void testLibraryDatasetToHistory() {
    HistoryDetails historyDetails = new HistoryDetails();
    History createdHistory = new History();
    createdHistory.setId(HISTORY_ID);
    when(historiesClient.createHistoryDataset(any(String.class), any(HistoryDataset.class))).thenReturn(historyDetails);
    assertNotNull(galaxyHistory.libraryDatasetToHistory(libraryFileId, createdHistory));
}

Example 14 with History

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

the class GalaxyHistoriesServiceTest method testConstructCollectionSuccess.

/**
 * Tests successfull construction of a dataset collection.
 * @throws ExecutionManagerException
 */
@Test
public void testConstructCollectionSuccess() throws ExecutionManagerException {
    CollectionResponse collectionResponse = new CollectionResponse();
    History history = new History();
    history.setId(HISTORY_ID);
    HistoryDatasetElement datasetElement = new HistoryDatasetElement();
    datasetElement.setId(DATA_ID);
    CollectionDescription description = new CollectionDescription();
    description.addDatasetElement(datasetElement);
    when(historiesClient.createDatasetCollection(eq(HISTORY_ID), any(CollectionDescription.class))).thenReturn(collectionResponse);
    assertEquals(collectionResponse, galaxyHistory.constructCollection(description, history));
}

Example 15 with History

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

the class AnalysisCollectionServiceGalaxyIT method testUploadSequenceFilesPairedFailForward.

/**
 * Tests failing to upload a paired-end sequence file to Galaxy and
 * constructing a collection due to no found forward file.
 *
 * @throws ExecutionManagerException
 */
@Test(expected = NoSuchElementException.class)
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testUploadSequenceFilesPairedFailForward() throws ExecutionManagerException {
    History history = new History();
    history.setName("testUploadSequenceFilesPairedFailForward");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
    History createdHistory = historiesClient.create(history);
    Library library = new Library();
    library.setName("testUploadSequenceFilesPairedFailForward");
    Library createdLibrary = librariesClient.createLibrary(library);
    Set<SequenceFilePair> sequenceFiles = Sets.newHashSet(databaseSetupGalaxyITService.setupSampleSequenceFileInDatabase(1L, pairSequenceFiles1AInvalidName, pairSequenceFiles2A));
    Map<Sample, IridaSequenceFilePair> sampleSequenceFilePairs = new HashMap<>(sequencingObjectService.getUniqueSamplesForSequencingObjects(sequenceFiles));
    analysisCollectionServiceGalaxy.uploadSequenceFilesPaired(sampleSequenceFilePairs, createdHistory, createdLibrary);
}