Examples with CollectionResponse com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse used on opensource projects

Example 1 with CollectionResponse

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

the class GalaxyHistoriesServiceIT method testConstructCollectionSuccess.

/**
 * Tests out successfully constructing a collection of datasets.
 * @throws ExecutionManagerException
 */
@Test
public void testConstructCollectionSuccess() throws ExecutionManagerException {
    History history = galaxyHistory.newHistoryForWorkflow();
    Dataset dataset1 = galaxyHistory.fileToHistory(dataFile, FILE_TYPE, history);
    Dataset dataset2 = galaxyHistory.fileToHistory(dataFile2, FILE_TYPE, history);
    assertNotNull(dataset1);
    assertNotNull(dataset2);
    String collectionName = "collection";
    CollectionDescription description = new CollectionDescription();
    description.setName(collectionName);
    description.setCollectionType(DatasetCollectionType.LIST.toString());
    HistoryDatasetElement element1 = new HistoryDatasetElement();
    element1.setId(dataset1.getId());
    element1.setName(dataset1.getName());
    description.addDatasetElement(element1);
    HistoryDatasetElement element2 = new HistoryDatasetElement();
    element2.setId(dataset2.getId());
    element2.setName(dataset2.getName());
    description.addDatasetElement(element2);
    CollectionResponse collectionResponse = galaxyHistory.constructCollection(description, history);
    assertNotNull(collectionResponse);
    assertEquals(DatasetCollectionType.LIST.toString(), collectionResponse.getCollectionType());
    assertEquals(history.getId(), collectionResponse.getHistoryId());
    assertEquals(2, collectionResponse.getElements().size());
}

Example 2 with CollectionResponse

use of com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse 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 3 with CollectionResponse

use of com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionResponse 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 4 with CollectionResponse

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

the class AnalysisWorkspaceServiceGalaxyTest method setup.

/**
 * Sets up variables for testing.
 *
 * @throws IOException
 * @throws GalaxyDatasetException
 * @throws UploadException
 */
@Before
public void setup() throws IOException, UploadException, GalaxyDatasetException {
    MockitoAnnotations.initMocks(this);
    sFileA = new SequenceFile(createTempFile("fileA", "fastq"));
    sFileB = new SequenceFile(createTempFile("fileB", "fastq"));
    sFileC = new SequenceFile(createTempFile("fileC", "fastq"));
    sObjA = new SingleEndSequenceFile(sFileA);
    sObjB = new SingleEndSequenceFile(sFileB);
    sObjC = new SingleEndSequenceFile(sFileC);
    sequenceFilePair = new SequenceFilePair(sFileB, sFileC);
    singleEndSequenceFile = sObjA;
    Sample sampleA = new Sample();
    sampleA.setSampleName("SampleA");
    Sample sampleB = new Sample();
    sampleB.setSampleName("SampleB");
    Sample sampleC = new Sample();
    sampleC.setSampleName("SampleC");
    sampleSingleSequenceFileMap = ImmutableMap.of(sampleA, singleEndSequenceFile);
    sampleSequenceFilePairMap = ImmutableMap.of(sampleB, sequenceFilePair);
    sampleSequenceFilePairMapSampleA = ImmutableMap.of(sampleA, sequenceFilePair);
    refFile = createTempFile("reference", "fasta");
    referenceFile = new ReferenceFile(refFile);
    inputFiles = new HashSet<>();
    inputFiles.addAll(Arrays.asList(sObjA, sObjB, sObjC));
    submission = AnalysisSubmission.builder(workflowId).name("my analysis").inputFiles(inputFiles).referenceFile(referenceFile).build();
    workflowHistory = new History();
    workflowHistory.setId(HISTORY_ID);
    workflowLibrary = new Library();
    workflowLibrary.setId(LIBRARY_ID);
    workflowDetails = new WorkflowDetails();
    workflowDetails.setId(WORKFLOW_ID);
    workflowPreparation = new AnalysisWorkspaceServiceGalaxy(galaxyHistoriesService, galaxyWorkflowService, galaxyLibrariesService, iridaWorkflowsService, analysisCollectionServiceGalaxy, analysisProvenanceServiceGalaxy, analysisParameterServiceGalaxy, sequencingObjectService);
    output1Dataset = new Dataset();
    output1Dataset.setId("1");
    output1Dataset.setName("output1.txt");
    output2Dataset = new Dataset();
    output2Dataset.setId("2");
    output2Dataset.setName("output2.txt");
    collectionResponseSingle = new CollectionResponse();
    collectionResponseSingle.setId(COLLECTION_SINGLE_ID);
    collectionResponsePaired = new CollectionResponse();
    collectionResponsePaired.setId(COLLECTION_PAIRED_ID);
    singleInputFiles = Sets.newHashSet(singleEndSequenceFile);
    pairedInputFiles = Sets.newHashSet(sequenceFilePair);
}

Example 5 with CollectionResponse

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

the class AnalysisCollectionServiceGalaxyIT method testUploadSequenceFilesPairedSuccess.

/**
 * Tests successfully uploading a paired-end sequence file to Galaxy and
 * constructing a collection.
 *
 * @throws ExecutionManagerException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testUploadSequenceFilesPairedSuccess() throws ExecutionManagerException {
    History history = new History();
    history.setName("testUploadSequenceFilesPaired");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
    History createdHistory = historiesClient.create(history);
    Library library = new Library();
    library.setName("testUploadSequenceFilesPaired");
    Library createdLibrary = librariesClient.createLibrary(library);
    Set<SequenceFilePair> sequenceFiles = Sets.newHashSet(databaseSetupGalaxyITService.setupSampleSequenceFileInDatabase(1L, pairSequenceFiles1A, pairSequenceFiles2A));
    Map<Sample, IridaSequenceFilePair> sampleSequenceFilePairs = new HashMap<>(sequencingObjectService.getUniqueSamplesForSequencingObjects(sequenceFiles));
    Sample sample1 = sampleRepository.findOne(1L);
    CollectionResponse collectionResponse = analysisCollectionServiceGalaxy.uploadSequenceFilesPaired(sampleSequenceFilePairs, createdHistory, createdLibrary);
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("history does not have correct number of files", 3, historyContents.size());
    Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
    assertTrue("the history should have a sequence file with name " + sequenceFilePathA.toFile().getName(), contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
    assertTrue("the history should have a file with name " + sequenceFilePath2A.toFile().getName(), contentsMap.containsKey(sequenceFilePath2A.toFile().getName()));
    assertTrue("the history should have a dataset collection with name " + INPUTS_PAIRED_NAME, contentsMap.containsKey(INPUTS_PAIRED_NAME));
    // verify correct collection has been created
    assertEquals("invalid type of dataset collection created", DatasetCollectionType.LIST_PAIRED.toString(), collectionResponse.getCollectionType());
    List<CollectionElementResponse> collectionElements = collectionResponse.getElements();
    assertEquals("invalid number of elements in the dataset collection", 1, collectionElements.size());
    Map<String, CollectionElementResponse> collectionElementsMap = collectionElementsAsMap(collectionElements);
    assertTrue("the dataset collection element should have name " + sample1.getSampleName(), collectionElementsMap.containsKey(sample1.getSampleName()));
    CollectionElementResponse sample1Response = collectionElementsMap.get(sample1.getSampleName());
    // verify collection has 2 files (paired end data)
    ElementResponse subElements = sample1Response.getResponseElement();
    assertEquals("invalid class for sub-element in dataset collection", CollectionResponse.class, subElements.getClass());
    CollectionResponse subElementsCollection = (CollectionResponse) subElements;
    assertEquals("invalid type for sub-element in dataset collection", DatasetCollectionType.PAIRED.toString(), subElementsCollection.getCollectionType());
    List<CollectionElementResponse> subCollectionElements = subElementsCollection.getElements();
    assertEquals("invalid number of files for paired dataset collection element", 2, subCollectionElements.size());
    Map<String, CollectionElementResponse> subCollectionElementsMap = collectionElementsAsMap(subCollectionElements);
    assertTrue("dataset collection should have a sub-element with name " + FORWARD_NAME, subCollectionElementsMap.containsKey(FORWARD_NAME));
    assertTrue("dataset collection should have a sub-element with name " + REVERSE_NAME, subCollectionElementsMap.containsKey(REVERSE_NAME));
    // verify paired-end files are correct type in collection
    CollectionElementResponse sequenceFile1 = subCollectionElementsMap.get(FORWARD_NAME);
    CollectionElementResponse sequenceFile2 = subCollectionElementsMap.get(REVERSE_NAME);
    assertEquals("the " + FORWARD_NAME + " sub-element should be a history dataset", HISTORY_DATASET_NAME, sequenceFile1.getElementType());
    assertEquals("the " + REVERSE_NAME + " sub-element should be a history dataset", HISTORY_DATASET_NAME, sequenceFile2.getElementType());
    // verify paired-end files are in correct order in collection
    ElementResponse sequenceFile1Response = sequenceFile1.getResponseElement();
    assertEquals("the " + FORWARD_NAME + " element is not of the correct type", Dataset.class, sequenceFile1Response.getClass());
    ElementResponse sequenceFile2Response = sequenceFile2.getResponseElement();
    assertEquals("the " + REVERSE_NAME + " element is not of the correct type", Dataset.class, sequenceFile2Response.getClass());
    Dataset sequenceFile1Dataset = (Dataset) sequenceFile1Response;
    assertEquals("forward file in Galaxy is named incorrectly", sequenceFilePathA.getFileName().toString(), sequenceFile1Dataset.getName());
    Dataset sequenceFile2Dataset = (Dataset) sequenceFile2Response;
    assertEquals("reverse file in Galaxy is named incorrectly", sequenceFilePath2A.getFileName().toString(), sequenceFile2Dataset.getName());
}