Examples with IridaSingleEndSequenceFile ca.corefacility.bioinformatics.irida.model.irida.IridaSingleEndSequenceFile used on opensource projects

Example 1 with IridaSingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.irida.IridaSingleEndSequenceFile in project irida by phac-nml.

the class AnalysisCollectionServiceGalaxyIT method testUploadSequenceFilesSingleSuccess.

/**
 * Tests successfully uploading a single end sequence file to Galaxy and
 * constructing a collection.
 *
 * @throws ExecutionManagerException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testUploadSequenceFilesSingleSuccess() throws ExecutionManagerException {
    History history = new History();
    history.setName("testUploadSequenceFilesSingleSuccess");
    HistoriesClient historiesClient = localGalaxy.getGalaxyInstanceAdmin().getHistoriesClient();
    LibrariesClient librariesClient = localGalaxy.getGalaxyInstanceAdmin().getLibrariesClient();
    History createdHistory = historiesClient.create(history);
    Library library = new Library();
    library.setName("testUploadSequenceFilesSingleSuccess");
    Library createdLibrary = librariesClient.createLibrary(library);
    Set<SingleEndSequenceFile> sequenceFiles = Sets.newHashSet(databaseSetupGalaxyITService.setupSequencingObjectInDatabase(1L, sequenceFilePathA));
    Map<Sample, IridaSingleEndSequenceFile> sampleSequenceFiles = new HashMap<>(sequencingObjectService.getUniqueSamplesForSequencingObjects(sequenceFiles));
    Sample sample1 = sampleRepository.findOne(1L);
    CollectionResponse collectionResponse = analysisCollectionServiceGalaxy.uploadSequenceFilesSingleEnd(sampleSequenceFiles, createdHistory, createdLibrary);
    // verify correct files have been uploaded
    List<HistoryContents> historyContents = historiesClient.showHistoryContents(createdHistory.getId());
    assertEquals("historyContents should have size 2", 2, historyContents.size());
    Map<String, HistoryContents> contentsMap = historyContentsAsMap(historyContents);
    assertTrue("sequenceFile should have been uploaded to history", contentsMap.containsKey(sequenceFilePathA.toFile().getName()));
    assertTrue("dataset collection with name " + INPUTS_SINGLE_NAME + " should have been created in history", contentsMap.containsKey(INPUTS_SINGLE_NAME));
    // verify correct collection has been created
    assertEquals("constructed dataset collection should have been " + DatasetCollectionType.LIST + " but is instead " + collectionResponse.getCollectionType(), DatasetCollectionType.LIST.toString(), collectionResponse.getCollectionType());
    List<CollectionElementResponse> collectionElements = collectionResponse.getElements();
    assertEquals("dataset collection should have only 1 element", 1, collectionElements.size());
    Map<String, CollectionElementResponse> collectionElementsMap = collectionElementsAsMap(collectionElements);
    assertTrue("dataset collection should have an element with the name " + sample1.getSampleName(), collectionElementsMap.containsKey(sample1.getSampleName()));
    CollectionElementResponse sample1Response = collectionElementsMap.get(sample1.getSampleName());
    assertEquals("invalid type for dataset element", HISTORY_DATASET_NAME, sample1Response.getElementType());
}

Example 2 with IridaSingleEndSequenceFile

use of ca.corefacility.bioinformatics.irida.model.irida.IridaSingleEndSequenceFile in project irida by phac-nml.

the class AnalysisCollectionServiceGalaxy method uploadSequenceFilesSingleEnd.

/**
 * Uploads a list of single sequence files belonging to the given samples to
 * Galaxy.
 *
 * @param sampleSequenceFiles
 *            A map between {@link Sample} and
 *            {@link IridaSingleEndSequenceFile}.
 * @param workflowHistory
 *            The history to upload the sequence files into.
 * @param workflowLibrary
 *            A temporary library to upload files into.
 * @return A CollectionResponse for the dataset collection constructed from
 *         the given files.
 * @throws ExecutionManagerException
 *             If there was an error uploading the files.
 */
public CollectionResponse uploadSequenceFilesSingleEnd(Map<Sample, ? extends IridaSingleEndSequenceFile> sampleSequenceFiles, History workflowHistory, Library workflowLibrary) throws ExecutionManagerException {
    CollectionDescription description = new CollectionDescription();
    description.setCollectionType(DatasetCollectionType.LIST.toString());
    description.setName(COLLECTION_NAME_SINGLE);
    Map<Path, Sample> samplesMap = new HashMap<>();
    for (Sample sample : sampleSequenceFiles.keySet()) {
        IridaSingleEndSequenceFile sequenceFile = sampleSequenceFiles.get(sample);
        samplesMap.put(sequenceFile.getSequenceFile().getFile(), sample);
    }
    // upload files to library and then to a history
    Set<Path> pathsToUpload = samplesMap.keySet();
    Map<Path, String> pathHistoryDatasetId = galaxyHistoriesService.filesToLibraryToHistory(pathsToUpload, InputFileType.FASTQ_SANGER, workflowHistory, workflowLibrary, DataStorage.LOCAL);
    for (Path sequenceFilePath : samplesMap.keySet()) {
        if (!pathHistoryDatasetId.containsKey(sequenceFilePath)) {
            throw new UploadException("Error, no corresponding history item found for " + sequenceFilePath);
        }
        Sample sample = samplesMap.get(sequenceFilePath);
        String datasetHistoryId = pathHistoryDatasetId.get(sequenceFilePath);
        HistoryDatasetElement datasetElement = new HistoryDatasetElement();
        datasetElement.setId(datasetHistoryId);
        datasetElement.setName(sample.getSampleName());
        description.addDatasetElement(datasetElement);
    }
    return galaxyHistoriesService.constructCollection(description, workflowHistory);
}