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

Example 1 with CollectionElementResponse

use of com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse 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());
}

Example 2 with CollectionElementResponse

use of com.github.jmchilton.blend4j.galaxy.beans.collection.response.CollectionElementResponse 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());
}