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

Example 66 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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);
}

Example 67 with Sample

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

the class AnalysisCollectionServiceGalaxyIT method testGetSequenceFileSingleSamplesSuccess.

/**
 * Tests successfully getting a map of samples and sequence files (single).
 *
 * @throws DuplicateSampleException
 */
@Test
@WithMockUser(username = "aaron", roles = "ADMIN")
public void testGetSequenceFileSingleSamplesSuccess() throws DuplicateSampleException {
    Set<SequencingObject> sequenceFiles = Sets.newHashSet(databaseSetupGalaxyITService.setupSequencingObjectInDatabase(1L, sequenceFilePathA));
    Sample sample = sampleRepository.findOne(1L);
    SequencingObject sequenceFile = sequenceFiles.iterator().next();
    Map<Sample, SequencingObject> sampleSequenceFiles = sequencingObjectService.getUniqueSamplesForSequencingObjects(sequenceFiles);
    assertEquals("sampleSequenceFiles map has size != 1", 1, sampleSequenceFiles.size());
    assertEquals("sampleSequenceFiles map does not have sequenceFile " + sequenceFile + " corresponding to sample " + sample, sequenceFile, sampleSequenceFiles.get(sample));
}

Example 68 with Sample

use of ca.corefacility.bioinformatics.irida.model.sample.Sample 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 69 with Sample

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

the class ProjectServiceImplIT method testShareSamplesWithOwner.

@Test
@WithMockUser(username = "user1", roles = "USER")
public void testShareSamplesWithOwner() {
    Project source = projectService.read(2L);
    Project destination = projectService.read(10L);
    Sample sample1 = sampleService.read(1L);
    Set<Sample> samples = Sets.newHashSet(sample1);
    List<ProjectSampleJoin> copiedSamples = projectService.shareSamples(source, destination, samples, true);
    assertEquals(samples.size(), copiedSamples.size());
    copiedSamples.forEach(j -> {
        assertTrue("Project should be owner for sample", j.isOwner());
    });
    assertNotNull("Samples should still exist in source project", projectSampleJoinRepository.readSampleForProject(source, sample1));
    assertNotNull("Sample should exist in destination project", projectSampleJoinRepository.readSampleForProject(destination, sample1));
}

Example 70 with Sample

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

the class ProjectServiceImplIT method testMoveLockedSamplesWithOwnerFail.

@Test(expected = AccessDeniedException.class)
@WithMockUser(username = "user1", roles = "USER")
public void testMoveLockedSamplesWithOwnerFail() {
    Project source = projectService.read(2L);
    Project destination = projectService.read(10L);
    List<Join<Project, Sample>> samplesForProject = sampleService.getSamplesForProject(source);
    Set<Sample> samples = samplesForProject.stream().map(j -> j.getObject()).collect(Collectors.toSet());
    projectService.moveSamples(source, destination, samples, true);
}