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

Example 76 with SequenceFile

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

the class ProjectSamplesControllerTest method testDownloadSamplesWithSameName.

@Test
public void testDownloadSamplesWithSameName() throws IOException {
    Project project = TestDataFactory.constructProject();
    Sample sample = TestDataFactory.constructSample();
    MockHttpServletResponse response = new MockHttpServletResponse();
    Path path = Paths.get(FILE_PATH);
    SequenceFile file = new SequenceFile(path);
    ImmutableList<SampleSequencingObjectJoin> filejoin = ImmutableList.of(new SampleSequencingObjectJoin(sample, new SingleEndSequenceFile(file)), new SampleSequencingObjectJoin(sample, new SingleEndSequenceFile(file)), new SampleSequencingObjectJoin(sample, new SingleEndSequenceFile(file)));
    when(projectService.read(project.getId())).thenReturn(project);
    when(sampleService.readMultiple(ImmutableList.of(sample.getId()))).thenReturn(ImmutableList.of(sample));
    when(sequencingObjectService.getSequencingObjectsForSample(sample)).thenReturn(filejoin);
    controller.downloadSamples(project.getId(), ImmutableList.of(sample.getId()), response);
    verify(projectService).read(project.getId());
    verify(sampleService).readMultiple(ImmutableList.of(sample.getId()));
    verify(sequencingObjectService).getSequencingObjectsForSample(sample);
    assertTrue("Response should contain a \"Content-Disposition\" header.", response.containsHeader("Content-Disposition"));
    assertEquals("Content-Disposition should include the file name", "attachment; filename=\"test_project.zip\"", response.getHeader("Content-Disposition"));
    try (ZipInputStream zipStream = new ZipInputStream(new ByteArrayInputStream(response.getContentAsByteArray()))) {
        Set<String> names = new HashSet<>();
        ZipEntry nextEntry = zipStream.getNextEntry();
        while (nextEntry != null) {
            names.add(nextEntry.getName());
            nextEntry = zipStream.getNextEntry();
        }
        assertEquals("should be 3 unique filenames", 3, names.size());
    }
}

Example 77 with SequenceFile

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

the class SamplesControllerTest method testDownloadAssembly.

@Test
public void testDownloadAssembly() throws IOException {
    HttpServletResponse response = new MockHttpServletResponse();
    Long sampleId = 1L;
    Long assemblyId = 3L;
    SequenceFile file = new SequenceFile(Paths.get("/tmp"));
    file.setId(2L);
    Sample sample = new Sample();
    GenomeAssembly genomeAssembly = TestDataFactory.constructGenomeAssembly();
    when(sampleService.read(sampleId)).thenReturn(sample);
    when(sampleService.getGenomeAssemblyForSample(sample, assemblyId)).thenReturn(genomeAssembly);
    when(readSamplePermission.isAllowed(any(Authentication.class), eq(sample))).thenReturn(true);
    controller.downloadAssembly(sampleId, assemblyId, response);
    verify(sampleService).read(sampleId);
    verify(sampleService).getGenomeAssemblyForSample(sample, assemblyId);
}

Example 78 with SequenceFile

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

the class SamplesControllerTest method testGetSampleFilesNoAccess.

@SuppressWarnings("unchecked")
@Test
public void testGetSampleFilesNoAccess() throws IOException {
    ExtendedModelMap model = new ExtendedModelMap();
    Long sampleId = 1L;
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile(Paths.get("/tmp"));
    file.setId(2L);
    Project project = new Project();
    List<SampleSequencingObjectJoin> files = Lists.newArrayList(new SampleSequencingObjectJoin(sample, new SingleEndSequenceFile(file)));
    when(sampleService.read(sampleId)).thenReturn(sample);
    when(sequencingObjectService.getSequencesForSampleOfType(sample, SingleEndSequenceFile.class)).thenReturn(files);
    when(updateSamplePermission.isAllowed(any(Authentication.class), eq(sample))).thenReturn(false);
    when(projectService.getProjectsForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true)));
    String sampleFiles = controller.getSampleFilesWithoutProject(model, sampleId);
    assertEquals(SamplesController.SAMPLE_FILES_PAGE, sampleFiles);
    assertFalse((boolean) model.get(SamplesController.MODEL_ATTR_CAN_MANAGE_SAMPLE));
    verify(sampleService).read(sampleId);
    verify(sequencingObjectService).getSequencesForSampleOfType(sample, SingleEndSequenceFile.class);
    verify(sequencingObjectService).getSequencesForSampleOfType(sample, SequenceFilePair.class);
}

Example 79 with SequenceFile

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

the class SequenceFileControllerTest method setUp.

@Before
public void setUp() {
    sequencingRunService = mock(SequencingRunService.class);
    analysisService = mock(AnalysisService.class);
    objectService = mock(SequencingObjectService.class);
    controller = new SequenceFileController(objectService, sequencingRunService, analysisService);
    Path path = Paths.get(FILE_PATH);
    SequenceFile file = new SequenceFile(path);
    file.setId(FILE_ID);
    SingleEndSequenceFile seqObject = new SingleEndSequenceFile(file);
    when(objectService.read(anyLong())).thenReturn(seqObject);
}

Example 80 with SequenceFile

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

the class ReadAnalysisSubmissionPermissionTest method setUp.

/**
 * Setup for tests
 */
@Before
public void setUp() {
    MockitoAnnotations.initMocks(this);
    readAnalysisSubmissionPermission = new ReadAnalysisSubmissionPermission(analysisSubmissionRepository, userRepository, sequencingObjectRepository, seqObjectPermission, pasRepository, readProjectPermission);
    inputSingleFiles = Sets.newHashSet(new SingleEndSequenceFile(new SequenceFile()));
}