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

Example 11 with SequenceFile

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

the class SampleSequenceFilesControllerTest method testAddNewSequenceFilePairToSample.

@Test
public void testAddNewSequenceFilePairToSample() throws IOException {
    Sample s = TestDataFactory.constructSample();
    String file1Name = "file1_R1_01.fastq.gz";
    String file2Name = "file2_R2_01.fastq.gz";
    SequenceFilePair pair = TestDataFactory.constructSequenceFilePair();
    Iterator<SequenceFile> iterator = pair.getFiles().iterator();
    SequenceFile sf1 = iterator.next();
    SequenceFile sf2 = iterator.next();
    sf1.setFile(Paths.get(file1Name));
    sf2.setFile(Paths.get(file2Name));
    sf1.setId(3245L);
    SampleSequencingObjectJoin sso = new SampleSequencingObjectJoin(s, pair);
    SequenceFileResource resource1 = new SequenceFileResource();
    SequenceFileResource resource2 = new SequenceFileResource();
    Path f1 = Files.createTempFile(null, null);
    Path f2 = Files.createTempFile(null, null);
    MockMultipartFile mmf1 = new MockMultipartFile(file1Name, file1Name, "blurgh1", FileCopyUtils.copyToByteArray(f1.toFile()));
    MockMultipartFile mmf2 = new MockMultipartFile(file2Name, file2Name, "blurgh2", FileCopyUtils.copyToByteArray(f2.toFile()));
    MockHttpServletResponse response = new MockHttpServletResponse();
    // mock out the service calls
    when(sampleService.read(s.getId())).thenReturn(s);
    when(sequencingObjectService.createSequencingObjectInSample(any(SequenceFilePair.class), Matchers.eq(s))).thenReturn(sso);
    ModelMap modelMap = controller.addNewSequenceFilePairToSample(s.getId(), mmf1, resource1, mmf2, resource2, response);
    verify(sampleService).read(s.getId());
    verify(sequencingObjectService).createSequencingObjectInSample(any(SequenceFilePair.class), Matchers.eq(s));
    Object o = modelMap.get(RESTGenericController.RESOURCE_NAME);
    assertNotNull("Object should not be null", o);
    assertTrue("Object should be an instance of SequenceFilePair", o instanceof SequenceFilePair);
    SequenceFilePair returnVal = (SequenceFilePair) o;
    Link selfCollection = returnVal.getLink(Link.REL_SELF);
    Link sampleRC = returnVal.getLink(RESTSampleSequenceFilesController.REL_SAMPLE);
    Link sampleSequenceFiles = returnVal.getLink(RESTSampleSequenceFilesController.REL_SAMPLE_SEQUENCE_FILES);
    String sampleLocation = "http://localhost/api/samples/" + s.getId();
    String pairLocation = sampleLocation + "/pairs/" + pair.getId();
    assertEquals("Pair location should be correct", pairLocation, selfCollection.getHref());
    assertEquals("Sample location should be correct", sampleLocation, sampleRC.getHref());
    assertEquals("Sequence file location should be correct", sampleLocation + "/sequenceFiles", sampleSequenceFiles.getHref());
    String sequenceFileLocation1 = pairLocation + "/files/" + sf1.getId();
    String sequenceFileLocation2 = pairLocation + "/files/" + sf2.getId();
    String[] sequenceFileLocs = new String[] { sequenceFileLocation1, sequenceFileLocation2 };
    String locationHeader = response.getHeader(HttpHeaders.LOCATION);
    assertEquals("The location header should have the self rel", pairLocation, locationHeader);
    Iterator<SequenceFile> filesIterator = returnVal.getFiles().iterator();
    for (int i = 0; i < 2; i++) {
        SequenceFile returnedFile = filesIterator.next();
        Link self = returnedFile.getLink(Link.REL_SELF);
        assertNotNull("Self link should not be null", self);
        assertEquals("Self reference should be correct", sequenceFileLocs[i], self.getHref());
    }
    assertEquals("HTTP status must be CREATED", HttpStatus.CREATED.value(), response.getStatus());
    Files.delete(f1);
    Files.delete(f2);
}

Example 12 with SequenceFile

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

the class SampleSequenceFilesControllerTest method testAddNewSequenceFileToSample.

@Test
public void testAddNewSequenceFileToSample() throws IOException {
    Sample s = TestDataFactory.constructSample();
    SingleEndSequenceFile so = TestDataFactory.constructSingleEndSequenceFile();
    SequenceFile sf = so.getSequenceFile();
    SampleSequencingObjectJoin sso = new SampleSequencingObjectJoin(s, so);
    SequenceFileResource resource = new SequenceFileResource();
    Path f = Files.createTempFile(null, null);
    MockMultipartFile mmf = new MockMultipartFile("filename", "filename", "blurgh", FileCopyUtils.copyToByteArray(f.toFile()));
    MockHttpServletResponse response = new MockHttpServletResponse();
    when(sampleService.read(s.getId())).thenReturn(s);
    when(sequencingObjectService.createSequencingObjectInSample(any(SingleEndSequenceFile.class), Matchers.eq(s))).thenReturn(sso);
    when(sequencingObjectService.read(so.getId())).thenReturn(so);
    ModelMap modelMap = controller.addNewSequenceFileToSample(s.getId(), mmf, resource, response);
    verify(sampleService).read(s.getId());
    verify(sampleService, times(1)).read(s.getId());
    verify(sequencingObjectService).createSequencingObjectInSample(any(SingleEndSequenceFile.class), Matchers.eq(s));
    Object o = modelMap.get(RESTGenericController.RESOURCE_NAME);
    assertNotNull("object must not be null", o);
    assertTrue("object must be a SequenceFile", o instanceof SequenceFile);
    SequenceFile sfr = (SequenceFile) o;
    assertEquals("response must have CREATED status", HttpStatus.CREATED.value(), response.getStatus());
    Link self = sfr.getLink(Link.REL_SELF);
    Link sampleSequenceFiles = sfr.getLink(RESTSampleSequenceFilesController.REL_SAMPLE_SEQUENCE_FILES);
    Link sample = sfr.getLink(RESTSampleSequenceFilesController.REL_SAMPLE);
    String sampleLocation = "http://localhost/api/samples/" + s.getId();
    String sequenceFileLocation = sampleLocation + "/unpaired/" + so.getIdentifier() + "/files/" + sf.getId();
    assertNotNull("self reference must exist", self);
    assertEquals("self reference must be correct", sequenceFileLocation, self.getHref());
    assertNotNull("sequence files link must exist", sampleSequenceFiles);
    assertEquals("sequence files location must be correct", sampleLocation + "/sequenceFiles", sampleSequenceFiles.getHref());
    assertNotNull("sample link must exist", sample);
    assertEquals("sample location must be correct", sampleLocation, sample.getHref());
    Files.delete(f);
}

Example 13 with SequenceFile

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

the class SampleSequenceFilesControllerTest method testGetSampleSequenceFiles.

@Test
public void testGetSampleSequenceFiles() throws IOException {
    Sample s = TestDataFactory.constructSample();
    SingleEndSequenceFile so = TestDataFactory.constructSingleEndSequenceFile();
    SampleSequencingObjectJoin r = new SampleSequencingObjectJoin(s, so);
    List<SampleSequencingObjectJoin> relationships = Lists.newArrayList(r);
    // mock out the service calls
    when(sampleService.read(s.getId())).thenReturn(s);
    when(sequencingObjectService.getSequencingObjectsForSample(s)).thenReturn(relationships);
    ModelMap modelMap = controller.getSampleSequenceFiles(s.getId());
    // verify that the service calls were used.
    verify(sampleService).read(s.getId());
    verify(sequencingObjectService).getSequencingObjectsForSample(s);
    Object o = modelMap.get(RESTGenericController.RESOURCE_NAME);
    assertTrue(o instanceof ResourceCollection);
    @SuppressWarnings("unchecked") ResourceCollection<SequenceFile> resources = (ResourceCollection<SequenceFile>) o;
    assertNotNull(resources);
    assertEquals(1, resources.size());
    Link selfCollection = resources.getLink(Link.REL_SELF);
    Link sample = resources.getLink(RESTSampleSequenceFilesController.REL_SAMPLE);
    String sampleLocation = "http://localhost/api/samples/" + s.getId();
    String sequenceFileLocation = sampleLocation + "/unpaired/" + so.getIdentifier() + "/files/" + so.getSequenceFile().getId();
    assertEquals(sampleLocation + "/sequenceFiles", selfCollection.getHref());
    assertEquals(sampleLocation, sample.getHref());
    // confirm that the self rel for an individual sequence file exists
    SequenceFile sfr = resources.iterator().next();
    Link self = sfr.getLink(Link.REL_SELF);
    assertEquals(sequenceFileLocation, self.getHref());
    assertEquals(so.getSequenceFile().getFile(), sfr.getFile());
}

Example 14 with SequenceFile

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

the class SampleServiceImplTest method sf.

private SequenceFile sf(Long id) {
    SequenceFile sf = new SequenceFile();
    sf.setId(id);
    try {
        sf.setFile(Files.createTempFile(null, null));
    } catch (IOException e) {
    }
    return sf;
}

Example 15 with SequenceFile

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

the class SampleServiceImplTest method testGetCoverageForSampleSuccess.

/**
 * Tests out successfully getting the coverage from a sample with a sequence
 * file.
 *
 * @throws SequenceFileAnalysisException
 * @throws AnalysisAlreadySetException
 */
@Test
public void testGetCoverageForSampleSuccess() throws SequenceFileAnalysisException, AnalysisAlreadySetException {
    Sample s1 = new Sample();
    s1.setId(1L);
    SequenceFile sf1 = new SequenceFile();
    sf1.setId(2222L);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(s1, new SingleEndSequenceFile(sf1));
    AnalysisFastQC analysisFastQC1 = AnalysisFastQC.sloppyBuilder().executionManagerAnalysisId("id").totalBases(1000L).build();
    sf1.setFastQCAnalysis(analysisFastQC1);
    when(ssoRepository.getSequencesForSample(s1)).thenReturn(Arrays.asList(join));
    when(analysisRepository.findFastqcAnalysisForSequenceFile(sf1)).thenReturn(analysisFastQC1);
    double coverage = sampleService.estimateCoverageForSample(s1, 500L);
    assertEquals(2.0, coverage, deltaFloatEquality);
}