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

Example 41 with SampleSequencingObjectJoin

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

the class SequencingObjectServiceImplIT method testGetUnpairedFilesForSampleWithNoPairs.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testGetUnpairedFilesForSampleWithNoPairs() {
    Sample s = sampleService.read(1L);
    Collection<SampleSequencingObjectJoin> sequencesForSampleOfType = objectService.getSequencesForSampleOfType(s, SingleEndSequenceFile.class);
    assertEquals(1, sequencesForSampleOfType.size());
    SampleSequencingObjectJoin join = sequencesForSampleOfType.iterator().next();
    assertEquals(new Long(2), join.getObject().getId());
}

Example 42 with SampleSequencingObjectJoin

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

the class SampleServiceImplTest method testGetTotalBasesForSampleSuccessTwo.

/**
 * Tests out successfully getting the total bases from a sample with two
 * sequence files.
 *
 * @throws SequenceFileAnalysisException
 * @throws AnalysisAlreadySetException
 */
@Test
public void testGetTotalBasesForSampleSuccessTwo() throws SequenceFileAnalysisException, AnalysisAlreadySetException {
    Sample s1 = new Sample();
    s1.setId(1L);
    SequenceFile sf1 = new SequenceFile();
    sf1.setId(2222L);
    SequenceFile sf2 = new SequenceFile();
    sf1.setId(3333L);
    SampleSequencingObjectJoin join1 = new SampleSequencingObjectJoin(s1, new SingleEndSequenceFile(sf1));
    SampleSequencingObjectJoin join2 = new SampleSequencingObjectJoin(s1, new SingleEndSequenceFile(sf2));
    AnalysisFastQC analysisFastQC1 = AnalysisFastQC.sloppyBuilder().executionManagerAnalysisId("id").totalBases(1000L).build();
    sf1.setFastQCAnalysis(analysisFastQC1);
    AnalysisFastQC analysisFastQC2 = AnalysisFastQC.sloppyBuilder().executionManagerAnalysisId("id2").totalBases(1000L).build();
    sf2.setFastQCAnalysis(analysisFastQC2);
    when(ssoRepository.getSequencesForSample(s1)).thenReturn(Arrays.asList(join1, join2));
    when(analysisRepository.findFastqcAnalysisForSequenceFile(sf1)).thenReturn(analysisFastQC1);
    when(analysisRepository.findFastqcAnalysisForSequenceFile(sf2)).thenReturn(analysisFastQC2);
    long actualBases = sampleService.getTotalBasesForSample(s1);
    assertEquals(2000, actualBases);
}

Example 43 with SampleSequencingObjectJoin

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

the class SampleServiceImplTest method testGetTotalBasesForSampleFailNoFastQC.

/**
 * Tests out failing to get the total bases from a sample with one sequence
 * file due to missing FastQC
 *
 * @throws SequenceFileAnalysisException
 */
@Test(expected = SequenceFileAnalysisException.class)
public void testGetTotalBasesForSampleFailNoFastQC() throws SequenceFileAnalysisException {
    Sample s1 = new Sample();
    s1.setId(1L);
    SequenceFile sf1 = new SequenceFile();
    sf1.setId(2222L);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(s1, new SingleEndSequenceFile(sf1));
    when(ssoRepository.getSequencesForSample(s1)).thenReturn(Arrays.asList(join));
    sampleService.getTotalBasesForSample(s1);
}

Example 44 with SampleSequencingObjectJoin

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

the class SequencingObjectServiceImpl method createSequencingObjectInSample.

/**
 * {@inheritDoc}
 */
@Override
@Transactional
@PreAuthorize("hasPermission(#sample, 'canUpdateSample')")
@LaunchesProjectEvent(DataAddedToSampleProjectEvent.class)
public SampleSequencingObjectJoin createSequencingObjectInSample(SequencingObject seqObject, Sample sample) {
    // create the sequencing object
    seqObject = create(seqObject);
    // save the new join
    SampleSequencingObjectJoin sampleSequencingObjectJoin = new SampleSequencingObjectJoin(sample, seqObject);
    return ssoRepository.save(sampleSequencingObjectJoin);
}

Example 45 with SampleSequencingObjectJoin

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

the class SequencingObjectServiceImpl method concatenateSequences.

/**
 * {@inheritDoc}
 */
@Override
@PreAuthorize("hasPermission(#toJoin, 'canReadSequencingObject') and hasPermission(#targetSample, 'canUpdateSample')")
@Transactional
public SampleSequencingObjectJoin concatenateSequences(List<SequencingObject> toJoin, String filename, Sample targetSample, boolean removeOriginals) throws ConcatenateException {
    SequencingObjectConcatenator<? extends SequencingObject> concatenator = SequencingObjectConcatenatorFactory.getConcatenator(toJoin);
    SequencingObject concatenated = concatenator.concatenateFiles(toJoin, filename);
    SampleSequencingObjectJoin created = createSequencingObjectInSample(concatenated, targetSample);
    concatenationRepository.save(new SequenceConcatenation(created.getObject(), toJoin));
    if (removeOriginals) {
        for (SequencingObject obj : toJoin) {
            SampleSequencingObjectJoin sampleForSequencingObject = ssoRepository.getSampleForSequencingObject(obj);
            ssoRepository.delete(sampleForSequencingObject);
        }
    }
    return created;
}