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

Example 11 with SampleSequencingObjectJoin

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

Example 12 with SampleSequencingObjectJoin

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

the class SampleServiceImplTest method testGetTotalBasesForSampleSuccessOne.

/**
 * Tests out successfully getting the total bases from a sample with one
 * sequence file.
 *
 * @throws SequenceFileAnalysisException
 * @throws AnalysisAlreadySetException
 */
@Test
public void testGetTotalBasesForSampleSuccessOne() 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);
    long actualBases = sampleService.getTotalBasesForSample(s1);
    assertEquals(1000, actualBases);
}

Example 13 with SampleSequencingObjectJoin

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

the class ProjectEventHandler method handleIndividualSequenceFileAddedEvent.

/**
 * Create {@link DataAddedToSampleProjectEvent} for all {@link Project}s a
 * {@link Sample} belongs to
 *
 * @param join
 *            a {@link SampleSequencingObjectJoin} to turn into a
 *            {@link DataAddedToSampleProjectEvent}
 */
private Collection<DataAddedToSampleProjectEvent> handleIndividualSequenceFileAddedEvent(SampleSequencingObjectJoin join) {
    Sample subject = join.getSubject();
    Collection<DataAddedToSampleProjectEvent> events = new ArrayList<>();
    List<Join<Project, Sample>> projectForSample = psjRepository.getProjectForSample(subject);
    for (Join<Project, Sample> psj : projectForSample) {
        events.add(eventRepository.save(new DataAddedToSampleProjectEvent(psj.getSubject(), subject)));
    }
    return events;
}

Example 14 with SampleSequencingObjectJoin

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

the class AssemblyFileProcessorTest method testAssembleFile.

@Test
public void testAssembleFile() {
    Long sequenceFileId = 1L;
    SequenceFilePair pair = new SequenceFilePair(new SequenceFile(Paths.get("file_R1_1.fastq.gz")), new SequenceFile(Paths.get("file_R2_1.fastq.gz")));
    Sample sample = new Sample();
    Project project = new Project();
    project.setAssembleUploads(true);
    when(objectRepository.findOne(sequenceFileId)).thenReturn(pair);
    when(ssoRepository.getSampleForSequencingObject(pair)).thenReturn(new SampleSequencingObjectJoin(sample, pair));
    when(psjRepository.getProjectForSample(sample)).thenReturn(ImmutableList.of(new ProjectSampleJoin(project, sample, true)));
    assertTrue("should want to assemble file", processor.shouldProcessFile(sequenceFileId));
    processor.process(pair);
    verify(submissionRepository).save(any(AnalysisSubmission.class));
}

Example 15 with SampleSequencingObjectJoin

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

the class AssemblyFileProcessorTest method testOneProjectEnabled.

@Test
public void testOneProjectEnabled() {
    SequenceFilePair pair = new SequenceFilePair(new SequenceFile(Paths.get("file_R1_1.fastq.gz")), new SequenceFile(Paths.get("file_R2_1.fastq.gz")));
    Sample sample = new Sample();
    Project project = new Project();
    project.setAssembleUploads(true);
    Project disabledProject = new Project();
    disabledProject.setAssembleUploads(false);
    when(ssoRepository.getSampleForSequencingObject(pair)).thenReturn(new SampleSequencingObjectJoin(sample, pair));
    when(psjRepository.getProjectForSample(sample)).thenReturn(ImmutableList.of(new ProjectSampleJoin(disabledProject, sample, true), new ProjectSampleJoin(project, sample, true)));
    processor.process(pair);
    verify(submissionRepository).save(any(AnalysisSubmission.class));
}