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

Example 21 with Sample

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

the class ProjectServiceImplTest method testGetProjectsForSample.

@Test
public void testGetProjectsForSample() {
    Sample sample = new Sample("my sample");
    @SuppressWarnings("unchecked") List<Join<Project, Sample>> projects = Lists.newArrayList(new ProjectSampleJoin(new Project("p1"), sample, true), new ProjectSampleJoin(new Project("p2"), sample, true));
    when(psjRepository.getProjectForSample(sample)).thenReturn(projects);
    List<Join<Project, Sample>> projectsForSample = projectService.getProjectsForSample(sample);
    assertEquals(2, projectsForSample.size());
    verify(psjRepository).getProjectForSample(sample);
}

Example 22 with Sample

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

the class SampleServiceImplTest method testRemoveSequenceFileFromSample.

@Test
public void testRemoveSequenceFileFromSample() {
    Sample s = new Sample();
    s.setId(1111L);
    SequenceFile sf = new SequenceFile();
    sf.setId(2222L);
    SingleEndSequenceFile obj = new SingleEndSequenceFile(sf);
    obj.setId(2L);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(s, obj);
    when(ssoRepository.readObjectForSample(s, obj.getId())).thenReturn(join);
    sampleService.removeSequencingObjectFromSample(s, obj);
    verify(ssoRepository).delete(join);
}

Example 23 with Sample

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

the class SampleServiceImplTest method testGetTotalBasesForSampleFailMultipleFastQC.

/**
 * Tests out failing to get the total bases from a sample with one sequence
 * file due to too many FastQC
 *
 * @throws SequenceFileAnalysisException
 */
@Test(expected = SequenceFileAnalysisException.class)
public void testGetTotalBasesForSampleFailMultipleFastQC() 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 24 with Sample

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

the class SampleServiceImplTest method s.

private Sample s(Long id) {
    Sample s = new Sample();
    s.setId(id);
    return s;
}

Example 25 with Sample

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

the class SampleServiceImplTest method testMergeSamples.

@Test
public void testMergeSamples() {
    // For every sample in toMerge, the service should:
    // 1. call SequenceFileRepository to get the sequence files in that
    // sample,
    // 2. call SequenceFileRepository to add the sequence files to
    // mergeInto,
    // 3. call SampleRepository to persist the sample as deleted.
    final int SIZE = 3;
    Sample s = s(1L);
    Project project = p(1L);
    Sample[] toMerge = new Sample[SIZE];
    SequenceFile[] toMerge_sf = new SequenceFile[SIZE];
    SequencingObject[] toMerge_so = new SequencingObject[SIZE];
    SampleSequencingObjectJoin[] s_so_joins = new SampleSequencingObjectJoin[SIZE];
    SampleSequencingObjectJoin[] s_so_original = new SampleSequencingObjectJoin[SIZE];
    ProjectSampleJoin[] p_s_joins = new ProjectSampleJoin[SIZE];
    List<Sample> mergeSamples = new ArrayList<>();
    for (long i = 0; i < SIZE; i++) {
        int p = (int) i;
        toMerge[p] = s(i + 2);
        mergeSamples.add(toMerge[p]);
        toMerge_sf[p] = sf(i + 2);
        toMerge_so[p] = so(i + 2);
        s_so_joins[p] = new SampleSequencingObjectJoin(s, toMerge_so[p]);
        p_s_joins[p] = new ProjectSampleJoin(project, toMerge[p], true);
        List<Join<Project, Sample>> projectSampleJoins = new ArrayList<>();
        projectSampleJoins.add(p_s_joins[p]);
        List<SampleSequencingObjectJoin> sampleSeqObjectJoins = new ArrayList<>();
        SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(toMerge[p], toMerge_so[p]);
        sampleSeqObjectJoins.add(join);
        s_so_original[p] = join;
        when(ssoRepository.getSequencesForSample(toMerge[p])).thenReturn(null);
        when(ssoRepository.getSequencesForSample(toMerge[p])).thenReturn(sampleSeqObjectJoins);
        when(ssoRepository.save(s_so_joins[p])).thenReturn(s_so_joins[p]);
        when(ssoRepository.readObjectForSample(toMerge[p], toMerge_so[p].getId())).thenReturn(join);
        when(psjRepository.getProjectForSample(toMerge[p])).thenReturn(projectSampleJoins);
        // for deletion
        when(psjRepository.readSampleForProject(project, toMerge[p])).thenReturn(p_s_joins[p]);
    }
    List<Join<Project, Sample>> joins = new ArrayList<>();
    joins.add(new ProjectSampleJoin(project, s, true));
    when(psjRepository.getProjectForSample(s)).thenReturn(joins);
    Sample saved = sampleService.mergeSamples(project, s, mergeSamples);
    verify(psjRepository).getProjectForSample(s);
    for (int i = 0; i < SIZE; i++) {
        verify(ssoRepository).getSequencesForSample(toMerge[i]);
        verify(ssoRepository).save(s_so_joins[i]);
        verify(ssoRepository).delete(s_so_original[i]);
        verify(sampleRepository).delete(toMerge[i].getId());
        verify(psjRepository).getProjectForSample(toMerge[i]);
        verify(psjRepository).delete(p_s_joins[i]);
    }
    assertEquals("The saved sample should be the same as the sample to merge into.", s, saved);
}