Examples with ProjectSampleJoin ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin used on opensource projects

Example 46 with ProjectSampleJoin

use of ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin in project irida by phac-nml.

the class ProjectServiceImplIT method testShareLockedSamplesWithoutOwner.

@Test
@WithMockUser(username = "user1", roles = "USER")
public void testShareLockedSamplesWithoutOwner() {
    Project source = projectService.read(2L);
    Project destination = projectService.read(10L);
    List<Join<Project, Sample>> samplesForProject = sampleService.getSamplesForProject(source);
    Set<Sample> samples = samplesForProject.stream().map(j -> j.getObject()).collect(Collectors.toSet());
    List<ProjectSampleJoin> copiedSamples = projectService.shareSamples(source, destination, samples, false);
    assertEquals(samples.size(), copiedSamples.size());
    copiedSamples.forEach(j -> {
        assertFalse("Project shouldn't be owner for sample", j.isOwner());
    });
    assertEquals("Samples should still exist in source project", Sets.newHashSet(1L, 2L), projectSampleJoinRepository.getSamplesForProject(source).stream().map(j -> j.getObject().getId()).collect(Collectors.toSet()));
    assertEquals("Samples should exist in destination project", Sets.newHashSet(1L, 2L), projectSampleJoinRepository.getSamplesForProject(destination).stream().map(j -> j.getObject().getId()).collect(Collectors.toSet()));
}

Example 47 with ProjectSampleJoin

use of ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin in project irida by phac-nml.

the class ProjectServiceImplTest method testRemoveSampleWithOtherLinksFromProject.

@Test
public void testRemoveSampleWithOtherLinksFromProject() {
    Sample s = new Sample("s1");
    Project p1 = new Project("p1");
    final ProjectSampleJoin j = new ProjectSampleJoin(p1, s, true);
    when(psjRepository.getProjectForSample(s)).thenReturn(ImmutableList.of(j));
    when(psjRepository.readSampleForProject(p1, s)).thenReturn(j);
    projectService.removeSampleFromProject(p1, s);
    verify(psjRepository).delete(j);
    verifyZeroInteractions(sampleRepository);
}

Example 48 with ProjectSampleJoin

use of ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin in project irida by phac-nml.

the class ProjectServiceImplTest method testAddSampleToProject.

@Test
public void testAddSampleToProject() {
    Sample s = new Sample();
    s.setSampleName("sample");
    s.setId(new Long(2222));
    Project p = project();
    ProjectSampleJoin join = new ProjectSampleJoin(p, s, true);
    when(psjRepository.save(join)).thenReturn(join);
    Join<Project, Sample> rel = projectService.addSampleToProject(p, s, true);
    verify(psjRepository).save(join);
    verify(sampleRepository).getSampleBySampleName(p, s.getSampleName());
    assertNotNull(rel);
    assertEquals(rel.getSubject(), p);
    assertEquals(rel.getObject(), s);
}

Example 49 with ProjectSampleJoin

use of ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin in project irida by phac-nml.

the class SampleServiceImplTest method testGetSampleForProject.

@Test
public void testGetSampleForProject() {
    Project p = new Project();
    p.setId(1111L);
    Sample s = new Sample();
    s.setId(2222L);
    ProjectSampleJoin join = new ProjectSampleJoin(p, s, true);
    when(sampleRepository.findOne(s.getId())).thenReturn(s);
    when(psjRepository.readSampleForProject(p, s)).thenReturn(join);
    sampleService.getSampleForProject(p, s.getId());
    verify(psjRepository).readSampleForProject(p, s);
}

Example 50 with ProjectSampleJoin

use of ca.corefacility.bioinformatics.irida.model.joins.impl.ProjectSampleJoin in project irida by phac-nml.

the class SampleServiceImplTest method testRejectSampleMergeDifferentProjects.

@Test
public void testRejectSampleMergeDifferentProjects() {
    Sample s1 = new Sample();
    s1.setId(1L);
    Sample s2 = new Sample();
    s2.setId(2L);
    Project p1 = new Project();
    p1.setId(1L);
    p1.setName("project 1");
    Project p2 = new Project();
    p2.setId(2L);
    p2.setName("project 2");
    List<Join<Project, Sample>> p1_s1 = new ArrayList<>();
    p1_s1.add(new ProjectSampleJoin(p1, s1, true));
    List<Join<Project, Sample>> p2_s2 = new ArrayList<>();
    p2_s2.add(new ProjectSampleJoin(p2, s2, true));
    when(psjRepository.getProjectForSample(s1)).thenReturn(p1_s1);
    when(psjRepository.getProjectForSample(s2)).thenReturn(p2_s2);
    try {
        sampleService.mergeSamples(p1, s1, Lists.newArrayList(s2));
        fail("Samples from different projects were allowed to be merged.");
    } catch (IllegalArgumentException e) {
    } catch (Exception e) {
        e.printStackTrace();
        fail("Failed for an unknown reason; stack trace preceded.");
    }
    verify(psjRepository).getProjectForSample(s1);
    verify(psjRepository).getProjectForSample(s2);
}