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

Example 16 with Sample

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

the class CartController method addProject.

/**
 * Add an entire {@link Project} to the cart
 *
 * @param projectId
 *            The ID of the {@link Project}
 * @return a map stating success
 */
@RequestMapping(value = "/project/{projectId}", method = RequestMethod.POST, consumes = MediaType.APPLICATION_JSON_VALUE)
@ResponseBody
public Map<String, Object> addProject(@PathVariable Long projectId) {
    Project project = projectService.read(projectId);
    List<Join<Project, Sample>> samplesForProject = sampleService.getSamplesForProject(project);
    Set<Sample> samples = samplesForProject.stream().map((j) -> {
        return j.getObject();
    }).collect(Collectors.toSet());
    getSelectedSamplesForProject(project).addAll(samples);
    return ImmutableMap.of("success", true);
}

Example 17 with Sample

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

the class ProjectServiceImplTest method testAddSampleWithSameSequencerId.

@Test(expected = EntityExistsException.class)
public void testAddSampleWithSameSequencerId() {
    Project p = project();
    Sample s = new Sample();
    Sample otherSample = new Sample("name");
    s.setSampleName("name");
    when(sampleRepository.getSampleBySampleName(p, s.getSampleName())).thenReturn(otherSample);
    projectService.addSampleToProject(p, s, true);
}

Example 18 with Sample

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

the class ProjectServiceImplTest method testAddSampleToProjectNoSamplePersistedInvalidSample.

@Test(expected = ConstraintViolationException.class)
public void testAddSampleToProjectNoSamplePersistedInvalidSample() {
    Project p = project();
    Sample s = new Sample();
    s.setSampleName("name");
    Set<ConstraintViolation<Sample>> violations = new HashSet<>();
    violations.add(ConstraintViolationImpl.forBeanValidation(null, null, Sample.class, null, null, null, null, null, null));
    when(validator.validate(s)).thenReturn(violations);
    projectService.addSampleToProject(p, s, true);
    verifyZeroInteractions(sampleRepository, psjRepository);
}

Example 19 with Sample

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

the class ProjectServiceImplTest method testAddSampleToProjectNoSamplePersisted.

@Test
public void testAddSampleToProjectNoSamplePersisted() {
    Project p = project();
    Sample s = new Sample();
    s.setSampleName("name");
    Set<ConstraintViolation<Sample>> noViolations = new HashSet<>();
    when(validator.validate(s)).thenReturn(noViolations);
    when(sampleRepository.save(s)).thenReturn(s);
    projectService.addSampleToProject(p, s, true);
    verify(sampleRepository).save(s);
    verify(psjRepository).save(new ProjectSampleJoin(p, s, true));
}

Example 20 with Sample

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

the class ProjectServiceImplTest method testRemoveSamplesFromProject.

@Test
public void testRemoveSamplesFromProject() {
    Project project = new Project();
    List<Sample> samples = ImmutableList.of(new Sample("s1"), new Sample("s2"));
    ProjectSampleJoin psj0 = new ProjectSampleJoin(project, samples.get(0), true);
    ProjectSampleJoin psj1 = new ProjectSampleJoin(project, samples.get(1), true);
    when(psjRepository.readSampleForProject(project, samples.get(0))).thenReturn(psj0);
    when(psjRepository.readSampleForProject(project, samples.get(1))).thenReturn(psj1);
    projectService.removeSamplesFromProject(project, samples);
    verify(psjRepository).delete(psj0);
    verify(psjRepository).delete(psj1);
}