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

Example 71 with Sample

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

the class ProjectServiceImplIT method testShareSamplesWithoutOwner.

@Test
@WithMockUser(username = "user1", roles = "USER")
public void testShareSamplesWithoutOwner() {
    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 72 with Sample

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

the class ProjectServiceImplIT method testMoveSamplesWithoutOwner.

@Test
@WithMockUser(username = "user1", roles = "USER")
public void testMoveSamplesWithoutOwner() {
    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> movedSamples = projectService.moveSamples(source, destination, samples, false);
    assertEquals(samples.size(), movedSamples.size());
    movedSamples.forEach(j -> {
        assertFalse("Project shouldn't be owner for sample", j.isOwner());
    });
    assertEquals("Samples should not exist in source project", Long.valueOf(0L), projectSampleJoinRepository.countSamplesForProject(source));
    assertEquals("Samples should exist in destination project", Sets.newHashSet(1L, 2L), projectSampleJoinRepository.getSamplesForProject(destination).stream().map(j -> j.getObject().getId()).collect(Collectors.toSet()));
}

Example 73 with Sample

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

the class ProjectServiceImplIT method s.

private Sample s() {
    Sample s = new Sample();
    s.setSampleName("Samplename");
    s.setDescription("Description");
    return s;
}

Example 74 with Sample

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

the class ProjectServiceImplIT method testShareSamplesWithOwnerRemoteFail.

@Test(expected = AccessDeniedException.class)
@WithMockUser(username = "user1", roles = "USER")
public void testShareSamplesWithOwnerRemoteFail() {
    Project source = projectService.read(11L);
    Project destination = projectService.read(10L);
    assertTrue("Source project should be a remote project for the test", source.isRemote());
    assertFalse("Destination project should not be a remote project for the test", destination.isRemote());
    Sample sample = sampleService.read(3L);
    Set<Sample> samples = Sets.newHashSet(sample);
    projectService.shareSamples(source, destination, samples, true);
}

Example 75 with Sample

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

the class ProjectServiceImplIT method testAddSampleToProjectAsSequencer.

@Test
@WithMockUser(username = "sequencer", roles = "SEQUENCER")
public void testAddSampleToProjectAsSequencer() {
    Project p = projectService.read(1L);
    Sample s = s();
    Join<Project, Sample> join = projectService.addSampleToProject(p, s, true);
    assertNotNull("Join should not be empty.", join);
    assertEquals("Wrong project in join.", p, join.getSubject());
    assertEquals("Wrong sample in join.", s, join.getObject());
}