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

Example 31 with ProjectSampleJoin

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

the class ProjectServiceImpl method moveSamples.

/**
 * {@inheritDoc}
 */
@Override
@Transactional
@LaunchesProjectEvent(SampleAddedProjectEvent.class)
@PreAuthorize("hasPermission(#source, 'isProjectOwner') and hasPermission(#destination, 'isProjectOwner') " + "and hasPermission(#samples, 'canReadSample') " + "and ((not #giveOwner) or hasPermission(#samples, 'canUpdateSample') )")
public List<ProjectSampleJoin> moveSamples(Project source, Project destination, Collection<Sample> samples, boolean giveOwner) {
    List<ProjectSampleJoin> newJoins = new ArrayList<>();
    for (Sample sample : samples) {
        ProjectSampleJoin newJoin = moveSampleBetweenProjects(source, destination, sample, giveOwner);
        logger.trace("Moved sample " + sample.getId() + " to project " + destination.getId());
        newJoins.add(newJoin);
    }
    return newJoins;
}

Example 32 with ProjectSampleJoin

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

the class ProjectEventHandlerTest method testHandleSequenceFileAddedEventMultipleProjects.

@SuppressWarnings("unchecked")
@Test
public void testHandleSequenceFileAddedEventMultipleProjects() {
    Class<? extends ProjectEvent> clazz = DataAddedToSampleProjectEvent.class;
    Project project = new Project("p1");
    Project project2 = new Project("p2");
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile();
    SingleEndSequenceFile seqObj = new SingleEndSequenceFile(file);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(sample, seqObj);
    when(psjRepository.getProjectForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true), new ProjectSampleJoin(project2, sample, true)));
    when(eventRepository.save(any(ProjectEvent.class))).thenReturn(new DataAddedToSampleProjectEvent(project, sample));
    Object[] args = {};
    MethodEvent methodEvent = new MethodEvent(clazz, join, args);
    handler.delegate(methodEvent);
    ArgumentCaptor<ProjectEvent> captor = ArgumentCaptor.forClass(ProjectEvent.class);
    verify(eventRepository, times(2)).save(captor.capture());
    List<ProjectEvent> allValues = captor.getAllValues();
    Set<Project> projects = Sets.newHashSet(project, project2);
    for (ProjectEvent event : allValues) {
        assertTrue(event instanceof DataAddedToSampleProjectEvent);
        Project eventProject = event.getProject();
        assertTrue(projects.contains(eventProject));
        projects.remove(eventProject);
    }
    verify(projectRepository, times(2)).save(project);
}

Example 33 with ProjectSampleJoin

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

the class ProjectEventHandlerTest method testHandleSequenceFileAddedEventSingle.

@SuppressWarnings("unchecked")
@Test
public void testHandleSequenceFileAddedEventSingle() {
    Class<? extends ProjectEvent> clazz = DataAddedToSampleProjectEvent.class;
    Project project = new Project();
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile();
    SingleEndSequenceFile seqObj = new SingleEndSequenceFile(file);
    SampleSequencingObjectJoin join = new SampleSequencingObjectJoin(sample, seqObj);
    when(psjRepository.getProjectForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true)));
    when(eventRepository.save(any(ProjectEvent.class))).thenReturn(new DataAddedToSampleProjectEvent(project, sample));
    Object[] args = {};
    MethodEvent methodEvent = new MethodEvent(clazz, join, args);
    handler.delegate(methodEvent);
    ArgumentCaptor<ProjectEvent> captor = ArgumentCaptor.forClass(ProjectEvent.class);
    verify(eventRepository).save(captor.capture());
    ProjectEvent event = captor.getValue();
    assertTrue(event instanceof DataAddedToSampleProjectEvent);
    verify(projectRepository).save(any(Project.class));
    verify(sampleRepository).save(any(Sample.class));
}

Example 34 with ProjectSampleJoin

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

the class ProjectSamplesControllerTest method testShareSampleToProject.

@SuppressWarnings("unchecked")
@Test
public void testShareSampleToProject() {
    Long projectId = 1L;
    List<Long> sampleIds = ImmutableList.of(2L, 3L);
    Long newProjectId = 4L;
    boolean removeFromOriginal = false;
    Project oldProject = new Project("oldProject");
    Project newProject = new Project("newProject");
    Sample s2 = new Sample("s2");
    Sample s3 = new Sample("s3");
    ArrayList<Sample> sampleList = Lists.newArrayList(s2, s3);
    boolean owner = true;
    ArrayList<ProjectSampleJoin> joins = Lists.newArrayList(new ProjectSampleJoin(newProject, s2, owner), new ProjectSampleJoin(newProject, s3, owner));
    when(projectService.read(projectId)).thenReturn(oldProject);
    when(projectService.read(newProjectId)).thenReturn(newProject);
    when(sampleService.readMultiple(any(Iterable.class))).thenReturn(sampleList);
    when(projectService.shareSamples(oldProject, newProject, sampleList, owner)).thenReturn(joins);
    controller.shareSampleToProject(projectId, sampleIds, newProjectId, removeFromOriginal, true, Locale.US);
    verify(projectService).read(projectId);
    verify(projectService).read(newProjectId);
    verify(projectService).shareSamples(oldProject, newProject, sampleList, owner);
}

Example 35 with ProjectSampleJoin

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

the class SamplesControllerTest method testGetSampleFilesNoAccess.

@SuppressWarnings("unchecked")
@Test
public void testGetSampleFilesNoAccess() throws IOException {
    ExtendedModelMap model = new ExtendedModelMap();
    Long sampleId = 1L;
    Sample sample = new Sample();
    SequenceFile file = new SequenceFile(Paths.get("/tmp"));
    file.setId(2L);
    Project project = new Project();
    List<SampleSequencingObjectJoin> files = Lists.newArrayList(new SampleSequencingObjectJoin(sample, new SingleEndSequenceFile(file)));
    when(sampleService.read(sampleId)).thenReturn(sample);
    when(sequencingObjectService.getSequencesForSampleOfType(sample, SingleEndSequenceFile.class)).thenReturn(files);
    when(updateSamplePermission.isAllowed(any(Authentication.class), eq(sample))).thenReturn(false);
    when(projectService.getProjectsForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true)));
    String sampleFiles = controller.getSampleFilesWithoutProject(model, sampleId);
    assertEquals(SamplesController.SAMPLE_FILES_PAGE, sampleFiles);
    assertFalse((boolean) model.get(SamplesController.MODEL_ATTR_CAN_MANAGE_SAMPLE));
    verify(sampleService).read(sampleId);
    verify(sequencingObjectService).getSequencesForSampleOfType(sample, SingleEndSequenceFile.class);
    verify(sequencingObjectService).getSequencesForSampleOfType(sample, SequenceFilePair.class);
}