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

Example 21 with ProjectSampleJoin

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

the class ProjectSamplesControllerTest method testGetAjaxProjectSampleModels.

@SuppressWarnings("unchecked")
@Test
public void testGetAjaxProjectSampleModels() {
    Sample sample = TestDataFactory.constructSample();
    when(projectService.read(anyLong())).thenReturn(project);
    when(sampleService.getSamplesForProject(any(Project.class))).thenReturn(ImmutableList.of(new ProjectSampleJoin(project, sample, true)));
    when(sampleService.getFilteredSamplesForProjects(any(List.class), any(List.class), any(String.class), any(String.class), any(String.class), any(Date.class), any(Date.class), any(Integer.class), any(Integer.class), any(Sort.class))).thenReturn(TestDataFactory.getPageOfProjectSampleJoin());
    DataTablesParams params = mock(DataTablesParams.class);
    when(params.getSort()).thenReturn(new Sort(Direction.ASC, "sample.sampleName"));
    DataTablesResponse response = controller.getProjectSamples(1L, params, ImmutableList.of(), ImmutableList.of(), new UISampleFilter(), Locale.US);
    List<DataTablesResponseModel> data = response.getData();
    assertEquals("Has the correct number of samples", 1, data.size());
    DTProjectSamples sampleData = (DTProjectSamples) data.get(0);
    assertEquals("Has the correct sample", "Joined Sample", sampleData.getSampleName());
}

Example 22 with ProjectSampleJoin

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

the class SamplesControllerTest method testGetSampleFiles.

@SuppressWarnings("unchecked")
@Test
public void testGetSampleFiles() 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(projectService.getProjectsForSample(sample)).thenReturn(Lists.newArrayList(new ProjectSampleJoin(project, sample, true)));
    when(updateSamplePermission.isAllowed(any(Authentication.class), eq(sample))).thenReturn(true);
    String sampleFiles = controller.getSampleFilesWithoutProject(model, sampleId);
    assertEquals(SamplesController.SAMPLE_FILES_PAGE, sampleFiles);
    assertTrue((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);
}

Example 23 with ProjectSampleJoin

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

the class ReadSamplePermissionTest method testGrantPermissionWithDomainObject.

@Test
public void testGrantPermissionWithDomainObject() {
    String username = "fbristow";
    User u = new User();
    u.setUsername(username);
    Project p = new Project();
    Sample s = new Sample();
    List<Join<Project, User>> projectUsers = new ArrayList<>();
    projectUsers.add(new ProjectUserJoin(p, u, ProjectRole.PROJECT_USER));
    List<Join<Project, Sample>> projectSampleList = new ArrayList<>();
    projectSampleList.add(new ProjectSampleJoin(p, s, true));
    when(psjRepository.getProjectForSample(s)).thenReturn(projectSampleList);
    when(sampleRepository.findOne(1L)).thenReturn(s);
    when(readProjectPermission.isAllowed(any(), eq(p))).thenReturn(true);
    Authentication auth = new UsernamePasswordAuthenticationToken("fbristow", "password1");
    assertTrue("permission was not granted.", readSamplePermission.isAllowed(auth, s));
    verify(psjRepository).getProjectForSample(s);
    // we didn't need to load the domain object for this test.
    verifyZeroInteractions(sampleRepository);
}

Example 24 with ProjectSampleJoin

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

the class ReadSamplePermissionTest method testGrantPermission.

@Test
public void testGrantPermission() {
    String username = "fbristow";
    User u = new User();
    u.setUsername(username);
    Project p = new Project();
    Sample s = new Sample();
    List<Join<Project, User>> projectUsers = new ArrayList<>();
    projectUsers.add(new ProjectUserJoin(p, u, ProjectRole.PROJECT_USER));
    List<Join<Project, Sample>> projectSampleList = new ArrayList<>();
    projectSampleList.add(new ProjectSampleJoin(p, s, true));
    when(psjRepository.getProjectForSample(s)).thenReturn(projectSampleList);
    when(sampleRepository.findOne(1L)).thenReturn(s);
    when(readProjectPermission.isAllowed(any(), eq(p))).thenReturn(true);
    Authentication auth = new UsernamePasswordAuthenticationToken("fbristow", "password1");
    assertTrue("permission was not granted.", readSamplePermission.isAllowed(auth, 1L));
    verify(sampleRepository).findOne(1L);
    verify(psjRepository).getProjectForSample(s);
    verify(readProjectPermission).isAllowed(any(), eq(p));
}

Example 25 with ProjectSampleJoin

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

the class UpdateSamplePermissionTest method testGrantPermissionWithOneProject.

@Test
public void testGrantPermissionWithOneProject() {
    final Project p1 = new Project();
    final Project p2 = new Project();
    final Sample s = new Sample();
    when(projectSampleJoinRepository.getProjectForSample(s)).thenReturn(ImmutableList.of(new ProjectSampleJoin(p1, s, true), new ProjectSampleJoin(p2, s, true)));
    when(projectOwnerPermission.isAllowed(auth, p1)).thenReturn(false);
    when(projectOwnerPermission.isAllowed(auth, p2)).thenReturn(true);
    assertTrue("Permission to update sample should be given.", updateSamplePermission.isAllowed(auth, s));
}