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

Example 51 with Join

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

the class ProjectServiceImplIT method testRemoveSampleFromProject.

@Test
@WithMockUser(username = "admin", roles = "ADMIN")
public void testRemoveSampleFromProject() {
    Sample s = sampleService.read(1L);
    Project p2 = projectService.read(2L);
    Project p3 = projectService.read(3L);
    projectService.removeSampleFromProject(p2, s);
    projectService.removeSampleFromProject(p3, s);
    Collection<Join<Project, Sample>> samples = sampleService.getSamplesForProject(p3);
    assertTrue("No samples should be assigned to project.", samples.isEmpty());
    assertFalse("sample should be deleted because it was detached", sampleService.exists(s.getId()));
}

Example 52 with Join

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

the class ReferenceFileServiceImplIT method testDeleteReferenceFile.

@Test
@WithMockUser(username = "fbristow", roles = "USER")
public void testDeleteReferenceFile() {
    Project p = projectService.read(1L);
    List<Join<Project, ReferenceFile>> prs = referenceFileService.getReferenceFilesForProject(p);
    assertEquals("Wrong number of reference files for project.", 1, prs.size());
    ReferenceFile rf = prs.iterator().next().getObject();
    assertEquals("Wrong reference file attached to project.", Long.valueOf(1), rf.getId());
    referenceFileService.delete(rf.getId());
    p = projectService.read(1L);
    prs = referenceFileService.getReferenceFilesForProject(p);
    assertEquals("No more reference files should be in the project.", 0, prs.size());
}

Example 53 with Join

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

the class ProjectServiceImplTest method testUpdateProjectUserJoin.

@Test
public void testUpdateProjectUserJoin() throws ProjectWithoutOwnerException {
    Project project = new Project("Project 1");
    User user = new User();
    User user2 = new User();
    ProjectRole projectRole = ProjectRole.PROJECT_USER;
    ProjectUserJoin oldJoin = new ProjectUserJoin(project, user, ProjectRole.PROJECT_OWNER);
    @SuppressWarnings("unchecked") List<Join<Project, User>> owners = Lists.newArrayList(new ProjectUserJoin(project, user, ProjectRole.PROJECT_OWNER), new ProjectUserJoin(project, user2, ProjectRole.PROJECT_OWNER));
    when(pujRepository.getProjectJoinForUser(project, user)).thenReturn(oldJoin);
    when(pujRepository.save(oldJoin)).thenReturn(oldJoin);
    when(pujRepository.getUsersForProjectByRole(project, ProjectRole.PROJECT_OWNER)).thenReturn(owners);
    Join<Project, User> updateUserProjectRole = projectService.updateUserProjectRole(project, user, projectRole);
    assertNotNull(updateUserProjectRole);
    ProjectUserJoin newJoin = (ProjectUserJoin) updateUserProjectRole;
    assertEquals(projectRole, newJoin.getProjectRole());
    verify(pujRepository).getProjectJoinForUser(project, user);
    verify(pujRepository).getUsersForProjectByRole(project, ProjectRole.PROJECT_OWNER);
    verify(pujRepository).save(oldJoin);
}

Example 54 with Join

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

the class ProjectServiceImplTest method testGetProjectsForUser.

@Test
public void testGetProjectsForUser() {
    final User u = new User();
    final Project p1 = new Project("p1");
    final Project p2 = new Project("p2");
    final UserGroup ug = new UserGroup("group");
    final ProjectUserJoin puj = new ProjectUserJoin(p1, u, ProjectRole.PROJECT_OWNER);
    final UserGroupProjectJoin ugpj = new UserGroupProjectJoin(p2, ug, ProjectRole.PROJECT_OWNER);
    when(pujRepository.getProjectsForUser(u)).thenReturn(ImmutableList.of(puj));
    when(ugpjRepository.findProjectsByUser(u)).thenReturn(ImmutableList.of(ugpj));
    final List<Join<Project, User>> projects = projectService.getProjectsForUser(u);
    assertEquals("User should be in 2 projects.", 2, projects.size());
    assertTrue("Should have found user project join.", projects.stream().anyMatch(p -> p.getSubject().equals(p1)));
    assertTrue("Should have found group project join.", projects.stream().anyMatch(p -> p.getSubject().equals(p2)));
}

Example 55 with Join

use of ca.corefacility.bioinformatics.irida.model.joins.Join 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);
}