Examples with Cohort org.pmiops.workbench.model.Cohort used on opensource projects

Example 16 with Cohort

use of org.pmiops.workbench.model.Cohort in project workbench by all-of-us.

the class CohortsControllerTest method testUpdateCohortInvalidEtagsThrow.

@Test
public void testUpdateCohortInvalidEtagsThrow() throws Exception {
    Cohort cohort = createDefaultCohort();
    cohort = cohortsController.createCohort(workspace.getNamespace(), workspace.getId(), cohort).getBody();
    // TODO: Refactor to be a @Parameterized test case.
    List<String> cases = ImmutableList.of("", "hello, world", "\"\"", "\"\"1234\"\"", "\"-1\"");
    for (String etag : cases) {
        try {
            cohortsController.updateCohort(workspace.getNamespace(), workspace.getId(), cohort.getId(), new Cohort().name("updated-name").etag(etag));
            fail(String.format("expected BadRequestException for etag: %s", etag));
        } catch (BadRequestException e) {
        // expected
        }
    }
}

Example 17 with Cohort

use of org.pmiops.workbench.model.Cohort in project workbench by all-of-us.

the class CohortsControllerTest method testUpdateCohort.

@Test
public void testUpdateCohort() throws Exception {
    Cohort cohort = createDefaultCohort();
    cohort = cohortsController.createCohort(workspace.getNamespace(), workspace.getId(), cohort).getBody();
    cohort.setName("updated-name");
    Cohort updated = cohortsController.updateCohort(workspace.getNamespace(), workspace.getId(), cohort.getId(), cohort).getBody();
    cohort.setEtag(updated.getEtag());
    assertThat(updated).isEqualTo(cohort);
    cohort.setName("updated-name2");
    updated = cohortsController.updateCohort(workspace.getNamespace(), workspace.getId(), cohort.getId(), cohort).getBody();
    cohort.setEtag(updated.getEtag());
    assertThat(updated).isEqualTo(cohort);
    Cohort got = cohortsController.getCohort(workspace.getNamespace(), workspace.getId(), cohort.getId()).getBody();
    assertThat(got).isEqualTo(cohort);
}

Example 18 with Cohort

use of org.pmiops.workbench.model.Cohort in project workbench by all-of-us.

the class CohortsControllerTest method testMaterializeCohortWorkspaceNotFound.

@Test(expected = NotFoundException.class)
public void testMaterializeCohortWorkspaceNotFound() throws Exception {
    Cohort cohort = createDefaultCohort();
    cohort = cohortsController.createCohort(workspace.getNamespace(), workspace.getId(), cohort).getBody();
    WorkspaceAccessLevel owner = WorkspaceAccessLevel.OWNER;
    String workspaceName = "badWorkspace";
    org.pmiops.workbench.firecloud.model.WorkspaceResponse fcResponse = new org.pmiops.workbench.firecloud.model.WorkspaceResponse();
    fcResponse.setAccessLevel(owner.toString());
    when(fireCloudService.getWorkspace(WORKSPACE_NAMESPACE, workspaceName)).thenReturn(fcResponse);
    when(workspaceService.getWorkspaceAccessLevel(WORKSPACE_NAMESPACE, workspaceName)).thenThrow(new NotFoundException());
    MaterializeCohortRequest request = new MaterializeCohortRequest();
    request.setCohortName(cohort.getName());
    cohortsController.materializeCohort(WORKSPACE_NAMESPACE, workspaceName, request);
}

Example 19 with Cohort

use of org.pmiops.workbench.model.Cohort in project workbench by all-of-us.

the class WorkspacesControllerTest method testCloneWorkspaceWithCohorts.

@Test
public void testCloneWorkspaceWithCohorts() throws Exception {
    CdrVersionContext.setCdrVersion(cdrVersion);
    Workspace workspace = createDefaultWorkspace();
    workspace = workspacesController.createWorkspace(workspace).getBody();
    Cohort c1 = createDefaultCohort("c1");
    c1 = cohortsController.createCohort(workspace.getNamespace(), workspace.getId(), c1).getBody();
    Cohort c2 = createDefaultCohort("c2");
    c2 = cohortsController.createCohort(workspace.getNamespace(), workspace.getId(), c2).getBody();
    stubBigQueryCohortCalls();
    CreateReviewRequest reviewReq = new CreateReviewRequest();
    reviewReq.setSize(1);
    CohortReview cr1 = cohortReviewController.createCohortReview(workspace.getNamespace(), workspace.getId(), c1.getId(), cdrVersion.getCdrVersionId(), reviewReq).getBody();
    reviewReq.setSize(2);
    CohortReview cr2 = cohortReviewController.createCohortReview(workspace.getNamespace(), workspace.getId(), c2.getId(), cdrVersion.getCdrVersionId(), reviewReq).getBody();
    stubGetWorkspace(workspace.getNamespace(), workspace.getName(), LOGGED_IN_USER_EMAIL, WorkspaceAccessLevel.OWNER);
    CloneWorkspaceRequest req = new CloneWorkspaceRequest();
    Workspace modWorkspace = new Workspace();
    modWorkspace.setName("cloned");
    modWorkspace.setNamespace("cloned-ns");
    ResearchPurpose modPurpose = new ResearchPurpose();
    modPurpose.setAncestry(true);
    modWorkspace.setResearchPurpose(modPurpose);
    req.setWorkspace(modWorkspace);
    stubGetWorkspace(modWorkspace.getNamespace(), modWorkspace.getName(), LOGGED_IN_USER_EMAIL, WorkspaceAccessLevel.OWNER);
    Workspace cloned = workspacesController.cloneWorkspace(workspace.getNamespace(), workspace.getId(), req).getBody().getWorkspace();
    List<Cohort> cohorts = cohortsController.getCohortsInWorkspace(cloned.getNamespace(), cloned.getId()).getBody().getItems();
    Map<String, Cohort> cohortsByName = Maps.uniqueIndex(cohorts, c -> c.getName());
    assertThat(cohortsByName.keySet()).containsExactlyElementsIn(ImmutableSet.of("c1", "c2"));
    assertThat(cohorts.stream().map(c -> c.getId()).collect(Collectors.toList())).containsNoneOf(c1.getId(), c2.getId());
    CohortReview gotCr1 = cohortReviewController.getParticipantCohortStatuses(cloned.getNamespace(), cloned.getId(), cohortsByName.get("c1").getId(), cdrVersion.getCdrVersionId(), new ParticipantCohortStatuses().pageFilterType(PageFilterType.PARTICIPANTCOHORTSTATUSES)).getBody();
    assertThat(gotCr1.getReviewSize()).isEqualTo(cr1.getReviewSize());
    assertThat(gotCr1.getParticipantCohortStatuses()).isEqualTo(cr1.getParticipantCohortStatuses());
    CohortReview gotCr2 = cohortReviewController.getParticipantCohortStatuses(cloned.getNamespace(), cloned.getId(), cohortsByName.get("c2").getId(), cdrVersion.getCdrVersionId(), new ParticipantCohortStatuses().pageFilterType(PageFilterType.PARTICIPANTCOHORTSTATUSES)).getBody();
    assertThat(gotCr2.getReviewSize()).isEqualTo(cr2.getReviewSize());
    assertThat(gotCr2.getParticipantCohortStatuses()).isEqualTo(cr2.getParticipantCohortStatuses());
    assertThat(ImmutableSet.of(gotCr1.getCohortReviewId(), gotCr2.getCohortReviewId())).containsNoneOf(cr1.getCohortReviewId(), cr2.getCohortId());
}