Examples with CdrVersion org.pmiops.workbench.db.model.CdrVersion used on opensource projects

Example 6 with CdrVersion

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

the class CohortBuilderControllerMockTest method getCriteriaByTypeAndParentIdIcd10.

@Test
public void getCriteriaByTypeAndParentIdIcd10() throws Exception {
    org.pmiops.workbench.cdr.model.Criteria expectedCriteria = new org.pmiops.workbench.cdr.model.Criteria().id(1L).type("ICD10").name("DIAGNOSIS CODES").group(true).selectable(true).count("0").conceptId("0");
    when(mockCdrVersionDao.findOne(1L)).thenReturn(new CdrVersion());
    when(mockCriteriaDao.findCriteriaByTypeAndParentIdOrderByCodeAsc("ICD10", 0L)).thenReturn(Arrays.asList(expectedCriteria));
    assertCriteria(controller.getCriteriaByTypeAndParentId(1L, "ICD10", 0L), new Criteria().id(1L).type("ICD10").name("DIAGNOSIS CODES").group(true).selectable(true).count(0L).conceptId(0L));
    verify(mockCdrVersionDao).findOne(1L);
    verify(mockCriteriaDao).findCriteriaByTypeAndParentIdOrderByCodeAsc("ICD10", 0L);
    verifyNoMoreInteractions(mockCriteriaDao, mockCdrVersionDao);
}

Example 7 with CdrVersion

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

the class CohortBuilderControllerMockTest method getCriteriaByTypeAndSubtypeDemographics.

@Test
public void getCriteriaByTypeAndSubtypeDemographics() throws Exception {
    org.pmiops.workbench.cdr.model.Criteria expectedCriteria = new org.pmiops.workbench.cdr.model.Criteria().id(1L).type("DEMO").subtype("RACE").name("African American").group(false).selectable(true).count("100").conceptId("0");
    when(mockCdrVersionDao.findOne(1L)).thenReturn(new CdrVersion());
    when(mockCriteriaDao.findCriteriaByTypeAndSubtypeOrderByNameAsc("DEMO", "RACE")).thenReturn(Arrays.asList(expectedCriteria));
    assertCriteria(controller.getCriteriaByTypeAndSubtype(1l, "DEMO", "RACE"), new Criteria().id(1L).type("DEMO").subtype("RACE").name("African American").group(false).selectable(true).count(100L).conceptId(0L));
    verify(mockCdrVersionDao).findOne(1L);
    verify(mockCriteriaDao).findCriteriaByTypeAndSubtypeOrderByNameAsc("DEMO", "RACE");
    verifyNoMoreInteractions(mockCriteriaDao, mockCdrVersionDao);
}

Example 8 with CdrVersion

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

the class CohortsControllerTest method setUp.

@Before
public void setUp() throws Exception {
    User user = new User();
    user.setEmail("bob@gmail.com");
    user.setUserId(123L);
    user.setDisabled(false);
    user.setEmailVerificationStatus(EmailVerificationStatus.SUBSCRIBED);
    user = userDao.save(user);
    when(userProvider.get()).thenReturn(user);
    cdrVersion = new CdrVersion();
    cdrVersion.setName(CDR_VERSION_NAME);
    cdrVersionDao.save(cdrVersion);
    searchRequest = SearchRequests.males();
    cohortCriteria = new Gson().toJson(searchRequest);
    workspace = new Workspace();
    workspace.setName(WORKSPACE_NAME);
    workspace.setNamespace(WORKSPACE_NAMESPACE);
    workspace.setDataAccessLevel(DataAccessLevel.PROTECTED);
    workspace.setResearchPurpose(new ResearchPurpose());
    workspace.setCdrVersionId(String.valueOf(cdrVersion.getCdrVersionId()));
    CLOCK.setInstant(NOW);
    WorkspacesController workspacesController = new WorkspacesController(workspaceService, cdrVersionDao, userDao, userProvider, fireCloudService, cloudStorageService, CLOCK, "https://api.blah.com", userService);
    stubGetWorkspace(WORKSPACE_NAMESPACE, WORKSPACE_NAME, "bob@gmail.com", WorkspaceAccessLevel.OWNER);
    workspace = workspacesController.createWorkspace(workspace).getBody();
    this.cohortsController = new CohortsController(workspaceService, cohortDao, cdrVersionDao, cohortReviewDao, cohortMaterializationService, userProvider, CLOCK);
}

Example 9 with CdrVersion

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

the class WorkspacesControllerTest method setUp.

@Before
public void setUp() {
    User user = new User();
    user.setEmail(LOGGED_IN_USER_EMAIL);
    user.setUserId(123L);
    user.setFreeTierBillingProjectName("TestBillingProject1");
    user.setDisabled(false);
    user.setEmailVerificationStatus(EmailVerificationStatus.SUBSCRIBED);
    user = userDao.save(user);
    when(userProvider.get()).thenReturn(user);
    workspacesController.setUserProvider(userProvider);
    cdrVersion = new CdrVersion();
    cdrVersion.setName("1");
    // set the db name to be empty since test cases currently
    // run in the workbench schema only.
    cdrVersion.setCdrDbName("");
    cdrVersion = cdrVersionDao.save(cdrVersion);
    cdrVersionId = Long.toString(cdrVersion.getCdrVersionId());
    CLOCK.setInstant(NOW);
}

Example 10 with CdrVersion

use of org.pmiops.workbench.db.model.CdrVersion 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());
}