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

Example 6 with Workspace

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

the class CohortReviewControllerTest method getParticipantCohortAnnotations.

@Test
public void getParticipantCohortAnnotations() throws Exception {
    long cohortReviewId = 1;
    when(cohortReviewService.findCohort(cohortId)).thenReturn(createCohort(cohortId, workspaceId, null));
    when(cohortReviewService.validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.READER)).thenReturn(new Workspace());
    when(cohortReviewService.findCohortReview(cohortId, cdrVersionId)).thenReturn(createCohortReview(0, cohortId, cohortReviewId, cdrVersionId, null));
    when(cohortReviewService.findParticipantCohortAnnotations(cohortReviewId, participantId)).thenReturn(new ArrayList<>());
    reviewController.getParticipantCohortAnnotations(namespace, name, cohortId, cdrVersionId, participantId);
    verify(cohortReviewService).findCohort(cohortId);
    verify(cohortReviewService).validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.READER);
    verify(cohortReviewService).findCohortReview(cohortId, cdrVersionId);
    verify(cohortReviewService).findParticipantCohortAnnotations(cohortReviewId, participantId);
    verifyNoMoreMockInteractions();
}

Example 7 with Workspace

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

the class CohortReviewControllerTest method assertFindByCohortIdAndCdrVersionId.

private void assertFindByCohortIdAndCdrVersionId(String namespace, String name, long cohortId, long cdrVersionId, Integer page, Integer pageSize, SortOrder sortOrder, ParticipantCohortStatusColumns sortColumn) {
    Integer pageParam = page == null ? 0 : page;
    Integer pageSizeParam = pageSize == null ? 25 : pageSize;
    sortColumn = (sortColumn == null || sortColumn.name().equals(sortColumn.PARTICIPANTID)) ? ParticipantCohortStatusColumns.PARTICIPANTID : sortColumn;
    sortOrder = sortOrder == null ? SortOrder.ASC : sortOrder;
    ParticipantCohortStatusKey key = new ParticipantCohortStatusKey().cohortReviewId(cohortId).participantId(participantId);
    final Date dob = new Date(System.currentTimeMillis());
    ParticipantCohortStatus dbParticipant = new ParticipantCohortStatus().participantKey(key).status(CohortStatus.INCLUDED).birthDate(dob).ethnicityConceptId(1L).genderConceptId(1L).raceConceptId(1L);
    org.pmiops.workbench.model.ParticipantCohortStatus respParticipant = new org.pmiops.workbench.model.ParticipantCohortStatus().participantId(1L).status(CohortStatus.INCLUDED).birthDate(dob.getTime()).ethnicityConceptId(1L).genderConceptId(1L).raceConceptId(1L);
    org.pmiops.workbench.model.CohortReview respCohortReview = new org.pmiops.workbench.model.CohortReview().cohortReviewId(1L).cohortId(cohortId).cdrVersionId(cdrVersionId).matchedParticipantCount(1000L).reviewedCount(0L).reviewSize(200L).page(pageParam).pageSize(pageSizeParam).sortOrder(sortOrder.toString()).sortColumn(sortColumn.toString()).participantCohortStatuses(Arrays.asList(respParticipant));
    List<ParticipantCohortStatus> participants = new ArrayList<ParticipantCohortStatus>();
    participants.add(dbParticipant);
    CohortReview cohortReviewAfter = new CohortReview();
    cohortReviewAfter.setCohortReviewId(1L);
    cohortReviewAfter.setCohortId(cohortId);
    cohortReviewAfter.setCdrVersionId(cdrVersionId);
    cohortReviewAfter.setMatchedParticipantCount(1000);
    cohortReviewAfter.setReviewSize(200);
    cohortReviewAfter.setCreationTime(new Timestamp(System.currentTimeMillis()));
    Cohort cohort = new Cohort();
    cohort.setWorkspaceId(1);
    Map<String, Map<Long, String>> concepts = new HashMap<>();
    concepts.put(GenderRaceEthnicityType.RACE.name(), new HashMap<>());
    concepts.put(GenderRaceEthnicityType.GENDER.name(), new HashMap<>());
    concepts.put(GenderRaceEthnicityType.ETHNICITY.name(), new HashMap<>());
    GenderRaceEthnicityConcept greConcept = new GenderRaceEthnicityConcept(concepts);
    when(cohortReviewService.findCohortReview(cohortId, cdrVersionId)).thenReturn(cohortReviewAfter);
    when(cohortReviewService.findAll(key.getCohortReviewId(), Collections.<Filter>emptyList(), new PageRequest(pageParam, pageSizeParam, sortOrder, sortColumn.toString()))).thenReturn(participants);
    when(cohortReviewService.validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.READER)).thenReturn(new Workspace());
    when(cohortReviewService.findCohort(cohortId)).thenReturn(cohort);
    ParticipantCohortStatuses request = new ParticipantCohortStatuses();
    request.page(page);
    request.pageSize(pageSize);
    request.sortOrder(sortOrder);
    request.sortColumn(sortColumn);
    request.pageFilterType(PageFilterType.PARTICIPANTCOHORTSTATUSES);
    ResponseEntity<org.pmiops.workbench.model.CohortReview> response = reviewController.getParticipantCohortStatuses(namespace, name, cohortId, cdrVersionId, request);
    org.pmiops.workbench.model.CohortReview actualCohortReview = response.getBody();
    respCohortReview.setCreationTime(actualCohortReview.getCreationTime());
    assertEquals(respCohortReview, response.getBody());
    verify(cohortReviewService, atLeast(1)).validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.READER);
    verify(cohortReviewService, atLeast(1)).findCohortReview(cohortId, cdrVersionId);
    verify(cohortReviewService, times(1)).findAll(key.getCohortReviewId(), Collections.<Filter>emptyList(), new PageRequest(pageParam, pageSizeParam, sortOrder, sortColumn.toString()));
    verify(cohortReviewService, atLeast(1)).findCohort(cohortId);
    verifyNoMoreMockInteractions();
}

Example 8 with Workspace

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

the class CohortReviewControllerTest method createWorkspace.

private Workspace createWorkspace(long workspaceId, String namespace, String name) {
    Workspace workspace = new Workspace();
    workspace.setWorkspaceId(workspaceId);
    workspace.setWorkspaceNamespace(namespace);
    workspace.setFirecloudName(name);
    return workspace;
}

Example 9 with Workspace

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

the class CohortReviewControllerTest method deleteParticipantCohortAnnotation.

@Test
public void deleteParticipantCohortAnnotation() throws Exception {
    when(cohortReviewService.findCohort(cohortId)).thenReturn(createCohort(cohortId, workspaceId, null));
    when(cohortReviewService.validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.WRITER)).thenReturn(new Workspace());
    when(cohortReviewService.findCohortReview(cohortId, cdrVersionId)).thenReturn(createCohortReview(0, cohortId, cohortReviewId, cdrVersionId, null));
    when(cohortReviewService.findParticipantCohortStatus(cohortReviewId, participantId)).thenReturn(new ParticipantCohortStatus());
    doNothing().when(cohortReviewService).deleteParticipantCohortAnnotation(1L, cohortReviewId, participantId);
    reviewController.deleteParticipantCohortAnnotation(namespace, name, cohortId, cdrVersionId, participantId, 1L);
    verify(cohortReviewService).findCohort(cohortId);
    verify(cohortReviewService).validateMatchingWorkspace(namespace, name, workspaceId, WorkspaceAccessLevel.WRITER);
    verify(cohortReviewService).findCohortReview(cohortId, cdrVersionId);
    verify(cohortReviewService).findParticipantCohortStatus(cohortReviewId, participantId);
    verify(cohortReviewService).deleteParticipantCohortAnnotation(1L, cohortReviewId, participantId);
    verifyNoMoreMockInteractions();
}

Example 10 with Workspace

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

the class CohortAnnotationDefinitionControllerTest method updateCohortAnnotationDefinition_BadWorkspace.

@Test
public void updateCohortAnnotationDefinition_BadWorkspace() throws Exception {
    String namespace = "aou-test";
    String name = "test";
    long cohortId = 1;
    long annotationDefinitionId = 1;
    long workspaceId = 1;
    long badWorkspaceId = 0;
    Cohort cohort = createCohort(workspaceId);
    Workspace workspace = createWorkspace(namespace, name, badWorkspaceId);
    ModifyCohortAnnotationDefinitionRequest request = new ModifyCohortAnnotationDefinitionRequest();
    WorkspaceAccessLevel owner = WorkspaceAccessLevel.OWNER;
    when(workspaceService.enforceWorkspaceAccessLevel(namespace, name, WorkspaceAccessLevel.WRITER)).thenReturn(owner);
    when(cohortDao.findOne(cohortId)).thenReturn(cohort);
    when(workspaceService.getRequired(namespace, name)).thenReturn(workspace);
    try {
        cohortAnnotationDefinitionController.updateCohortAnnotationDefinition(namespace, name, cohortId, annotationDefinitionId, request);
        fail("Should have thrown a NotFoundException!");
    } catch (NotFoundException e) {
        assertEquals("Not Found: No workspace matching workspaceNamespace: " + namespace + ", workspaceId: " + name, e.getMessage());
    }
    verify(cohortDao, times(1)).findOne(cohortId);
    verify(workspaceService, times(1)).getRequired(namespace, name);
    verify(workspaceService).enforceWorkspaceAccessLevel(namespace, name, WorkspaceAccessLevel.WRITER);
    verifyNoMoreMockInteractions();
}