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

Example 16 with Cohort

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

the class WorkspaceServiceImpl method saveAndCloneCohorts.

@Override
@Transactional
public Workspace saveAndCloneCohorts(Workspace from, Workspace to) {
    // Save the workspace first to allocate an ID.
    Workspace saved = workspaceDao.save(to);
    for (Cohort fromCohort : from.getCohorts()) {
        Cohort c = new Cohort();
        c.setCriteria(fromCohort.getCriteria());
        c.setDescription(fromCohort.getDescription());
        c.setName(fromCohort.getName());
        c.setType(fromCohort.getType());
        c.setCreator(saved.getCreator());
        c.setWorkspaceId(saved.getWorkspaceId());
        c.setCreationTime(saved.getCreationTime());
        c.setLastModifiedTime(saved.getLastModifiedTime());
        c.setVersion(1);
        cohortService.saveAndCloneReviews(fromCohort, c);
    }
    return saved;
}

Example 17 with Cohort

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

the class CohortAnnotationDefinitionControllerTest method getCohortAnnotationDefinition.

@Test
public void getCohortAnnotationDefinition() throws Exception {
    String namespace = "aou-test";
    String name = "test";
    long cohortId = 1;
    long workspaceId = 1;
    long annotationDefinitionId = 1;
    String columnName = "name";
    Cohort cohort = createCohort(workspaceId);
    Workspace workspace = createWorkspace(namespace, name, workspaceId);
    org.pmiops.workbench.db.model.CohortAnnotationDefinition cohortAnnotationDefinition = createDBCohortAnnotationDefinition(cohortId, annotationDefinitionId, AnnotationType.STRING, columnName);
    WorkspaceAccessLevel owner = WorkspaceAccessLevel.OWNER;
    when(workspaceService.enforceWorkspaceAccessLevel(namespace, name, WorkspaceAccessLevel.READER)).thenReturn(owner);
    when(cohortDao.findOne(cohortId)).thenReturn(cohort);
    when(workspaceService.getRequired(namespace, name)).thenReturn(workspace);
    when(cohortAnnotationDefinitionDao.findByCohortIdAndCohortAnnotationDefinitionId(cohortId, annotationDefinitionId)).thenReturn(cohortAnnotationDefinition);
    CohortAnnotationDefinition responseDefinition = cohortAnnotationDefinitionController.getCohortAnnotationDefinition(namespace, name, cohortId, annotationDefinitionId).getBody();
    CohortAnnotationDefinition expectedResponse = createClientCohortAnnotationDefinition(annotationDefinitionId, cohortId, columnName, AnnotationType.STRING);
    assertEquals(expectedResponse, responseDefinition);
    verify(cohortDao, times(1)).findOne(cohortId);
    verify(workspaceService, times(1)).getRequired(namespace, name);
    verify(cohortAnnotationDefinitionDao, times(1)).findByCohortIdAndCohortAnnotationDefinitionId(cohortId, annotationDefinitionId);
    verify(workspaceService).enforceWorkspaceAccessLevel(namespace, name, WorkspaceAccessLevel.READER);
    verifyNoMoreMockInteractions();
}

Example 18 with Cohort

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

the class CohortAnnotationDefinitionControllerTest method createCohortAnnotationDefinition_BadWorkspace.

@Test
public void createCohortAnnotationDefinition_BadWorkspace() throws Exception {
    String namespace = "aou-test";
    String name = "test";
    long cohortId = 1;
    long workspaceId = 1;
    long badWorkspaceId = 0;
    Cohort cohort = createCohort(workspaceId);
    Workspace workspace = createWorkspace(namespace, name, badWorkspaceId);
    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.createCohortAnnotationDefinition(namespace, name, cohortId, new CohortAnnotationDefinition());
        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();
}

Example 19 with Cohort

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

the class CohortAnnotationDefinitionControllerTest method createCohortAnnotationDefinition.

@Test
public void createCohortAnnotationDefinition() throws Exception {
    String namespace = "aou-test";
    String name = "test";
    long cohortId = 1;
    long workspaceId = 1;
    long annotationDefinitionId = 1;
    final String columnName = "testing";
    Cohort cohort = createCohort(workspaceId);
    Workspace workspace = createWorkspace(namespace, name, workspaceId);
    CohortAnnotationDefinition request = createClientCohortAnnotationDefinition(annotationDefinitionId, cohortId, columnName, AnnotationType.STRING);
    org.pmiops.workbench.db.model.CohortAnnotationDefinition dbCohortAnnotationDefinition = createDBCohortAnnotationDefinition(cohortId, annotationDefinitionId, request.getAnnotationType(), request.getColumnName());
    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);
    when(cohortAnnotationDefinitionDao.save(dbCohortAnnotationDefinition)).thenReturn(dbCohortAnnotationDefinition);
    when(cohortAnnotationDefinitionDao.findByCohortIdAndColumnName(cohortId, columnName)).thenReturn(null);
    CohortAnnotationDefinition expectedResponse = createClientCohortAnnotationDefinition(annotationDefinitionId, cohortId, columnName, AnnotationType.STRING);
    CohortAnnotationDefinition response = cohortAnnotationDefinitionController.createCohortAnnotationDefinition(namespace, name, cohortId, request).getBody();
    assertEquals(expectedResponse, response);
    verify(cohortDao, times(1)).findOne(cohortId);
    verify(workspaceService, times(1)).getRequired(namespace, name);
    verify(cohortAnnotationDefinitionDao, times(1)).save(dbCohortAnnotationDefinition);
    verify(cohortAnnotationDefinitionDao, times(1)).findByCohortIdAndColumnName(cohortId, columnName);
    verify(workspaceService).enforceWorkspaceAccessLevel(namespace, name, WorkspaceAccessLevel.WRITER);
    verifyNoMoreMockInteractions();
}

Example 20 with Cohort

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

the class CohortAnnotationDefinitionControllerTest method createCohort.

private Cohort createCohort(long workspaceId) {
    Cohort cohort = new Cohort();
    cohort.setWorkspaceId(workspaceId);
    return cohort;
}