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

Example 11 with ResearchPurpose

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

the class WorkspacesControllerTest method testCloneWithMassiveNotebook.

@Test(expected = FailedPreconditionException.class)
public void testCloneWithMassiveNotebook() throws Exception {
    Workspace workspace = createDefaultWorkspace();
    workspace = workspacesController.createWorkspace(workspace).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);
    org.pmiops.workbench.firecloud.model.Workspace fcWorkspace = createFcWorkspace(modWorkspace.getNamespace(), modWorkspace.getName(), LOGGED_IN_USER_EMAIL);
    fcWorkspace.setBucketName("bucket2");
    stubGetWorkspace(fcWorkspace, WorkspaceAccessLevel.OWNER);
    Blob bigNotebook = mockBlob(BUCKET_NAME, "notebooks/nb.ipynb");
    // 5 GB.
    when(bigNotebook.getSize()).thenReturn(5_000_000_000L);
    when(cloudStorageService.getBlobList(BUCKET_NAME, "notebooks")).thenReturn(ImmutableList.of(bigNotebook));
    workspacesController.cloneWorkspace(workspace.getNamespace(), workspace.getId(), req).getBody().getWorkspace();
}

Example 12 with ResearchPurpose

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

the class WorkspacesControllerTest method testApproveWorkspace.

@Test
public void testApproveWorkspace() throws Exception {
    Workspace ws = createDefaultWorkspace();
    ResearchPurpose researchPurpose = ws.getResearchPurpose();
    researchPurpose.setApproved(null);
    researchPurpose.setTimeReviewed(null);
    workspacesController.createWorkspace(ws);
    ResearchPurposeReviewRequest request = new ResearchPurposeReviewRequest();
    request.setApproved(true);
    workspacesController.reviewWorkspace(ws.getNamespace(), ws.getName(), request);
    stubGetWorkspace(ws.getNamespace(), ws.getName(), ws.getCreator(), WorkspaceAccessLevel.OWNER);
    ws = workspacesController.getWorkspace(ws.getNamespace(), ws.getName()).getBody().getWorkspace();
    researchPurpose = ws.getResearchPurpose();
    assertThat(researchPurpose.getApproved()).isTrue();
}

Example 13 with ResearchPurpose

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

the class WorkspacesController method cloneWorkspace.

@Override
public ResponseEntity<CloneWorkspaceResponse> cloneWorkspace(String workspaceNamespace, String workspaceId, CloneWorkspaceRequest body) {
    Workspace workspace = body.getWorkspace();
    if (Strings.isNullOrEmpty(workspace.getNamespace())) {
        throw new BadRequestException("missing required field 'workspace.namespace'");
    } else if (Strings.isNullOrEmpty(workspace.getName())) {
        throw new BadRequestException("missing required field 'workspace.name'");
    } else if (workspace.getResearchPurpose() == null) {
        throw new BadRequestException("missing required field 'workspace.researchPurpose'");
    }
    User user = userProvider.get();
    if (workspaceService.getByName(workspace.getNamespace(), workspace.getName()) != null) {
        throw new ConflictException(String.format("Workspace %s/%s already exists", workspace.getNamespace(), workspace.getName()));
    }
    // Retrieving the workspace is done first, which acts as an access check.
    String fromBucket = null;
    try {
        fromBucket = fireCloudService.getWorkspace(workspaceNamespace, workspaceId).getWorkspace().getBucketName();
    } catch (ApiException e) {
        if (e.getCode() == 404) {
            log.log(Level.INFO, "Firecloud workspace not found", e);
            throw new NotFoundException(String.format("workspace %s/%s not found or not accessible", workspaceNamespace, workspaceId));
        }
        log.log(Level.SEVERE, "Firecloud server error", e);
        throw new ServerErrorException();
    }
    org.pmiops.workbench.db.model.Workspace fromWorkspace = workspaceService.getRequiredWithCohorts(workspaceNamespace, workspaceId);
    if (fromWorkspace == null) {
        throw new NotFoundException(String.format("Workspace %s/%s not found", workspaceNamespace, workspaceId));
    }
    FirecloudWorkspaceId fcWorkspaceId = generateFirecloudWorkspaceId(workspace.getNamespace(), workspace.getName());
    fireCloudService.cloneWorkspace(workspaceNamespace, workspaceId, fcWorkspaceId.getWorkspaceNamespace(), fcWorkspaceId.getWorkspaceName());
    org.pmiops.workbench.firecloud.model.Workspace toFcWorkspace = null;
    try {
        toFcWorkspace = fireCloudService.getWorkspace(fcWorkspaceId.getWorkspaceNamespace(), fcWorkspaceId.getWorkspaceName()).getWorkspace();
    } catch (ApiException e) {
        log.log(Level.SEVERE, "Firecloud error retrieving newly cloned workspace", e);
        throw new ServerErrorException();
    }
    // feasibly copy within a single API request.
    for (Blob b : cloudStorageService.getBlobList(fromBucket, NOTEBOOKS_WORKSPACE_DIRECTORY)) {
        if (!NOTEBOOK_PATTERN.matcher(b.getName()).matches()) {
            continue;
        }
        if (b.getSize() != null && b.getSize() / 1e6 > MAX_NOTEBOOK_SIZE_MB) {
            throw new FailedPreconditionException(String.format("workspace %s/%s contains a notebook larger than %dMB: '%s'; cannot clone - please " + "remove this notebook, reduce its size, or contact the workspace owner", workspaceNamespace, workspaceId, MAX_NOTEBOOK_SIZE_MB, b.getName()));
        }
        cloudStorageService.copyBlob(b.getBlobId(), BlobId.of(toFcWorkspace.getBucketName(), b.getName()));
    }
    // The final step in the process is to clone the AoU representation of the
    // workspace. The implication here is that we may generate orphaned
    // Firecloud workspaces / buckets, but a user should not be able to see
    // half-way cloned workspaces via AoU - so it will just appear as a
    // transient failure.
    org.pmiops.workbench.db.model.Workspace toWorkspace = FROM_CLIENT_WORKSPACE.apply(body.getWorkspace());
    org.pmiops.workbench.db.model.Workspace dbWorkspace = new org.pmiops.workbench.db.model.Workspace();
    Timestamp now = new Timestamp(clock.instant().toEpochMilli());
    dbWorkspace.setFirecloudName(fcWorkspaceId.getWorkspaceName());
    dbWorkspace.setWorkspaceNamespace(fcWorkspaceId.getWorkspaceNamespace());
    dbWorkspace.setCreator(user);
    dbWorkspace.setCreationTime(now);
    dbWorkspace.setLastModifiedTime(now);
    dbWorkspace.setVersion(1);
    dbWorkspace.setName(toWorkspace.getName());
    ResearchPurpose researchPurpose = body.getWorkspace().getResearchPurpose();
    setResearchPurposeDetails(dbWorkspace, researchPurpose);
    if (researchPurpose.getReviewRequested()) {
        // Use a consistent timestamp.
        dbWorkspace.setTimeRequested(now);
    }
    dbWorkspace.setReviewRequested(researchPurpose.getReviewRequested());
    // Clone the previous description, by default.
    if (Strings.isNullOrEmpty(toWorkspace.getDescription())) {
        dbWorkspace.setDescription(fromWorkspace.getDescription());
    } else {
        dbWorkspace.setDescription(toWorkspace.getDescription());
    }
    dbWorkspace.setCdrVersion(fromWorkspace.getCdrVersion());
    dbWorkspace.setDataAccessLevel(fromWorkspace.getDataAccessLevel());
    writeWorkspaceConfigFile(toFcWorkspace, dbWorkspace.getCdrVersion());
    org.pmiops.workbench.db.model.WorkspaceUserRole permissions = new org.pmiops.workbench.db.model.WorkspaceUserRole();
    permissions.setRole(WorkspaceAccessLevel.OWNER);
    permissions.setWorkspace(dbWorkspace);
    permissions.setUser(user);
    dbWorkspace.addWorkspaceUserRole(permissions);
    dbWorkspace = workspaceService.saveAndCloneCohorts(fromWorkspace, dbWorkspace);
    CloneWorkspaceResponse resp = new CloneWorkspaceResponse();
    resp.setWorkspace(TO_SINGLE_CLIENT_WORKSPACE_FROM_FC_AND_DB.apply(dbWorkspace, toFcWorkspace));
    return ResponseEntity.ok(resp);
}