use of org.pmiops.workbench.model.Workspace 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();
}
use of org.pmiops.workbench.model.Workspace in project workbench by all-of-us.
the class WorkspacesControllerTest method testReaderUpdateWorkspaceThrows.
@Test(expected = ForbiddenException.class)
public void testReaderUpdateWorkspaceThrows() throws Exception {
Workspace ws = createDefaultWorkspace();
ws = workspacesController.createWorkspace(ws).getBody();
ws.setName("updated-name");
UpdateWorkspaceRequest request = new UpdateWorkspaceRequest();
request.setWorkspace(ws);
stubGetWorkspace(ws.getNamespace(), ws.getId(), ws.getCreator(), WorkspaceAccessLevel.READER);
Workspace updated = workspacesController.updateWorkspace(ws.getNamespace(), ws.getId(), request).getBody();
}
use of org.pmiops.workbench.model.Workspace in project workbench by all-of-us.
the class WorkspacesController method updateWorkspace.
@Override
public ResponseEntity<Workspace> updateWorkspace(String workspaceNamespace, String workspaceId, UpdateWorkspaceRequest request) {
org.pmiops.workbench.db.model.Workspace dbWorkspace = workspaceService.getRequired(workspaceNamespace, workspaceId);
workspaceService.enforceWorkspaceAccessLevel(workspaceNamespace, workspaceId, WorkspaceAccessLevel.WRITER);
Workspace workspace = request.getWorkspace();
if (workspace == null) {
throw new BadRequestException("No workspace provided in request");
}
if (Strings.isNullOrEmpty(workspace.getEtag())) {
throw new BadRequestException("Missing required update field 'etag'");
}
int version = Etags.toVersion(workspace.getEtag());
if (dbWorkspace.getVersion() != version) {
throw new ConflictException("Attempted to modify outdated workspace version");
}
if (workspace.getDataAccessLevel() != null && !dbWorkspace.getDataAccessLevel().equals(workspace.getDataAccessLevel())) {
throw new BadRequestException("Attempted to change data access level");
}
if (workspace.getDescription() != null) {
dbWorkspace.setDescription(workspace.getDescription());
}
if (workspace.getName() != null) {
dbWorkspace.setName(workspace.getName());
}
// TODO: handle research purpose
setCdrVersionId(dbWorkspace, workspace.getCdrVersionId());
// The version asserted on save is the same as the one we read via
// getRequired() above, see RW-215 for details.
dbWorkspace = workspaceService.saveWithLastModified(dbWorkspace);
return ResponseEntity.ok(TO_SINGLE_CLIENT_WORKSPACE.apply(dbWorkspace));
}
use of org.pmiops.workbench.model.Workspace 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);
}
use of org.pmiops.workbench.model.Workspace in project workbench by all-of-us.
the class WorkspacesController method constructListWorkspaceFromDb.
// This does not populate the list of underserved research groups.
private static final Workspace constructListWorkspaceFromDb(org.pmiops.workbench.db.model.Workspace workspace, ResearchPurpose researchPurpose) {
FirecloudWorkspaceId workspaceId = workspace.getFirecloudWorkspaceId();
Workspace result = new Workspace().etag(Etags.fromVersion(workspace.getVersion())).lastModifiedTime(workspace.getLastModifiedTime().getTime()).creationTime(workspace.getCreationTime().getTime()).dataAccessLevel(workspace.getDataAccessLevel()).name(workspace.getName()).id(workspaceId.getWorkspaceName()).namespace(workspaceId.getWorkspaceNamespace()).description(workspace.getDescription()).researchPurpose(researchPurpose);
if (workspace.getCreator() != null) {
result.setCreator(workspace.getCreator().getEmail());
}
if (workspace.getCdrVersion() != null) {
result.setCdrVersionId(String.valueOf(workspace.getCdrVersion().getCdrVersionId()));
}
result.setUserRoles(workspace.getWorkspaceUserRoles().stream().map(TO_CLIENT_USER_ROLE).collect(Collectors.toList()));
return result;
}
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