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

Example 1 with FirecloudWorkspaceId

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

the class WorkspacesController method createWorkspace.

@Override
public ResponseEntity<Workspace> createWorkspace(Workspace workspace) {
    if (Strings.isNullOrEmpty(workspace.getNamespace())) {
        throw new BadRequestException("missing required field 'namespace'");
    } else if (Strings.isNullOrEmpty(workspace.getName())) {
        throw new BadRequestException("missing required field 'name'");
    } else if (workspace.getResearchPurpose() == null) {
        throw new BadRequestException("missing required field 'researchPurpose'");
    } else if (workspace.getDataAccessLevel() == null) {
        throw new BadRequestException("missing required field 'dataAccessLevel'");
    }
    User user = userProvider.get();
    org.pmiops.workbench.db.model.Workspace existingWorkspace = workspaceService.getByName(workspace.getNamespace(), workspace.getName());
    if (existingWorkspace != null) {
        throw new ConflictException(String.format("Workspace %s/%s already exists", workspace.getNamespace(), workspace.getName()));
    }
    // Note: please keep any initialization logic here in sync with CloneWorkspace().
    FirecloudWorkspaceId workspaceId = generateFirecloudWorkspaceId(workspace.getNamespace(), workspace.getName());
    FirecloudWorkspaceId fcWorkspaceId = workspaceId;
    org.pmiops.workbench.firecloud.model.Workspace fcWorkspace = null;
    for (int attemptValue = 0; attemptValue < MAX_FC_CREATION_ATTEMPT_VALUES; attemptValue++) {
        try {
            fcWorkspace = attemptFirecloudWorkspaceCreation(fcWorkspaceId);
            break;
        } catch (ConflictException e) {
            if (attemptValue >= 5) {
                throw e;
            } else {
                fcWorkspaceId = new FirecloudWorkspaceId(workspaceId.getWorkspaceNamespace(), workspaceId.getWorkspaceName() + Integer.toString(attemptValue));
            }
        }
    }
    Timestamp now = new Timestamp(clock.instant().toEpochMilli());
    org.pmiops.workbench.db.model.Workspace dbWorkspace = new org.pmiops.workbench.db.model.Workspace();
    dbWorkspace.setFirecloudName(fcWorkspaceId.getWorkspaceName());
    dbWorkspace.setWorkspaceNamespace(fcWorkspaceId.getWorkspaceNamespace());
    dbWorkspace.setCreator(user);
    dbWorkspace.setCreationTime(now);
    dbWorkspace.setLastModifiedTime(now);
    dbWorkspace.setVersion(1);
    setCdrVersionId(dbWorkspace, workspace.getCdrVersionId());
    writeWorkspaceConfigFile(fcWorkspace, dbWorkspace.getCdrVersion());
    org.pmiops.workbench.db.model.Workspace reqWorkspace = FROM_CLIENT_WORKSPACE.apply(workspace);
    // TODO: enforce data access level authorization
    dbWorkspace.setDataAccessLevel(reqWorkspace.getDataAccessLevel());
    dbWorkspace.setName(reqWorkspace.getName());
    dbWorkspace.setDescription(reqWorkspace.getDescription());
    // Ignore incoming fields pertaining to review status; clients can only request a review.
    setResearchPurposeDetails(dbWorkspace, workspace.getResearchPurpose());
    if (reqWorkspace.getReviewRequested()) {
        // Use a consistent timestamp.
        dbWorkspace.setTimeRequested(now);
    }
    dbWorkspace.setReviewRequested(reqWorkspace.getReviewRequested());
    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.getDao().save(dbWorkspace);
    return ResponseEntity.ok(TO_SINGLE_CLIENT_WORKSPACE_FROM_FC_AND_DB.apply(dbWorkspace, fcWorkspace));
}

Example 2 with FirecloudWorkspaceId

use of org.pmiops.workbench.db.model.Workspace.FirecloudWorkspaceId 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);
}

Example 3 with FirecloudWorkspaceId

use of org.pmiops.workbench.db.model.Workspace.FirecloudWorkspaceId 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;
}