Workbench CLI commands

Prior reading: Command-line interface overview

Purpose: This document provides a list of the Workbench CLI commands and information about their usage. For a full list of commands that includes details about sub-command arguments, see the CLI Reference.

List available commands

Usage: wb [COMMAND]
The Workbench CLI allows advanced users to interact with Workbench workspaces
and resources, and to perform administrative actions.
Commands:
  auth                            Commands to manage user credentials.
  bq                              Call bq in the Workbench workspace.
  cluster                         Use spark clusters in the workspace.
  config                          Commands to configure the CLI.
  pod, crg                        Manage Workbench pods.
  cromwell                        Commands related to Cromwell workflows.
  folder                          Commands related to folder.
  gcloud                          Call gcloud in the Workbench workspace.
  git                             Call git in the Workbench workspace.
  group                           Manage groups of Workbench users.
  gsutil                          Call gsutil in the Workbench workspace.
  nextflow                        Call nextflow in the Workbench workspace.
  notebook                        Use Notebooks in the workspace.
  organization, org               Manage Workbench organizations.
  resolve                         Resolve a resource to its cloud id or path.
  resource                        Manage references and controlled resources in the workspace.
  security                        Manage Workbench security credentials such as SSH keys.
  server                          Connect to a Workbench server.
  status                          Print details about the current workspace and server.
  utility                         Run third-party tools in the workspace.
  version                         Get the installed version.
  workspace                       Set up a Workbench workspace.
  app                             This command is deprecated. Please use `utility` instead.

Standalone commands

The status command prints details about the current workspace and server.

ℹ️ wb status

The version command prints the installed version.

ℹ️ wb version

The gcloud, git, gsutil, bq, and nextflow commands call third-party applications in the context of a Verily Workbench workspace.

ℹ️ wb gcloud ℹ️ wb git ℹ️ wb gsutil ℹ️ wb bq ℹ️ wb nextflow

The resolve command is an alias for the wb resource resolve command.

ℹ️ wb resolve

Groupings of sub-commands

The other commands are groupings of sub-commands, described in the sections below.

• auth Authentication
• config Config
• cromwell Cromwell
• git Git
• group Groups
• gsutil gsutil
• notebook Notebooks
• org or organization Organization
• resource Resources
• security Security
• server Server
• utility Utility
• workspace Workspace

Authentication

Usage: wb auth [COMMAND]
Commands to manage user credentials.
Commands:
  login   Authorize the CLI to access Workbench APIs and data with user credentials.
  revoke  Revoke credentials from an account.
  status  Print details about the currently authorized account.

ℹ️ wb auth

The Workbench CLI authenticates users with the Google OAuth 2.0 installed application flow.

Only one user can be logged in at a time. Call wb auth login to login as a different user.

You don't need to login again after switching workspaces. You will need to login again after switching servers, because different Workbench deployments may have different OAuth flows.

By default, the CLI opens a browser window for the user to click through the OAuth flow. For some use cases (e.g., Cloud Shell, cloud app), this isn't practical because there is no default (or any) browser on the machine. The CLI has a browser option that controls this behavior: wb config set browser MANUAL means the user can copy the URL into a browser on a different machine (e.g., their laptop), complete the login prompt, and then copy/paste the response token back into the shell prompt. For example:

> wb config set browser MANUAL
Browser launch mode for login is MANUAL (CHANGED).

> wb auth login
Please open the following address in a browser on any machine:
  https://accounts.google.com/o/oauth2/auth?access_type=offline&approval_prompt=force&client_id=[...]
Please enter code: *****
Login successful: testuser@gmail.com

Config

Usage: wb config [COMMAND]
Commands to configure the CLI.
Commands:
  get   Get a configuration property value.
  list  List all configuration properties and their values.
  set   Set a configuration property value.

ℹ️ wb config

These commands are property getters and setters for configuring the Workbench CLI. Currently the available configuration properties are:

OPTION                VALUE                                          DESCRIPTION
utility-mode          LOCAL_PROCESS                                  Check/Configure the way tools are launched.
aws-vault-path        /usr/local/bin/aws-vault                       Get/Set the location of aws-vault executable.
browser               AUTO                                           Check/Configure whether a browser is launched automatically during the login process.
cache-with-aws-vault  false                                          Get/Set whether aws-vault is used for caching.
default-resource-id   (unset)                                        Get/Set the ID of resource to treat as default.
format                TEXT                                           Get/Set the default output format option.
image                 us-east1-docker.pkg.dev/terra-vdevel-happy...  Get/Set the Docker image used for launching applications.
logging               OFF                                            Get/Set the logging level. 
resource-limit        1000                                           Get/Set the maximum number of resources allowed per workspace.
server                verily                                         Get/Set the Workbench server the CLI connects to.
wb-path               /usr/local/bin/wb                              Get/Set the location of wb executable.
workspace             (unset)                                        Get the current Workbench workspace./Set the workspace to an existing one.

Cromwell

Utility commands for using the Cromwell workflow engine with Workbench.

Usage: wb cromwell [COMMAND]
Commands related to Cromwell workflows.
Commands:
  generate-config  Generate cromwell.conf under the user-specified path.

ℹ️ wb cromwell

To use Cromwell to run a WDL workflow in an app:

• Run:

  wb cromwell generate-config \
      (--workspace-bucket-name=bucket_name | --google-bucket-name=gs://my-bucket) \
      [--dir=my/path]
  

• Either workspace-bucket-name or google-bucket-name is required to specify the bucket used by Cromwell for workflow orchestration.
  • workspace-bucket-name is a Workbench resource name.
  • google-bucket-name is a Google Cloud Storage bucket name. If google-bucket-name does not begin with the gs:// prefix, it will be automatically added.
• Run java -Dconfig.file=path/to/cromwell.conf -jar cromwell/cromwell-81.jar server. This starts Cromwell server on localhost:8000.
• In another terminal window, run cromshell. Enter localhost:8000 for cromwell server.
• Start workflow through cromshell: e.g., cromshell submit workflow.wdl inputs.json [options.json] [dependencies.zip]

For more information, see here.

Git

Usage: wb git [COMMAND]
Call git command in the wb workspace. Besides calling normal Git operation, this command allow cloning git-repo resources in the workspace.
Commands:
  all        Clone all the git-repo resources in the workspace. Usage: wb git clone --all
  resource   Clone specified git-repo resources in the workspace. Usage: wb git clone --resource=<repoResource1Name> --resource=<repoResource2Name>

ℹ️ wb git

To add a Git repo:

> wb resource add-ref git-repo --id=<resource_id> --repo-url=<repo_url>

Groups

Usage: wb group [COMMAND]
Manage groups of Workbench users.
Commands:
  add-user     Add a user to a group with a given policy.
  create       Create a new Workbench group.
  delete       Delete an existing Workbench group.
  describe     Describe the group.
  list         List the groups to which the current user belongs.
  list-users   List the users in a group.
  remove-user  Remove a user from a group with a given policy.

ℹ️ wb group

Workbench contains a directory-like system for managing groups of users. These commands are utility wrappers around the group management API endpoints.

Say a Workbench group's email is mygroup@mydomain.com. The option for the --name flag is mygroup, not mygroup@mydomain.com:

> wb group list-users --name=mygroup

Adding a member to a Workbench group implicitly adds their workspace service accounts. For example, say wb-user is added to mygroup@mydomain.com. When mygroup is granted access to a resource, wb-user is able to access that resource from any of their workspaces.

gsutil

You can run wb gsutil or wb gcloud alpha storage. gcloud alpha storage is a newer version of gsutil. It doesn't support everything, but what it does support may be significantly faster.

ℹ️ wb gsutil

Notebooks

Usage: wb notebook [COMMAND]
Commands:
Use Notebooks in the workspace.
  start  Start a stopped Notebook instance within your workspace.
  stop   Stop a running Notebook instance within your workspace.
  launch Launch a running Notebook instance within your workspace.

ℹ️ wb notebook

You can create a GCP Notebook controlled resource with wb resource create gcp-notebook --id=<resourceid> [--workspace=<id>] and a AWS Notebook controlled resource with wb resource create sagemaker-notebook. The stop, start, and launch commands are provided for convenience.

You can also stop and start the gcp-notebook using the gcloud notebooks instances start/stop commands.

Organization

Usage: wb organization [COMMAND]
Manage Workbench organizations.
Commands:
  access    Request temporary access to an organization.
  create    Create a new organization.
  delete    Delete an existing organization.
  describe  Describe the organization.
  list      List organizations.
  role      Manage organization roles.
  update    Update an existing organization.
  user      Manage users within Workbench organizations.

ℹ️ wb organization

User changes

Run the wb org user command with any of the follow sub-commands to manage Workbench organization users.

Usage: wb organization user [COMMAND]
Manage users within Workbench organizations.
Commands:
  archive   Archive a disabled user in an organization.
  describe  Describe a user.
  disable   Disable an enabled user in an organization.
  enable    Re-enable a disabled user in an organization.
  invite    Invite a user to an organization.
  list      List organization users.

ℹ️ wb organization user

Resources

Usage: wb resource [COMMAND]
Manage references and controlled resources in the workspace.
Commands:
  add-ref, add-referenced    Add a new referenced resource.
  check-access               Check if you have access to a referenced resource.
  credentials                Retrieve temporary credentials to access a cloud resource.
  create, create-controlled  Add a new controlled resource.
  delete                     Delete a resource from the workspace.
  describe                   Describe a resource.
  list                       List all resources.
  list-tree                  List all resources and folders in tree view.
  mount                      Mounts all workspace bucket resources.
  move                       Move resource to a folder.
  open-console               Retrieve console link to access a cloud resource.
  resolve                    Resolve a resource to its cloud id or path.
  unmount                    Unmounts all workspace bucket resources.
  update                     Update the properties of a resource.

ℹ️ wb resource

A controlled resource is a cloud resource that is managed by Workbench. It exists within the current workspace context (e.g., a bucket within the workspace Google project). You can create these with the create command.

A referenced resource is a cloud resource that is NOT managed by Workbench. It exists outside the current workspace context (e.g., a BigQuery dataset hosted outside of Workbench or in another workspace). You can add these with the add-ref command. The workspace currently supports the following referenced resources:

• bq-dataset
• bq-table
• gcs-bucket
• gcs-object
• git-repo
• s3-external-bucket
• s3-folder

The check-access command lets you see whether you have access to a particular resource. This is useful when a different user created or added the resource and subsequently shared the workspace with you. check-access currently always returns true for git-repo reference type because workspaces don't support authentication to external Git services yet.

The list of resources in a workspace is maintained on the Workbench Workspace Manager server. The CLI caches this list of resources locally. Third-party tools can access resource details via environment variables (e.g., $WORKBENCH_mybucket holds the gs:// URL of the workspace bucket resource named mybucket). The CLI updates the cache on every call to a wb resource command. If you are working in a shared workspace, you can run wb resource list (for example) to pick up any changes that your collaborators have made.

Cloud Storage bucket lifecycle rules

Cloud Storage bucket lifecycle rules are specified by passing a JSON-formatted file path to the wb resource create gcs-bucket command. The expected JSON structure matches the one used by the gsutil lifecycle command. This structure is a subset of the Cloud Storage resource specification . Below are some example file contents for specifying a lifecycle rule.

(1) Change the storage class to ARCHIVE after 10 days.

{
  "rule": [
    {
      "action": {
        "type": "SetStorageClass",
        "storageClass": "ARCHIVE"
      },
      "condition": {
        "age": 10
      }
    }
  ]
}

(2) Delete any objects with storage class STANDARD that were created before December 3, 2007.

{
  "rule": [
    {
      "action": {
        "type": "Delete"
      },
      "condition": {
        "createdBefore": "2007-12-03",
        "matchesStorageClass": ["STANDARD"]
      }
    }
  ]
}

(3) Delete any objects that are more than 365 days old.

{
  "rule": [
    {
      "action": {
        "type": "Delete"
      },
      "condition": {
        "age": 365
      }
    }
  ]
}

There is also a command shortcut for specifying this type of lifecycle rule in example 3:

wb resource create gcs-bucket --id=<mybucket> --bucket-name=<mybucket> --auto-delete=365

Cloud Storage bucket object reference

A reference to a Cloud Storage bucket object can be created by calling

wb resource add-ref gcs-object --id=<referenceid> --bucket-name=<mybucket> --object-name=<myobject>

Reference to a file or folder

A file or folder is treated as an object in a Cloud Storage bucket. By either creating a folder through the cloud console UI or copying an existing folder of files to the Cloud Storage bucket, a user can create a folder or file object. The user can then create a reference to the folder/file if they have at least READER access to the bucket and/or READER access to the folder/file.

Reference to multiple objects under a folder

Different from other referenced resource type, there is also support for creating a reference to objects in the folder. For instance, a user may create a a foo/ folder with bar.txt and secret.txt in it. If the user has at least READER access to foo/ folder, they have access to anything in the foo/ folder. So they can add a reference to foo/bar.txt, foo/\* or foo/\*.txt.

Update a referenced resource

Users can update the name and description of a referenced resource. Users can also update a referenced resource to another of the same type. For instance, if a user creates a referenced resource to BigQuery dataset foo and later on wants to point to BigQuery dataset bar in the same project, one can use wb resource update --id=<fooReferenceId> --new-dataset-id=bar to update the reference. However, users are not allowed to update the reference to a different type (e.g., updating a dataset reference to a data table reference is not allowed).

Mounting workspace resources

Users can mount Cloud Storage buckets and referenced folder objects locally to the user's home directory in $HOME/workspace/ by running wb resource mount.

Users can specify the --id flag with the ID of a Cloud Storage bucket or object resource to only mount that individual resource. This flag is useful for remounting a resource that had failed to mount or has been moved to a different folder in the workspace.

By default, controlled Cloud Storage buckets and referenced folder objects created by the user will be mounted with read-write permissions while controlled buckets created by other users and referenced bucket folders will be mounted with read-only permissions. Users can override this default behavior by specifying the --read-only flag. Ex: wb resource mount --read-only for all mounts to be read-only or wb resource mount --id=mybucket --read-only=false for all mounts to be read-write.

Users can specify the --disable-cache flag to disable file metadata caching and file type caching for objects in the mounted buckets. List operations such as ls will be slower, but will reflect the most up-to-date state of the bucket. This is useful when working with collaborators in a shared workspace. See more details in the gcsfuse repository.

Mount failures

If a mount has failed, an empty directory will be left at mount point with the resource name and a suffix error string indicating the failure. Users can remount the bucket with wb resource mount after resolving bucket access or bucket reference issues.

Unmounting a single resource can fail if the resource has been renamed or moved to a different workspace folder. In this case, users can either run wb resource unmount to unmount all mounted resources in $HOME/workspace/. Alternatively, users can directly list out all mounted file systems with mount and then unmount the resource using its mount path with fusermount -u (for Linux) or umount (for MacOS).

Security

Usage: wb security [COMMAND]
Manage Workbench security credentials such as SSH keys.
Commands:
  ssh-key  Get, generate, or add Workbench-managed SSH key pairs.

wb security ssh-key helps Workbench support source control in a notebook environment. It handles the ssh key of the current user. There is one Workbench SSH key per user. With this SSH key, you can perform source control in a Workbench-managed notebook instance using Git.

Usage: wb security ssh-key [COMMAND]
Get, generate, or add Workbench-managed SSH key pairs.
Commands:
  get       Get a Workbench generated and managed SSH key.
  generate  Generate a Workbench-managed SSH key.
  add       Save your Workbench SSH key to ~/.ssh and add it to ssh-agent.

To set up an SSH key, run wb security ssh-key add to add the Workbench SSH key to your local machine. You should see in the output an SSH public key starting with ssh-rsa. Copy the public key from the command output and add it to GitHub, as per these instructions.

If you think your key is compromised (e.g., the private key on your local machine is leaked to another user), you must delete the key from your GitHub account and run wb security ssh-key generate to generate a new Workbench SSH key. Once a new key is generated, you need to associate this new key with your GitHub account again.

Server

Usage: wb server [COMMAND]
Connect to a Workbench server.
Commands:
  list          List all available Workbench servers.
  list-regions  List the valid regions for a cloud platform.
  set           Set the Workbench server to connect to.
  status        Print status and details of the Workbench server context.

ℹ️ wb server

A Workbench server or app is a set of connected Workbench services (e.g., Workspace Manager, Data Repo, SAM).

Workspaces exist on a single server, so switching servers will change the list of workspaces available to you.

Utility

Usage: wb utility [COMMAND]
Run third-party tools in the workspace.
Commands:
  execute  [FOR DEBUG] Execute a command in the tool container for the
             Workbench workspace, with no setup.
  list     List the supported tools.

ℹ️ wb utility

The Workbench CLI allows running supported third-party tools within the context of a workspace. To see supported tools, run wb utility list.

The utility-mode configuration property controls how tools are run (e.g., either in a Docker container, or as a local child process).

Nextflow and the gcloud SDK are the first examples of supported third-party tools.

If you pass the --workspace flag, it must come immediately after the tool:

# Works
> wb bq --workspace=<workspace-id> ls

# Doesn't work, --workspace is passed to bq instead of Workbench
> wb bq ls --workspace=<workspace-id>

For creating resources such as a BigQuery dataset or Cloud Storage bucket, you must create them through Workbench rather than GCP tools. This is because Workbench configures permissions for you.

# Works
> wb resource create gcs-bucket --id=<resource-id>

# Doesn't work
> wb gsutil mb gs://<bucket-name>

Workspace

Usage: wb workspace [COMMAND]
Set up a Workbench workspace.
Commands:
  access           Request temporary access to a workspace.
  add-user         Add a user or group to the workspace.
  configure-aws    Generate an AWS configuration file for a workspace.
  create           Create a new workspace.
  delete           Delete an existing workspace.
  delete-property  Delete the workspace properties.
  describe         Describe the existing workspace.
  duplicate        Duplicate an existing workspace.
  list             List all workspaces the current user can access.
  list-users       List the users of the workspace.
  remove-user      Remove a user or group from the workspace.
  set              Set the workspace to an existing one.
  set-property     Set the workspace properties.
  update           Update an existing workspace.

ℹ️ wb workspace

A Workbench workspace is backed by a Google project. Creating/deleting a workspace also creates/deletes the project.

Folder

Usage: wb folder [COMMAND]
Commands related to folder.
Commands:
  tree          Show the folder hierarchy.
  set-property  Set the folder properties.
  create        Create a folder.
  delete        Delete a folder.
  update        Update a folder.

ℹ️ wb folder