Terralab CLI

PLEASE NOTE: This CLI and service are still in development. This CLI can not yet be used to run imputation as described here.

Overview

The Terralab CLI provides a command-line interface with which to interact with the Terra Scientific Pipelines Service, or Teaspoons.

Currently, Terralab supports running Genotype Imputation (for public release in early 2025).

Note that in order to use Terralab and Teaspoons, you must have a Terra account.

User instructions coming soon.

Installation

You can install the Terralab CLI from PyPi using your favorite package management tool.

For example, run

pip install terralab-cli

Using the CLI

Once installed, to run the CLI, run the following command:

terralab COMMAND [ARGS]

For example, to list the pipelines you can run using Terralab, run the following command:

terralab pipelines list

(Internal) WIP documentation for the CLI.

Python CLI structure

The CLI code is structured as follows:

terra-scientific-pipelines-service-cli
├── terralab
│   └── commands
│   │   └── __init__.py
│   │   └── auth_commands.py
│   │   └── pipelines_commands.py
│   └── logic
│   │   └── __init__.py
│   │   └── auth_logic.py
│   │   └── pipelines_logic.py
│   └── __init__.py
│   └── auth_helper.py
│   └── cli.py
│   └── client.py
│   └── config.py
│   └── teaspoons
├── tests
│   └── commands
│   │   └── test_auth_commands.py
│   │   └── test_pipelines_commands.py
│   └── logic
│   │   └── test_auth_logic.py
│   │   └── test_pipelines_logic.py
│   └── __init__.py
│   └── auth_helper.py
│   └── cli.py
│   └── client.py
│   └── config.py
│   └── terralab
├── .gitignore
├── .terralab-cli-config
├── poetry.lock
├── pyproject.toml
├── README.md

In the terralab directory, we have the following files and subdirectories:

• auth_helper.py contains the code for authenticating with the Terra Scientific Pipelines Service (Terra, via b2c).
• cli.py is the entrypoint for the CLI. It configures logging and assembles the CLI sub-modules that are defined in commands/.
• client.py contains the code for wrapping API calls to the Terra Scientific Pipelines Service.
• config.py contains the code for managing the CLI configuration via environment variables.
• utils.py contains utility functions that are used across the CLI.
• The commands directory contains the CLI sub-modules. This is effectively the controller layer for the CLI.
• The logic directory contains the business logic for the CLI, including calling Terra Scientific Pipelines Service APIs via the thin teaspoons_client, which is autogenerated and published by the Terra Scientific Pipelines Service repository.

In the tests directory, we have test files that can be run with pytest.

Development

See CONTRIBUTING.md.