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Command line interface for interacting with the Terra Scientific Pipelines Service, or Teaspoons.
PLEASE NOTE: This CLI and service are still in development. This CLI can not yet be used to run imputation as described here.
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.
You can install the Terralab CLI from PyPi using your favorite package management tool.
For example, run
pip install terralab-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.
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.commands
directory contains the CLI sub-modules. This is effectively the controller layer for the CLI.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.
See CONTRIBUTING.md.
FAQs
Command line interface for interacting with the Terra Scientific Pipelines Service, or Teaspoons.
We found that terralab-cli demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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