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This package implements a Python interface to the B-Fabric system. Several pieces of functionality are available:

  • Python API:
    • General client for all B-Fabric web service operations (CRUD) and configuration management.
    • A relational API for low-boilerplate read access to the B-Fabric system.
  • Scripts: Several scripts we use more or less frequently to interact with the system.
  • A REST API: A REST API to interact with the B-Fabric system. This allows us to interact with B-Fabric from R using bfabricShiny.

Please see below for how to install bfabricPy.

Installation

The bfabric and bfabric-scripts packages are available on PyPI. If you want to use the API in your code the bfabric package already provides all relevant functionality, whereas bfabric-scripts will provide several command line tools to interact with the B-Fabric system.

Installing the tool

If you are only interested in running the command line scripts, installation with uv tool is recommended as it will create a separate virtual environment for bfabric-scripts and make it possible to upgrade your installation later easily.

uv tool install -p 3.13 bfabric-scripts

You can upgrade this installation to the most recent version later with:

uv tool upgrade bfabric-scripts

Declaring a package dependency

If you want to add it to a pyproject.toml, simply add bfabric to your dependencies:

[project]
dependencies = [
    "bfabric==x.y.z"
]

where you replace x.y.z with the version you want to use.

If you instead want to install a development version, you can specify the git repository and branch to use:

[project]
dependencies = [
    "bfabric @ git+https://github.com/fgcz/bfabricPy.git@stable&subdirectory=bfabric#egg=bfabric",
]

Configuration

Create a file as follows: (note: the password is not your login password, but the web service password available on your profile page)

# ~/.bfabricpy.yml

GENERAL:
  default_config: PRODUCTION

PRODUCTION:
  login: yourBfabricLogin
  password: yourBfabricWebPassword
  base_url: https://fgcz-bfabric.uzh.ch/bfabric

You can also append an additional config section for the TEST instance which will be used for instance when running the integration tests:

TEST:
  login: yourBfabricLogin
  password: yourBfabricWebPassword
  base_url: https://fgcz-bfabric-test.uzh.ch/bfabric

When you run an application using bfabricPy, and it does not explicitly set the config when calling Bfabric.from_config, you can adjust the environment that is used by setting the environemnt variable BFABRICPY_CONFIG_ENV to the name of the config section you want to use. Command line scripts will log the user and base URL that is used, so you can verify that you are indeed using the correct environment.