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This package connects the bfabric system to the python and R world while providing a JSON and REST interface using Flask. The bfabricShiny R package is an extension and provides code snippets and sample implementation for a seamless R shiny bfabric integration. For more advanced users the bfabricPy package also provides a powerful query interface on the command-line though using the provided scripts.

Please see below for how to install bfabricPy.

Installation

The package is not available on PyPI as of now, but can be installed directly from GitHub and a stable branch is available for your convenience.

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

pipx install "git+https://github.com/fgcz/bfabricPy.git@stable"

Note that pipx is also useful in scripts, if you want to run a particular version without forcing the global installation of that version (simply replace "stable" with a tag of your chosing):

pipx run --spec "git+https://github.com/fgcz/bfabricPy.git@stable" bfabric_read.py --help

If you want to add it to a pyproject.toml the syntax for specifying a git dependency is as follows:

[project]
dependencies = [
    "bfabric @ git+https://github.com/fgcz/bfabricPy.git@stable"
]

Updating

If you installed with pipx, you can update the package to the most recent release with the following command:

pipx upgrade 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.