https://github.com/fgcz/bfabricpy

API and commad line tools for b-fabric
https://github.com/fgcz/bfabricpy

api bfabric python3 rest-api shiny-r soap wsdl

Last synced: about 2 months ago
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API and commad line tools for b-fabric

• Host: GitHub
• URL: https://github.com/fgcz/bfabricpy
• Owner: fgcz
• License: gpl-3.0
• Created: 2015-02-04T13:27:27.000Z (over 10 years ago)
• Default Branch: main
• Last Pushed: 2025-07-22T11:42:41.000Z (3 months ago)
• Last Synced: 2025-07-22T13:23:28.516Z (3 months ago)
• Topics: api, bfabric, python3, rest-api, shiny-r, soap, wsdl
• Language: Python
• Homepage: https://fgcz.github.io/bfabricPy/
• Size: 7.61 MB
• Stars: 5
• Watchers: 7
• Forks: 1
• Open Issues: 15
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: COPYING

Awesome Lists containing this project

README

          
# bfabricPy

[![PR Checks](https://github.com/fgcz/bfabricPy/actions/workflows/run_unit_tests.yml/badge.svg)](https://github.com/fgcz/bfabricPy/actions/workflows/run_unit_tests.yml)

[![Nightly Integration Tests](https://github.com/fgcz/bfabricPy-tests/actions/workflows/nightly_tests.yml/badge.svg)](https://github.com/fgcz/bfabricPy-tests/actions/workflows/nightly_tests.yml)

[![EDBT'10](https://img.shields.io/badge/EDBT-10.1145%2F1739041.1739135-brightgreen)](https://doi.org/10.1145/1739041.1739135)

[![JIB](https://img.shields.io/badge/JIB-10.1515%2Fjib.2022.0031-brightgreen)](https://doi.org/10.1515/jib-2022-0031)

[![PyPI - bfabric](https://img.shields.io/pypi/v/bfabric?label=bfabric&logo=python&logoColor=white)](https://pypi.org/project/bfabric/)

[![PyPI - bfabric-scripts](https://img.shields.io/pypi/v/bfabric-scripts?label=bfabric-scripts&logo=python&logoColor=white)](https://pypi.org/project/bfabric-scripts/)

[![PyPI - bfabric-app-runner](https://img.shields.io/pypi/v/bfabric-app-runner?label=bfabric-app-runner&logo=python&logoColor=white)](https://pypi.org/project/bfabric-app-runner/)

## Documentation

| Package            | Link                                                                 | Change Log                                                                                                               |

| ------------------ | -------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------ |

| bfabric            | [https://fgcz.github.io/bfabricPy](https://fgcz.github.io/bfabricPy) | [bfabric/docs/changelog.md](https://github.com/fgcz/bfabricPy/blob/main/bfabric/docs/changelog.md)                       |

| bfabric-scripts    | [https://fgcz.github.io/bfabricPy](https://fgcz.github.io/bfabricPy) | [bfabric_scripts/docs/changelog.md](https://github.com/fgcz/bfabricPy/blob/main/bfabric_scripts/docs/changelog.md)       |

| bfabric-app-runner | https://fgcz.github.io/bfabricPy/app_runner/                         | [bfabric_app_runner/docs/changelog.md](https://github.com/fgcz/bfabricPy/blob/main/bfabric_app_runner/docs/changelog.md) |

## Introduction

This package implements a Python interface to the [B-Fabric](https://fgcz-bfabric.uzh.ch/bfabric/) 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](https://github.com/cpanse/bfabricShiny).

## Howto cite?

Panse, Christian, Trachsel, Christian and Türker, Can. "Bridging data management platforms and visualization tools to enable ad-hoc and smart analytics in life sciences" Journal of Integrative Bioinformatics, 2022, pp. 20220031. [doi: 10.1515/jib-2022-0031](https://doi.org/10.1515/jib-2022-0031).