From 825ef41f95353a153cfefd3f3240a46ac62d23ea Mon Sep 17 00:00:00 2001 From: Leonardo Schwarz Date: Wed, 16 Oct 2024 16:11:22 +0200 Subject: [PATCH] improve readme --- README.md | 21 +++++++++++++++------ docs/index.md | 11 ++++++++--- 2 files changed, 23 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 7c3b7b4f..f3670939 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,25 @@ +# 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) -# bfabricPy - -This package connects the [bfabric](https://fgcz-bfabric.uzh.ch/bfabric/) system to the [python](https://www.python.org/) and [R](https://cran.r-project.org/) world while providing a JSON and REST interface using [Flask](https://www.fullstackpython.com). -The [bfabricShiny](https://github.com/cpanse/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. +## Documentation You can find the up-to-date documentation at [https://fgcz.github.io/bfabricPy](https://fgcz.github.io/bfabricPy). -# Howto cite? +## 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). diff --git a/docs/index.md b/docs/index.md index 92983fc7..ac58235e 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,8 +1,13 @@ # Home -This package connects the [bfabric](https://fgcz-bfabric.uzh.ch/bfabric/) system to the [python](https://www.python.org/) and [R](https://cran.r-project.org/) world while providing a JSON and REST interface using [Flask](https://www.fullstackpython.com). -The [bfabricShiny](https://github.com/cpanse/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. +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). Please see below for how to install bfabricPy.