bfabric
Python client for the B-Fabric API — the system that runs the Functional Genomics Center Zurich (FGCZ), covering project and service management, data production, annotation, search and analysis workflows.
- A general client for all B-Fabric web service operations (CRUD) and configuration management.
- A relational API for low-boilerplate read access to B-Fabric entities.
Installation
pip install bfabric
One extra is available: bfabric[transfer] adds
resource download and upload.
Usage
Credentials are read from ~/.bfabricpy.yml:
from bfabric import Bfabric
client = Bfabric.connect()
results = client.read(endpoint="workunit", obj={}, max_results=5)
for workunit in results:
print(workunit["id"], workunit.get("status"))
See the getting started guide for configuring the client, and the user guides for the relational entity API, caching and error handling.
Links
This package is part of the bfabricPy monorepo, which also publishes bfabric-scripts (command line tools) and bfabric-app-runner (application workflows).
How to 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.
3 maintainers
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