What's the current version for each biological database?
Project description
Bioversions
What's the current version for each biological database?
A daily updated static listing of all current versions (that are incorporated) can be found at https://biopragmatics.github.io/bioversions.
🚀 Installation
$ pip install bioversions
💪 Usage
import bioversions
assert bioversions.get_version('biogrid') == '4.2.192', 'This was true on Dec 5th, 2020!'
# If you want more information, use the resolve() function
bioversion = bioversions.resolve('biogrid')
assert bioversion.version == '4.2.192'
By default, the results are cached and only refreshed once per day with the help
of cachier. The cache is stored in ~/.data/bioversions. The cache location
can be overridden by setting the
BIOVERSIONS_HOME environment variable via pystow.
🌐 Web Application
While https://biopragmatics.github.io/bioversions provides a daily updated static listing of the database, you can run a dynamic version with an API from your shell with:
$ bioversions web
Options can be listed with bioversions web --help.
You can navigate to http://localhost:5000 to see all versions as HTML or programmatically resolve given databases with
the
http://localhost:5000/database/<name> endpoint like in the following:
import requests
res = requests.get('http://localhost:5000/database/biogrid').json()
assert res['success']
assert res['result']['name'] == 'BioGRID'
assert res['result']['version'] == '4.2.192', 'This was true on Dec 5th, 2020!'
CLI Usage
You can use bioversions get to incorporate the latest versions in your shell scripts or REPL usage like in:
$ wget "https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive/BIOGRID-$(bioversions get biogrid)/BIOGRID-ALL-$(bioversions get biogrid).mitab.zip"
🙏 Contributing
To add more databases to the list, you can create a new submodule of
bioversions.sources and extend the bioversions.utils.Getter class to identify the most recent version for your
target database. See
bioversions.sources.biogrid as an example.
👋 Attribution
⚖️ License
Code is licensed under the MIT License.
🎁 Support
The Bioversions service was developed by the INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS) at Harvard Medical School.
💰 Funding
The development of the Bioregistry is funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).
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