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).
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
File details
Details for the file bioversions-0.4.21.tar.gz.
File metadata
- Download URL: bioversions-0.4.21.tar.gz
- Upload date:
- Size: 182.4 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/0.9.1 urllib3/1.26.9 tqdm/4.63.0 importlib-metadata/4.11.3 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.10.2
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | e830313458bfc1df22a82a3299b2628e7dfbcb9b5351bc905f2454f5e4b543be |
|
| MD5 | 150f54e3f5dae0214ff573aa61527772 |
|
| BLAKE2b-256 | f8b7d1729d1fdfecd3a2b0860d049c58a1ff35925c169dae86cda60a989ceec0 |
Provenance
File details
Details for the file bioversions-0.4.21-py3-none-any.whl.
File metadata
- Download URL: bioversions-0.4.21-py3-none-any.whl
- Upload date:
- Size: 49.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: twine/3.8.0 pkginfo/1.8.2 readme-renderer/34.0 requests/2.27.1 requests-toolbelt/0.9.1 urllib3/1.26.9 tqdm/4.63.0 importlib-metadata/4.11.3 keyring/23.5.0 rfc3986/2.0.0 colorama/0.4.4 CPython/3.10.2
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 | 121fe1529acf75b6dc7558b32cd47a717b71663df64ee5b4bf7d86f1e2929f4c |
|
| MD5 | d0d5cf5347ee778c799c3f28d66319e3 |
|
| BLAKE2b-256 | 723ffdc1ff0605ac3837c174930ed298f577b4f8d0aab4f20f7e8872c7e54b69 |
