Create end-user GAF validation SOP / tooling

[kltm]

This is coming out of a meeting and email thread with Markus K.

The given file is currently at:
http://skyhook.berkeleybop.org/ecocyc-2024-04-19-upstream.gaf.gz

The idea would be to either provide a "simple" SOP for using ontobio to generate reports on a GAF locally or create a forking template to do the same w/GHA resources.

Tagging @pgaudet

[kltm]

This is an easy recipe to get local reports, if you have docker available:

Get image and setup environment:

docker run -it geneontology/dev-base:ea32b54c822f7a3d9bf20c78208aca452af7ee80_2023-08-28T125255 bash
mkdir -p /opt/go-site
cd /opt/ && git clone -b master https://github.com/geneontology/go-site.git
cd /opt/go-site/scripts && pip3 install -r requirements.txt
cd /opt/go-site/pipeline && pip3 install -r requirements.txt

Get files:

cd /tmp
wget http://snapshot.geneontology.org/ontology/go.json
wget http://skyhook.berkeleybop.org/ecocyc-2024-04-19-upstream.gaf.gz
gunzip ecocyc-2024-04-19-upstream.gaf.gz

Run code and produce reports; this produces a report.md file and a report.json file:

ontobio-parse-assocs.py --resource go.json --file ecocyc-2024-04-19-upstream.gaf --report-md report.md --report-json report.json --rule all validate

More reading on ontobio tool usage: https://ontobio.readthedocs.io/en/latest/commandline.html#go-rules .