updating gpi parsing to allow for version 2.0. Tests for changes

biolink / ontobio

python library for working with ontologies and ontology associations

https://ontobio.readthedocs.io/en/latest/

BSD 3-Clause "New" or "Revised" License

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updating gpi parsing to allow for version 2.0. Tests for changes #509

Closed dougli1sqrd closed 3 years ago

dougli1sqrd commented 3 years ago

This change allows parsers to parse GPI 2.0 as well when processing GPAD/GAF. Currently this is just for reading, and does not write GPI 2.0 yet.

The changes are tested, I plan on doing some more tests replicating the pipeline to make sure everything is good.

kltm commented 3 years ago

A quick look seems to reveal nothing not expected, with tests included. Seems good to me. Would like input from @dustine32

dougli1sqrd commented 3 years ago

@dustine32 and I looked through some files we ran using this PR to detect any anomolies in gpad 2.0 parsing and output, as well as the pipeline validate.py script and are satisfied that this is working properly.