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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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Gocamgen reporting changes and deleting gpad_extensions_mapper #542

Closed dustine32 closed 3 years ago

dustine32 commented 3 years ago

This writes out the GPAD parser GO rules report in gpad2gocams along with adding an errors container for passing model translation error data (e.g. Couldn't get regulates relation from logical definition of a term) to the translation report.

Also, completely dropped gpad_extensions_mapper.py and refactored the remaining (though already commented out) gocamgen code that was referencing it. Removing the rigged is_cool conditional caused the enormous tab-shift as seen in the diff.

@kltm According to @dougli1sqrd, the code I just removed was initially causing some problems in testing of ontobio's static analysis tools. Do you have a way for us to test this is fixed now? Eric pasted the error results of some isolate following_rules command?

kltm commented 3 years ago

@dustine32 For this merge, I'll defer to @dougli1sqrd .

I wouldn't worry too much about the static code testing for the moment, but you can see some of the commands and where this is coming from over here: https://github.com/berkeleybop/bbops/issues/6