adding sssom support - Githubissues

monarch-initiative / koza

Data transformation framework for LinkML data models

https://koza.monarchinitiative.org/

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

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adding sssom support #109

Closed glass-ships closed 1 year ago

glass-ships commented 1 year ago

addresses #108 fix #110

Tasks:

[x] Add SSSOM mapping functionality in Koza writers
[x] Still need to do something else
[x] Add testing (still need narrow match and broad match tests, but in another PR)
[x] Update documentation
[x] ~~Clarify existing examples (this can/should probably be a separate issue)~~ see #113
[ ] Add example w/ sssom config

glass-ships commented 1 year ago

Where does the config live that says: "use narrow matches for node replacement" vs "us only exact matches for node replacement"?

I... don't know if we have one, to be honest

glass-ships commented 1 year ago

Oh, so in response to the config question- I think for now we might just bring this in with only "exact match", and open it up to include narrow in another PR

matentzn commented 1 year ago

Restricting to exact sounds good as a first safe step, but you may loose quite a bit of relevant Information. I think it's worth making that configurable via some property like "merge_on_property".

glass-ships commented 1 year ago

nice one @hrshdhgd thanks for taking a look at that!!

glass-ships commented 1 year ago

is there anything preventing this from being merged as is?

glass-ships commented 1 year ago

There's a lot of formatting noise in this now, but the relevant changes are in:

model/config/sssom_config.py
tsv_writer
jsonl_writer
example usage in tests/unit/test_sssom_mapping.py