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INCATools / ontology-access-kit

Ontology Access Kit: A python library and command line application for working with ontologies
https://incatools.github.io/ontology-access-kit/
Apache License 2.0
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Externalize OntoPortal client functions (e.g., for BioPortal, AgroPortal, EcoPortal) #168

Open cthoyt opened 2 years ago

cthoyt commented 2 years ago

I have previous written a harness for accessing the API for OntoPortal instances in the Bioregistry project. I spun that code out into a clean project at https://github.com/cthoyt/ontoportal-client. I'd be happy to move that to a different namespace if other people want to contribute to it.

pkalita-lbl commented 2 years ago

Hey @cthoyt I took a look at ontoportal-client and it seems like it could drop in pretty easily. I did notice that there was a recent change to make the client name a class variable. It turns out I think that would actually help make the integration into OAK a bit easier. Wondering if you have plans to make a release with those changes any time in the near future?

cthoyt commented 2 years ago

Yes I can drop a release anytime, it’s quite easy with the Tox configuration

pkalita-lbl commented 2 years ago

Here's a draft PR: https://github.com/INCATools/ontology-access-kit/pull/204 (still have some tests to fix!)

Having the name class variable would just simply this bit here. OntoPortalInterface could use that name for the API key lookup instead of having implementation classes define it in addition to the OntoPortalClient class to use.

It's a fairly minor difference so if you want to make a release I'll gladly pick up the new version, otherwise I don't see much harm in updating it later.

cmungall commented 2 years ago

thanks!

reopening as we still only using the inner layer of ontoportal-client (the bit that returns json).

there is still more to be done to move some parts of oaklib.impl.ontoportal into ontoportal-client, see:

https://github.com/cthoyt/ontoportal-client/issues/3

but if you like you can reclose this and open more specific issues, e.g for different components like annotator/search/ancestors