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Externalize OLS implementation#270

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cmungall merged 9 commits into
INCATools:mainfrom
cthoyt:ols-client
Sep 13, 2022
Merged

Externalize OLS implementation#270
cmungall merged 9 commits into
INCATools:mainfrom
cthoyt:ols-client

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@cthoyt
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@cthoyt cthoyt commented Sep 9, 2022

This PR switches out interaction with the EBI's ontology lookup service using the ols-client package, similarly to how we externalized some functionality for OntoPortal instances in #204.

Further, this enables interaction with alternative OLS instances like the TIB Hannover one. Probably of interest to @StroemPhi.

This PR switches out interaction with the EBI's ontology lookup service using the `ols-client` package, which enables interaction with alternative OLS instances like the TIB Hannover one. Probably of interest to @StroemPhi
@StroemPhi
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Oooh cool! Thank you @cthoyt, am definitely interested!
Although I must admit, I didn't have the time yet to actually test OAK. I only read the paper draft and thus only have a sense of how useful it can be. I did bring this up to Oliver and our devs, but will propably need to carve out some more prio points for this somehow. ;)

@cmungall
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Thanks @cthoyt this is awesome! I have no idea why that 3.10 test is failing

@StroemPhi if you can install a python module you can be doing awesome things on the command line in seconds, ping me on slack with what kind of thing you’d find most useful

@cmungall
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I think rebase should fix (gets rid of the problematic switch on the nx code) but odd how it got into this state in the first place

@cmungall cmungall merged commit be8c773 into INCATools:main Sep 13, 2022
@cthoyt cthoyt deleted the ols-client branch September 13, 2022 20:39
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3 participants