Add oaklib (libraries in path and runoak CLI) to ODK

[kltm]

This is a request to add OAK (ontology access kit) to the ODK.

https://github.com/INCATools/ontology-access-kit

Tagging @cmungall

[matentzn]

What is needed, just a PR on https://github.com/INCATools/ontology-development-kit/blob/master/requirements.txt.full?

[gouttegd]

It is on PyPI (despite what the README says) under the name oaklib, and it does not seem to have any non-Python dependencies, so yes, it shouldn’t require anything more than updating that file.

[matentzn]

Thank you @gouttegd :)

The tool does so many things, not sure if it has some undocumented dependencies, like dot or similar.

[gouttegd]

Argh, the viz command requires obographviz which requires Node.js!

(Runs away in fear)

[cmungall]

It is an optional dependency not required for many operations But point taken maybe time to either deploy using server less or implement the kgviz style sheet standard in python

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On Thu, Apr 21, 2022 at 3:55 AM Damien Goutte-Gattat < ***@***.***> wrote: Argh, the viz command requires obographviz <https://github.com/cmungall/obographviz> which requires Node.js! (*Runs away in fear*) — Reply to this email directly, view it on GitHub <#584 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOMSKHRSFMSAOUG7TALVGEXYJANCNFSM5T5WPIKQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[gouttegd]

Only for creating graph images, if I understand correctly?

But still, that may be useful and after all one point of the ODK is to provide the tools ontology editors/engineers might need, without asking them to deal with Python or Node packages.

I did a quick check, apparently adding Node.js, NPM, and the Node packages required by obographviz would add ~100 MB to the ODK. If there’s a need for OAK’s viz command, I’d be in favour of adding that to odkfull.

[cmungall]

you would need dot/gv too. But I imagine that would be useful in other scenarios too. So let's do it!

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On Thu, Apr 21, 2022 at 8:32 AM Damien Goutte-Gattat < ***@***.***> wrote: Only for creating graph images, if I understand correctly? But still, that may be useful and after all one point of the ODK is to provide the tools ontology editors/engineers might need, without asking them to deal with Python or Node packages. I did a quick check, apparently adding Node.js, NPM, and the Node packages required by obographviz would add ~100 MB to the ODK. If there’s a need for OAK’s viz command, I’d be in favour of adding that to odkfull. — Reply to this email directly, view it on GitHub <#584 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOP6TYNCCGV5Z2RMQZTVGFYHRANCNFSM5T5WPIKQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>