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obophenotype / ncbitaxon

Build for NCBITaxon
BSD 3-Clause "New" or "Revised" License
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Changing purls to GitHub and Release plan #36

Open matentzn opened 4 years ago

matentzn commented 4 years ago

We have now changed the primary release purls to github releases. However, I have no idea how to handle any old versions (in the OBO yaml config).. Should we create links to any old versions manually? If so, someone with access should provide a list of old version paths or, better yet, edit the ncbitaxon.yaml.

The second thing are the subsets; I just added them to the github release the same way I add the primary artefacts, hope that is ok.

Lastly, how often do we want ncbitaxon to be released properly? Monthly? Quarterly?

matentzn commented 4 years ago

FYI @jamesaoverton @wdduncan

matentzn commented 4 years ago

Another question: What about the mapping pipeline in the mapping subfolder?

jamesaoverton commented 4 years ago

The taxdmp.zip is updated every Friday, I think. They archive one per month. In my opinion, once per month is fine. I'd kinda like to add a link from the OWL to the exact source file, which would only make sense for monthly.

I'm fine with using GitHub Releases, except that it sounds like it took forever to upload the big files. Will that be a problem every time?

matentzn commented 4 years ago

My connection at home is super slow, that's all. I would like to script the release eventually, then it can be run from any server. I think its fine - certainly better then to point to the Jenkins job output, which is much more wobbly.. I agree with month per month, but I think once per two months would also be fine.. What do the other think?

balhoff commented 4 years ago

The version IRI doesn't resolve; is it meant to?

jamesaoverton commented 4 years ago

They didn’t resolve before, did they?

https://github.com/OBOFoundry/purl.obolibrary.org/blob/master/config/ncbitaxon.yml

It would be better if they did, though.

cmungall commented 4 years ago

no they never resolved.

cmungall commented 4 years ago

@matentzn looks like you are using the mi jenkins - not enough memory on the obolibrary.io one?

(given the manual steps not clear jenkins helps that much vs a release manager just doing this on their desktop/laptop...?)

btw I have python for wrapping the pushing to gh releases in mondo, been meaning to move to odk

matentzn commented 4 years ago

@cmungall If you would share the GitHub release script that would be great - I can adapt for our purposes (we would like it independent of ODK).

Yeah, seems like the process needs more memory (more memory than any potential release manager like @wdduncan would have on their laptop) - that's why its currently deployed on MI (it wont run regularly - needs to be triggered manually, so it does not consume resources). Is there hope to bump the obofoundry Jenkins to something more like 32 GB?

I added paths to version iris here:

However, at first I used the usual redirect for version IRIs with this /releases/ substring, but turns out ncbitaxon version IRI does not have that (http://purl.obolibrary.org/obo/ncbitaxon/2020-04-18/ncbitaxon.owl). Let me know if you want this changed (http://purl.obolibrary.org/obo/ncbitaxon/releases/2020-04-18/ncbitaxon.owl).