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brain-bican / models

BICAN data models
https://brain-bican.github.io/models/
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Green Table Additions #20

Closed puja-trivedi closed 2 months ago

satra commented 9 months ago

shouldn't this only add the yaml file? the rest should be auto generated on merge.

puja-trivedi commented 9 months ago

@satra - if you look at the workflow it is generated on "push" as well as "pull request". Although it might make more sense to change it to "merge". 

name: generating other formats

on:
  push:
  pull_request:
satra commented 9 months ago

sorry i had forgotten. the conflicts misled me. yes, it would be good to test that the autogeneration works, but the actual autogeneration could happen when ready to merge, or when a label is set on the PR.

djarecka commented 8 months ago

@puja-trivedi - perhaps you didn't pull the changes to autogenerated formats and that's why you have the conflicts?

satra commented 8 months ago

@puja-trivedi - is this the latest version of the green sheets/minimal metadata release? (and could you please fix the conflicts?)

puja-trivedi commented 8 months ago

@puja-trivedi - is this the latest version of the green sheets/minimal metadata release? (and could you please fix the conflicts?)

Is there a specific date associated with the latest version of the green table you are thinking of? I haven't looked at the green table in a few weeks (ever since I created the PR). I am waiting to update the model further until Patrick merges his PR since I have been told that the tables on that repo are the "truth" and I should use those from now on.

satra commented 8 months ago

I am waiting to update the model further until Patrick merges his PR

no you should use patrick's PR, but don't wait for it to be merged. just use that info to update this. note the commit that you are working off of, and any changes relative to that commit can be incorporated later.

puja-trivedi commented 8 months ago

@satra - In last week's biolink meeting, Pam suggested that we could use Biolink:Procedure for the orange boxes and Biolink:MaterialSample for the purple boxes. Would you be able to take a look at these classes? I wanted to run it by you before I update the model.

satra commented 8 months ago

go for it.

puja-trivedi commented 8 months ago

the checks are currently failing due to a linkml issue.

Update: All checks are passing now (using the advice provided on the issue). Had to add "linkml-runtime == 1.6.0" to pyproject.toml temporarily to fix issue.