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adding ccn2 schema and restructure the repo #1
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@djarecka - can this be updated to using slots (see: #1) also can you add a github workflow that runs cc: @sooyounga |
@satra - after moving to slots and removing I understood from the biolink guide that if i add I will work on tests now. |
I believe And as I mentioned in the slack, seems like to official guidance from linkml is that we use a different naming convention: https://linkml.io/linkml/schemas/linter.html#standard-naming |
regarding validate, this would be more on the test side perhaps. |
In the guide you sent it was I have to say that it's not clear to me why I would like to use |
looks like biolink is using the python API, so will write the tests using it |
@satra - I've added some simple tests, we should have more, but perhaps we can start from here. I'm planning to create a GA action for this, but I want to ask what else would you want as a GA? During the call you mentioned about publishing the json file automatically, but I'm not sure where do you want to publish. I took from biolink structure and created dirs for json and python versions, but I don't think they are creating these automatically... |
if indeed they don't have full automations, what do you think, should we generate the schema and models in a separate repo or this one? GA would allow us to write to a different repo on merge into master. so this would only contain yaml files, and perhaps GA to generate docs. |
perhaps I was wrong and they do generate it in GA, now when I'm checking their workflows it looks like they are adding some artifacts in the repo: https://github.com/biolink/biolink-model/blob/master/.github/workflows/regenerate-artifacts.yml#L45 I thought that there had different day of modification last time I checked, but now it looks like they were all changed 6h ago... I can try to add something similar tomorrow, will just focus on json and python for now |
@satra - do you have any linting rules you want to add? https://linkml.io/linkml/schemas/linter.html for now I just disabled the naming warnings, since we don't want to use it. I was also thinking a bit more about the organization, and now I think that perhaps pydantic schemas, the ones that will be mostly used in other libraries, should be pushed to a separate repo. I understand that the repo with the pydantin schemas would be published in PyPI? |
the original schema from: https://github.com/brain-bican/CCN2/blob/main/src/schema/schema.json
A draft of linkml file with some issues/questions (search "todo").
ccn.json created with:
gen-json-schema ccn.yaml > ccn.json
EDIT