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phenopackets / phenopacket-schema

Repository for the GA4GH phenopacket schema
https://phenopacket-schema.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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trouble running protobuf-jsonschema with v2 paths #319

Open cmungall opened 3 years ago

cmungall commented 3 years ago

I'm trying protobuf-jsonschema, it used to work on v1 but it's having issues with paths..

I don't know if protobuf-jsonschema isn't following the spec or it's some configuration

I'm trying to follow the structure but am a bit flummoxed by symlinks like this:

https://github.com/phenopackets/phenopacket-schema/blob/v2/src/main/proto/ga4gh/vrs/v1/vrs.proto

[sorry if this not so helpful about to head out, wanted to make an issue before I forgot, sorry about lack of detail]

pnrobinson commented 3 years ago

Please put validation issues in this repo https://github.com/phenopackets/phenopacket-validator I am experimenting with code to create phenopackets and with no claims for beauty here is a repo that creates rare, cancer, and COVID phenopackets that can be used for the phenopacket validator https://github.com/pnrobinson/phepagen I have finished about 80% of the JSON Schema by hand, and everything seems to be working except for the action field of medicalAction (https://phenopacket-schema.readthedocs.io/en/v2/medical-action.html). For some reason the oneOf is not being captured by the JSON Schema, I cannot figure out where the problem is.

cmungall commented 3 years ago

I was able to find vrs.proto here:

https://github.com/phenopackets/phenopacket-schema/issues/219#issuecomment-818665809