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cmungall / linkml-phenopackets

EXPERIMENTAL rendering of phenopackets in linkml
https://cmungall.github.io/linkml-phenopackets/
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include package information in the LinkML yaml for phenopackets.yaml #3

Open sierra-moxon opened 2 years ago

sierra-moxon commented 2 years ago

To convert to valid proto files, we need to include package designations in the header.

Something like: https://github.com/phenopackets/phenopacket-schema/blob/master/src/main/proto/phenopackets/schema/v2/phenopackets.proto

package org.phenopackets.schema.v2;

import "phenopackets/schema/v2/core/base.proto";
import "phenopackets/schema/v2/core/biosample.proto";
import "phenopackets/schema/v2/core/disease.proto";
import "phenopackets/schema/v2/core/interpretation.proto";
import "phenopackets/schema/v2/core/individual.proto";
import "phenopackets/schema/v2/core/measurement.proto";
import "phenopackets/schema/v2/core/medical_action.proto";
import "phenopackets/schema/v2/core/meta_data.proto";
import "phenopackets/schema/v2/core/pedigree.proto";
import "phenopackets/schema/v2/core/phenotypic_feature.proto";

Can we include this somehow in the metadata in LinkML or can we get it from the schemaname somehow?

sierra-moxon commented 2 years ago

One giant proto file is doable, then you don't need the imports, but this would break downstream software that is dependent on independent proto files per domain.

Maybe we just need a click parameter in LinkML protogen to reflect the yaml files in the generated proto files, with imports according to yaml file imports.