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Verifier not accepting CUSTOM for HandoverType #83

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costero-e opened this issue May 26, 2023 · 4 comments
Closed

Verifier not accepting CUSTOM for HandoverType #83

costero-e opened this issue May 26, 2023 · 4 comments

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@costero-e
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costero-e commented May 26, 2023

When I execute Beacon Verifier and the schema being verified has the generic CUSTOM in HandoverType, the Verifier complains about the schema because CUSTOM doesn't match the OntologyTerm.json nomenclature when looking at beaconCommonComponents.json reference.
I would suggest to add CUSTOM like an Ontology, with a fake Ontology Id part. For example:

"HandoverType": {
"$ref": "./ontologyTerm.json",
"description": "Handover type, as an Ontology_term object with CURIE syntax for the `id` value. Use `CUSTOM:000001` for the `id` when no ontology is available.",
"examples": [
{
"id": "EFO:0004157",
"label": "BAM format"
},
{
"id": "CUSTOM:000001",
"label": "download genomic variants in .pgxseg file format"
}
]
},
@mbaudis
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mbaudis commented May 26, 2023

@costero-e Good point; I've changed our's to be CURIE-compliant (before they had additional : in their ids):

{
    "description": "retrieve data of the phenopackets matched by the query",
    "handoverType": {
        "id": "pgx:HO.phenopackets",
        "label": "Phenopackets"
    },
    "url": "https://progenetix.org/beacon/individuals?accessid=4410bfb5-0200-4311-9865-2b95e84efcd1&requestedSchema=phenopacket&variantsaccessid=a7fe2f25-5a26-47b3-a93c-cf2d4fcad90a"
},

pgx is actually a registered prefix.

@costero-e
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costero-e commented May 26, 2023

Yes, nice example, thank you @mbaudis . That's what I had to do for our Beacon to pass the Verifier (change CUSTOM to an ontology nomenclature). So is it already obvious that CUSTOM has to be an ontology and not the word "CUSTOM" itself or it would be better to make a PR and change CUSTOM for CUSTOM:01 or something like that?

mbaudis added a commit that referenced this issue Jun 10, 2023
This is a pure documentation change for the handover format. Addresses #83
@mbaudis
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mbaudis commented Jun 10, 2023

@costero-e please see 11312cd Also, IMO #82 should be merged @jrambla ...

@costero-e
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Ok, I addressed all the fixes from schema-urgent-fixes branch in this PR #85. If @jrambla and @mbaudis can you review and accept the PR we can move on.

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