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VRS references fix #185

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merged 1 commit into from
Nov 24, 2024
Merged

VRS references fix #185

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4 changes: 2 additions & 2 deletions bin/beacon_yaml2md.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -729,9 +729,9 @@ sub add_properties_vrs {
my ( $property, $data ) = @_;
my %url = (
'SequenceExpression' =>
'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/',
'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/',
'CopyNumber' =>
'https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/'
'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/'
);
if ( exists $url{$property} ) {
$data->{properties} =
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2 changes: 1 addition & 1 deletion bin/deref_schemas/obj/CopyNumber.yaml
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@@ -1,4 +1,4 @@
---
CopyNumber:
properties: '[VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber)'
properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber)'
type: allOf
2 changes: 1 addition & 1 deletion docs/schemas-md/obj/CopyNumber.md
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Original file line number Diff line number Diff line change
@@ -1,3 +1,3 @@
|Term | Description | Type | Properties | Example | Enum|
| ---| ---| ---| ---| ---| --- |
| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber) | NA | NA|
| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber) | NA | NA|
6 changes: 3 additions & 3 deletions models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
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Expand Up @@ -272,7 +272,7 @@
"type": "string"
},
"location": {
"$ref": "https://raw.githubusercontent.com/ga4gh/vrs/main/schema/vrs.json#/definitions/Location"
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location"
},
"referenceBases": {
"description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.",
Expand Down Expand Up @@ -557,10 +557,10 @@
"variation": {
"oneOf": [
{
"$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/MolecularVariation"
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation"
},
{
"$ref": "https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/SystemicVariation"
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation"
},
{
"$ref": "#/$defs/LegacyVariation"
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6 changes: 3 additions & 3 deletions models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
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Expand Up @@ -10,8 +10,8 @@ required:
properties:
variation:
oneOf:
- $ref: https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/MolecularVariation
- $ref: https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/SystemicVariation
- $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation
- $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation
- $ref: '#/$defs/LegacyVariation'
variantInternalId:
description: >-
Expand Down Expand Up @@ -51,7 +51,7 @@ $defs:
- location
properties:
location:
$ref: https://raw.githubusercontent.com/ga4gh/vrs/main/schema/vrs.json#/definitions/Location
$ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location
variantType:
description: >-
The `variantType` declares the nature of the variation in relation
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