diff --git a/bin/beacon_yaml2md.pl b/bin/beacon_yaml2md.pl index 96e59c17..9fc75fe5 100755 --- a/bin/beacon_yaml2md.pl +++ b/bin/beacon_yaml2md.pl @@ -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} ) { $data->{properties} = diff --git a/bin/deref_schemas/obj/CopyNumber.yaml b/bin/deref_schemas/obj/CopyNumber.yaml index 0ac7b7d7..37906e03 100644 --- a/bin/deref_schemas/obj/CopyNumber.yaml +++ b/bin/deref_schemas/obj/CopyNumber.yaml @@ -1,4 +1,4 @@ --- CopyNumber: - properties: '[VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber)' + properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber)' type: allOf diff --git a/docs/schemas-md/obj/CopyNumber.md b/docs/schemas-md/obj/CopyNumber.md index f4738d0f..88e7a5ee 100644 --- a/docs/schemas-md/obj/CopyNumber.md +++ b/docs/schemas-md/obj/CopyNumber.md @@ -1,3 +1,3 @@ |Term | Description | Type | Properties | Example | Enum| | ---| ---| ---| ---| ---| --- | -| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://raw.githubusercontent.com/ga4gh/vrs/1.2/schema/vrs.json#/definitions/CopyNumber) | NA | NA| +| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber) | NA | NA| diff --git a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json index 5ec02a7f..394bef5c 100644 --- a/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json +++ b/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json @@ -272,7 +272,7 @@ "type": "string" }, "location": { - "$ref": "https://raw.githubusercontent.com/ga4gh/vrs/main/schema/vrs.json#/definitions/Location" + "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location" }, "referenceBases": { "description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.", @@ -557,10 +557,10 @@ "variation": { "oneOf": [ { - "$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" diff --git a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml index 96c3dbff..b5e5cc9e 100644 --- a/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml +++ b/models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml @@ -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: >- @@ -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