VRS references from 1.2 => 1.3

The Beacon schema for genomic allows 3 options:

* VRS MolecularVariation
* VRS SystemicVariation
* Beacon LegacyVariation (which adopts the VRS location object but uses separate definitions otherwise)

Unfortunately, during Beacon v2 approval only VRS 1.2. was available and then explicitly referenced in the schema. It fast superseded by 1.3 which allows a *much* better definition of "Systemic Variations" such as CNV.

This PR changes all VRS references from 1.2 => 1.3 and should be very welcome to implementers (1.3. has been the longstanding standard now until the future 2.x is out; in fact, the `bycon` based implementations such as progenetix.org have been using it for their Beacons for ~2years).

bin/beacon_yaml2md.pl

@@ -729,9 +729,9 @@ sub add_properties_vrs {
     my ( $property, $data ) = @_;
     my %url = (
         'SequenceExpression' =>
-'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/',
+'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/',
         'CopyNumber' =>
-'https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/'
+'https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/'
     );
     if ( exists $url{$property} ) {
         $data->{properties} =

bin/deref_schemas/obj/CopyNumber.yaml

@@ -1,4 +1,4 @@
 ---
 CopyNumber:
-  properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber)'
+  properties: '[VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber)'
   type: allOf

docs/schemas-md/obj/CopyNumber.md

@@ -1,3 +1,3 @@
 |Term | Description | Type | Properties | Example | Enum|
 | ---| ---| ---| ---| ---| --- |
-| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/CopyNumber) | NA | NA|
+| CopyNumber | NA | allOf | [VRS definition for CopyNumber](https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/CopyNumber) | NA | NA|

models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json

@@ -1,5 +1,5 @@
 {
-    "$comment": "version: ga4gh-beacon-variant-v2.0.0",
+    "$comment": "version: ga4gh-beacon-variant-v2.1.0",
     "$defs": {
         "CaseLevelVariant": {
             "description": "",
@@ -272,7 +272,7 @@
                     "type": "string"
                 },
                 "location": {
-                    "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location"
+                    "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location"
                 },
                 "referenceBases": {
                     "description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n  as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n  trimmed, inserted sequence being indicated in `AlternateBases`.",
@@ -557,10 +557,10 @@
         "variation": {
             "oneOf": [
                 {
-                    "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation"
+                    "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation"
                 },
                 {
-                    "$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation"
+                    "$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation"
                 },
                 {
                     "$ref": "#/$defs/LegacyVariation"

models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml

@@ -1,6 +1,6 @@
 $schema: https://json-schema.org/draft/2020-12/schema
 title: Genomic Variation
-$comment: 'version: ga4gh-beacon-variant-v2.0.0'
+$comment: 'version: ga4gh-beacon-variant-v2.1.0'
 description: >-
   Schema for a genomic variant entry.
 type: object
@@ -10,8 +10,8 @@ required:
 properties:
   variation:
     oneOf:
-      - $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: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation
+      - $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation
       - $ref: '#/$defs/LegacyVariation'
   variantInternalId:
     description: >-
@@ -51,7 +51,7 @@ $defs:
       - location
     properties:
       location:
-        $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location
+        $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location
       variantType:
         description: >-
           The `variantType` declares the nature of the variation in relation