From 5a97fd46ea07e9913acf3d808630e691364a5a9d Mon Sep 17 00:00:00 2001
From: Lawrence Babb <lbabb@broadinstitute.org>
Date: Tue, 17 Sep 2024 22:24:44 -0400
Subject: [PATCH] fixed schema id refs & SM update

---
 schema/cat-vrs/core/cat-vrs-core-source.yaml     | 14 +++++++-------
 .../profiles/cat-vrs-profiles-source.yaml        | 16 ++++++++--------
 submodules/vrs                                   |  2 +-
 3 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/schema/cat-vrs/core/cat-vrs-core-source.yaml b/schema/cat-vrs/core/cat-vrs-core-source.yaml
index b0455f8..e26ad08 100644
--- a/schema/cat-vrs/core/cat-vrs-core-source.yaml
+++ b/schema/cat-vrs/core/cat-vrs-core-source.yaml
@@ -36,8 +36,8 @@ $defs:
           this categorical variant.
         items:
           oneOf:
-            - $ref: /ga4gh/schema/vrs/2.x/json/Variation
-            - $ref: /ga4gh/schema/gks-common/1.x/data-types/json/IRI
+            - $ref: /ga4gh/schema/vrs/2.0.0-connect.2024-09.1/json/Variation
+            - $ref: /ga4gh/schema/gks-common/1.0.0-connect.2024-09.1/data-types/json/IRI
       constraints:
         type: array
         ordered: false
@@ -77,9 +77,9 @@ $defs:
         description: 'MUST be "DefiningContextConstraint"'
       definingContext:
         oneOf:
-          - $ref: /ga4gh/schema/vrs/2.x/json/Variation
-          - $ref: /ga4gh/schema/vrs/2.x/json/Location
-          - $ref: /ga4gh/schema/gks-common/1.x/data-types/json/IRI
+          - $ref: /ga4gh/schema/vrs/2.0.0-connect.2024-09.1/json/Variation
+          - $ref: /ga4gh/schema/vrs/2.0.0-connect.2024-09.1/json/Location
+          - $ref: /ga4gh/schema/gks-common/1.0.0-connect.2024-09.1/data-types/json/IRI
       relations:
         type: array
         ordered: false
@@ -112,7 +112,7 @@ $defs:
       copies:
         oneOf:
           - type: integer
-          - $ref: /ga4gh/schema/vrs/2.x/json/Range
+          - $ref: /ga4gh/schema/vrs/2.0.0-connect.2024-09.1/json/Range
     required:
       - copies
 
@@ -129,7 +129,7 @@ $defs:
         default: CopyChangeConstraint
         description: 'MUST be "CopyChangeConstraint"'
       copyChange:
-        $ref: /ga4gh/schema/gks-common/1.x/data-types/json/Coding
+        $ref: /ga4gh/schema/gks-common/1.0.0-connect.2024-09.1/data-types/json/Coding
         items:
           properties:
             code:
diff --git a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml b/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml
index 8734c1f..e14c279 100644
--- a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml
+++ b/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml
@@ -19,7 +19,7 @@ $defs:
       constraints:
         contains:
           allOf:
-            - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint"
+            - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/DefiningContextConstraint"
             - type: object
               properties:
                 relations:
@@ -35,7 +35,7 @@ $defs:
       that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).
     allOf:
       - $ref: "#/$defs/ProteinSequenceConsequenceProperties"
-      - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant"
+      - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/CategoricalVariant"
 
   CanonicalAlleleProperties:
     type: object
@@ -46,7 +46,7 @@ $defs:
       constraints:
         contains:
           allOf:
-            - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint"
+            - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/DefiningContextConstraint"
             - type: object
               properties:
                 relations:
@@ -65,7 +65,7 @@ $defs:
       across different genome assemblies and associated cDNA transcript representations.
     allOf:
       - $ref: "#/$defs/CanonicalAlleleProperties"
-      - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant"
+      - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/CategoricalVariant"
 
   CategoricalCnvProperties:
     type: object
@@ -77,7 +77,7 @@ $defs:
         allOf:
           - contains:
               allOf:
-                - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint"
+                - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/DefiningContextConstraint"
                 - type: object
                   properties:
                     relations:
@@ -85,8 +85,8 @@ $defs:
                         const: sequence_liftover
           - contains:
               anyOf:
-                - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint"
-                - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint"
+                - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/CopyCountConstraint"
+                - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/CopyChangeConstraint"
 
   CategoricalCnv:
     maturity: draft
@@ -94,4 +94,4 @@ $defs:
       A representation of the constraints for matching knowledge about CNVs.
     allOf:
       - $ref: "#/$defs/CategoricalCnvProperties"
-      - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant"
\ No newline at end of file
+      - $ref: "/ga4gh/schema/cat-vrs/1.0.0-connect.2024-09.1/core/json/CategoricalVariant"
\ No newline at end of file
diff --git a/submodules/vrs b/submodules/vrs
index b277adb..37b80cc 160000
--- a/submodules/vrs
+++ b/submodules/vrs
@@ -1 +1 @@
-Subproject commit b277adb4f69da056db6172fcb128c8234668110d
+Subproject commit 37b80cc27e9caecce0f1fcc4dbb06755a5f33a9b