Issue #597 - remove and refactor CNVs

schema/vrs/def/CopyNumberChange.rst

@@ -23,7 +23,7 @@ An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a
 
 **Information Model**
 
-Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
+Some CopyNumberChange attributes are inherited from :ref:`Variation`.
 
 .. list-table::
    :class: clean-wrap
@@ -80,16 +80,16 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
       - :ref:`Expression`
       - 0..m
       - 
-   *  - location
-      - 
-      - :ref:`iriReference` | :ref:`Location`
-      - 1..1
-      - A location for which the number of systemic copies is described.
    *  - type
       - 
       - string
       - 1..1
       - MUST be "CopyNumberChange"
+   *  - location
+      - 
+      - :ref:`iriReference` | :ref:`Location`
+      - 1..1
+      - The location of the subject of the copy change.
    *  - copyChange
       - 
       - :ref:`Coding`

schema/vrs/def/CopyNumberCount.rst

@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. note:: This data class is at a **trial use** maturity level and may \
+    change in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**
@@ -23,7 +23,7 @@ The absolute count of discrete copies of a :ref:`Location` or :ref:`Gene`, withi
 
 **Information Model**
 
-Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
+Some CopyNumberCount attributes are inherited from :ref:`Variation`.
 
 .. list-table::
    :class: clean-wrap
@@ -80,16 +80,16 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
       - :ref:`Expression`
       - 0..m
       - 
-   *  - location
-      - 
-      - :ref:`iriReference` | :ref:`Location`
-      - 1..1
-      - A location for which the number of systemic copies is described.
    *  - type
       - 
       - string
       - 1..1
       - MUST be "CopyNumberCount"
+   *  - location
+      - 
+      - :ref:`iriReference` | :ref:`Location`
+      - 1..1
+      - The location of the subject of the copy count.
    *  - copies
       - 
       - integer | :ref:`Range`

schema/vrs/json/CopyNumberChange

@@ -56,6 +56,12 @@
             "$ref": "/ga4gh/schema/vrs/2.x/json/Expression"
          }
       },
+      "type": {
+         "type": "string",
+         "const": "CopyNumberChange",
+         "default": "CopyNumberChange",
+         "description": "MUST be \"CopyNumberChange\""
+      },
       "location": {
          "oneOf": [
             {
@@ -65,13 +71,7 @@
                "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
-         "description": "A location for which the number of systemic copies is described."
-      },
-      "type": {
-         "type": "string",
-         "const": "CopyNumberChange",
-         "default": "CopyNumberChange",
-         "description": "MUST be \"CopyNumberChange\""
+         "description": "The location of the subject of the copy change."
       },
       "copyChange": {
          "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding",

schema/vrs/json/CopyNumberCount

@@ -3,7 +3,7 @@
    "$id": "https://w3id.org/ga4gh/schema/vrs/2.x/json/CopyNumberCount",
    "title": "CopyNumberCount",
    "type": "object",
-   "maturity": "draft",
+   "maturity": "trial use",
    "ga4ghDigest": {
       "keys": [
          "copies",
@@ -56,6 +56,12 @@
             "$ref": "/ga4gh/schema/vrs/2.x/json/Expression"
          }
       },
+      "type": {
+         "type": "string",
+         "const": "CopyNumberCount",
+         "default": "CopyNumberCount",
+         "description": "MUST be \"CopyNumberCount\""
+      },
       "location": {
          "oneOf": [
             {
@@ -65,13 +71,7 @@
                "$ref": "/ga4gh/schema/gks-core/1.x/json/iriReference"
             }
          ],
-         "description": "A location for which the number of systemic copies is described."
-      },
-      "type": {
-         "type": "string",
-         "const": "CopyNumberCount",
-         "default": "CopyNumberCount",
-         "description": "MUST be \"CopyNumberCount\""
+         "description": "The location of the subject of the copy count."
       },
       "copies": {
          "oneOf": [

schema/vrs/vrs-source.yaml

@@ -191,30 +191,15 @@ $defs:
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # SystemicVariation
 
-  CopyNumber:
-    maturity: draft
-    ga4ghDigest:
-      keys:
-        - location
-    inherits: SystemicVariation
-    description: >-
-      A measure of the copies of a :ref:`Location` within a system (e.g. genome, cell, etc.)
-    heritableProperties:
-      location:
-        oneOf:
-          - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference"
-          - $ref: "#/$defs/Location"
-        description: >-
-          A location for which the number of systemic copies is described.
-    heritableRequired: [ "location" ]
-
+
   CopyNumberCount:
-    maturity: draft
+    maturity: trial use
     ga4ghDigest:
       keys:
+        - location
         - copies
       prefix: CN
-    inherits: CopyNumber
+    inherits: SystemicVariation
     type: object
     description: >-
       The absolute count of discrete copies of a :ref:`Location` or :ref:`Gene`,
@@ -226,21 +211,28 @@ $defs:
         default: "CopyNumberCount"
         description: >-
           MUST be "CopyNumberCount"
+      location:
+        oneOf:
+          - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference"
+          - $ref: "#/$defs/Location"
+        description: >-
+          The location of the subject of the copy count.
       copies:
         oneOf:
           - type: integer
           - $ref: "#/$defs/Range"
         description: >-
           The integral number of copies of the subject in a system
-    required: [ "copies" ]
+    required: [ "location", "copies" ]
 
   CopyNumberChange:
     maturity: draft
     ga4ghDigest:
       keys:
+        - location
         - copyChange
       prefix: CX
-    inherits: CopyNumber
+    inherits: SystemicVariation
     type: object
     description: >-
       An assessment of the copy number of a :ref:`Location` or a :ref:`Gene` within a system (e.g. genome, cell,
@@ -252,13 +244,19 @@ $defs:
         default: "CopyNumberChange"
         description: >-
           MUST be "CopyNumberChange"
+      location:
+        oneOf:
+          - $ref: "/ga4gh/schema/gks-core/1.x/json/iriReference"
+          - $ref: "#/$defs/Location"
+        description: >-
+          The location of the subject of the copy change.
       copyChange:
         $ref: "/ga4gh/schema/gks-core/1.x/json/Coding"
         description: >-
           MUST be a :ref:`Coding` representing one of "EFO:0030069" (complete genomic loss), "EFO:0020073" (high-level loss),
           "EFO:0030068" (low-level loss), "EFO:0030067" (loss), "EFO:0030064" (regional base ploidy),
           "EFO:0030070" (gain), "EFO:0030071" (low-level gain), "EFO:0030072" (high-level gain).
-    required: [ "copyChange" ]
+    required: [ "location", "copyChange" ]
 
   # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   # Locations