Update vrs (#49)

* update MSP / submodule
* update submodule to vrs/common ballot.

.requirements.txt

@@ -2,6 +2,6 @@ pytest
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2
 pyyaml
-ga4gh.gks.metaschema==0.3.0b11
+ga4gh.gks.metaschema==0.3.0b12
 jsonschema
 referencing

schema/cat-vrs/cat-vrs-source.yaml

@@ -20,8 +20,9 @@ $defs:
 
   CategoricalVariation:
     inherits: gks.core-im:DomainEntity
+    maturity: draft
     description: >-
-      A representation of a categorically-defined domain for variation, in which individual 
+      A representation of a categorically-defined domain for variation, in which individual
       contextual variation instances may be members of the domain.
     oneOf:
       - $ref: "#/$defs/CanonicalAllele"
@@ -37,19 +38,19 @@ $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-ballot.2024-08.1/json/Variation"
+            - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI"
 
   ProteinSequenceConsequence:
-    maturity: draft
     type: object
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
       A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature
       of the genetic code, there are often several genomic changes that can cause a protein sequence consequence.
       The protein sequence consequence, like a :ref:`CanonicalAllele`, is defined by an
-      `Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#variation>` that is representative of a collection
-      of congruent Protein Alleles that share the same altered codon(s).
+      `Allele <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#>`
+      that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).
     properties:
       type:
         extends: type
@@ -58,21 +59,21 @@ $defs:
         description: 'MUST be "ProteinSequenceConsequence"'
       definingContext:
         oneOf:
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Allele"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele"
+          - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI"
         description: >-
-          The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
-          object that is congruent with (projects to the same codons) as alleles on other protein reference 
+          The `Allele <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#>`_
+          object that is congruent with (projects to the same codons) as alleles on other protein reference
           sequences.
     required:
       - definingContext
 
   CanonicalAllele:
-    maturity: draft
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
-      A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#variation>` 
-      that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid 
+      A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#>`_
+      that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid
       change on different underlying reference sequences. Congruent representations of an Allele often exist
       across different genome assemblies and associated cDNA transcript representations.
     type: object
@@ -84,25 +85,25 @@ $defs:
         description: 'MUST be "CanonicalAllele"'
       definingContext:
         oneOf:
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Allele"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Allele"
+          - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI"
         description: >-
-          The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_
+          The `Allele <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#>`_
           object that is congruent with variants on alternate reference sequences.
     required:
       - definingContext
 
   CategoricalCnv:
-    maturity: draft
     type: object
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
-      A categorical variation domain is defined first by a sequence derived from a canonical `Location 
-      <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#Location>`_ , which is representative of 
-      a collection of congruent Locations. The change or count of this sequence is also described, either
-      by a numeric value (e.g. "3 or more copies") or categorical representation (e.g. "high-level gain"). 
-      Categorical CNVs may optionally be defined by rules specifying the location match characteristics for 
-      member CNVs.
+      A categorical variation domain is defined first by a sequence derived from a canonical `SequenceLocation
+      <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/LocationAndReference/SequenceLocation.html>`_ ,
+      which is representative of a collection of congruent Locations. The change or count of this sequence is
+      also described, either by a numeric value (e.g. "3 or more copies") or categorical representation
+      (e.g. "high-level gain"). Categorical CNVs may optionally be defined by rules specifying the location
+      match characteristics for member CNVs.
     properties:
       type:
         extends: type
@@ -111,43 +112,43 @@ $defs:
         description: 'MUST be "CategoricalCnv"'
       location:
         oneOf:
-          - $ref: "/ga4gh/schema/vrs/2.x/json/SequenceLocation"
-          - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/SequenceLocation"
+          - $ref: "/ga4gh/schema/gks-common/1.0.0-ballot.2024-08.1/data-types/json/IRI"
         description: >-
-          A `VRS Location <https://vrs.ga4gh.org/en/2.x/concepts/location/SequenceLocation.html>`_
-          object that represents a sequence derived from that location, and is congruent with locations 
+          A `SequenceLocation <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/LocationAndReference/SequenceLocation.html>`_
+          object that represents a sequence derived from that location, and is congruent with locations
           on alternate reference sequences.
       locationMatchCharacteristic:
         type: string
         enum: ['exact', 'partial', 'subinterval', 'superinterval']
         description: >-
-          The characteristics of a valid match between a contextual CNV location (the query) and the 
-          Categorical CNV location (the domain), when both query and domain are represented on the same 
-          reference sequence. An `exact` match requires the location of the query and domain to be identical. 
+          The characteristics of a valid match between a contextual CNV location (the query) and the
+          Categorical CNV location (the domain), when both query and domain are represented on the same
+          reference sequence. An `exact` match requires the location of the query and domain to be identical.
           A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match
           requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue
           of overlap between the query and domain.
       copyChange:
         type: string
         enum: [ "EFO:0030069", "EFO:0020073", "EFO:0030068", "EFO:0030067", "EFO:0030064", "EFO:0030070", "EFO:0030071", "EFO:0030072" ]
         description: >-
-          A representation of the change in copies of a sequence in a system. MUST be 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" 
+          A representation of the change in copies of a sequence in a system. MUST be 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).
       copies:
         oneOf:
           - type: integer
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
         description: >-
           The integral number of copies of the subject in a system.
     required:
       - location
 
   DescribedVariation:
-    maturity: draft
     type: object
     inherits: CategoricalVariation
+    maturity: draft
     description: >-
       Some categorical variation concepts are supported by custom nomenclatures or text-descriptive
       representations for which a categorical variation model does not exist. DescribedVariation is
@@ -162,12 +163,12 @@ $defs:
       label:
         extends: label
         description: >-
-          A primary label for the categorical variation. This required property should provide a 
+          A primary label for the categorical variation. This required property should provide a
           short and descriptive textual representation of the concept.
       description:
         extends: description
         description: >-
-          A textual description of the domain of variation that should match the categorical 
+          A textual description of the domain of variation that should match the categorical
           variation entity.
     required:
       - label
@@ -221,12 +222,12 @@ $defs:
 
 
   NumberCount:
-    maturity: draft
     # ga4ghDigest:
     #   keys:
     #     - numberCount
     type: object
     # inherits: QuantityVariance
+    maturity: draft
     description: >-
       The absolute count of a discrete assayable unit (e.g. chromosome, gene, or sequence).
     properties:
@@ -239,19 +240,19 @@ $defs:
       count:
         oneOf:
           - type: integer
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
         description: >-
           The integral quantity or quantity range of the subject in a system
     required: [ "count" ]
 
 
   NumberChange:
-    maturity: draft
     # ga4ghDigest:
     #   keys:
     #     - numberChange
     #   prefix: CX
     type: object
+    maturity: draft
     description: >-
       A quantitative assessment of a unit within a system (e.g. genome, cell,
       etc.) relative to a baseline quantity.
@@ -265,7 +266,7 @@ $defs:
       change:
         oneOf:
           - type: integer
-          - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+          - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
           - copyChange:
             type: string
             enum: [ "EFO:0030069", "EFO:0020073", "EFO:0030068", "EFO:0030067", "EFO:0030064", "EFO:0030070",
@@ -278,9 +279,9 @@ $defs:
         required: [ "change" ]
 
   QuantityVariance:
-    maturity: draft
     type: object
     # inherits: NumberCount
+    maturity: draft
     description: >-
       The Quantity Variance class captures one axis of variation in the generalized model of categorical
       variation.  It is used to model quantitative measure changes in a given biological level of
@@ -322,7 +323,7 @@ $defs:
   #     copies:
   #       oneOf:
   #         - type: integer
-  #         - $ref: "/ga4gh/schema/vrs/2.x/json/Range"
+  #         - $ref: "/ga4gh/schema/vrs/2.0.0-ballot.2024-08.1/json/Range"
   #       description: >-
   #         The integral number of copies of the subject in a system.
   #   required:
@@ -340,6 +341,7 @@ $defs:
 
   CategoricalVariant:
     inherits: gks.core-im:DomainEntity
+    maturity: draft
     description: >-
       A top-level representation of a categorically-defined domain for variation across one or multiple biological levels in which individual contextual variants may be members of the domain.
     # type: object

schema/cat-vrs/def/CanonicalAllele.rst

@@ -1,6 +1,6 @@
 **Computational Definition**
 
-A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#variation>`  that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid  change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.
+A canonical allele is defined by an `Allele <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#>`_ that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.
 
 **Information Model**
 
@@ -33,22 +33,22 @@ Some CanonicalAllele attributes are inherited from :ref:`CategoricalVariation`.
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - mappings
-      - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
+      - :ref:`ConceptMapping`
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - members
-      - `Variation </ga4gh/schema/vrs/2.x/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - :ref:`Variation` | :ref:`IRI`
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
    *  - type
       - string
       - 1..1
       - MUST be "CanonicalAllele"
    *  - definingContext
-      - `Allele </ga4gh/schema/vrs/2.x/json/Allele>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - :ref:`Allele` | :ref:`IRI`
       - 1..1
-      - The `VRS Allele <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#allele>`_ object that is congruent with variants on alternate reference sequences.
+      - The `Allele <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/MolecularVariation/Allele.html#>`_ object that is congruent with variants on alternate reference sequences.

schema/cat-vrs/def/CategoricalCnv.rst

@@ -1,6 +1,6 @@
 **Computational Definition**
 
-A categorical variation domain is defined first by a sequence derived from a canonical `Location  <https://vrs.ga4gh.org/en/2.0/terms_and_model.html#Location>`_ , which is representative of  a collection of congruent Locations. The change or count of this sequence is also described, either by a numeric value (e.g. "3 or more copies") or categorical representation (e.g. "high-level gain").  Categorical CNVs may optionally be defined by rules specifying the location match characteristics for  member CNVs.
+A categorical variation domain is defined first by a sequence derived from a canonical `SequenceLocation <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/LocationAndReference/SequenceLocation.html>`_ , which is representative of a collection of congruent Locations. The change or count of this sequence is also described, either by a numeric value (e.g. "3 or more copies") or categorical representation (e.g. "high-level gain"). Categorical CNVs may optionally be defined by rules specifying the location match characteristics for member CNVs.
 
 **Information Model**
 
@@ -33,34 +33,34 @@ Some CategoricalCnv attributes are inherited from :ref:`CategoricalVariation`.
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
-      - `Extension </ga4gh/schema/gks-common/1.x/data-types/json/Extension>`_
+      - :ref:`Extension`
       - 0..m
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - mappings
-      - `ConceptMapping </ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping>`_
+      - :ref:`ConceptMapping`
       - 0..m
       - A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation.
    *  - members
-      - `Variation </ga4gh/schema/vrs/2.x/json/Variation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - :ref:`Variation` | :ref:`IRI`
       - 0..m
       - A non-exhaustive list of VRS variation contexts that satisfy the constraints of this categorical variant.
    *  - type
       - string
       - 1..1
       - MUST be "CategoricalCnv"
    *  - location
-      - `SequenceLocation </ga4gh/schema/vrs/2.x/json/SequenceLocation>`_ | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - :ref:`SequenceLocation` | :ref:`IRI`
       - 1..1
-      - A `VRS Location <https://vrs.ga4gh.org/en/2.x/concepts/location/SequenceLocation.html>`_ object that represents a sequence derived from that location, and is congruent with locations  on alternate reference sequences.
+      - A `SequenceLocation <https://vrs.ga4gh.org/en/2.0.0-ballot.2024-08/concepts/LocationAndReference/SequenceLocation.html>`_ object that represents a sequence derived from that location, and is congruent with locations on alternate reference sequences.
    *  - locationMatchCharacteristic
       - string
       - 0..1
-      - The characteristics of a valid match between a contextual CNV location (the query) and the  Categorical CNV location (the domain), when both query and domain are represented on the same  reference sequence. An `exact` match requires the location of the query and domain to be identical.  A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue of overlap between the query and domain.
+      - The characteristics of a valid match between a contextual CNV location (the query) and the Categorical CNV location (the domain), when both query and domain are represented on the same reference sequence. An `exact` match requires the location of the query and domain to be identical. A `subinterval` match requires the query to be a subinterval of the domain. A `superinterval` match requires the query to be a superinterval of the domain. A `partial` match requires at least 1 residue of overlap between the query and domain.
    *  - copyChange
       - string
       - 0..1
-      - A representation of the change in copies of a sequence in a system. MUST be 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).
+      - A representation of the change in copies of a sequence in a system. MUST be 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).
    *  - copies
-      - integer | `Range </ga4gh/schema/vrs/2.x/json/Range>`_
+      - integer | :ref:`Range`
       - 0..1
       - The integral number of copies of the subject in a system.