addresses #465 and disables out-of-scope classes

ga4gh · Feb 10, 2024 · cf58308 · cf58308
1 parent 5ace850
commit cf58308
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diff --git a/schema/defs/vrs/Adjacency.rst b/schema/defs/vrs/Adjacency.rst
@@ -32,14 +32,14 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - MUST be "Adjacency".
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - expressions
           - :ref:`Expression`
           - 0..m

diff --git a/schema/defs/vrs/Allele.rst b/schema/defs/vrs/Allele.rst
@@ -32,14 +32,14 @@ Some Allele attributes are inherited from :ref:`Variation`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - MUST be "Allele"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - expressions
           - :ref:`Expression`
           - 0..m

diff --git a/schema/defs/vrs/CopyNumber.rst b/schema/defs/vrs/CopyNumber.rst
@@ -32,14 +32,14 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - 
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - expressions
           - :ref:`Expression`
           - 0..m

diff --git a/schema/defs/vrs/CopyNumberChange.rst b/schema/defs/vrs/CopyNumberChange.rst
@@ -32,14 +32,14 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - MUST be "CopyNumberChange"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - expressions
           - :ref:`Expression`
           - 0..m

diff --git a/schema/defs/vrs/CopyNumberCount.rst b/schema/defs/vrs/CopyNumberCount.rst
@@ -32,14 +32,14 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - MUST be "CopyNumberCount"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - expressions
           - :ref:`Expression`
           - 0..m

diff --git a/schema/defs/vrs/Ga4ghIdentifiableObject.rst b/schema/defs/vrs/Ga4ghIdentifiableObject.rst
@@ -4,7 +4,7 @@ A contextual value object for which a GA4GH computed identifier can be created.
 
     **Information Model**
 
-Some Ga4ghIdentifiableObject attributes are inherited from :ref:`ValueObject`.
+Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core:Entity`.
 
     .. list-table::
        :class: clean-wrap
@@ -32,11 +32,11 @@ Some Ga4ghIdentifiableObject attributes are inherited from :ref:`ValueObject`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - 
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
diff --git a/schema/defs/vrs/Genotype.rst b/schema/defs/vrs/Genotype.rst
diff --git a/schema/defs/vrs/GenotypeMember.rst b/schema/defs/vrs/GenotypeMember.rst
diff --git a/schema/defs/vrs/Haplotype.rst b/schema/defs/vrs/Haplotype.rst
@@ -32,14 +32,14 @@ Some Haplotype attributes are inherited from :ref:`Variation`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - MUST be "Haplotype"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - expressions
           - :ref:`Expression`
           - 0..m

diff --git a/schema/defs/vrs/LengthExpression.rst b/schema/defs/vrs/LengthExpression.rst
@@ -32,10 +32,6 @@ Some LengthExpression attributes are inherited from :ref:`SequenceExpression`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 1..1

diff --git a/schema/defs/vrs/LiteralSequenceExpression.rst b/schema/defs/vrs/LiteralSequenceExpression.rst
@@ -32,10 +32,6 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 1..1

diff --git a/schema/defs/vrs/ReferenceLengthExpression.rst b/schema/defs/vrs/ReferenceLengthExpression.rst
@@ -32,10 +32,6 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 1..1

diff --git a/schema/defs/vrs/SequenceExpression.rst b/schema/defs/vrs/SequenceExpression.rst
@@ -4,7 +4,7 @@ An expression describing a :ref:`Sequence`.
 
     **Information Model**
 
-Some SequenceExpression attributes are inherited from :ref:`ValueObject`.
+Some SequenceExpression attributes are inherited from :ref:`gks.core:Entity`.
 
     .. list-table::
        :class: clean-wrap
@@ -32,10 +32,6 @@ Some SequenceExpression attributes are inherited from :ref:`ValueObject`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 1..1

diff --git a/schema/defs/vrs/SequenceLocation.rst b/schema/defs/vrs/SequenceLocation.rst
@@ -32,14 +32,14 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - MUST be "SequenceLocation"
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - sequenceReference
           - `IRI <gks.common.json#/$defs/IRI>`_ | :ref:`SequenceReference`
           - 0..1

diff --git a/schema/defs/vrs/SequenceReference.rst b/schema/defs/vrs/SequenceReference.rst
@@ -4,7 +4,7 @@ A sequence of nucleic or amino acid character codes.
 
     **Information Model**
 
-Some SequenceReference attributes are inherited from :ref:`ValueObject`.
+Some SequenceReference attributes are inherited from :ref:`gks.core:Entity`.
 
     .. list-table::
        :class: clean-wrap
@@ -32,10 +32,6 @@ Some SequenceReference attributes are inherited from :ref:`ValueObject`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1

diff --git a/schema/defs/vrs/ValueObject.rst b/schema/defs/vrs/ValueObject.rst
@@ -1,38 +1,3 @@
 **Computational Definition**
 
-A contextual value whose equality is based on value, not identity. All VRS Value Objects may have computed digests from the VRS Computed Identifier algorithm. See https://en.wikipedia.org/wiki/Value_object for more on Value Objects.
-
-    **Information Model**
-
-Some ValueObject attributes are inherited from :ref:`gks.core:Entity`.
-
-    .. list-table::
-       :class: clean-wrap
-       :header-rows: 1
-       :align: left
-       :widths: auto
-
-       *  - Field
-          - Type
-          - Limits
-          - Description
-       *  - id
-          - string
-          - 0..1
-          - The 'logical' identifier of the entity in the system of record, e.g. a UUID. This 'id' is  unique within a given system. The identified entity may have a different 'id' in a different  system, or may refer to an 'id' for the shared concept in another system (e.g. a CURIE).
-       *  - label
-          - string
-          - 0..1
-          - A primary label for the entity.
-       *  - description
-          - string
-          - 0..1
-          - A free-text description of the entity.
-       *  - extensions
-          - `Extension <gks.common.json#/$defs/Extension>`_
-          - 0..m
-          - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
+A contextual value whose equality is based on value, not identity. See https://en.wikipedia.org/wiki/Value_object for more on Value Objects.
diff --git a/schema/defs/vrs/Variation.rst b/schema/defs/vrs/Variation.rst
@@ -32,14 +32,14 @@ Some Variation attributes are inherited from :ref:`Ga4ghIdentifiableObject`.
           - `Extension <gks.common.json#/$defs/Extension>`_
           - 0..m
           - 
-       *  - digest
-          - string
-          - 0..1
-          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - type
           - string
           - 0..1
           - 
+       *  - digest
+          - string
+          - 0..1
+          - A sha512t24u digest created using the VRS Computed Identifier algorithm.
        *  - expressions
           - :ref:`Expression`
           - 0..m