update gks-core SM, adjust refs and rebuild (ga4gh#575)

* update gks-core SM, adjust refs and rebuild * added Element PR from gks-core to add Extensions * udpated current schema diagram * Added Element to Imported Classes doc * added the class diagram to the appendix and a reference from the Concepts page
clingen-data-model · Oct 31, 2024 · 2d69dc1 · 2d69dc1
1 parent 9bae4ce
commit 2d69dc1
Show file tree

Hide file tree

Showing 58 changed files with 151 additions and 145 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -1,4 +1,3 @@
-[submodule "schema/gks-common"]
-	path = submodules/gks-common
-	url = https://github.com/ga4gh/gks-common.git
-	branch = 1.x
+[submodule "submodules/gks-core"]
+	path = submodules/gks-core
+	url = https://github.com/ga4gh/gks-core.git
diff --git a/docs/source/appendices/class_diagram.rst b/docs/source/appendices/class_diagram.rst
@@ -0,0 +1,9 @@
+.. _ClassDiagram:
+
+Class Diagram
+!!!!!!!!!!!!!
+
+.. figure:: ../images/schema-current.png
+
+   Current VRS Class Inheritance Diagram
+
diff --git a/docs/source/concepts/AdditionalDataTypes/Code.rst b/docs/source/concepts/AdditionalDataTypes/Code.rst
@@ -3,4 +3,4 @@
 Code
 !!!!
 
-.. include::  ../../def/gks.common/core-im/Code.rst
+.. include::  ../../def/gks-core/Code.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/Coding.rst b/docs/source/concepts/AdditionalDataTypes/Coding.rst
@@ -3,4 +3,4 @@
 Coding
 !!!!!!
 
-.. include::  ../../def/gks.common/core-im/Coding.rst
+.. include::  ../../def/gks-core/Coding.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/Element.rst b/docs/source/concepts/AdditionalDataTypes/Element.rst
@@ -0,0 +1,6 @@
+.. _Element:
+
+Element
+!!!!!!
+
+.. include::  ../../def/gks-core/Element.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/Entity.rst b/docs/source/concepts/AdditionalDataTypes/Entity.rst
@@ -3,4 +3,4 @@
 Entity
 !!!!!!
 
-.. include::  ../../def/gks.common/core-im/Entity.rst
+.. include::  ../../def/gks-core/Entity.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/Extension.rst b/docs/source/concepts/AdditionalDataTypes/Extension.rst
@@ -3,4 +3,4 @@
 Extension
 !!!!!!!!!
 
-.. include::  ../../def/gks.common/core-im/Extension.rst
+.. include::  ../../def/gks-core/Extension.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/IRI.rst b/docs/source/concepts/AdditionalDataTypes/IRI.rst
@@ -3,4 +3,4 @@
 IRI
 !!!
 
-.. include::  ../../def/gks.common/core-im/IRI.rst
+.. include::  ../../def/gks-core/IRI.rst
diff --git a/docs/source/concepts/AdditionalDataTypes/index.rst b/docs/source/concepts/AdditionalDataTypes/index.rst
@@ -93,7 +93,8 @@ Work Stream as common data classes.
    :titlesonly:
 
    Entity
+   Element
    Extension
-   IRI
    Coding
    Code
+   IRI
diff --git a/docs/source/concepts/index.rst b/docs/source/concepts/index.rst
@@ -2,7 +2,7 @@ Concepts
 !!!!!!!!
 
 VRS is a collection of data models or concepts that are used together to represent molecular 
-and systemic variation.
+and systemic variation. An inhertiance view is available in the :ref:`ClassDiagram` appendix.
 These models exist across several related domains:
 
 - :ref:`MolecularVariation`: models that describe variation on a contiguous molecule

diff --git a/docs/source/def/gks-core b/docs/source/def/gks-core
@@ -0,0 +1 @@
+../../../schema/gks-core/def
diff --git a/docs/source/def/gks.common/core-im b/docs/source/def/gks.common/core-im
diff --git a/docs/source/def/gks.common/data-types b/docs/source/def/gks.common/data-types
diff --git a/docs/source/images/schema-current.png b/docs/source/images/schema-current.png
diff --git a/docs/source/images/schema-future.png b/docs/source/images/schema-future.png
diff --git a/docs/source/rst_epilog b/docs/source/rst_epilog
@@ -29,7 +29,7 @@
 .. |varnomen| replace:: `HGVS Variant Nomenclature <https://varnomen.hgvs.org/>`__
 .. |vrs-python| replace:: `GA4GH VRS Python Implementation <https://github.com/ga4gh/vrs-python/>`__
 .. |vrs| replace:: `VRS <https://github.com/ga4gh/vrs/>`__
-.. |gks-common| replace:: `GKS Common <https://github.com/ga4gh/gks-common/>`__
+.. |gks-core| replace:: `GKS Common <https://github.com/ga4gh/gks-core/>`__
 
 
 .. |eg| replace:: *e.g.,*

diff --git a/docs/source/schema.rst b/docs/source/schema.rst
diff --git a/schema/core-im b/schema/core-im
diff --git a/schema/domain-entities b/schema/domain-entities
diff --git a/schema/gks-core b/schema/gks-core
@@ -0,0 +1 @@
+../submodules/gks-core/schema/gks-core
diff --git a/schema/vrs/def/Adjacency.rst b/schema/vrs/def/Adjacency.rst
@@ -1,12 +1,11 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**
 
-The `Adjacency` class can represent either the termination of a sequence or the adjoining of the end of a sequence with the beginning of an adjacent sequence, potentially with an intervening linker sequence.
+The `Adjacency` class represents the adjoining of the end of a sequence with the beginning of an adjacent sequence, potentially with an intervening linker sequence.
 
 **Information Model**
 

diff --git a/schema/vrs/def/Allele.rst b/schema/vrs/def/Allele.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/CisPhasedBlock.rst b/schema/vrs/def/CisPhasedBlock.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/CopyNumber.rst b/schema/vrs/def/CopyNumber.rst
@@ -1,3 +1,9 @@
+
+.. warning:: This data class is at a **draft** maturity level and may change
+    significantly in future releases. Maturity levels are described in 
+    the :ref:`maturity-model`.
+
+
 **Computational Definition**
 
 A measure of the copies of a :ref:`Location` within a system (e.g. genome, cell, etc.)

diff --git a/schema/vrs/def/Expression.rst b/schema/vrs/def/Expression.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**
@@ -10,6 +9,7 @@ Representation of a variation by a specified nomenclature or syntax for a Variat
 
 **Information Model**
 
+Some Expression attributes are inherited from :ref:`gks-core:Element`.
 
 .. list-table::
    :class: clean-wrap
@@ -21,6 +21,14 @@ Representation of a variation by a specified nomenclature or syntax for a Variat
       - Type
       - Limits
       - Description
+   *  - id
+      - string
+      - 0..1
+      - The 'logical' identifier of the data element in the system of record, e.g. a UUID.  This 'id' is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
+   *  - extensions
+      - :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.
    *  - syntax
       - string
       - 1..1

diff --git a/schema/vrs/def/Ga4ghIdentifiableObject.rst b/schema/vrs/def/Ga4ghIdentifiableObject.rst
@@ -1,10 +1,15 @@
+
+.. 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**
 
 An object for which a GA4GH computed identifier can be created.
 
 **Information Model**
 
-Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core-im:Entity`.
+Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks-core:Entity`.
 
 .. list-table::
    :class: clean-wrap

diff --git a/schema/vrs/def/LiteralSequenceExpression.rst b/schema/vrs/def/LiteralSequenceExpression.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/Range.rst b/schema/vrs/def/Range.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/ReferenceLengthExpression.rst b/schema/vrs/def/ReferenceLengthExpression.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/Residue.rst b/schema/vrs/def/Residue.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/SequenceExpression.rst b/schema/vrs/def/SequenceExpression.rst
@@ -1,10 +1,15 @@
+
+.. 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**
 
 An expression describing a :ref:`Sequence`.
 
 **Information Model**
 
-Some SequenceExpression attributes are inherited from :ref:`gks.core-im:Entity`.
+Some SequenceExpression attributes are inherited from :ref:`gks-core:Entity`.
 
 .. list-table::
    :class: clean-wrap

diff --git a/schema/vrs/def/SequenceLocation.rst b/schema/vrs/def/SequenceLocation.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/SequenceReference.rst b/schema/vrs/def/SequenceReference.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**
@@ -10,7 +9,7 @@ A sequence of nucleic or amino acid character codes.
 
 **Information Model**
 
-Some SequenceReference attributes are inherited from :ref:`gks.core-im:Entity`.
+Some SequenceReference attributes are inherited from :ref:`gks-core:Entity`.
 
 .. list-table::
    :class: clean-wrap

diff --git a/schema/vrs/def/SequenceString.rst b/schema/vrs/def/SequenceString.rst
@@ -1,7 +1,6 @@
 
-.. warning:: This data class is at a **draft** maturity level and may change
-    significantly in future releases. Maturity levels are described in 
-    the :ref:`maturity-model`.
+.. 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**

diff --git a/schema/vrs/def/TraversalBlock.rst b/schema/vrs/def/TraversalBlock.rst
@@ -10,7 +10,7 @@ A component used to describe the orientation of applicable molecular variation w
 
 **Information Model**
 
-Some TraversalBlock attributes are inherited from :ref:`gks.core-im:Entity`.
+Some TraversalBlock attributes are inherited from :ref:`gks-core:Entity`.
 
 .. list-table::
    :class: clean-wrap

diff --git a/schema/vrs/def/Variation.rst b/schema/vrs/def/Variation.rst
@@ -1,3 +1,8 @@
+
+.. 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**
 
 A representation of the state of one or more biomolecules.
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,4 +3,4 @@ @@
     Code
     !!!!
-    .. include::  ../../def/gks.common/core-im/Code.rst
+    .. include::  ../../def/gks-core/Code.rst