Merge branch '2.x' into seqref-updates

ga4gh · Nov 26, 2024 · 0d510f8 · 0d510f8
2 parents cd9fe2c + cad2d56
commit 0d510f8
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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/.requirements.txt b/.requirements.txt
@@ -3,7 +3,7 @@ jsonschema
 referencing
 ipython
 pyyaml
-ga4gh.gks.metaschema==0.3.0b14
+ga4gh.gks.metaschema==0.3.0b17
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2
 jupyterlab

diff --git a/docs/source/appendices/class_diagram.rst b/docs/source/appendices/class_diagram.rst
@@ -0,0 +1,14 @@
+.. _ClassDiagram:
+
+Class Diagram
+!!!!!!!!!!!!!
+
+Below is a class diagram of the VRS schema which provides a visual representation
+of the class inheritance only not associations. Each class within the diagram is
+tagged with the maturity level of the class in the upper right corner. The maturity
+levels are defined in the :ref:`feature-maturity-levels` section.
+
+.. figure:: ../images/schema-current.png
+
+   Current VRS Class Inheritance Diagram
+
diff --git a/docs/source/appendices/index.rst b/docs/source/appendices/index.rst
@@ -4,18 +4,8 @@ Appendices
 .. toctree::
    :maxdepth: 2
 
-   getting_involved    
-   design_decisions
-   development_process
+   class_diagram
    maturity_model
-   future_plans
-
-   implementations
-   relationships
-   associating_annotations
-   equivalence
    ga4gh_identifiers
    truncated_digest_collision_analysis
-
-   faq
    glossary
diff --git a/docs/source/appendices/maturity_model.rst b/docs/source/appendices/maturity_model.rst
@@ -43,9 +43,14 @@ adoption by the community.
     model, enabling adopters to engage at a time that is appropriate for their 
     organizational needs.*
 
+.. _feature-maturity-levels:
+
 Feature Maturity levels
 @@@@@@@@@@@@@@@@@@@@@@@
 
+It may be helpful to visualize the application of maturity levels by viewing the 
+current :ref:`classDiagram`.
+
 .. figure:: ../images/maturity_levels.png
     :width: 800
 

diff --git a/docs/source/concepts/AdditionalDataTypes/Code.rst b/docs/source/concepts/AdditionalDataTypes/Code.rst
@@ -1,6 +1,6 @@
-.. _Code:
+.. _code:
 
-Code
+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
diff --git a/docs/source/concepts/AdditionalDataTypes/index.rst b/docs/source/concepts/AdditionalDataTypes/index.rst
@@ -69,19 +69,19 @@ Range
 
 .. include:: ../../def/vrs/Range.rst
 
-.. _Residue:
+.. _residue:
 
-Residue
+residue
 #######
 
-.. include:: ../../def/vrs/Residue.rst
+.. include:: ../../def/vrs/residue.rst
 
-.. _SequenceString:
+.. _sequenceString:
 
-SequenceString
+sequenceString
 ##############
 
-.. include:: ../../def/vrs/SequenceString.rst
+.. include:: ../../def/vrs/sequenceString.rst
 
 Imported Classes
 @@@@@@@@@@@@@@@@
@@ -93,7 +93,8 @@ Work Stream as common data classes.
    :titlesonly:
 
    Entity
+   Element
    Extension
-   IRI
    Coding
-   Code
+   code
+   iriReference
diff --git a/docs/source/concepts/AdditionalDataTypes/iriReference.rst b/docs/source/concepts/AdditionalDataTypes/iriReference.rst
@@ -0,0 +1,6 @@
+.. _iriReference:
+
+iriReference
+!!!!!!!!!!!!
+
+.. include::  ../../def/gks-core/iriReference.rst
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
@@ -19,3 +19,4 @@ These models exist across several related domains:
     LocationAndReference/index
     SequenceExpression/index
     AdditionalDataTypes/index
+
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 +1,25 @@
+.. 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`.
 
-.. 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**
 
-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.
+
+**GA4GH Digest**
+
+.. list-table::
+    :class: clean-wrap
+    :header-rows: 1
+    :align: left
+    :widths: auto
+
+    *  - Prefix
+       - Keys
+
+    *  - AJ
+       - ['adjoinedSequences', 'linker', 'type']
+
 
 **Information Model**
 
@@ -19,50 +32,77 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
    :widths: auto
 
    *  - Field
+      - Flags
       - 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, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
    *  - label
+      - 
       - string
       - 0..1
       - A primary name for the entity.
    *  - description
+      - 
       - string
       - 0..1
       - A free-text description of the Entity.
    *  - alternativeLabels
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - string
       - 0..m
       - Alternative name(s) for the Entity.
    *  - extensions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :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.
    *  - digest
+      - 
       - string
       - 0..1
       - A sha512t24u digest created using the VRS Computed Identifier algorithm.
    *  - expressions
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Unordered">&#8942;</span>
       - :ref:`Expression`
       - 0..m
       - 
    *  - type
+      - 
       - string
       - 1..1
       - MUST be "Adjacency".
    *  - adjoinedSequences
-      - :ref:`IRI` | :ref:`Location`
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #B2DFEE; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Ordered">&#8595;</span>
+      - :ref:`iriReference` | :ref:`Location`
       - 2..2
       - The terminal sequence or pair of adjoined sequences that defines in the adjacency.
    *  - linker
+      - 
       - :ref:`SequenceExpression`
       - 0..1
       - The sequence found between adjoined sequences.
    *  - homology
+      - 
+                        .. raw:: html
+
+                            <span style="background-color: #D3D3D3; color: black; padding: 2px 6px; border: 1px solid black; border-radius: 3px; font-weight: bold; display: inline-block; margin-bottom: 5px;" title="Draft Maturity Level">D</span>
       - boolean
       - 0..1
       - A flag indicating if coordinate ambiguity in the adjoined sequences is from sequence homology (true) or other uncertainty, such as instrument ambiguity (false).
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,4 +3,4 @@ @@
     Coding
     !!!!!!
-    .. include::  ../../def/gks.common/core-im/Coding.rst
+    .. include::  ../../def/gks-core/Coding.rst