udpate SM & MSP (#584)

ga4gh · Nov 7, 2024 · 8d533d6 · 8d533d6
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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==0.3.0b16
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2
 jupyterlab

diff --git a/schema/vrs/def/Adjacency.rst b/schema/vrs/def/Adjacency.rst
@@ -1,12 +1,26 @@
-
 .. 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`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 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**
 
 Some Adjacency attributes are inherited from :ref:`Variation`.
@@ -18,50 +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
+      - 
+                        .. 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).
diff --git a/schema/vrs/def/Allele.rst b/schema/vrs/def/Allele.rst
@@ -1,12 +1,26 @@
-
 .. 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`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 The state of a molecule at a :ref:`Location`.
 
+**GA4GH Digest**
+
+.. list-table::
+    :class: clean-wrap
+    :header-rows: 1
+    :align: left
+    :widths: auto
+
+    *  - Prefix
+       - Keys
+
+    *  - VA
+       - ['location', 'state', 'type']
+
+
 **Information Model**
 
 Some Allele attributes are inherited from :ref:`Variation`.
@@ -18,46 +32,66 @@ Some Allele 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 "Allele"
    *  - location
+      - 
       - :ref:`iriReference` | :ref:`Location`
       - 1..1
       - The location of the Allele
    *  - state
+      - 
       - :ref:`SequenceExpression`
       - 1..1
       - An expression of the sequence state
diff --git a/schema/vrs/def/CisPhasedBlock.rst b/schema/vrs/def/CisPhasedBlock.rst
@@ -1,12 +1,26 @@
-
 .. 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`.
-                      
-                    
+     in future releases. Maturity levels are described in
+    the :ref:`maturity-model`.
+
 **Computational Definition**
 
 An ordered set of co-occurring :ref:`variants <Variation>` on the same molecule.
 
+**GA4GH Digest**
+
+.. list-table::
+    :class: clean-wrap
+    :header-rows: 1
+    :align: left
+    :widths: auto
+
+    *  - Prefix
+       - Keys
+
+    *  - CPB
+       - ['members', 'type']
+
+
 **Information Model**
 
 Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
@@ -18,46 +32,69 @@ Some CisPhasedBlock 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 "CisPhasedBlock"
    *  - members
+      - 
+                        .. 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:`Allele` | :ref:`iriReference`
       - 2..m
       - A list of :ref:`Alleles <Allele>` that are found in-cis on a shared molecule.
    *  - sequenceReference
+      - 
       - :ref:`SequenceReference`
       - 0..1
       - An optional Sequence Reference on which all of the in-cis Alleles are found. When defined, this may be used to implicitly define the `sequenceReference` attribute for each of the CisPhasedBlock member Alleles.