update MSP

ga4gh · Sep 6, 2024 · c429f75 · c429f75
1 parent c57ede1
commit c429f75
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Showing 18 changed files with 28 additions and 28 deletions.
diff --git a/.requirements.txt b/.requirements.txt
@@ -3,7 +3,7 @@ jsonschema
 referencing
 ipython
 pyyaml
-ga4gh.gks.metaschema==0.3.0b11
+ga4gh.gks.metaschema==0.3.0b12
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.2
 jupyterlab

diff --git a/schema/vrs/def/Adjacency.rst b/schema/vrs/def/Adjacency.rst
@@ -33,7 +33,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
       - 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.
    *  - digest
@@ -49,7 +49,7 @@ Some Adjacency attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "Adjacency".
    *  - adjoinedSequences
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 2..2
       - The terminal sequence or pair of adjoined sequences that defines in the adjacency.
    *  - linker

diff --git a/schema/vrs/def/Allele.rst b/schema/vrs/def/Allele.rst
@@ -33,7 +33,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
       - 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.
    *  - digest
@@ -49,7 +49,7 @@ Some Allele attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "Allele"
    *  - location
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - The location of the Allele
    *  - state

diff --git a/schema/vrs/def/CisPhasedBlock.rst b/schema/vrs/def/CisPhasedBlock.rst
@@ -33,7 +33,7 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
       - 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.
    *  - digest
@@ -49,7 +49,7 @@ Some CisPhasedBlock attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "CisPhasedBlock"
    *  - members
-      - :ref:`Allele` | `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_
+      - :ref:`Allele` | :ref:`IRI`
       - 2..m
       - A list of :ref:`Alleles <Allele>` that are found in-cis on a shared molecule.
    *  - sequenceReference

diff --git a/schema/vrs/def/CopyNumber.rst b/schema/vrs/def/CopyNumber.rst
@@ -37,7 +37,7 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
       - 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.
    *  - digest
@@ -49,6 +49,6 @@ Some CopyNumber attributes are inherited from :ref:`Variation`.
       - 0..m
       - 
    *  - location
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.
diff --git a/schema/vrs/def/CopyNumberChange.rst b/schema/vrs/def/CopyNumberChange.rst
@@ -33,7 +33,7 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
       - 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.
    *  - digest
@@ -45,14 +45,14 @@ Some CopyNumberChange attributes are inherited from :ref:`CopyNumber`.
       - 0..m
       - 
    *  - location
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.
    *  - type
       - string
       - 1..1
       - MUST be "CopyNumberChange"
    *  - copyChange
-      - `Coding <../data-types/data-types-source.json#/$defs/Coding>`_
+      - :ref:`Coding`
       - 1..1
       - MUST be a `Coding` representing 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).
diff --git a/schema/vrs/def/CopyNumberCount.rst b/schema/vrs/def/CopyNumberCount.rst
@@ -33,7 +33,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
       - 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.
    *  - digest
@@ -45,7 +45,7 @@ Some CopyNumberCount attributes are inherited from :ref:`CopyNumber`.
       - 0..m
       - 
    *  - location
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - A location for which the number of systemic copies is described.
    *  - type

diff --git a/schema/vrs/def/DerivativeMolecule.rst b/schema/vrs/def/DerivativeMolecule.rst
@@ -33,7 +33,7 @@ Some DerivativeMolecule attributes are inherited from :ref:`Variation`.
       - 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.
    *  - digest
@@ -49,7 +49,7 @@ Some DerivativeMolecule attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "DerivativeMolecule".
    *  - components
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`TraversalBlock`
+      - :ref:`IRI` | :ref:`TraversalBlock`
       - 2..m
       - The molecular components that constitute the derivative molecule.
    *  - circular

diff --git a/schema/vrs/def/Ga4ghIdentifiableObject.rst b/schema/vrs/def/Ga4ghIdentifiableObject.rst
@@ -37,7 +37,7 @@ Some Ga4ghIdentifiableObject attributes are inherited from :ref:`gks.core-im:Ent
       - 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.
    *  - digest

diff --git a/schema/vrs/def/LengthExpression.rst b/schema/vrs/def/LengthExpression.rst
@@ -33,7 +33,7 @@ Some LengthExpression attributes are inherited from :ref:`SequenceExpression`.
       - 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.
    *  - type

diff --git a/schema/vrs/def/LiteralSequenceExpression.rst b/schema/vrs/def/LiteralSequenceExpression.rst
@@ -33,7 +33,7 @@ Some LiteralSequenceExpression attributes are inherited from :ref:`SequenceExpre
       - 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.
    *  - type

diff --git a/schema/vrs/def/ReferenceLengthExpression.rst b/schema/vrs/def/ReferenceLengthExpression.rst
@@ -33,7 +33,7 @@ Some ReferenceLengthExpression attributes are inherited from :ref:`SequenceExpre
       - 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.
    *  - type

diff --git a/schema/vrs/def/SequenceExpression.rst b/schema/vrs/def/SequenceExpression.rst
@@ -33,7 +33,7 @@ Some SequenceExpression attributes are inherited from :ref:`gks.core-im:Entity`.
       - 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.
    *  - type

diff --git a/schema/vrs/def/SequenceLocation.rst b/schema/vrs/def/SequenceLocation.rst
@@ -33,7 +33,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
       - 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.
    *  - digest
@@ -45,7 +45,7 @@ Some SequenceLocation attributes are inherited from :ref:`Ga4ghIdentifiableObjec
       - 1..1
       - MUST be "SequenceLocation"
    *  - sequenceReference
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`SequenceReference`
+      - :ref:`IRI` | :ref:`SequenceReference`
       - 0..1
       - A reference to a :ref:`Sequence` on which the location is defined.
    *  - start

diff --git a/schema/vrs/def/SequenceReference.rst b/schema/vrs/def/SequenceReference.rst
@@ -33,7 +33,7 @@ Some SequenceReference attributes are inherited from :ref:`gks.core-im:Entity`.
       - 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.
    *  - type

diff --git a/schema/vrs/def/Terminus.rst b/schema/vrs/def/Terminus.rst
@@ -33,7 +33,7 @@ Some Terminus attributes are inherited from :ref:`Variation`.
       - 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.
    *  - digest
@@ -49,6 +49,6 @@ Some Terminus attributes are inherited from :ref:`Variation`.
       - 1..1
       - MUST be "Terminus".
    *  - location
-      - `IRI </ga4gh/schema/gks-common/1.x/data-types/json/IRI>`_ | :ref:`Location`
+      - :ref:`IRI` | :ref:`Location`
       - 1..1
       - The location of the terminus.
diff --git a/schema/vrs/def/TraversalBlock.rst b/schema/vrs/def/TraversalBlock.rst
@@ -33,7 +33,7 @@ Some TraversalBlock attributes are inherited from :ref:`gks.core-im:Entity`.
       - 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.
    *  - type

diff --git a/schema/vrs/def/Variation.rst b/schema/vrs/def/Variation.rst
@@ -37,7 +37,7 @@ Some Variation attributes are inherited from :ref:`Ga4ghIdentifiableObject`.
       - 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.
    *  - digest