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SMU, datatype merge, doc fixes #56

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Oct 10, 2024
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SMU, datatype merge, doc fixes #56

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1 change: 0 additions & 1 deletion docs/source/def
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1 change: 1 addition & 0 deletions docs/source/def-core
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@@ -0,0 +1 @@
../../schema/cat-vrs/core/def
1 change: 1 addition & 0 deletions docs/source/def-profiles
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../../schema/cat-vrs/profiles/def
23 changes: 8 additions & 15 deletions docs/source/schema.rst
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Expand Up @@ -19,11 +19,11 @@ JSON files for each class in the schema (|vrs_json|).
Contributions to the schema MUST be written in the YAML document.


.. _CategoricalVariationSchemata:
.. _CategoricalVariation:
.. _CategoricalVariantSchemata:
.. _CategoricalVariant:

Categorical Variation Schemata
@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
Categorical Variant Schemata
@@@@@@@@@@@@@@@@@@@@@@@@@@@@

THIS SECTION WILL GET UPDATEED WHEN I HAVE SCHEMATA READY
PLEASE CHECK BACK IN THE FUTURE!
Expand All @@ -33,32 +33,25 @@ PLEASE CHECK BACK IN THE FUTURE!
:alt: An irresistably cute kittynaut beckoning you to enter the Cat-VRS.
:align: center

.. include:: def/CategoricalVariation.rst
.. include:: def-core/CategoricalVariant.rst

.. _CanonicalAllele:

Canonical Allele
################

.. include:: def/CanonicalAllele.rst

.. _DescribedVariation:

Described Variation
###################

.. include:: def/DescribedVariation.rst
.. include:: def-profiles/CanonicalAllele.rst

.. _CategoricalCnv:

Categorical Copy Number
#######################

.. include:: def/CategoricalCnv.rst
.. include:: def-profiles/CategoricalCnv.rst

.. _ProteinSequenceConsequence:

Protein Sequence Consequence
############################

.. include:: def/ProteinSequenceConsequence.rst
.. include:: def-profiles/ProteinSequenceConsequence.rst
7 changes: 3 additions & 4 deletions schema/cat-vrs/core/cat-vrs-core-source.yaml
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Expand Up @@ -6,7 +6,6 @@ strict: true

imports:
gks.core-im: ../../core-im/core-im-source.yaml
gks.data-types: ../../data-types/data-types-source.yaml
vrs: ../../vrs/vrs-source.yaml

$defs:
Expand Down Expand Up @@ -37,7 +36,7 @@ $defs:
items:
oneOf:
- $ref: /ga4gh/schema/vrs/2.x/json/Variation
- $ref: /ga4gh/schema/gks-common/1.x/data-types/json/IRI
- $ref: /ga4gh/schema/gks-common/1.x/core-im/json/IRI
constraints:
type: array
ordered: false
Expand Down Expand Up @@ -79,7 +78,7 @@ $defs:
oneOf:
- $ref: /ga4gh/schema/vrs/2.x/json/Variation
- $ref: /ga4gh/schema/vrs/2.x/json/Location
- $ref: /ga4gh/schema/gks-common/1.x/data-types/json/IRI
- $ref: /ga4gh/schema/gks-common/1.x/core-im/json/IRI
relations:
type: array
ordered: false
Expand Down Expand Up @@ -129,7 +128,7 @@ $defs:
default: CopyChangeConstraint
description: 'MUST be "CopyChangeConstraint"'
copyChange:
$ref: /ga4gh/schema/gks-common/1.x/data-types/json/Coding
$ref: /ga4gh/schema/gks-common/1.x/core-im/json/Coding
items:
properties:
code:
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6 changes: 3 additions & 3 deletions schema/cat-vrs/core/json/CategoricalVariant
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Expand Up @@ -31,7 +31,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Extension"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension"
},
"description": "A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.",
"$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems."
Expand All @@ -40,7 +40,7 @@
"type": "array",
"ordered": false,
"items": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/ConceptMapping"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/ConceptMapping"
},
"description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation."
},
Expand All @@ -58,7 +58,7 @@
"items": {
"oneOf": [
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
},
{
"$ref": "/ga4gh/schema/vrs/2.x/json/Variation"
Expand Down
2 changes: 1 addition & 1 deletion schema/cat-vrs/core/json/CopyChangeConstraint
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Expand Up @@ -13,7 +13,7 @@
"description": "MUST be \"CopyChangeConstraint\""
},
"copyChange": {
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding",
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding",
"items": {
"properties": {
"code": {
Expand Down
2 changes: 1 addition & 1 deletion schema/cat-vrs/core/json/DefiningContextConstraint
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Expand Up @@ -15,7 +15,7 @@
"definingContext": {
"oneOf": [
{
"$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI"
"$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI"
},
{
"$ref": "/ga4gh/schema/vrs/2.x/json/Location"
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1 change: 0 additions & 1 deletion schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml
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Expand Up @@ -5,7 +5,6 @@ type: object

imports:
gks.core-im: ../../core-im/core-im-source.yaml
gks.data-types: ../../data-types/data-types-source.yaml
vrs: ../../vrs/vrs-source.yaml
cat.core: ../core/cat-vrs-core-source.yaml

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1 change: 0 additions & 1 deletion schema/data-types
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2 changes: 1 addition & 1 deletion submodules/vrs
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Submodule vrs updated 25 files
+9 −4 CONTRIBUTING.md
+0 −25 LICENSE
+1 −1 docs/source/concepts/AdditionalDataTypes/Code.rst
+1 −1 docs/source/concepts/AdditionalDataTypes/Coding.rst
+1 −1 docs/source/concepts/AdditionalDataTypes/Extension.rst
+1 −1 docs/source/concepts/AdditionalDataTypes/IRI.rst
+1 −1 docs/source/concepts/MolecularVariation/index.rst
+1 −1 docs/source/concepts/SequenceExpression/index.rst
+1 −1 docs/source/concepts/SystemicVariation/index.rst
+0 −1 schema/data-types
+2 −2 schema/vrs/json/Adjacency
+2 −2 schema/vrs/json/Allele
+2 −2 schema/vrs/json/CisPhasedBlock
+4 −4 schema/vrs/json/CopyNumberChange
+2 −2 schema/vrs/json/CopyNumberCount
+2 −2 schema/vrs/json/DerivativeMolecule
+1 −1 schema/vrs/json/LengthExpression
+1 −1 schema/vrs/json/LiteralSequenceExpression
+1 −1 schema/vrs/json/ReferenceLengthExpression
+2 −2 schema/vrs/json/SequenceLocation
+1 −1 schema/vrs/json/SequenceReference
+2 −2 schema/vrs/json/Terminus
+1 −1 schema/vrs/json/TraversalBlock
+8 −13 schema/vrs/vrs-source.yaml
+1 −1 submodules/gks-common
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