diff --git a/docs/source/def b/docs/source/def deleted file mode 120000 index 75475c0..0000000 --- a/docs/source/def +++ /dev/null @@ -1 +0,0 @@ -../../schema/catvrs/def \ No newline at end of file diff --git a/docs/source/def-core b/docs/source/def-core new file mode 120000 index 0000000..069f033 --- /dev/null +++ b/docs/source/def-core @@ -0,0 +1 @@ +../../schema/cat-vrs/core/def \ No newline at end of file diff --git a/docs/source/def-profiles b/docs/source/def-profiles new file mode 120000 index 0000000..226c3eb --- /dev/null +++ b/docs/source/def-profiles @@ -0,0 +1 @@ +../../schema/cat-vrs/profiles/def \ No newline at end of file diff --git a/docs/source/schema.rst b/docs/source/schema.rst index 1a3f078..f601531 100644 --- a/docs/source/schema.rst +++ b/docs/source/schema.rst @@ -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! @@ -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 diff --git a/schema/cat-vrs/core/cat-vrs-core-source.yaml b/schema/cat-vrs/core/cat-vrs-core-source.yaml index f7bc9f4..29f66a9 100644 --- a/schema/cat-vrs/core/cat-vrs-core-source.yaml +++ b/schema/cat-vrs/core/cat-vrs-core-source.yaml @@ -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: @@ -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 @@ -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 @@ -129,7 +128,7 @@ $defs: default: CopyChangeConstraint description: 'MUST be "CopyChangeConstraint"' copyChange: - $ref: /ga4gh/schema/gks-common/1.x/data-types/json/Coding + $ref: /ga4gh/schema/gks-common/1.x/core-im/json/Coding items: properties: code: diff --git a/schema/cat-vrs/core/json/CategoricalVariant b/schema/cat-vrs/core/json/CategoricalVariant index 24087bc..c3f4fcd 100644 --- a/schema/cat-vrs/core/json/CategoricalVariant +++ b/schema/cat-vrs/core/json/CategoricalVariant @@ -31,7 +31,7 @@ "type": "array", "ordered": false, "items": { - "$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." @@ -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." }, @@ -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" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" diff --git a/schema/cat-vrs/core/json/CopyChangeConstraint b/schema/cat-vrs/core/json/CopyChangeConstraint index 100a129..44af32f 100644 --- a/schema/cat-vrs/core/json/CopyChangeConstraint +++ b/schema/cat-vrs/core/json/CopyChangeConstraint @@ -13,7 +13,7 @@ "description": "MUST be \"CopyChangeConstraint\"" }, "copyChange": { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding", + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding", "items": { "properties": { "code": { diff --git a/schema/cat-vrs/core/json/DefiningContextConstraint b/schema/cat-vrs/core/json/DefiningContextConstraint index 065c167..c301919 100644 --- a/schema/cat-vrs/core/json/DefiningContextConstraint +++ b/schema/cat-vrs/core/json/DefiningContextConstraint @@ -15,7 +15,7 @@ "definingContext": { "oneOf": [ { - "$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" diff --git a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml b/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml index abda788..b1441e9 100644 --- a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml +++ b/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml @@ -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 diff --git a/schema/data-types b/schema/data-types deleted file mode 120000 index 9d641ef..0000000 --- a/schema/data-types +++ /dev/null @@ -1 +0,0 @@ -../submodules/vrs/schema/data-types \ No newline at end of file diff --git a/submodules/vrs b/submodules/vrs index 890db40..5749b54 160000 --- a/submodules/vrs +++ b/submodules/vrs @@ -1 +1 @@ -Subproject commit 890db4004a41feb80f1a93006bc70aa40c948ad3 +Subproject commit 5749b541cd7158358ebe977e7e371fce722369fe