From ddbed32baf8e6b22b5c640b4fd73d1b64fbc90a1 Mon Sep 17 00:00:00 2001 From: Lawrence Babb Date: Thu, 10 Oct 2024 16:04:11 -0400 Subject: [PATCH] SMU datatype merge to core-im --- schema/data-types | 1 - schema/vrs/json/Adjacency | 4 ++-- schema/vrs/json/Allele | 4 ++-- schema/vrs/json/CisPhasedBlock | 4 ++-- schema/vrs/json/CopyNumberChange | 8 ++++---- schema/vrs/json/CopyNumberCount | 4 ++-- schema/vrs/json/DerivativeMolecule | 4 ++-- schema/vrs/json/LengthExpression | 2 +- schema/vrs/json/LiteralSequenceExpression | 2 +- schema/vrs/json/ReferenceLengthExpression | 2 +- schema/vrs/json/SequenceLocation | 4 ++-- schema/vrs/json/SequenceReference | 2 +- schema/vrs/json/Terminus | 4 ++-- schema/vrs/json/TraversalBlock | 2 +- schema/vrs/vrs-source.yaml | 21 ++++++++------------- submodules/gks-common | 2 +- 16 files changed, 32 insertions(+), 38 deletions(-) delete mode 120000 schema/data-types diff --git a/schema/data-types b/schema/data-types deleted file mode 120000 index 7af4510a..00000000 --- a/schema/data-types +++ /dev/null @@ -1 +0,0 @@ -../submodules/gks-common/schema/data-types \ No newline at end of file diff --git a/schema/vrs/json/Adjacency b/schema/vrs/json/Adjacency index 5f5b8da6..1283335a 100644 --- a/schema/vrs/json/Adjacency +++ b/schema/vrs/json/Adjacency @@ -39,7 +39,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -72,7 +72,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ] }, diff --git a/schema/vrs/json/Allele b/schema/vrs/json/Allele index 86ea7a29..18277bf2 100644 --- a/schema/vrs/json/Allele +++ b/schema/vrs/json/Allele @@ -39,7 +39,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -68,7 +68,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ], "description": "The location of the Allele" diff --git a/schema/vrs/json/CisPhasedBlock b/schema/vrs/json/CisPhasedBlock index 19e87192..10cc7232 100644 --- a/schema/vrs/json/CisPhasedBlock +++ b/schema/vrs/json/CisPhasedBlock @@ -38,7 +38,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -72,7 +72,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/Allele" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ] }, diff --git a/schema/vrs/json/CopyNumberChange b/schema/vrs/json/CopyNumberChange index 0c79b221..1c43eccf 100644 --- a/schema/vrs/json/CopyNumberChange +++ b/schema/vrs/json/CopyNumberChange @@ -39,7 +39,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -62,7 +62,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ], "description": "A location for which the number of systemic copies is described." @@ -74,8 +74,8 @@ "description": "MUST be \"CopyNumberChange\"" }, "copyChange": { - "description": "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).", - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/Coding" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding", + "description": "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)." } }, "required": [ diff --git a/schema/vrs/json/CopyNumberCount b/schema/vrs/json/CopyNumberCount index aa35d009..804c0577 100644 --- a/schema/vrs/json/CopyNumberCount +++ b/schema/vrs/json/CopyNumberCount @@ -39,7 +39,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -62,7 +62,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ], "description": "A location for which the number of systemic copies is described." diff --git a/schema/vrs/json/DerivativeMolecule b/schema/vrs/json/DerivativeMolecule index dd82a489..7dc0d93e 100644 --- a/schema/vrs/json/DerivativeMolecule +++ b/schema/vrs/json/DerivativeMolecule @@ -38,7 +38,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -71,7 +71,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/TraversalBlock" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ] }, diff --git a/schema/vrs/json/LengthExpression b/schema/vrs/json/LengthExpression index 0277eb1c..78fa17da 100644 --- a/schema/vrs/json/LengthExpression +++ b/schema/vrs/json/LengthExpression @@ -37,7 +37,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." diff --git a/schema/vrs/json/LiteralSequenceExpression b/schema/vrs/json/LiteralSequenceExpression index 775fadfe..688c4b0f 100644 --- a/schema/vrs/json/LiteralSequenceExpression +++ b/schema/vrs/json/LiteralSequenceExpression @@ -37,7 +37,7 @@ "type": "array", "ordered": false, "items": { - "$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." diff --git a/schema/vrs/json/ReferenceLengthExpression b/schema/vrs/json/ReferenceLengthExpression index 44f57aac..07e4d326 100644 --- a/schema/vrs/json/ReferenceLengthExpression +++ b/schema/vrs/json/ReferenceLengthExpression @@ -38,7 +38,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." diff --git a/schema/vrs/json/SequenceLocation b/schema/vrs/json/SequenceLocation index e8bd9041..fde190c3 100644 --- a/schema/vrs/json/SequenceLocation +++ b/schema/vrs/json/SequenceLocation @@ -40,7 +40,7 @@ "type": "array", "ordered": false, "items": { - "$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." @@ -62,7 +62,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceReference" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ], "description": "A reference to a Sequence on which the location is defined." diff --git a/schema/vrs/json/SequenceReference b/schema/vrs/json/SequenceReference index 2d817f16..49408e42 100644 --- a/schema/vrs/json/SequenceReference +++ b/schema/vrs/json/SequenceReference @@ -37,7 +37,7 @@ "type": "array", "ordered": false, "items": { - "$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." diff --git a/schema/vrs/json/Terminus b/schema/vrs/json/Terminus index b1b92310..b96cde2e 100644 --- a/schema/vrs/json/Terminus +++ b/schema/vrs/json/Terminus @@ -38,7 +38,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." @@ -67,7 +67,7 @@ "$ref": "/ga4gh/schema/vrs/2.x/json/SequenceLocation" }, { - "$ref": "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" } ], "description": "The location of the terminus." diff --git a/schema/vrs/json/TraversalBlock b/schema/vrs/json/TraversalBlock index 6b36a44b..d5dab041 100644 --- a/schema/vrs/json/TraversalBlock +++ b/schema/vrs/json/TraversalBlock @@ -38,7 +38,7 @@ "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.", "$comment": "Extension objects have a key-value data structure that allows definition of custom fields in the data itself. Extensions are not expected to be natively understood, but may be used for pre-negotiated exchange of message attributes between systems." diff --git a/schema/vrs/vrs-source.yaml b/schema/vrs/vrs-source.yaml index 64982738..94a4d827 100644 --- a/schema/vrs/vrs-source.yaml +++ b/schema/vrs/vrs-source.yaml @@ -16,11 +16,6 @@ strict: true imports: gks.core-im: ../core-im/core-im-source.yaml - gks.data-types: ../data-types/data-types-source.yaml - -namespaces: - gks.core-im: ../core-im/core-im-source.json#/$defs/ - gks.data-types: ../data-types/data-types-source.json#/$defs/ $defs: # VRS definitions are presented top-down. Everything rolls up to @@ -143,7 +138,7 @@ $defs: MUST be "Allele" location: oneOf: - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" - $ref: "#/$defs/Location" description: >- The location of the Allele @@ -178,7 +173,7 @@ $defs: items: oneOf: - $ref: "#/$defs/Allele" - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" description: >- A list of :ref:`Alleles ` that are found in-cis on a shared molecule. sequenceReference: @@ -203,7 +198,7 @@ $defs: heritableProperties: location: oneOf: - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" - $ref: "#/$defs/Location" description: >- A location for which the number of systemic copies is described. @@ -254,7 +249,7 @@ $defs: description: >- MUST be "CopyNumberChange" copyChange: - $refCurie: gks.data-types:Coding + $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/Coding" description: >- MUST be a :ref:`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), @@ -292,7 +287,7 @@ $defs: description: MUST be "SequenceLocation" sequenceReference: oneOf: - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" - $ref: "#/$defs/SequenceReference" description: A reference to a :ref:`Sequence` on which the location is defined. start: @@ -519,7 +514,7 @@ $defs: ordered: true items: oneOf: - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" - $ref: "#/$defs/Location" description: The terminal sequence or pair of adjoined sequences that defines in the adjacency. minItems: 2 @@ -556,7 +551,7 @@ $defs: description: MUST be "Terminus". location: oneOf: - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" - $ref: "#/$defs/Location" description: The location of the terminus. required: @@ -585,7 +580,7 @@ $defs: ordered: true items: oneOf: - - $ref: "/ga4gh/schema/gks-common/1.x/data-types/json/IRI" + - $ref: "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" - $ref: "#/$defs/TraversalBlock" description: >- The molecular components that constitute the derivative molecule. diff --git a/submodules/gks-common b/submodules/gks-common index 1cf59456..0018c1b7 160000 --- a/submodules/gks-common +++ b/submodules/gks-common @@ -1 +1 @@ -Subproject commit 1cf59456983d6dfe843b2b1f278510fa1b9a5762 +Subproject commit 0018c1b7546559efbf5c2cc4090c6a2f9854316f