From 2b2aeec42f873d1b7b30dbe0d072945f18f66b30 Mon Sep 17 00:00:00 2001 From: Larry Babb Date: Thu, 31 Oct 2024 20:58:01 -0400 Subject: [PATCH] update SM gks-core reorg (#62) --- schema/Makefile | 5 ++ schema/cat-vrs/Makefile | 47 ++++++++++++++++--- ...ource.yaml => cat-vrs-recipes-source.yaml} | 26 +++++----- ...s-core-source.yaml => cat-vrs-source.yaml} | 14 +++--- schema/cat-vrs/core/Makefile | 44 ----------------- .../{profiles => }/def/CanonicalAllele.rst | 6 +++ .../def/CanonicalAlleleProperties.rst | 6 +++ .../{profiles => }/def/CategoricalCnv.rst | 6 +++ .../def/CategoricalCnvProperties.rst | 6 +++ .../{core => }/def/CategoricalVariant.rst | 8 +++- schema/cat-vrs/{core => }/def/Constraint.rst | 6 +++ .../{core => }/def/CopyChangeConstraint.rst | 6 +++ .../{core => }/def/CopyCountConstraint.rst | 6 +++ .../def/DefiningContextConstraint.rst | 6 +++ .../def/ProteinSequenceConsequence.rst | 0 .../ProteinSequenceConsequenceProperties.rst | 6 +++ .../{profiles => }/json/CanonicalAllele | 6 +-- .../json/CanonicalAlleleProperties | 4 +- .../{profiles => }/json/CategoricalCnv | 6 +-- .../json/CategoricalCnvProperties | 8 ++-- .../{core => }/json/CategoricalVariant | 14 +++--- schema/cat-vrs/{core => }/json/Constraint | 8 ++-- .../{core => }/json/CopyChangeConstraint | 4 +- .../{core => }/json/CopyCountConstraint | 2 +- .../{core => }/json/DefiningContextConstraint | 4 +- .../json/ProteinSequenceConsequence | 6 +-- .../json/ProteinSequenceConsequenceProperties | 4 +- schema/cat-vrs/profiles/Makefile | 44 ----------------- schema/cat-vrs/profiles/prune.mk | 11 ----- schema/cat-vrs/{core => }/prune.mk | 0 schema/core-im | 1 - schema/domain-entities | 1 - schema/gks-core | 1 + submodules/vrs | 2 +- 34 files changed, 161 insertions(+), 163 deletions(-) create mode 100644 schema/Makefile rename schema/cat-vrs/{profiles/cat-vrs-profiles-source.yaml => cat-vrs-recipes-source.yaml} (77%) rename schema/cat-vrs/{core/cat-vrs-core-source.yaml => cat-vrs-source.yaml} (91%) delete mode 100644 schema/cat-vrs/core/Makefile rename schema/cat-vrs/{profiles => }/def/CanonicalAllele.rst (73%) rename schema/cat-vrs/{profiles => }/def/CanonicalAlleleProperties.rst (58%) rename schema/cat-vrs/{profiles => }/def/CategoricalCnv.rst (55%) rename schema/cat-vrs/{profiles => }/def/CategoricalCnvProperties.rst (58%) rename schema/cat-vrs/{core => }/def/CategoricalVariant.rst (84%) rename schema/cat-vrs/{core => }/def/Constraint.rst (60%) rename schema/cat-vrs/{core => }/def/CopyChangeConstraint.rst (67%) rename schema/cat-vrs/{core => }/def/CopyCountConstraint.rst (67%) rename schema/cat-vrs/{core => }/def/DefiningContextConstraint.rst (84%) rename schema/cat-vrs/{profiles => }/def/ProteinSequenceConsequence.rst (100%) rename schema/cat-vrs/{profiles => }/def/ProteinSequenceConsequenceProperties.rst (59%) rename schema/cat-vrs/{profiles => }/json/CanonicalAllele (71%) rename schema/cat-vrs/{profiles => }/json/CanonicalAlleleProperties (85%) rename schema/cat-vrs/{profiles => }/json/CategoricalCnv (53%) rename schema/cat-vrs/{profiles => }/json/CategoricalCnvProperties (74%) rename schema/cat-vrs/{core => }/json/CategoricalVariant (85%) rename schema/cat-vrs/{core => }/json/Constraint (52%) rename schema/cat-vrs/{core => }/json/CopyChangeConstraint (86%) rename schema/cat-vrs/{core => }/json/CopyCountConstraint (89%) rename schema/cat-vrs/{core => }/json/DefiningContextConstraint (91%) rename schema/cat-vrs/{profiles => }/json/ProteinSequenceConsequence (71%) rename schema/cat-vrs/{profiles => }/json/ProteinSequenceConsequenceProperties (80%) delete mode 100644 schema/cat-vrs/profiles/Makefile delete mode 100644 schema/cat-vrs/profiles/prune.mk rename schema/cat-vrs/{core => }/prune.mk (100%) delete mode 120000 schema/core-im delete mode 120000 schema/domain-entities create mode 120000 schema/gks-core diff --git a/schema/Makefile b/schema/Makefile new file mode 100644 index 0000000..2bf505f --- /dev/null +++ b/schema/Makefile @@ -0,0 +1,5 @@ +all: + (cd cat-vrs; make all) + +clean: + (cd cat-vrs; make clean) \ No newline at end of file diff --git a/schema/cat-vrs/Makefile b/schema/cat-vrs/Makefile index cb70e14..7575c82 100644 --- a/schema/cat-vrs/Makefile +++ b/schema/cat-vrs/Makefile @@ -1,11 +1,44 @@ -all: core-build profiles-build +.SECONDARY: +.DELETE_ON_ERROR: -core-build: - (cd core; make all) +BUILD_DIR := build +DEF_DIR := def +JSON_DIR := json +IMPORT_DIR := import -profiles-build: - (cd profiles; make all) +vpath %tag $(BUILD_DIR) +vpath %.classes $(BUILD_DIR) + +SOURCES := $(wildcard *-source.yaml) +TAGS := $(SOURCES:-source.yaml=.tag) +IMPORTS := $(wildcard $(IMPORT_DIR)/*-source.yaml) + +all: build-ordered ${TAGS} prune-tag + +build-ordered: | $(BUILD_DIR) + +$(BUILD_DIR): + mkdir $(BUILD_DIR) + +%.tag: %.classes %.json-tag %.defs-tag + touch $(BUILD_DIR)/$@ + +%.classes: %-source.yaml + source2classes $< >${BUILD_DIR}/$@ + +%.json-tag: %-source.yaml ${IMPORTS} + source2splitjs $< + touch $(BUILD_DIR)/$@ + +%.defs-tag: %-source.yaml ${IMPORTS} + y2t $< + touch $(BUILD_DIR)/$@ + +prune-tag: ${TAGS} + $(MAKE) -f prune.mk + touch $(BUILD_DIR)/$@ clean: - (cd core; make clean) - (cd profiles; make clean) \ No newline at end of file + rm $(BUILD_DIR)/* + rm $(DEF_DIR)/* + rm $(JSON_DIR)/* diff --git a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml b/schema/cat-vrs/cat-vrs-recipes-source.yaml similarity index 77% rename from schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml rename to schema/cat-vrs/cat-vrs-recipes-source.yaml index b1441e9..4e846d0 100644 --- a/schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml +++ b/schema/cat-vrs/cat-vrs-recipes-source.yaml @@ -1,12 +1,12 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/cat-vrs-profiles-source.yaml" -title: GA4GH-Cat-VRS-Definitions +$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/cat-vrs-recipes-source.yaml" +title: GA4GH-Cat-VRS-Recipe-Definitions type: object imports: - gks.core-im: ../../core-im/core-im-source.yaml - vrs: ../../vrs/vrs-source.yaml - cat.core: ../core/cat-vrs-core-source.yaml + gks.core-im: ../gks-core/gks-core-source.yaml + vrs: ../vrs/vrs-source.yaml + cat-vrs: ./cat-vrs-source.yaml $defs: ProteinSequenceConsequenceProperties: @@ -18,7 +18,7 @@ $defs: constraints: contains: allOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" - type: object properties: relations: @@ -37,7 +37,7 @@ $defs: that is representative of a collection of congruent Protein Alleles that share the same altered codon(s). allOf: - $ref: "#/$defs/ProteinSequenceConsequenceProperties" - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" CanonicalAlleleProperties: type: object @@ -48,7 +48,7 @@ $defs: constraints: contains: allOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" - type: object properties: relations: @@ -71,7 +71,7 @@ $defs: across different genome assemblies and associated cDNA transcript representations. allOf: - $ref: "#/$defs/CanonicalAlleleProperties" - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant" + - $ref: "/ga4gh/schema/cat-vrs/1.x/core/CategoricalVariant" CategoricalCnvProperties: type: object @@ -83,7 +83,7 @@ $defs: allOf: - contains: allOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" - type: object properties: relations: @@ -91,8 +91,8 @@ $defs: const: sequence_liftover - contains: anyOf: - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint" - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" required: - constraints @@ -103,4 +103,4 @@ $defs: A representation of the constraints for matching knowledge about CNVs. allOf: - $ref: "#/$defs/CategoricalCnvProperties" - - $ref: "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant" \ No newline at end of file + - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" \ No newline at end of file diff --git a/schema/cat-vrs/core/cat-vrs-core-source.yaml b/schema/cat-vrs/cat-vrs-source.yaml similarity index 91% rename from schema/cat-vrs/core/cat-vrs-core-source.yaml rename to schema/cat-vrs/cat-vrs-source.yaml index 04a4fea..0f87a7a 100644 --- a/schema/cat-vrs/core/cat-vrs-core-source.yaml +++ b/schema/cat-vrs/cat-vrs-source.yaml @@ -1,12 +1,12 @@ $schema: "https://json-schema.org/draft/2020-12/schema" -$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/core/cat-vrs-core-source.yaml" +$id: "https://w3id.org/ga4gh/schema/cat-vrs/1.x/cat-vrs-source.yaml" title: GA4GH-Cat-VRS-Definitions type: object strict: true imports: - gks.core-im: ../../core-im/core-im-source.yaml - vrs: ../../vrs/vrs-source.yaml + gks-core: ../gks-core/gks-core-source.yaml + vrs: ../vrs/vrs-source.yaml $defs: @@ -16,7 +16,7 @@ $defs: CategoricalVariant: type: object - inherits: gks.core-im:DomainEntity + inherits: gks-core:DomainEntity maturity: draft description: >- A representation of a categorically-defined domain for variation, in which individual @@ -36,7 +36,7 @@ $defs: items: oneOf: - $ref: /ga4gh/schema/vrs/2.x/json/Variation - - $ref: /ga4gh/schema/gks-common/1.x/core-im/json/IRI + - $ref: /ga4gh/schema/gks-core/1.x/gks-core/json/IRI constraints: type: array ordered: false @@ -78,7 +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/core-im/json/IRI + - $ref: /ga4gh/schema/gks-core/1.x/json/IRI relations: type: array ordered: false @@ -129,7 +129,7 @@ $defs: default: CopyChangeConstraint description: 'MUST be "CopyChangeConstraint"' copyChange: - $ref: /ga4gh/schema/gks-common/1.x/core-im/json/Coding + $ref: /ga4gh/schema/gks-core/1.x/json/Coding items: properties: code: diff --git a/schema/cat-vrs/core/Makefile b/schema/cat-vrs/core/Makefile deleted file mode 100644 index 7575c82..0000000 --- a/schema/cat-vrs/core/Makefile +++ /dev/null @@ -1,44 +0,0 @@ -.SECONDARY: -.DELETE_ON_ERROR: - -BUILD_DIR := build -DEF_DIR := def -JSON_DIR := json -IMPORT_DIR := import - -vpath %tag $(BUILD_DIR) -vpath %.classes $(BUILD_DIR) - -SOURCES := $(wildcard *-source.yaml) -TAGS := $(SOURCES:-source.yaml=.tag) -IMPORTS := $(wildcard $(IMPORT_DIR)/*-source.yaml) - -all: build-ordered ${TAGS} prune-tag - -build-ordered: | $(BUILD_DIR) - -$(BUILD_DIR): - mkdir $(BUILD_DIR) - -%.tag: %.classes %.json-tag %.defs-tag - touch $(BUILD_DIR)/$@ - -%.classes: %-source.yaml - source2classes $< >${BUILD_DIR}/$@ - -%.json-tag: %-source.yaml ${IMPORTS} - source2splitjs $< - touch $(BUILD_DIR)/$@ - -%.defs-tag: %-source.yaml ${IMPORTS} - y2t $< - touch $(BUILD_DIR)/$@ - -prune-tag: ${TAGS} - $(MAKE) -f prune.mk - touch $(BUILD_DIR)/$@ - -clean: - rm $(BUILD_DIR)/* - rm $(DEF_DIR)/* - rm $(JSON_DIR)/* diff --git a/schema/cat-vrs/profiles/def/CanonicalAllele.rst b/schema/cat-vrs/def/CanonicalAllele.rst similarity index 73% rename from schema/cat-vrs/profiles/def/CanonicalAllele.rst rename to schema/cat-vrs/def/CanonicalAllele.rst index 53c3e0a..6a91d2e 100644 --- a/schema/cat-vrs/profiles/def/CanonicalAllele.rst +++ b/schema/cat-vrs/def/CanonicalAllele.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** A canonical allele is defined by an `Allele `_ that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations. diff --git a/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst b/schema/cat-vrs/def/CanonicalAlleleProperties.rst similarity index 58% rename from schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst rename to schema/cat-vrs/def/CanonicalAlleleProperties.rst index 5bb090e..7aa176f 100644 --- a/schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst +++ b/schema/cat-vrs/def/CanonicalAlleleProperties.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** Cat-VRS Constraints found in Canonical Alleles. diff --git a/schema/cat-vrs/profiles/def/CategoricalCnv.rst b/schema/cat-vrs/def/CategoricalCnv.rst similarity index 55% rename from schema/cat-vrs/profiles/def/CategoricalCnv.rst rename to schema/cat-vrs/def/CategoricalCnv.rst index 4fd465e..6a34694 100644 --- a/schema/cat-vrs/profiles/def/CategoricalCnv.rst +++ b/schema/cat-vrs/def/CategoricalCnv.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** A representation of the constraints for matching knowledge about CNVs. diff --git a/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst b/schema/cat-vrs/def/CategoricalCnvProperties.rst similarity index 58% rename from schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst rename to schema/cat-vrs/def/CategoricalCnvProperties.rst index acdd353..271e301 100644 --- a/schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst +++ b/schema/cat-vrs/def/CategoricalCnvProperties.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** Cat-VRS Constraints found in CategoricalCnvs. diff --git a/schema/cat-vrs/core/def/CategoricalVariant.rst b/schema/cat-vrs/def/CategoricalVariant.rst similarity index 84% rename from schema/cat-vrs/core/def/CategoricalVariant.rst rename to schema/cat-vrs/def/CategoricalVariant.rst index 1c6b844..314f2b5 100644 --- a/schema/cat-vrs/core/def/CategoricalVariant.rst +++ b/schema/cat-vrs/def/CategoricalVariant.rst @@ -1,10 +1,16 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** A representation of a categorically-defined domain for variation, in which individual contextual variation instances may be members of the domain. **Information Model** -Some CategoricalVariant attributes are inherited from :ref:`gks.core-im:DomainEntity`. +Some CategoricalVariant attributes are inherited from :ref:`gks-core:DomainEntity`. .. list-table:: :class: clean-wrap diff --git a/schema/cat-vrs/core/def/Constraint.rst b/schema/cat-vrs/def/Constraint.rst similarity index 60% rename from schema/cat-vrs/core/def/Constraint.rst rename to schema/cat-vrs/def/Constraint.rst index 574e0f4..b3d3bb8 100644 --- a/schema/cat-vrs/core/def/Constraint.rst +++ b/schema/cat-vrs/def/Constraint.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** Constraints are used to construct an intensional semantics of categorical variant types. diff --git a/schema/cat-vrs/core/def/CopyChangeConstraint.rst b/schema/cat-vrs/def/CopyChangeConstraint.rst similarity index 67% rename from schema/cat-vrs/core/def/CopyChangeConstraint.rst rename to schema/cat-vrs/def/CopyChangeConstraint.rst index 681e5bc..fc22e11 100644 --- a/schema/cat-vrs/core/def/CopyChangeConstraint.rst +++ b/schema/cat-vrs/def/CopyChangeConstraint.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** A representation of copy number change diff --git a/schema/cat-vrs/core/def/CopyCountConstraint.rst b/schema/cat-vrs/def/CopyCountConstraint.rst similarity index 67% rename from schema/cat-vrs/core/def/CopyCountConstraint.rst rename to schema/cat-vrs/def/CopyCountConstraint.rst index 639c778..1931447 100644 --- a/schema/cat-vrs/core/def/CopyCountConstraint.rst +++ b/schema/cat-vrs/def/CopyCountConstraint.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** The absolute number of copies in a system diff --git a/schema/cat-vrs/core/def/DefiningContextConstraint.rst b/schema/cat-vrs/def/DefiningContextConstraint.rst similarity index 84% rename from schema/cat-vrs/core/def/DefiningContextConstraint.rst rename to schema/cat-vrs/def/DefiningContextConstraint.rst index 393e272..e385556 100644 --- a/schema/cat-vrs/core/def/DefiningContextConstraint.rst +++ b/schema/cat-vrs/def/DefiningContextConstraint.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** The location or location-state, congruent with other reference sequences, about which categorical variation is being described. diff --git a/schema/cat-vrs/profiles/def/ProteinSequenceConsequence.rst b/schema/cat-vrs/def/ProteinSequenceConsequence.rst similarity index 100% rename from schema/cat-vrs/profiles/def/ProteinSequenceConsequence.rst rename to schema/cat-vrs/def/ProteinSequenceConsequence.rst diff --git a/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst b/schema/cat-vrs/def/ProteinSequenceConsequenceProperties.rst similarity index 59% rename from schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst rename to schema/cat-vrs/def/ProteinSequenceConsequenceProperties.rst index 0b1eaef..f0660e3 100644 --- a/schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst +++ b/schema/cat-vrs/def/ProteinSequenceConsequenceProperties.rst @@ -1,3 +1,9 @@ + +.. warning:: This data class is at a **draft** maturity level and may change + significantly in future releases. Maturity levels are described in + the :ref:`maturity-model`. + + **Computational Definition** Cat-VRS Constraints found in Protein Sequence Consequences. diff --git a/schema/cat-vrs/profiles/json/CanonicalAllele b/schema/cat-vrs/json/CanonicalAllele similarity index 71% rename from schema/cat-vrs/profiles/json/CanonicalAllele rename to schema/cat-vrs/json/CanonicalAllele index 631d42c..19eff05 100644 --- a/schema/cat-vrs/profiles/json/CanonicalAllele +++ b/schema/cat-vrs/json/CanonicalAllele @@ -1,16 +1,16 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/CanonicalAllele", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CanonicalAllele", "title": "CanonicalAllele", "type": "object", "maturity": "draft", "description": "A canonical allele is defined by an [Allele](https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#) that is representative of a collection of congruent Alleles, each of which depict the same nucleic acid change on different underlying reference sequences. Congruent representations of an Allele often exist across different genome assemblies and associated cDNA transcript representations.", "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/profiles/json/CanonicalAlleleProperties" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CanonicalAlleleProperties" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" } ] } \ No newline at end of file diff --git a/schema/cat-vrs/profiles/json/CanonicalAlleleProperties b/schema/cat-vrs/json/CanonicalAlleleProperties similarity index 85% rename from schema/cat-vrs/profiles/json/CanonicalAlleleProperties rename to schema/cat-vrs/json/CanonicalAlleleProperties index f4cc583..38215a5 100644 --- a/schema/cat-vrs/profiles/json/CanonicalAlleleProperties +++ b/schema/cat-vrs/json/CanonicalAlleleProperties @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/CanonicalAlleleProperties", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CanonicalAlleleProperties", "title": "CanonicalAlleleProperties", "type": "object", "maturity": "draft", @@ -10,7 +10,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/profiles/json/CategoricalCnv b/schema/cat-vrs/json/CategoricalCnv similarity index 53% rename from schema/cat-vrs/profiles/json/CategoricalCnv rename to schema/cat-vrs/json/CategoricalCnv index 8d4d83c..86ea53b 100644 --- a/schema/cat-vrs/profiles/json/CategoricalCnv +++ b/schema/cat-vrs/json/CategoricalCnv @@ -1,16 +1,16 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/CategoricalCnv", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalCnv", "title": "CategoricalCnv", "type": "object", "maturity": "draft", "description": "A representation of the constraints for matching knowledge about CNVs.", "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/profiles/json/CategoricalCnvProperties" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalCnvProperties" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" } ] } \ No newline at end of file diff --git a/schema/cat-vrs/profiles/json/CategoricalCnvProperties b/schema/cat-vrs/json/CategoricalCnvProperties similarity index 74% rename from schema/cat-vrs/profiles/json/CategoricalCnvProperties rename to schema/cat-vrs/json/CategoricalCnvProperties index 4f0ad60..c0762dc 100644 --- a/schema/cat-vrs/profiles/json/CategoricalCnvProperties +++ b/schema/cat-vrs/json/CategoricalCnvProperties @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/CategoricalCnvProperties", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalCnvProperties", "title": "CategoricalCnvProperties", "type": "object", "maturity": "draft", @@ -12,7 +12,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" }, { "type": "object", @@ -31,10 +31,10 @@ "contains": { "anyOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" } ] } diff --git a/schema/cat-vrs/core/json/CategoricalVariant b/schema/cat-vrs/json/CategoricalVariant similarity index 85% rename from schema/cat-vrs/core/json/CategoricalVariant rename to schema/cat-vrs/json/CategoricalVariant index c3f4fcd..29b2d5e 100644 --- a/schema/cat-vrs/core/json/CategoricalVariant +++ b/schema/cat-vrs/json/CategoricalVariant @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant", "title": "CategoricalVariant", "type": "object", "maturity": "draft", @@ -31,7 +31,7 @@ "type": "array", "ordered": false, "items": { - "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Extension" + "$ref": "/ga4gh/schema/gks-core/1.x/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/core-im/json/ConceptMapping" + "$ref": "/ga4gh/schema/gks-core/1.x/json/ConceptMapping" }, "description": "A list of mappings to concepts in terminologies or code systems. Each mapping should include a coding and a relation." }, @@ -58,7 +58,7 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" + "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Variation" @@ -72,13 +72,13 @@ "items": { "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" } ] } diff --git a/schema/cat-vrs/core/json/Constraint b/schema/cat-vrs/json/Constraint similarity index 52% rename from schema/cat-vrs/core/json/Constraint rename to schema/cat-vrs/json/Constraint index 6b341e5..f7ddbdb 100644 --- a/schema/cat-vrs/core/json/Constraint +++ b/schema/cat-vrs/json/Constraint @@ -1,19 +1,19 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/core/json/Constraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/Constraint", "title": "Constraint", "type": "object", "maturity": "draft", "description": "Constraints are used to construct an intensional semantics of categorical variant types.", "oneOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" } ] } \ No newline at end of file diff --git a/schema/cat-vrs/core/json/CopyChangeConstraint b/schema/cat-vrs/json/CopyChangeConstraint similarity index 86% rename from schema/cat-vrs/core/json/CopyChangeConstraint rename to schema/cat-vrs/json/CopyChangeConstraint index 44af32f..6de3d40 100644 --- a/schema/cat-vrs/core/json/CopyChangeConstraint +++ b/schema/cat-vrs/json/CopyChangeConstraint @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/core/json/CopyChangeConstraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CopyChangeConstraint", "title": "CopyChangeConstraint", "type": "object", "maturity": "draft", @@ -13,7 +13,7 @@ "description": "MUST be \"CopyChangeConstraint\"" }, "copyChange": { - "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/Coding", + "$ref": "/ga4gh/schema/gks-core/1.x/json/Coding", "items": { "properties": { "code": { diff --git a/schema/cat-vrs/core/json/CopyCountConstraint b/schema/cat-vrs/json/CopyCountConstraint similarity index 89% rename from schema/cat-vrs/core/json/CopyCountConstraint rename to schema/cat-vrs/json/CopyCountConstraint index 5bb682d..e1bcb69 100644 --- a/schema/cat-vrs/core/json/CopyCountConstraint +++ b/schema/cat-vrs/json/CopyCountConstraint @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/core/json/CopyCountConstraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/CopyCountConstraint", "title": "CopyCountConstraint", "type": "object", "maturity": "draft", diff --git a/schema/cat-vrs/core/json/DefiningContextConstraint b/schema/cat-vrs/json/DefiningContextConstraint similarity index 91% rename from schema/cat-vrs/core/json/DefiningContextConstraint rename to schema/cat-vrs/json/DefiningContextConstraint index e576fc2..867dc28 100644 --- a/schema/cat-vrs/core/json/DefiningContextConstraint +++ b/schema/cat-vrs/json/DefiningContextConstraint @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint", "title": "DefiningContextConstraint", "type": "object", "maturity": "draft", @@ -15,7 +15,7 @@ "definingContext": { "oneOf": [ { - "$ref": "/ga4gh/schema/gks-common/1.x/core-im/json/IRI" + "$ref": "/ga4gh/schema/gks-core/1.x/json/IRI" }, { "$ref": "/ga4gh/schema/vrs/2.x/json/Location" diff --git a/schema/cat-vrs/profiles/json/ProteinSequenceConsequence b/schema/cat-vrs/json/ProteinSequenceConsequence similarity index 71% rename from schema/cat-vrs/profiles/json/ProteinSequenceConsequence rename to schema/cat-vrs/json/ProteinSequenceConsequence index 93b6fe2..cbd25cf 100644 --- a/schema/cat-vrs/profiles/json/ProteinSequenceConsequence +++ b/schema/cat-vrs/json/ProteinSequenceConsequence @@ -1,15 +1,15 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/ProteinSequenceConsequence", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/ProteinSequenceConsequence", "title": "ProteinSequenceConsequence", "type": "object", "description": "A change that occurs in a protein sequence as a result of genomic changes. Due to the degenerate nature of the genetic code, there are often several genomic changes that can cause a protein sequence consequence. The protein sequence consequence, like a CanonicalAllele, is defined by an [Allele](https://vrs.ga4gh.org/en/2.x/concepts/MolecularVariation/Allele.html#) that is representative of a collection of congruent Protein Alleles that share the same altered codon(s).", "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/profiles/json/ProteinSequenceConsequenceProperties" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/ProteinSequenceConsequenceProperties" }, { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/CategoricalVariant" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant" } ] } \ No newline at end of file diff --git a/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties b/schema/cat-vrs/json/ProteinSequenceConsequenceProperties similarity index 80% rename from schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties rename to schema/cat-vrs/json/ProteinSequenceConsequenceProperties index d983263..e4fd32a 100644 --- a/schema/cat-vrs/profiles/json/ProteinSequenceConsequenceProperties +++ b/schema/cat-vrs/json/ProteinSequenceConsequenceProperties @@ -1,6 +1,6 @@ { "$schema": "https://json-schema.org/draft/2020-12/schema", - "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/profiles/json/ProteinSequenceConsequenceProperties", + "$id": "https://w3id.org/ga4gh/schema/cat-vrs/1.x/json/ProteinSequenceConsequenceProperties", "title": "ProteinSequenceConsequenceProperties", "type": "object", "maturity": "draft", @@ -10,7 +10,7 @@ "contains": { "allOf": [ { - "$ref": "/ga4gh/schema/cat-vrs/1.x/core/json/DefiningContextConstraint" + "$ref": "/ga4gh/schema/cat-vrs/1.x/json/DefiningContextConstraint" }, { "type": "object", diff --git a/schema/cat-vrs/profiles/Makefile b/schema/cat-vrs/profiles/Makefile deleted file mode 100644 index 7575c82..0000000 --- a/schema/cat-vrs/profiles/Makefile +++ /dev/null @@ -1,44 +0,0 @@ -.SECONDARY: -.DELETE_ON_ERROR: - -BUILD_DIR := build -DEF_DIR := def -JSON_DIR := json -IMPORT_DIR := import - -vpath %tag $(BUILD_DIR) -vpath %.classes $(BUILD_DIR) - -SOURCES := $(wildcard *-source.yaml) -TAGS := $(SOURCES:-source.yaml=.tag) -IMPORTS := $(wildcard $(IMPORT_DIR)/*-source.yaml) - -all: build-ordered ${TAGS} prune-tag - -build-ordered: | $(BUILD_DIR) - -$(BUILD_DIR): - mkdir $(BUILD_DIR) - -%.tag: %.classes %.json-tag %.defs-tag - touch $(BUILD_DIR)/$@ - -%.classes: %-source.yaml - source2classes $< >${BUILD_DIR}/$@ - -%.json-tag: %-source.yaml ${IMPORTS} - source2splitjs $< - touch $(BUILD_DIR)/$@ - -%.defs-tag: %-source.yaml ${IMPORTS} - y2t $< - touch $(BUILD_DIR)/$@ - -prune-tag: ${TAGS} - $(MAKE) -f prune.mk - touch $(BUILD_DIR)/$@ - -clean: - rm $(BUILD_DIR)/* - rm $(DEF_DIR)/* - rm $(JSON_DIR)/* diff --git a/schema/cat-vrs/profiles/prune.mk b/schema/cat-vrs/profiles/prune.mk deleted file mode 100644 index 5d52ce5..0000000 --- a/schema/cat-vrs/profiles/prune.mk +++ /dev/null @@ -1,11 +0,0 @@ -BUILD_DIR := build -SOURCES := $(wildcard *-source.yaml) -CLASS_FILTER_FILES = $(SOURCES:%-source.yaml=${BUILD_DIR}/%.classes) -FILTER_CLASSES := $(shell cat ${CLASS_FILTER_FILES}) -FILTER_JSONS = $(FILTER_CLASSES:%=json/%) -FILTER_DEFS = $(FILTER_CLASSES:%=def/%.rst) - -.DEFAULT: prune - -prune: $(filter-out ${FILTER_JSONS} ${FILTER_DEFS},$(wildcard def/* json/*)) - $(if $^,rm $^) \ No newline at end of file diff --git a/schema/cat-vrs/core/prune.mk b/schema/cat-vrs/prune.mk similarity index 100% rename from schema/cat-vrs/core/prune.mk rename to schema/cat-vrs/prune.mk diff --git a/schema/core-im b/schema/core-im deleted file mode 120000 index 98b8af6..0000000 --- a/schema/core-im +++ /dev/null @@ -1 +0,0 @@ -../submodules/vrs/submodules/gks-common/schema/core-im \ No newline at end of file diff --git a/schema/domain-entities b/schema/domain-entities deleted file mode 120000 index a18d7b7..0000000 --- a/schema/domain-entities +++ /dev/null @@ -1 +0,0 @@ -../submodules/vrs/submodules/gks-common/schema/domain-entities \ No newline at end of file diff --git a/schema/gks-core b/schema/gks-core new file mode 120000 index 0000000..eeba6fc --- /dev/null +++ b/schema/gks-core @@ -0,0 +1 @@ +../submodules/vrs/submodules/gks-core/schema/gks-core \ No newline at end of file diff --git a/submodules/vrs b/submodules/vrs index f2ec1ba..24c6405 160000 --- a/submodules/vrs +++ b/submodules/vrs @@ -1 +1 @@ -Subproject commit f2ec1ba41c03ddde2c28ff39726dbb634fe9a7c2 +Subproject commit 24c64057c81ebab9cf0b34d7f2db4eb90df7262e