update SM gks-core reorg (#62)

schema/Makefile

@@ -0,0 +1,5 @@
+all:
+	(cd cat-vrs; make all)
+
+clean:
+	(cd cat-vrs; make clean)

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)
+	rm $(BUILD_DIR)/*
+	rm $(DEF_DIR)/*
+	rm $(JSON_DIR)/*

schema/cat-vrs/profiles/cat-vrs-profiles-source.yaml → 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
@@ -83,16 +83,16 @@ $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:
                       contains:
                         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"
+      - $ref: "/ga4gh/schema/cat-vrs/1.x/json/CategoricalVariant"

schema/cat-vrs/core/cat-vrs-core-source.yaml → 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:

schema/cat-vrs/profiles/def/CanonicalAllele.rst → 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 <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.

schema/cat-vrs/profiles/def/CanonicalAlleleProperties.rst → 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.

schema/cat-vrs/profiles/def/CategoricalCnv.rst → 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.

schema/cat-vrs/profiles/def/CategoricalCnvProperties.rst → 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.

schema/cat-vrs/core/def/CategoricalVariant.rst → 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

schema/cat-vrs/core/def/Constraint.rst → 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.

schema/cat-vrs/core/def/CopyChangeConstraint.rst → 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

schema/cat-vrs/core/def/CopyCountConstraint.rst → 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

schema/cat-vrs/core/def/DefiningContextConstraint.rst → 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.

schema/cat-vrs/profiles/def/ProteinSequenceConsequenceProperties.rst → 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.

schema/cat-vrs/profiles/json/CanonicalAllele → 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"
       }
    ]
 }

schema/cat-vrs/profiles/json/CanonicalAlleleProperties → 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",