Moved outstanding exp-func-imp PR into this PR with latest reorg

.requirements.txt

@@ -2,7 +2,7 @@ pytest
 sphinx ~= 7.2
 sphinx-rtd-theme ~= 1.3
 pyyaml
-ga4gh.gks.metaschema==0.3.0b14
+ga4gh.gks.metaschema==0.3.0b16
 jsonschema
 referencing
 jupyterlab

schema/Makefile

@@ -1,7 +1,15 @@
-all: va-base
+all: base-all acmg-2015-all
 
-va-base:
+clean: base-clean acmg-2015-clean
+
+base-all:
 	(cd va-spec/base; make all)
 
-clean:
-	(cd va-spec/base; make clean)
+acmg-2015-all:
+	(cd va-spec/acmg-2015; make all)
+
+base-clean:
+	(cd va-spec/base; make clean)
+
+acmg-2015-clean:
+	(cd va-spec/acmg-2015; make clean)

schema/va-spec/acmg-2015/Makefile

@@ -0,0 +1,44 @@
+.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)/*

schema/va-spec/acmg-2015/def/VariantPathogenicityStatement.rst

@@ -0,0 +1,22 @@
+.. 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 Statement describing the role of a variant in causing an inherited condition.
+
+**Information Model**
+
+
+.. list-table::
+   :class: clean-wrap
+   :header-rows: 1
+   :align: left
+   :widths: auto
+
+   *  - Field
+      - Flags
+      - Type
+      - Limits
+      - Description

schema/va-spec/acmg-2015/json/VariantPathogenicityStatement

@@ -0,0 +1,19 @@
+{
+   "$schema": "https://json-schema.org/draft/2020-12/schema",
+   "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/json/VariantPathogenicityStatement",
+   "title": "VariantPathogenicityStatement",
+   "maturity": "draft",
+   "description": "A Statement describing the role of a variant in causing an inherited condition.",
+   "allOf": [
+      {
+         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPathogenicityStatement"
+      },
+      {
+         "properties": {
+            "classification": {
+               "description": "The ACMG 2015 classification of the variant's pathogenicity."
+            }
+         }
+      }
+   ]
+}

schema/va-spec/acmg-2015/pathogenicity-statement-profile-source.yaml

@@ -0,0 +1,32 @@
+$schema: "https://json-schema.org/draft/2020-12/schema"
+$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/acmg-2015/pathogenicity-statement-profile-source.yaml"
+title: ACMG 2015 Variant Pathogenicity Statement Standard Profile
+strict: true
+
+imports:
+  va-spec: ../base/pathogenicity-statement-profile-source.yaml
+  cat-vrs: ../../cat-vrs/cat-vrs-source.yaml
+  vrs: ../../vrs/vrs-source.yaml
+  gks-core: ../../gks-core/gks-core-source.yaml
+
+$defs:
+  VariantPathogenicityStatement:
+    maturity: draft
+    description: >-
+      A Statement describing the role of a variant in causing an inherited condition.
+    allOf:
+    - $ref: "/ga4gh/schema/va-spec/1.x/base/VariantPathogenicityStatement"
+    - properties:
+        classification:
+          # this is a MappableConcept but we would ideally like to specify a value set with meta characteristics to validate with some consistency
+          # type: string
+          # enum:
+          #   - pathogenic
+          #   - likely pathogenic
+          #   - uncertain significance
+          #   - likely benign
+          #   - benign
+          description: >-
+            The ACMG 2015 classification of the variant's pathogenicity.
+
+

schema/va-spec/acmg-2015/prune.mk

@@ -0,0 +1,11 @@
+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 $^)

schema/va-spec/base/caf-study-result-source.yaml → schema/va-spec/base/cohort-allele-frequency-study-result-profile-source.yaml

@@ -1,5 +1,5 @@
 $schema: "https://json-schema.org/draft/2020-12/schema"
-$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/caf-study-result-source.yaml"
+$id: "https://w3id.org/ga4gh/schema/va-spec/1.x/base/cohort-allele-frequency-study-result-profile-source.yaml"
 title: Cohort Allele Frequency Study Result Standard Profile
 strict: true