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

docs/source/standard-profiles/index.rst → docs/source/base-profiles/index.rst

@@ -1,11 +1,11 @@
-.. _standard-profiles:
+.. _base-profiles:
 
-Standard Profiles
-!!!!!!!!!!!!!!!!!
+Base Profiles
+!!!!!!!!!!!!!
 
 ``PREREQUISITES:`` :ref:`Introduction <introduction>`,  :ref:`Core Information Model <gks-core>`
 
-**VA Standard Profiles** are the end product of the VA Modeling Framework, providing standard models that will be used by the GA4GH community to store and exchange variant data. They are built as specializations of the :ref:`Statement<Statement>`, :ref:`Study Result<StudyResult>`, or :ref:`EvidenceLine<EvidenceLine>` classes in the Core-IM, each supporting a specific type of knowledge about genetic variation.  
+**VA Base Profiles** are the end product of the VA Modeling Framework for exchanging variant knowledge. They are built as specializations of the :ref:`Statement<Statement>`, :ref:`Study Result<StudyResult>`, or :ref:`EvidenceLine<EvidenceLine>` classes in the Core-IM, each supporting a specific type of knowledge about genetic variation.  
 
  * **Statement Profiles** are used to represent discrete assertions of general **knowledge** about a variant (e.g. a pathogenicity classification).  
 

docs/source/standard-profiles/statement-profiles.rst → docs/source/base-profiles/statement-profiles.rst

@@ -25,32 +25,27 @@ Below are the **Standard Statement Profiles** currently defined as part of the V
 Variant Pathogenicity Statement
 ###############################
 
-An example of data structured using this Standard Profile can be found `here <https://va-ga4gh.readthedocs.io/en/stable/examples/variant-pathogenicity-statement.html>`_.
-
-.. include::  ../../../schema/profiles/def/VariantPathogenicityStatement.rst
-
+.. include::  ../def/va-spec/VariantPathogenicityStatement.rst
 
 Variant Oncogenicity Study Statement
 ####################################
 
-.. include::  ../../../schema/profiles/def/VariantOncogenicityStudyStatement.rst
-
+.. include::  ../def/va-spec/VariantOncogenicityStudyStatement.rst
 
 Variant Therapeutic Response Study Statement
 #############################################
 
-.. include::  ../../../schema/profiles/def/VariantTherapeuticResponseStudyStatement.rst
+.. include::  ../def/va-spec/VariantTherapeuticResponseStudyStatement.rst
 
 .. _variant-diagnostic-statement-profile:
 
 Variant Diagnostic Study Statement
 ##################################
 
-.. include::  ../../../schema/profiles/def/VariantDiagnosticStudyStatement.rst
-
+.. include::  ../def/va-spec/VariantDiagnosticStudyStatement.rst
 
 Variant Prognostic Study Statement
 ##################################
 
-.. include::  ../../../schema/profiles/def/VariantPrognosticStudyStatement.rst
+.. include::  ../def/va-spec/VariantPrognosticStudyStatement.rst
 

docs/source/community-profiles/acmg-2015.rst

@@ -0,0 +1,13 @@
+.. _acmg-2015:
+
+ACMG/AMP 2015 Community Profiles
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+Below are the **ACMG/AMP 2015 Community Profiles**.
+
+.. _acmg-2015-statement-profile:
+
+Variant Pathogenicity Statement (ACMG 2015)
+###########################################
+
+.. include::  ../def/va-spec.acmg-2015/VariantPathogenicityStatement.rst

docs/source/community-profiles/index.rst

@@ -0,0 +1,16 @@
+.. _community-profiles:
+
+Community Profiles
+!!!!!!!!!!!!!!!!!!
+
+``PREREQUISITES:`` :ref:`Introduction <introduction>`,  :ref:`Core Information Model <gks-core>`
+
+**VA Community Profiles** are constrained specializations of :ref:`base-profiles`.
+
+ * **ACMG/AMP 2015 Profiles** are used to represent data from the ACMG 2015 variant pathogenicity guidelines.
+
+.. toctree::
+   :maxdepth: 4
+   :titlesonly:
+
+   acmg-2015

docs/source/def/cat-vrs

@@ -0,0 +1 @@
+../../../schema/cat-vrs/def

docs/source/def/gks-core

@@ -0,0 +1 @@
+../../../schema/gks-core/def

docs/source/def/va-spec

@@ -0,0 +1 @@
+../../../schema/va-spec/base/def

docs/source/def/va-spec.acmg-2015

@@ -0,0 +1 @@
+../../../schema/va-spec/acmg-2015/def

docs/source/def/vrs

@@ -0,0 +1 @@
+../../../schema/vrs/def

docs/source/index.rst

@@ -15,8 +15,8 @@ Readers may wish to review this :ref:`annotated data example <variant-pathogenic
    Resources to help implementers begin working with the VA-Spec.
 * :ref:`Core Information Model (Core-IM) <gks-core>`
    Detailed descriptions and implementation guidance for the classes and attributes in the foundational Core-IM.
-* :ref:`Standard Profiles <standard-profiles>`
-   Detailed descriptions and implementation guidance for Statement and Study Result Profiles provided as standards for representing variant knowledge. 
+* :ref:`Base Profiles <base-profiles>`
+   Detailed descriptions and implementation guidance for Statement and Study Result Profiles for representing variant knowledge. 
 * :ref:`Profiling Methodology <profiling-methodology>`
    Instructions and resources for creating or expanding Statement and Study Result Profiles through the SEPIO profiling process.
 * :ref:`Modeling Foundations <modeling-foundations>`
@@ -40,7 +40,8 @@ If you have questions or feedback, please reach out to the VA Team on `Slack <ht
    introduction
    quick-start
    core-information-model/index
-   standard-profiles/index
+   base-profiles/index
+   community-profiles/index
    profiling-methodology
    modeling-foundations
    reference-implementation

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/example-rst-output-for-allof-classes.rst

@@ -0,0 +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 Statement describing the role of a variant in causing an inherited condition.
+
+**Profile Conditions**
+
+This class adds the following conditions to the :ref:`variant-pathogenicity-evidence-line-profile`:
+
+- `VariantPathogenicityStatement.classification` is additionally defined as 
+  *The ACMG 2015 classification of the variant's pathogenicity*.
+    - `.classification.label` is constrained to values `pathogenic`, `likely pathogenic`,
+      `uncertain significance`, `likely benign`, and `benign`.

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

@@ -0,0 +1,33 @@
+$schema: "https://json-schema.org/draft/2020-12/schema"
+$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-evidence-line-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:
+  VariantPathogenicityFunctionalImpactEvidenceLine:
+    maturity: draft
+    description: >-
+      An Evidence Line providing information about the functional impact of a variant on a gene or gene product.
+    allOf:
+    - $ref: "/ga4gh/schema/va-spec/1.x/base/VariantPathogenicityEvidenceLine"
+    - properties:
+        strengthOfEvidenceProvided:           # TO DO: Ensure that the enum below covers terms needed for initial adopters. Merge https://github.com/ga4gh/gks-core/pull/78 which updates the core IM to allow this property to take a string so we can define the enum here. Think about if we need the 'PS'/'BS' parts of enum value labels - as this bakes in direction, and is duplicative as the 'specifiedBy' attribute reports the ACMG criterion applied. 
+          extends: strengthOfEvidenceProvided
+          type: string                       # Note that in the core model, the data type for this attribute was changed to be a MappableConcept. How then can we define a set of allowable values?  Do we even want to do this in the base profile at all (maybe this constraint goes in a Community Profile)?
+          enum:
+            - PS3_Strong
+            - PS3_Moderate
+            - PS3_Supporting
+            - BS3_Strong
+            - BS3_Moderate
+            - BS3_Supporting
+          description: >-
+            The strength of support that an Evidence Line is determined to provide for or against
+            the pathogenicity of the assessed variant. Strength is evaluated relative to the direction
+            indicated by the directionOfEvidenceProvided attribute.            

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 $^)