gks-tech sync prep: reorg core/va classes and get tests working (#217)

* gks-tech sync prep: reorg core/va classes and get tests working * changes from 2024-11-13 gks-tech sync review * gks-tech-updates from 11-15-2024 mtg * final change before 11/15/24 sync meeting * DRY refactor SubjectVariant in propositions * evidence code enum revision (#218) * update oncogenicity proposition to current va-spec model (#219) * init trial use coverage tests * revise available attributes in base models * bring test examples in line with schema changes * add coverage exception config --------- Co-authored-by: Alex H. Wagner, PhD <Alex.Wagner@nationwidechildrens.org>
ga4gh · Nov 19, 2024 · 27ac565 · 27ac565
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diff --git a/docs/source/base-profiles/statement-profiles.rst b/docs/source/base-profiles/statement-profiles.rst
@@ -1,51 +1,51 @@
 .. _statement-profiles:
 
-Statement Profiles
+Proposition Profiles
 !!!!!!!!!!!!!!!!!!
 
-In the **GKS-Core-IM**, each discrete assertion of knowledge is captured in a self-contained ``Statement`` object which roots a :ref:`data structure <core-im-statement-data-structure>` supporting rich and flexible descriptions of the evidence and provenance supporting this knowledge. 
+In the **GKS-Core-IM**, each discrete assertion of knowledge is captured in a self-contained ``Proposition`` object which roots a :ref:`data structure <core-im-statement-data-structure>` supporting rich and flexible descriptions of the evidence and provenance supporting this knowledge. 
 
-**Statement Profiles** are defined as specializations of this Core-IM ``Statement`` class, to provide a concrete schema for representing a particular type of Variant knowledge (e.g. variant pathogenicity classifications).
+**Proposition Profiles** are defined as specializations of this Core-IM ``Proposition`` class, to provide a concrete schema for representing a particular type of Variant knowledge (e.g. variant pathogenicity classifications).
 
-The basic structure of Statement Profiles built on the Core-IM is illustrated below. The process used to specialize this structure for a specific Statement type is described in the :ref:`Profiling Methodology<profiling-methodology>`.
+The basic structure of Proposition Profiles built on the Core-IM is illustrated below. The process used to specialize this structure for a specific Statement type is described in the :ref:`Profiling Methodology<profiling-methodology>`.
 
 .. _statement-data-structure:
 
 .. figure:: ../images/statement-data-structure.png
 
    Statement Data Structure
 
-   **Legend** A view of the core data structure rooted by the Statement class, which can be leveraged in defining a Statement Profile. This view focuses on the most important and commonly used attributes and relationships in the model. Note that specific subtypes of InformtionEntity are listed at the bottom of this Class, but not shown for space.  See Core-IM pags for these classes for details. 
+   **Legend** A view of the core data structure rooted by the Statement class, which can be leveraged in defining a Proposition Profile. This view focuses on the most important and commonly used attributes and relationships in the model. Note that specific subtypes of InformtionEntity are listed at the bottom of this Class, but not shown for space.  See Core-IM pags for these classes for details. 
 ---------
 
-Below are the **Standard Statement Profiles** currently defined as part of the VA-Spec, and available for adoption or extension by Driver Project implementations. **JSON Schema** for each Profile can be found `here <https://github.com/ga4gh/va-spec/tree/1.x/schema/profiles/json>`_. 
+Below are the **Standard Proposition Profiles** currently defined as part of the VA-Spec, and available for adoption or extension by Driver Project implementations. **JSON Schema** for each Profile can be found `here <https://github.com/ga4gh/va-spec/tree/1.x/schema/profiles/json>`_. 
 
-.. _variant-pathogenicity-statement-profile:
+.. _variant-pathogenicity-proposition-profile:
 
-Variant Pathogenicity Statement
-###############################
+Variant Pathogenicity Proposition
+#################################
 
-.. include::  ../def/va-spec/VariantPathogenicityStatement.rst
+.. include::  ../def/va-spec/VariantPathogenicityProposition.rst
 
-Variant Oncogenicity Study Statement
-####################################
+Variant Oncogenicity Study Proposition
+######################################
 
-.. include::  ../def/va-spec/VariantOncogenicityStudyStatement.rst
+.. include::  ../def/va-spec/VariantOncogenicityStudyProposition.rst
 
-Variant Therapeutic Response Study Statement
-#############################################
+Variant Therapeutic Response Study Proposition
+##############################################
 
-.. include::  ../def/va-spec/VariantTherapeuticResponseStudyStatement.rst
+.. include::  ../def/va-spec/VariantTherapeuticResponseStudyProposition.rst
 
 .. _variant-diagnostic-statement-profile:
 
-Variant Diagnostic Study Statement
-##################################
+Variant Diagnostic Study Proposition
+####################################
 
-.. include::  ../def/va-spec/VariantDiagnosticStudyStatement.rst
+.. include::  ../def/va-spec/VariantDiagnosticStudyProposition.rst
 
-Variant Prognostic Study Statement
-##################################
+Variant Prognostic Study Proposition
+####################################
 
-.. include::  ../def/va-spec/VariantPrognosticStudyStatement.rst
+.. include::  ../def/va-spec/VariantPrognosticStudyProposition.rst
 
diff --git a/docs/source/base-profiles/study-result-profiles.rst b/docs/source/base-profiles/study-result-profiles.rst
@@ -14,10 +14,10 @@ Cohort Allele Frequency Study Result
 ####################################
 
 
-.. include::  ../../../schema/profiles/def/CohortAlleleFrequencyStudyResult.rst
+.. include::  ../def/va-spec/CohortAlleleFrequencyStudyResult.rst
 
 
-Assay Variant Effect Measurement Study Result
-#############################################
+Experimental Variant Functional Impact Study Result
+###################################################
 
-.. include::  ../../../schema/profiles/def/AssayVariantEffectMeasurementStudyResult.rst
+.. include::  ../def/va-spec/ExperimentalVariantFunctionalImpactStudyResult.rst
diff --git a/docs/source/core-information-model/data-types.rst b/docs/source/core-information-model/data-types.rst
@@ -11,26 +11,26 @@ Complex Data Types
 Coding
 ******
 
-.. include::  ../../../schema/gks-core/def/Coding.rst
+.. include::  ../def/gks-core/Coding.rst
 
 .. _Extension:
 
 Extension
 *********
-.. include::  ../../../schema/gks-core/def/Extension.rst
+.. include::  ../def/gks-core/Extension.rst
 
 
 .. _RecordMetadata:
 
 RecordMetadata
 **************
 
-.. include::  ../../../schema/gks-core/def/RecordMetadata.rst
+.. include::  ../def/va-spec/RecordMetadata.rst
 
 ConceptMapping
 **************
 
-.. include::  ../../../schema/gks-core/def/ConceptMapping.rst
+.. include::  ../def/gks-core/ConceptMapping.rst
 
 Simple Data Types
 ###################
@@ -40,27 +40,27 @@ Simple Data Types
 code
 ****
 
-.. include::  ../../../schema/gks-core/def/code.rst
+.. include::  ../def/gks-core/code.rst
 
 
 .. _iriReference:
 
 iriReference
 ************
 
-.. include::  ../../../schema/gks-core/def/iriReference.rst
+.. include::  ../def/gks-core/iriReference.rst
 
 .. _date:
 
 date
 ****
 
-.. include::  ../../../schema/gks-core/def/date.rst
+.. include::  ../def/gks-core/date.rst
 
 
 .. _datetime:
 
 datetime
 ********
 
-.. include::  ../../../schema/gks-core/def/datetime.rst
+.. include::  ../def/gks-core/datetime.rst
diff --git a/docs/source/core-information-model/entities/activities/contribution.rst b/docs/source/core-information-model/entities/activities/contribution.rst
@@ -3,4 +3,4 @@
 Contribution
 !!!!!!!!!!!!
 
-.. include::  ../../../../../schema/gks-core/def/Contribution.rst
+.. include::  ../../../def/va-spec/Contribution.rst
diff --git a/docs/source/core-information-model/entities/activities/index.rst b/docs/source/core-information-model/entities/activities/index.rst
@@ -3,7 +3,7 @@
 Activity
 !!!!!!!!
 
-.. include::  ../../../../../schema/gks-core/def/Activity.rst  
+.. include::  ../../../def/va-spec/Activity.rst  
 
 Subclasses
 

diff --git a/docs/source/core-information-model/entities/agent.rst b/docs/source/core-information-model/entities/agent.rst
@@ -3,4 +3,4 @@
 Agent
 !!!!!
 
-.. include::  ../../../../schema/gks-core/def/Agent.rst
+.. include::  ../../def/va-spec/Agent.rst
diff --git a/docs/source/core-information-model/entities/characteristic.rst b/docs/source/core-information-model/entities/characteristic.rst
@@ -3,4 +3,4 @@
 Characteristic
 !!!!!!!!!!!!!!
 
-.. include::  ../../../../schema/gks-core/def/Characteristic.rst
+.. include::  ../../def/va-spec/Characteristic.rst
diff --git a/docs/source/core-information-model/entities/domain-entities/conditions/index.rst b/docs/source/core-information-model/entities/domain-entities/conditions/index.rst
@@ -3,7 +3,7 @@
 Condition
 !!!!!!!!!
 
-  .. include::  ../../../../../../schema/domain-entities/def/Condition.rst
+  .. include::  ../../../../def/va-spec/Condition.rst
 
 
 **Subclasses**

diff --git a/...source/core-information-model/entities/domain-entities/conditions/trait-set.rst b/...source/core-information-model/entities/domain-entities/conditions/trait-set.rst
@@ -3,7 +3,7 @@
 Trait Set
 !!!!!!!!!
 
-.. include::  ../../../../../../schema/domain-entities/def/TraitSet.rst
+.. include::  ../../../../def/va-spec/TraitSet.rst
 
 
 
diff --git a/docs/source/core-information-model/entities/domain-entities/gene.rst b/docs/source/core-information-model/entities/domain-entities/gene.rst
@@ -3,4 +3,4 @@
 Gene
 !!!!
 
-.. include::  ../../../../../schema/domain-entities/def/Gene.rst  
+.. include::  ../../../def/va-spec/Gene.rst  
diff --git a/docs/source/core-information-model/entities/domain-entities/index.rst b/docs/source/core-information-model/entities/domain-entities/index.rst
@@ -3,8 +3,6 @@
 Domain Entity
 !!!!!!!!!!!!!
 
-.. include::  ../../../../../schema/core-im/def/DomainEntity.rst
-
 .. core-im-class-hierarchy:
 
 

diff --git a/docs/source/core-information-model/entities/index.rst b/docs/source/core-information-model/entities/index.rst
@@ -3,7 +3,7 @@
 Entity
 !!!!!!
 
-.. include::  ../../../../schema/gks-core/def/Entity.rst
+.. include::  ../../def/gks-core/Entity.rst
 
 
 **Subclasses**

diff --git a/docs/source/core-information-model/entities/information-entities/dataset.rst b/docs/source/core-information-model/entities/information-entities/dataset.rst
@@ -4,4 +4,4 @@ Data Set
 !!!!!!!!
 
 
-.. include::  ../../../../../schema/gks-core/def/DataSet.rst
+.. include::  ../../../def/va-spec/DataSet.rst
diff --git a/docs/source/core-information-model/entities/information-entities/document.rst b/docs/source/core-information-model/entities/information-entities/document.rst
@@ -4,4 +4,4 @@ Document
 !!!!!!!!
 
 
-.. include::  ../../../../../schema/gks-core/def/Document.rst
+.. include::  ../../../def/va-spec/Document.rst
diff --git a/docs/source/core-information-model/entities/information-entities/evidence-line.rst b/docs/source/core-information-model/entities/information-entities/evidence-line.rst
@@ -3,7 +3,7 @@
 Evidence Line
 !!!!!!!!!!!!!
 
-.. include::  ../../../../../schema/gks-core/def/EvidenceLine.rst  
+.. include::  ../../../def/va-spec/EvidenceLine.rst  
 
 **IMPLEMENTATION GUIDANCE**
 

diff --git a/docs/source/core-information-model/entities/information-entities/index.rst b/docs/source/core-information-model/entities/information-entities/index.rst
@@ -3,7 +3,7 @@
 Information Entity
 !!!!!!!!!!!!!!!!!!
 
-.. include::  ../../../../../schema/gks-core/def/InformationEntity.rst  
+.. include::  ../../../def/va-spec/InformationEntity.rst  
 
 **Subclasses**
 

diff --git a/docs/source/core-information-model/entities/information-entities/method.rst b/docs/source/core-information-model/entities/information-entities/method.rst
@@ -3,4 +3,4 @@
 Method
 !!!!!!
 
-.. include::  ../../../../../schema/gks-core/def/Method.rst
+.. include::  ../../../def/va-spec/Method.rst
diff --git a/docs/source/core-information-model/entities/information-entities/statement.rst b/docs/source/core-information-model/entities/information-entities/statement.rst
@@ -4,7 +4,7 @@ Statement
 !!!!!!!!!
 
 
-.. include::  ../../../../../schema/gks-core/def/Statement.rst
+.. include::  ../../../def/va-spec/Statement.rst
 
 ----------
 

diff --git a/docs/source/core-information-model/entities/information-entities/study-result.rst b/docs/source/core-information-model/entities/information-entities/study-result.rst
@@ -3,7 +3,7 @@
 Study Result
 !!!!!!!!!!!!
 
-.. include::  ../../../../../schema/gks-core/def/StudyResult.rst
+.. include::  ../../../def/va-spec/StudyResult.rst
 
 ---------
 

diff --git a/docs/source/core-information-model/entities/study-group.rst b/docs/source/core-information-model/entities/study-group.rst
@@ -3,4 +3,4 @@
 Study Group
 !!!!!!!!!!!
 
-.. include::  ../../../../schema/gks-core/def/StudyGroup.rst
+.. include::  ../../def/va-spec/StudyGroup.rst
diff --git a/schema/Makefile b/schema/Makefile
@@ -1,6 +1,6 @@
-all: base-all acmg-2015-all ave-2024-all aac-2017-all ccv-2022-all
+all: base-all acmg-2015-all aac-2017-all ccv-2022-all
 
-clean: base-clean acmg-2015-clean ave-2024-clean aac-2017-clean ccv-2022-clean
+clean: base-clean acmg-2015-clean aac-2017-clean ccv-2022-clean
 
 base-all:
 	(cd va-spec/base; make all)
@@ -14,12 +14,6 @@ acmg-2015-all:
 acmg-2015-clean:
 	(cd va-spec/acmg-2015; make clean)
 
-ave-2024-all:
-	(cd va-spec/ave-2024; make all)	
-
-ave-2024-clean:
-	(cd va-spec/ave-2024; make clean)
-
 aac-2017-all:
 	(cd va-spec/aac-2017; make all)	
 

diff --git a/schema/va-spec/aac-2017/diagnostic-study-statement-profile-source.yaml b/schema/va-spec/aac-2017/diagnostic-study-statement-profile-source.yaml
@@ -4,7 +4,7 @@ title: AAC 2017 Variant Diagnostic Study Statement
 strict: true
 
 imports:
-  va-base: ../base/diagnostic-study-proposition-profile-source.yaml
+  va-spec: ../base/va-spec-source.yaml
   gks-core: ../../gks-core/gks-core-source.yaml
 
 $defs:
@@ -19,7 +19,7 @@ $defs:
     - $ref: "/ga4gh/schema/gks-core/1.x/json/Statement"
     - properties:
         proposition:
-          $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyProposition"
+          $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticProposition"
           description: >-
             The proposition for which the study provides evidence - that the subject variant
             is associated with the object condition.
diff --git a/schema/va-spec/aac-2017/json/VariantDiagnosticStudyStatement b/schema/va-spec/aac-2017/json/VariantDiagnosticStudyStatement
@@ -6,12 +6,12 @@
    "description": "A statement reporting a conclusion from a single study about whether a variant is associated with a disease (a diagnostic inclusion criterion), or absence of a disease (diagnostic exclusion criterion) - based on interpretation of the study's results.",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/gks-core/1.x/json/Statement"
+         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
       },
       {
          "properties": {
             "proposition": {
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticStudyProposition",
+               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantDiagnosticProposition",
                "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object condition."
             }
          }

diff --git a/schema/va-spec/aac-2017/json/VariantPrognosticStudyStatement b/schema/va-spec/aac-2017/json/VariantPrognosticStudyStatement
@@ -6,12 +6,12 @@
    "description": "A statement reporting a conclusion from a single study about whether a variant is associated with a disease prognosis - based on interpretation of the study's results.",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/gks-core/1.x/json/Statement"
+         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
       },
       {
          "properties": {
             "proposition": {
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyProposition",
+               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticProposition",
                "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object condition."
             }
          }

diff --git a/schema/va-spec/aac-2017/json/VariantTherapeuticResponseStudyStatement b/schema/va-spec/aac-2017/json/VariantTherapeuticResponseStudyStatement
@@ -6,12 +6,12 @@
    "description": "A statement reporting a conclusion from a single study about whether a variant is associated with a therapeutic response (positive or negative) - based on interpretation of the study's results.",
    "allOf": [
       {
-         "$ref": "/ga4gh/schema/gks-core/1.x/json/Statement"
+         "$ref": "/ga4gh/schema/va-spec/1.x/base/json/Statement"
       },
       {
          "properties": {
             "proposition": {
-               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseStudyProposition",
+               "$ref": "/ga4gh/schema/va-spec/1.x/base/json/VariantTherapeuticResponseProposition",
                "description": "The proposition for which the study provides evidence - that the subject variant is associated with the object therapeutic response. "
             }
          }

diff --git a/schema/va-spec/aac-2017/prognostic-study-statement-profile-source.yaml b/schema/va-spec/aac-2017/prognostic-study-statement-profile-source.yaml
@@ -4,7 +4,7 @@ title: AAC 2017 Variant Prognostic Study Statement
 strict: true
 
 imports:
-  va-base: ../base/prognostic-study-proposition-profile-source.yaml
+  va-spec: ../base/va-spec-source.yaml
   gks-core: ../../gks-core/gks-core-source.yaml
 
 $defs:
@@ -18,7 +18,7 @@ $defs:
     - $ref: "/ga4gh/schema/gks-core/1.x/json/Statement"
     - properties:
         proposition:
-          $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticStudyProposition"
+          $ref: "/ga4gh/schema/va-spec/1.x/base/json/VariantPrognosticProposition"
           description: >-
             The proposition for which the study provides evidence - that the subject variant
             is associated with the object condition.
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,4 +3,4 @@ @@
     Agent
     !!!!!
-    .. include::  ../../../../schema/gks-core/def/Agent.rst
+    .. include::  ../../def/va-spec/Agent.rst
Original file line number	Diff line number	Diff line change
Expand Up		@@ -4,4 +4,4 @@ Data Set
		!!!!!!!!


		.. include:: ../../../../../schema/gks-core/def/DataSet.rst
		.. include:: ../../../def/va-spec/DataSet.rst
Original file line number	Diff line number	Diff line change
Expand Up		@@ -4,4 +4,4 @@ Document
		!!!!!!!!


		.. include:: ../../../../../schema/gks-core/def/Document.rst
		.. include:: ../../../def/va-spec/Document.rst