Domain entities to Trial Use (#232)

* add group classes * TraitSet to TU * add TherapyGroup to TU
ga4gh · Nov 27, 2024 · 0bc7d16 · 0bc7d16
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Showing 14 changed files with 51 additions and 21 deletions.
diff --git a/schema/va-spec/base/def/Condition.rst b/schema/va-spec/base/def/Condition.rst
@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. note:: This data class is at a **trial use** maturity level and may \
+    change in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**

diff --git a/schema/va-spec/base/def/Therapeutic.rst b/schema/va-spec/base/def/Therapeutic.rst
@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. note:: This data class is at a **trial use** maturity level and may \
+    change in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**

diff --git a/schema/va-spec/base/def/TherapyGroup.rst b/schema/va-spec/base/def/TherapyGroup.rst
@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. note:: This data class is at a **trial use** maturity level and may \
+    change in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**
@@ -36,7 +36,7 @@ Some TherapyGroup attributes are inherited from :ref:`gks-core:Element`.
       - A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
    *  - groupType
       - 
-      - string
+      - :ref:`MappableConcept`
       - 0..1
       - The type of the therapy group.
    *  - therapies

diff --git a/schema/va-spec/base/def/TraitSet.rst b/schema/va-spec/base/def/TraitSet.rst
@@ -1,5 +1,5 @@
-.. warning:: This data class is at a **draft** maturity level and may \
-    change significantly in future releases. Maturity \
+.. note:: This data class is at a **trial use** maturity level and may \
+    change in future releases. Maturity \
     levels are described in the :ref:`maturity-model`.
 
 **Computational Definition**

diff --git a/schema/va-spec/base/domain-entities-source.yaml b/schema/va-spec/base/domain-entities-source.yaml
@@ -9,7 +9,7 @@ imports:
 $defs:
   # Condition data structure for consolidating the different forms of conditions, individual vs co-occurring traits
   Condition:
-    maturity: draft
+    maturity: trial use
     description: >-
       A set of traits (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents
       the object of a Variant Pathogenicity statement.
@@ -20,7 +20,7 @@ $defs:
   # TraitSet data structure to provide support for co-occuring traits (i.e. diseases, phenotypes, etc.)
   TraitSet:
     type: object
-    maturity: draft
+    maturity: trial use
     inherits: gks-core:Element
     description: >-
       A set of conditions (diseases, phenotypes, traits) that are co-occurring.
@@ -36,7 +36,7 @@ $defs:
 
   # Therapeutic
   Therapeutic:
-    maturity: draft
+    maturity: trial use
     description: >-
       A group of therapies (TherapyGroup) or a single therapy (drug, procedure, behavioral intervention, etc.).
     oneOf:
@@ -46,13 +46,13 @@ $defs:
   # TherapyGroup data structure to provide support for combination therapies (i.e. drug treatment, etc.)
   TherapyGroup:
     type: object
-    maturity: draft
+    maturity: trial use
     inherits: gks-core:Element
     description: >-
       A group of therapies that are applied together to treat a condition.
     properties:
       groupType:
-        type: string
+        $ref: "/ga4gh/schema/gks-core/1.x/json/MappableConcept"
         description: The type of the therapy group.
       therapies:
         type: array

diff --git a/schema/va-spec/base/json/Condition b/schema/va-spec/base/json/Condition
@@ -2,7 +2,7 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Condition",
    "title": "Condition",
-   "maturity": "draft",
+   "maturity": "trial use",
    "description": "A set of traits (TraitSet) or a single trait (Disease, Phenotype, etc.) that represents the object of a Variant Pathogenicity statement.",
    "oneOf": [
       {

diff --git a/schema/va-spec/base/json/Therapeutic b/schema/va-spec/base/json/Therapeutic
@@ -2,7 +2,7 @@
    "$schema": "https://json-schema.org/draft/2020-12/schema",
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/Therapeutic",
    "title": "Therapeutic",
-   "maturity": "draft",
+   "maturity": "trial use",
    "description": "A group of therapies (TherapyGroup) or a single therapy (drug, procedure, behavioral intervention, etc.).",
    "oneOf": [
       {

diff --git a/schema/va-spec/base/json/TherapyGroup b/schema/va-spec/base/json/TherapyGroup
@@ -3,7 +3,7 @@
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TherapyGroup",
    "title": "TherapyGroup",
    "type": "object",
-   "maturity": "draft",
+   "maturity": "trial use",
    "description": "A group of therapies that are applied together to treat a condition.",
    "properties": {
       "id": {
@@ -20,7 +20,7 @@
          "$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."
       },
       "groupType": {
-         "type": "string",
+         "$ref": "/ga4gh/schema/gks-core/1.x/json/MappableConcept",
          "description": "The type of the therapy group."
       },
       "therapies": {

diff --git a/schema/va-spec/base/json/TraitSet b/schema/va-spec/base/json/TraitSet
@@ -3,7 +3,7 @@
    "$id": "https://w3id.org/ga4gh/schema/va-spec/1.x/base/json/TraitSet",
    "title": "TraitSet",
    "type": "object",
-   "maturity": "draft",
+   "maturity": "trial use",
    "description": "A set of conditions (diseases, phenotypes, traits) that are co-occurring.",
    "properties": {
       "id": {

diff --git a/tests/fixtures/therapy-group.yaml b/tests/fixtures/therapy-group.yaml
@@ -0,0 +1,8 @@
+id: civic.theragroup:e1090
+therapies:
+  - primaryCode: ncit:C1005
+    label: Arsenic Trioxide
+  - primaryCode: C900
+    label: Tretinoin
+groupType:
+  primaryCode: combination
diff --git a/tests/fixtures/traitset.yaml b/tests/fixtures/traitset.yaml
@@ -0,0 +1,6 @@
+id: traitset001
+traits:
+  - primaryCode: HP:0025769
+    label: Disordered formal thought process
+  - primaryCode: HP:0033051
+    label: Impaired executive functioning
diff --git a/tests/test_definitions.yaml b/tests/test_definitions.yaml
@@ -24,6 +24,14 @@ tests:
     namespace: va-spec.base
     definition: StudyGroup
 
+  # test domain entities
+  - test_file: traitset.yaml
+    namespace: va-spec.base
+    definition: TraitSet
+  - test_file: therapy-group.yaml
+    namespace: va-spec.base
+    definition: TherapyGroup
+
   # test propositions
   - test_file: EVFI-proposition.yaml
     namespace: va-spec.base

diff --git a/tests/test_examples.py b/tests/test_examples.py
@@ -5,7 +5,7 @@
 def _get_trial_use_classes():
     return set([x for x in js_def if x.startswith('va-spec') and js_def[x]['maturity'] == 'trial use'])
 
-va_abstract_classes = {'va-spec.base:SubjectVariantProposition'}
+va_abstract_classes = {'va-spec.base:SubjectVariantProposition', 'va-spec.base:Condition', 'va-spec.base:Therapeutic'}
 
 def test_examples():
     with open(test_path / 'test_definitions.yaml') as def_file:

diff --git a/tests/tu_coverage_exceptions.yaml b/tests/tu_coverage_exceptions.yaml
@@ -106,4 +106,12 @@ va-spec.base:Method:
 
   # InformationEntity
   - specifiedBy
-  - contributions
+  - contributions
+
+va-spec.base:TraitSet:
+  # Element
+  - extensions
+
+va-spec.base:TherapyGroup:
+  # Element
+  - extensions