fix: criterion,recommendation saving

- removed criterion_concept_name from criterion table
- added concept_id, json, description argument contents to Criterion/Recommendation where required

Author: glichtner

execution_engine/execution_engine.py

@@ -350,11 +350,6 @@ def register_criterion(self, criterion: Criterion) -> None:
                             if hasattr(criterion, "concept")
                             else OMOPConcepts.UNKNOWN
                         ),
-                        criterion_concept_name=(
-                            criterion.concept.concept_name
-                            if hasattr(criterion, "concept")
-                            else "unknown"
-                        ),
                         criterion_json=criterion.json(),
                         criterion_description=criterion.description(),
                     )

execution_engine/omop/db/celida/tables.py

@@ -93,10 +93,9 @@ class Criterion(Base):  # noqa: D101
     criterion_description: Mapped[str]
     criterion_concept_id: Mapped[int] = mapped_column(
         BigInteger(),
-        # ForeignKey(f"{OMOP_SCHEMA_NAME}.concept.concept_id"),
+        ForeignKey(f"{OMOP_SCHEMA_NAME}.concept.concept_id"),
         index=True,
     )
-    criterion_concept_name: Mapped[str]
     criterion_json: Mapped[str]
     criterion_hash: Mapped[str] = mapped_column(String(64), index=True, unique=True)
 

tests/_fixtures/omop_fixture.py

@@ -154,6 +154,7 @@ def celida_recommendation(
             recommendation_url="https://example.com",
             recommendation_version="1.0",
             recommendation_package_version="1.0",
+            recommendation_description="my_description",
             recommendation_hash=hash("my_recommendation"),
             recommendation_json="{}".encode(),
             create_datetime=datetime.datetime.now(),
@@ -185,6 +186,8 @@ def celida_recommendation(
         criterion = Criterion(
             criterion_id=criterion_id,
             criterion_description="my_description",
+            criterion_concept_id=0,
+            criterion_json="{}".encode(),
             criterion_hash=hash("my_criterion"),
         )
         db_session.add(criterion)

tests/execution_engine/omop/criterion/test_criterion.py

@@ -194,6 +194,8 @@ def register_criterion(cls, criterion: Criterion, db_session):
             new_criterion = celida_tables.Criterion(
                 criterion_id=criterion.id,
                 criterion_description=criterion.description(),
+                criterion_concept_id=criterion.concept.concept_id,
+                criterion_json=criterion.json(),
                 criterion_hash=hash(criterion),
             )
             db_session.add(new_criterion)