Validate ORM relationships in tests

thehyve · Dec 19, 2024 · 5f6a02a · 5f6a02a
1 parent 6072df3
commit 5f6a02a
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Showing 9 changed files with 32 additions and 10 deletions.
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -1,8 +1,9 @@
 from contextlib import contextmanager
-from typing import Set
+from typing import Callable, Set
 
 import pytest
-from sqlalchemy import Connection, Engine, MetaData, create_engine
+from sqlalchemy import Connection, Engine, MetaData, create_engine, select
+from sqlalchemy.orm import Session
 from sqlalchemy.sql.ddl import CreateSchema, DropSchema
 from testcontainers.postgres import PostgresContainer
 
@@ -38,3 +39,16 @@ def temp_schemas(engine: Engine, schemas: Set[str]):
 def create_all_tables(engine: Engine, metadata: MetaData) -> None:
     with engine.begin() as conn:
         metadata.create_all(bind=conn)
+
+
+def validate_relationships(engine: Engine, table: Callable) -> None:
+    """
+    Query any table to make SQLAlchemy validate table relationships.
+
+    While SQLAlchemy's Metadata.create_all method will create the tables
+    in the database, it can still be that ORM FK relationships are
+    configured incorrectly. This will only become apparent upon first
+    using an ORM query. Hence, this simple session interaction.
+    """
+    with Session(engine) as session:
+        session.execute(select(table))
diff --git a/tests/omop_cdm/dynamic/cdm531/test_cdm531.py b/tests/omop_cdm/dynamic/cdm531/test_cdm531.py
@@ -2,7 +2,7 @@
 from sqlalchemy import Engine, inspect
 
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.dynamic.cdm_definitions import cdm531
 from tests.omop_cdm.table_sets import CDM531_NON_VOCAB, CUSTOM, VOCAB
 
@@ -21,3 +21,4 @@ def test_create_tables_cdm531(cdm531_engine: Engine):
         cdm_tables = inspect(cdm531_engine).get_table_names(SCHEMA_MAP[CDM_SCHEMA])
         assert set(vocab_tables) == VOCAB
         assert set(cdm_tables) == CDM531_NON_VOCAB | CUSTOM
+        validate_relationships(cdm531_engine, cdm531.Person)
diff --git a/tests/omop_cdm/dynamic/cdm54/test_cdm54.py b/tests/omop_cdm/dynamic/cdm54/test_cdm54.py
@@ -2,7 +2,7 @@
 from sqlalchemy import Engine, inspect
 
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.dynamic.cdm_definitions import cdm54
 from tests.omop_cdm.table_sets import CDM54_NON_VOCAB, CUSTOM, VOCAB
 
@@ -21,3 +21,4 @@ def test_create_tables_cdm54(cdm54_engine: Engine):
         cdm_tables = inspect(cdm54_engine).get_table_names(SCHEMA_MAP[CDM_SCHEMA])
         assert set(vocab_tables) == VOCAB
         assert set(cdm_tables) == CDM54_NON_VOCAB | CUSTOM
+        validate_relationships(cdm54_engine, cdm54.Person)
diff --git a/tests/omop_cdm/dynamic/cdm54_custom/test_cdm54_custom.py b/tests/omop_cdm/dynamic/cdm54_custom/test_cdm54_custom.py
@@ -2,7 +2,7 @@
 from sqlalchemy import BIGINT, Engine, inspect
 
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.dynamic.cdm_definitions import cdm54_custom
 from tests.omop_cdm.table_sets import CDM54_NON_VOCAB, CUSTOM
 
@@ -27,6 +27,7 @@ def _create_custom_cdm_tables(cdm54_custom_engine: Engine):
 def test_custom_table_is_created(cdm54_custom_engine: Engine):
     cdm_tables = inspect(cdm54_custom_engine).get_table_names(SCHEMA_MAP[CDM_SCHEMA])
     assert set(cdm_tables) == CDM54_NON_VOCAB | CUSTOM | {"cloudspine"}
+    validate_relationships(cdm54_custom_engine, cdm54_custom.Person)
 
 
 @pytest.mark.usefixtures("_create_custom_cdm_tables")

diff --git a/tests/omop_cdm/dynamic/cdm54_plus_legacy/test_legacy.py b/tests/omop_cdm/dynamic/cdm54_plus_legacy/test_legacy.py
@@ -2,7 +2,7 @@
 from sqlalchemy import Engine, inspect
 
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.dynamic.cdm_definitions import cdm54_plus_legacy
 from tests.omop_cdm.table_sets import CDM54_NON_VOCAB, CUSTOM, LEGACY, VOCAB
 
@@ -23,3 +23,4 @@ def test_create_tables_cdm54_plus_legacy(cdm54_legacy_engine: Engine):
             SCHEMA_MAP[CDM_SCHEMA]
         )
         assert set(cdm_tables) == VOCAB | CDM54_NON_VOCAB | LEGACY | CUSTOM
+        validate_relationships(cdm54_legacy_engine, cdm54_plus_legacy.Person)
diff --git a/tests/omop_cdm/dynamic/cdm600/test_cdm600.py b/tests/omop_cdm/dynamic/cdm600/test_cdm600.py
@@ -2,7 +2,7 @@
 from sqlalchemy import Engine, inspect
 
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.dynamic.cdm_definitions import cdm600
 from tests.omop_cdm.table_sets import CDM600_NON_VOCAB, CUSTOM, VOCAB
 
@@ -21,3 +21,4 @@ def test_create_tables_cdm600(cdm600_engine: Engine):
         cdm_tables = inspect(cdm600_engine).get_table_names(SCHEMA_MAP[CDM_SCHEMA])
         assert set(vocab_tables) == VOCAB
         assert set(cdm_tables) == CDM600_NON_VOCAB | CUSTOM
+        validate_relationships(cdm600_engine, cdm600.Person)
diff --git a/tests/omop_cdm/regular/cdm531/test_cdm531.py b/tests/omop_cdm/regular/cdm531/test_cdm531.py
@@ -3,7 +3,7 @@
 
 import src.omop_cdm.regular.cdm531 as cdm531
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.table_sets import CDM531_NON_VOCAB, VOCAB
 
 SCHEMA_MAP = {VOCAB_SCHEMA: "vocab531", CDM_SCHEMA: "cdm531"}
@@ -22,3 +22,4 @@ def test_create_tables_cdm531_regular(cdm531_regular_engine: Engine):
         cdm_tables = inspect(engine).get_table_names(SCHEMA_MAP[CDM_SCHEMA])
         assert set(vocab_tables) == VOCAB
         assert set(cdm_tables) == CDM531_NON_VOCAB
+        validate_relationships(cdm531_regular_engine, cdm531.Person)
diff --git a/tests/omop_cdm/regular/cdm54/test_cdm54.py b/tests/omop_cdm/regular/cdm54/test_cdm54.py
@@ -3,7 +3,7 @@
 
 import src.omop_cdm.regular.cdm54 as cdm54
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.table_sets import CDM54_NON_VOCAB, VOCAB
 
 SCHEMA_MAP = {VOCAB_SCHEMA: "vocab54", CDM_SCHEMA: "cdm54"}
@@ -22,3 +22,4 @@ def test_create_tables_cdm54_regular(cdm54_regular_engine: Engine):
         cdm_tables = inspect(engine).get_table_names(SCHEMA_MAP[CDM_SCHEMA])
         assert set(vocab_tables) == VOCAB
         assert set(cdm_tables) == CDM54_NON_VOCAB
+        validate_relationships(cdm54_regular_engine, cdm54.Person)
diff --git a/tests/omop_cdm/regular/cdm600/test_cdm600.py b/tests/omop_cdm/regular/cdm600/test_cdm600.py
@@ -3,7 +3,7 @@
 
 import src.omop_cdm.regular.cdm600 as cdm600
 from src.omop_cdm.constants import CDM_SCHEMA, VOCAB_SCHEMA
-from tests.conftest import create_all_tables, temp_schemas
+from tests.conftest import create_all_tables, temp_schemas, validate_relationships
 from tests.omop_cdm.table_sets import CDM600_NON_VOCAB, VOCAB
 
 SCHEMA_MAP = {VOCAB_SCHEMA: "vocab600", CDM_SCHEMA: "cdm600"}
@@ -22,3 +22,4 @@ def test_create_tables_cdm600_regular(cdm600_regular_engine: Engine):
         cdm_tables = inspect(engine).get_table_names(SCHEMA_MAP[CDM_SCHEMA])
         assert set(vocab_tables) == VOCAB
         assert set(cdm_tables) == CDM600_NON_VOCAB
+        validate_relationships(cdm600_regular_engine, cdm600.Person)