Cutover to duckdb for unit tests (#154)

* Cutover to duckdb for unit tests

* line breaks, export check

* Update test data for additional exports

cumulus_library/studies/core/manifest.toml

@@ -35,6 +35,9 @@ file_names = [
 export_list = [
     "core__count_patient",
     "core__count_encounter_month",
+    "core__count_encounter_service_month",
+    "core__count_encounter_priority_month",
+    'core__count_encounter_enc_type_month',
     "core__count_encounter_type",
     "core__count_encounter_type_month",
     "core__count_documentreference_month",

tests/conftest.py

@@ -9,17 +9,40 @@
 from cumulus_library.cli import StudyBuilder
 from cumulus_library.databases import create_db_backend
 
+MOCK_DATA_DIR = f"{Path(__file__).parent}/test_data/duckdb_data"
+
+
+def duckdb_args(args, tmp_path):
+    """Convenience function for adding duckdb args to a CLI mock"""
+    if args[0] == "build":
+        return args + [
+            "--db-type",
+            "duckdb",
+            "--load-ndjson-dir",
+            f"{MOCK_DATA_DIR}",
+            "--database",
+            f"{tmp_path}/duck.db",
+        ]
+    elif args[0] == "export":
+        return args + [
+            "--db-type",
+            "duckdb",
+            "--database",
+            f"{tmp_path}/duck.db",
+            f"{tmp_path}/counts",
+        ]
+    return args + ["--db-type", "duckdb", "--database", f"{tmp_path}/duck.db"]
+
 
 @pytest.fixture
 def mock_db():
     """Provides a DuckDatabaseBackend for local testing"""
-    data_dir = f"{Path(__file__).parent}/test_data/duckdb_data"
     with tempfile.TemporaryDirectory() as tmpdir:
         db = create_db_backend(
             {
                 "db_type": "duckdb",
                 "schema_name": f"{tmpdir}/duck.db",
-                "load_ndjson_dir": data_dir,
+                "load_ndjson_dir": MOCK_DATA_DIR,
             }
         )
         yield db