Add fixes to tests

VectorInstitute · Oct 6, 2023 · a93f989 · a93f989
1 parent 12e6e8b
commit a93f989
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Showing 7 changed files with 1,432 additions and 1,283 deletions.
diff --git a/poetry.lock b/poetry.lock
diff --git a/tests/cyclops/query/test_base.py b/tests/cyclops/query/test_base.py
@@ -8,7 +8,12 @@
 @pytest.mark.integration_test()
 def test_dataset_querier():
     """Test base querier methods using OMOPQuerier."""
-    querier = OMOPQuerier("cdm_synthea10", database="synthea_integration_test")
+    querier = OMOPQuerier(
+        database="synthea_integration_test",
+        schema_name="cdm_synthea10",
+        user="postgres",
+        password="pwd",
+    )
     assert len(querier.list_tables()) == 69
     assert len(querier.list_schemas()) == 4
     assert len(querier.list_tables(schema_name="cdm_synthea10")) == 43

diff --git a/tests/cyclops/query/test_eicu.py b/tests/cyclops/query/test_eicu.py
@@ -8,7 +8,12 @@
 @pytest.mark.integration_test()
 def test_eicu_querier():
     """Test EICUQuerier on eICU-CRD."""
-    querier = EICUQuerier(database="eicu")
+    querier = EICUQuerier(
+        database="eicu",
+        user="postgres",
+        password="pwd",
+    )
+
     patients = querier.eicu_crd.patient().run(limit=10)
     assert len(patients) == 10
     assert "age" in patients

diff --git a/tests/cyclops/query/test_interface.py b/tests/cyclops/query/test_interface.py
@@ -45,7 +45,12 @@ def test_query_interface(
 @pytest.mark.integration_test()
 def test_query_interface_integration():
     """Test QueryInterface with OMOPQuerier."""
-    synthea = OMOPQuerier("cdm_synthea10", database="synthea_integration_test")
+    synthea = OMOPQuerier(
+        database="synthea_integration_test",
+        schema_name="cdm_synthea10",
+        user="postgres",
+        password="pwd",
+    )
     visits = synthea.visit_occurrence()
     assert isinstance(visits, QueryInterface)
     visits_pd_df = visits.run()

diff --git a/tests/cyclops/query/test_mimiciv.py b/tests/cyclops/query/test_mimiciv.py
@@ -8,7 +8,12 @@
 @pytest.mark.integration_test()
 def test_mimiciv_querier():
     """Test MIMICQuerier on MIMICIV-2.0."""
-    querier = MIMICIVQuerier()
+    querier = MIMICIVQuerier(
+        database="mimiciv-2.0",
+        user="postgres",
+        password="pwd",
+    )
+
     patients = querier.patients().run(limit=10)
     assert len(patients) == 10
     assert "anchor_year_difference" in patients

diff --git a/tests/cyclops/query/test_omop.py b/tests/cyclops/query/test_omop.py
@@ -9,7 +9,12 @@
 @pytest.mark.integration_test()
 def test_omop_querier_synthea():
     """Test OMOPQuerier on synthea data."""
-    querier = OMOPQuerier("cdm_synthea10", database="synthea_integration_test")
+    querier = OMOPQuerier(
+        database="synthea_integration_test",
+        schema_name="cdm_synthea10",
+        user="postgres",
+        password="pwd",
+    )
     ops = qo.Sequential(
         qo.ConditionEquals("gender_source_value", "M"),
         qo.Rename({"race_source_value": "race"}),
@@ -36,6 +41,11 @@ def test_omop_querier_synthea():
 @pytest.mark.integration_test()
 def test_omop_querier_mimiciii():
     """Test OMOPQuerier on MIMICIII data."""
-    querier = OMOPQuerier("omop", database="mimiciii")
+    querier = OMOPQuerier(
+        database="mimiciii",
+        schema_name="omop",
+        user="postgres",
+        password="pwd",
+    )
     visits = querier.visit_occurrence().run()
     assert len(visits) == 58976
diff --git a/tests/cyclops/query/test_orm.py b/tests/cyclops/query/test_orm.py
@@ -11,7 +11,12 @@
 @pytest.mark.integration_test()
 def test_omop_querier():
     """Test ORM using OMOPQuerier."""
-    querier = OMOPQuerier("cdm_synthea10", database="synthea_integration_test")
+    querier = OMOPQuerier(
+        database="synthea_integration_test",
+        schema_name="cdm_synthea10",
+        user="postgres",
+        password="pwd",
+    )
     assert querier is not None
     db_ = querier.db
     visits_query = querier.visit_occurrence().query