Mock the Census API for tests so that Actions doesn't actually hit the API when running tests

containers/record-linkage/app/utils.py

@@ -4,6 +4,7 @@
 import subprocess
 from typing import Literal
 
+
 from app.config import get_settings
 from phdi.linkage import DIBBsConnectorClient
 

tests/fhir/geospatial/test_fhir_census_client.py

@@ -1,17 +1,30 @@
-from unittest import mock
+import copy
 import json
 import pathlib
-import copy
+import pytest
 
 from phdi.fhir.geospatial.census import CensusFhirGeocodeClient
 from phdi.geospatial.core import GeocodeResult
 
 
-def test_geocode_resource_census():
-    census_client = CensusFhirGeocodeClient()
-    assert census_client is not None
+FHIR_BUNDLE_PATH = pathlib.Path(__file__).parent.parent.parent / "assets" / "general"
+
+
+@pytest.fixture
+def patient_bundle_census():
+    with open(FHIR_BUNDLE_PATH / "patient_bundle_census.json") as file:
+        return json.load(file)
+
+
+@pytest.fixture
+def patient_bundle_census_extension():
+    with open(FHIR_BUNDLE_PATH / "patient_bundle_census_extension.json") as file:
+        return json.load(file)
+
 
-    geocoded_response = GeocodeResult(
+@pytest.fixture
+def geocoded_response():
+    return GeocodeResult(
         line=["239 Greene St", "Apt 4L"],
         city="NEW YORK",
         state="NY",
@@ -23,17 +36,28 @@ def test_geocode_resource_census():
         census_tract="59",
     )
 
-    bundle = json.load(
-        open(
-            pathlib.Path(__file__).parent.parent.parent
-            / "assets"
-            / "general"
-            / "patient_bundle_census.json"
-        )
+
+@pytest.fixture
+def census_client(monkeypatch, geocoded_response):
+    client = CensusFhirGeocodeClient()
+
+    def mock_geocode_from_dict(*args, **kwargs):
+        return geocoded_response
+
+    monkeypatch.setattr(
+        client._CensusFhirGeocodeClient__client,
+        "geocode_from_dict",
+        mock_geocode_from_dict,
     )
 
-    patient = bundle["entry"][1]["resource"]
-    standardized_patient = copy.deepcopy(patient)
+    return client
+
+
+def _get_patient_from_bundle(bundle):
+    return bundle["entry"][1]["resource"]
+
+
+def _extract_address(standardized_patient, geocoded_response, extension=False):
     address = standardized_patient["address"][0]
     address["city"] = geocoded_response.city
     address["state"] = geocoded_response.state
@@ -48,31 +72,61 @@ def test_geocode_resource_census():
             ],
         }
     )
-    address["_line"] = []
-    address["_line"].append(
-        {
-            "extension": [
-                {
-                    "url": "http://hl7.org/fhir/StructureDefinition/"
-                    + "iso21090-ADXP-censusTract",
-                    "valueString": "59",
-                }
-            ]
-        },
-    )
-    address["_line"].append(
-        {
+    if extension:
+        address["_line"][0]["extension"].append(
+            {
+                "url": "http://hl7.org/fhir/StructureDefinition/"
+                + "iso21090-ADXP-censusTract",
+                "valueString": "59",
+            }
+        )
+        address["_line"][1] = {
             "extension": [
                 {
                     "url": "http://hl7.org/fhir/StructureDefinition/"
                     + "iso21090-ADXP-censusTract",
                     "valueString": "59",
                 }
             ]
-        },
-    )
-    census_client.geocode_from_str = mock.Mock()
-    census_client.geocode_from_str.return_value = geocoded_response
+        }
+    else:
+        address["_line"] = []
+        address["_line"].append(
+            {
+                "extension": [
+                    {
+                        "url": "http://hl7.org/fhir/StructureDefinition/"
+                        + "iso21090-ADXP-censusTract",
+                        "valueString": "59",
+                    }
+                ]
+            },
+        )
+        address["_line"].append(
+            {
+                "extension": [
+                    {
+                        "url": "http://hl7.org/fhir/StructureDefinition/"
+                        + "iso21090-ADXP-censusTract",
+                        "valueString": "59",
+                    }
+                ]
+            },
+        )
+    return address
+
+
+def test_geocode_resource_census(
+    patient_bundle_census,
+    patient_bundle_census_extension,
+    geocoded_response,
+    census_client,
+):
+    assert census_client is not None
+
+    patient = _get_patient_from_bundle(patient_bundle_census)
+    standardized_patient = copy.deepcopy(patient)
+    _extract_address(standardized_patient, geocoded_response)
 
     # Case 1: Overwrite = False
     returned_patient = census_client.geocode_resource(patient, overwrite=False)
@@ -89,48 +143,9 @@ def test_geocode_resource_census():
     assert returned_patient == patient
 
     # Case 3: Patient already has an extension on line, and it's preserved.
-    bundle = json.load(
-        open(
-            pathlib.Path(__file__).parent.parent.parent
-            / "assets"
-            / "general"
-            / "patient_bundle_census_extension.json"
-        )
-    )
-
-    patient = bundle["entry"][1]["resource"]
+    patient = _get_patient_from_bundle(patient_bundle_census_extension)
     standardized_patient = copy.deepcopy(patient)
-
-    address = standardized_patient["address"][0]
-    address["city"] = geocoded_response.city
-    address["state"] = geocoded_response.state
-    address["postalCode"] = geocoded_response.postal_code
-    address["extension"] = []
-    address["extension"].append(
-        {
-            "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
-            "extension": [
-                {"url": "latitude", "valueDecimal": geocoded_response.lat},
-                {"url": "longitude", "valueDecimal": geocoded_response.lng},
-            ],
-        }
-    )
-    address["_line"][0]["extension"].append(
-        {
-            "url": "http://hl7.org/fhir/StructureDefinition/"
-            + "iso21090-ADXP-censusTract",
-            "valueString": "59",
-        }
-    )
-    address["_line"][1] = {
-        "extension": [
-            {
-                "url": "http://hl7.org/fhir/StructureDefinition/"
-                + "iso21090-ADXP-censusTract",
-                "valueString": "59",
-            }
-        ]
-    }
+    _extract_address(standardized_patient, geocoded_response, extension=True)
 
     # Case 3: Patient already has 1 extension on _line, and it's preserved.
     returned_patient = census_client.geocode_resource(patient, overwrite=True)
@@ -145,73 +160,15 @@ def test_geocode_resource_census():
     )
 
 
-def test_geocode_bundle_census():
-    census_client = CensusFhirGeocodeClient()
+def test_geocode_bundle_census(patient_bundle_census, geocoded_response, census_client):
     assert census_client is not None
 
-    geocoded_response = GeocodeResult(
-        line=["239 Greene St", "Apt 4L"],
-        city="NEW YORK",
-        state="NY",
-        lat=40.729656537689166,
-        lng=-73.99550002689155,
-        county_fips="36061",
-        county_name="New York",
-        postal_code="10003",
-        census_tract="59",
-    )
+    standardized_bundle = copy.deepcopy(patient_bundle_census)
+    patient = _get_patient_from_bundle(standardized_bundle)
+    _extract_address(patient, geocoded_response)
 
-    bundle = json.load(
-        open(
-            pathlib.Path(__file__).parent.parent.parent
-            / "assets"
-            / "general"
-            / "patient_bundle_census.json"
-        )
+    returned_bundle = census_client.geocode_bundle(
+        patient_bundle_census, overwrite=False
     )
-    standardized_bundle = copy.deepcopy(bundle)
-    patient = standardized_bundle["entry"][1]["resource"]
-    address = patient["address"][0]
-    address["city"] = geocoded_response.city
-    address["state"] = geocoded_response.state
-    address["postalCode"] = geocoded_response.postal_code
-    address["extension"] = []
-    address["extension"].append(
-        {
-            "url": "http://hl7.org/fhir/StructureDefinition/geolocation",
-            "extension": [
-                {"url": "latitude", "valueDecimal": geocoded_response.lat},
-                {"url": "longitude", "valueDecimal": geocoded_response.lng},
-            ],
-        }
-    )
-    address["_line"] = []
-    address["_line"].append(
-        {
-            "extension": [
-                {
-                    "url": "http://hl7.org/fhir/StructureDefinition/"
-                    + "iso21090-ADXP-censusTract",
-                    "valueString": "59",
-                }
-            ]
-        },
-    )
-    address["_line"].append(
-        {
-            "extension": [
-                {
-                    "url": "http://hl7.org/fhir/StructureDefinition/"
-                    + "iso21090-ADXP-censusTract",
-                    "valueString": "59",
-                }
-            ]
-        },
-    )
-
-    census_client.geocode_from_str = mock.Mock()
-    census_client.geocode_from_str.return_value = geocoded_response
-
-    returned_bundle = census_client.geocode_bundle(bundle, overwrite=False)
     assert standardized_bundle == returned_bundle
-    assert bundle != standardized_bundle
+    assert patient_bundle_census != standardized_bundle