add tests

FHIR-2646

Markdown.iml

@@ -5,6 +5,7 @@
     <content url="file://$MODULE_DIR$">
       <excludeFolder url="file://$MODULE_DIR$/.idea/copilot/chatSessions" />
     </content>
+    <orderEntry type="jdk" jdkName="Python 3.11 (venv4)" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
 </module>

build_support/pants/flake8.ini

@@ -12,5 +12,4 @@ max-complexity = 11
 ignore = E203,W503 
 per_file_ignores =
     ; Make flake8 ignore late module imports just like Ruff
-    utils/tests/*.py: E402
-    analyze_har_files/tests/*.py: E402
+    ; utils/tests/*.py: E402

jupyter/BUILD

@@ -8,3 +8,9 @@ python_sources(
     sources = ["dbgap_fhir.py"],
     dependencies = [":dbgap_fhir_requirements"],
 )
+
+python_test(
+    name = "dbgap_fhir_test",
+    source = "dbgap_fhir_test.py",
+    dependencies = [":dbgap_fhir_src"],
+)

jupyter/test_dbgap_fhir.py

@@ -0,0 +1,18 @@
+from unittest.mock import patch, MagicMock
+from jupyter.dbgap_fhir import DbGapFHIR, obs_to_df, prettyprint
+
+
+
+@patch('requests.Session')
+def test_run_query_with_limit(MockSession):
+    mock_session = MockSession.return_value
+    mock_response = MagicMock()
+    mock_response.json.return_value = {"entry": [{"resource": {"id": "1"}}]}
+    mock_response.content = b'{"entry": [{"resource": {"id": "1"}}]}'
+    mock_session.get.return_value = mock_response
+
+    client = DbGapFHIR(fhir_server="http://example.com")
+    result = client.run_query("Patient", limit=True)
+
+    assert len(result) == 1
+    assert result[0]["id"] == "1"