ci: add coverage checking to pytest runs

.github/workflows/ci.yaml

@@ -22,7 +22,7 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -33,7 +33,17 @@ jobs:
 
       - name: Test with pytest
         run: |
-          python -m pytest
+          python -m pytest --cov=cumulus_fhir_support --cov-report=xml
+
+      - name: Check coverage report
+        if: github.ref != 'refs/heads/main'
+        uses: orgoro/[email protected]
+        with:
+          coverageFile: coverage.xml
+          token: ${{ secrets.GITHUB_TOKEN }}
+          thresholdAll: .99
+          thresholdNew: 1
+          thresholdModified: 1
 
   lint:
     runs-on: ubuntu-latest

cumulus_fhir_support/json.py

@@ -44,7 +44,7 @@
 from typing import TYPE_CHECKING, Any, Iterable, Optional, Union
 
 if TYPE_CHECKING:
-    import fsspec
+    import fsspec  # pragma: no cover
 
 PathType = Union[str, pathlib.Path]
 ResourceType = Union[str, Iterable[str], None]

pyproject.toml

@@ -43,6 +43,7 @@ line-length = 100
 tests = [
     "ddt",
     "pytest",
+    "pytest-cov",
 ]
 dev = [
     "black >= 24, < 25",

tests/test_json.py

@@ -261,6 +261,12 @@ def fake_open(filename, mode, encoding):
         mock_fs.ls = fake_ls
         mock_fs.open = fake_open
 
+        # Missing dir
+        with self.assert_no_logs():
+            rows = support.read_multiline_json_from_dir("not-present", "Patient", fsspec_fs=mock_fs)
+        self.assertEqual([], list(rows))
+
+        # Dir exists
         with self.assert_no_logs():
             rows = support.read_multiline_json_from_dir("folder", "Patient", fsspec_fs=mock_fs)
         self.assertEqual(["P2", "P1"], [x["id"] for x in rows])

tests/test_schemas.py

@@ -1,6 +1,7 @@
 """Tests for schemas.py"""
 
 import unittest
+from unittest import mock
 
 import pyarrow
 
@@ -219,3 +220,15 @@ def test_contained_resources_empty(self):
         self.assertEqual(pyarrow.string(), contained_type.field("id").type)
         self.assertEqual(pyarrow.string(), contained_type.field("implicitRules").type)
         self.assertEqual(pyarrow.string(), contained_type.field("language").type)
+
+    @mock.patch("fhirclient.models.fhirelementfactory.FHIRElementFactory.instantiate")
+    def test_unexpected_fhir_type(self, mock_instantiate):
+        """Verify that we error out if an unknown FHIR type is provided"""
+        mock_resource = mock.MagicMock()
+        mock_resource.elementProperties.return_value = [
+            ("fieldBoolean", "fieldBoolean", bool, False, None, False),
+            ("fieldObject", "fieldObject", object, False, None, False),
+        ]
+        mock_instantiate.return_value = mock_resource
+        with self.assertRaisesRegex(ValueError, "Unexpected type: <class 'object'>"):
+            support.pyarrow_schema_from_rows("AllergyIntolerance")