fix: gracefully handle contained Medications

Previously, if a MedicationRequest.medicationReference pointed at a
contained Medication, we would raise an exception trying to handle it.

This commit makes sure that we gracefully ignore it and pass it through
to the output table.

cumulus_etl/etl/tasks/basic_tasks.py

@@ -52,9 +52,9 @@ def __init__(self, *args, **kwargs):
         # But let's try initially with keeping it around for the whole task.
         self.medication_ids = set()
 
-    def scrub_medication(self, medication: dict) -> bool:
+    def scrub_medication(self, medication: dict | None) -> bool:
         """Scrub incoming medication resources, returns False if it should be skipped"""
-        if not self.scrubber.scrub_resource(medication):  # standard scrubbing
+        if not medication or not self.scrubber.scrub_resource(medication):  # standard scrubbing
             return False
 
         # Normally the above is all we'd need to do.
@@ -75,12 +75,13 @@ async def fetch_medication(self, resource: dict) -> dict | None:
         if not reference:
             return None
 
-        # Don't duplicate medications we've already seen this run.
-        # This will still duplicate medications from previous runs, but avoiding that feels like more work than it's
-        # worth - just download em again and push em through (there might be updates to the resources, too!)
-        if reference in self.medication_ids:
-            return None
-        self.medication_ids.add(reference)
+        if not reference.startswith("#"):
+            # Don't duplicate medications we've already seen this run.
+            # This will still duplicate medications from previous runs, but avoiding that feels like more work than it's
+            # worth - just download em again and push em through (there might be updates to the resources, too!)
+            if reference in self.medication_ids:
+                return None
+            self.medication_ids.add(reference)
 
         try:
             medication = await fhir.download_reference(self.task_config.client, reference)

tests/etl/test_tasks.py

@@ -172,6 +172,22 @@ async def test_inline_codes(self):
         df2 = self.format2.write_records.call_args[0][0]
         self.assertTrue(df2.empty)
 
+    async def test_contained_medications(self):
+        """Verify that we pass it through and don't blow up"""
+        self.make_json("MedicationRequest.1", "A", medicationReference={"reference": "#123"})
+
+        await basic_tasks.MedicationRequestTask(self.job_config, self.scrubber).run()
+
+        # Confirm we wrote the basic MedicationRequest
+        self.assertEqual(1, self.format.write_records.call_count)
+        df = self.format.write_records.call_args[0][0]
+        self.assertEqual(f'#{self.codebook.db.resource_hash("123")}', df.iloc[0].medicationReference["reference"])
+
+        # Confirm we wrote an empty dataframe to the medication table
+        self.assertEqual(1, self.format2.write_records.call_count)
+        df2 = self.format2.write_records.call_args[0][0]
+        self.assertTrue(df2.empty)
+
     @mock.patch("cumulus_etl.fhir.download_reference")
     async def test_external_medications(self, mock_download):
         """Verify that we download referenced medications"""