Fixup FHIR Bundles (#232)

* Fixup FHIR compliance; add missing `resource` nesting

* Fixup code style

* Fixup tests

* Assign resource to new variable

patientsearch/api.py

@@ -629,7 +629,9 @@ def external_search(resource_type):
         audit_entry("multiple patients returned from PDMP", extra=extra, level="warn")
 
     if external_match_count:
-        external_search_bundle["entry"][0].setdefault("id", local_fhir_patient["id"])
+        external_search_bundle["entry"][0]["resource"].setdefault(
+            "id", local_fhir_patient["id"]
+        )
 
     message = "PDMP found match" if external_match_count else "fEMR found match"
     audit_entry(message, extra=extra)

patientsearch/models/sync.py

@@ -16,7 +16,8 @@ def add_identifier_to_resource_type(bundle, resource_type, identifier):
     if "entry" not in result:
         return result
 
-    for resource in result["entry"]:
+    for entry in result["entry"]:
+        resource = entry["resource"]
         if resource.get("resourceType") != resource_type:
             continue
         identifiers = resource.get("identifier", [])
@@ -164,11 +165,12 @@ def sync_bundle(token, bundle, consider_active=False):
         raise ValueError(f"Expected bundle; can't process {bundle.get('resourceType')}")
 
     for entry in bundle.get("entry"):
+        resource = entry["resource"]
         # Restrict to what is expected for now
-        if entry["resourceType"] != "Patient":
-            raise ValueError(f"Can't sync resourceType {entry['resourceType']}")
+        if resource["resourceType"] != "Patient":
+            raise ValueError(f"Can't sync resourceType {resource['resourceType']}")
 
-        patient = sync_patient(token, entry, consider_active)
+        patient = sync_patient(token, resource, consider_active)
         # TODO handle multiple external matches (if it ever happens!)
         # currently returning first
         return patient

tests/test_sync.py

@@ -150,8 +150,8 @@ def test_adding_identifier(external_patient_search):
     result = add_identifier_to_resource_type(external_patient_search, "Patient", ident)
     assert result != external_patient_search
     for entry in result["entry"]:
-        assert len(entry["identifier"]) == 1
-        assert entry["identifier"][0] == ident
+        assert len(entry["resource"]["identifier"]) == 1
+        assert entry["resource"]["identifier"][0] == ident
 
 
 def test_existing(

tests/test_sync/external_patient_active_search.json

@@ -1,6 +1,7 @@
 {
-    "entry": [
-      {
+  "entry": [
+    {
+      "resource": {
         "active": true,
         "birthDate": "1977-01-12",
         "gender": "male",
@@ -10,8 +11,8 @@
         },
         "resourceType": "Patient"
       }
-    ],
-    "resourceType": "Bundle",
-    "type": "searchset"
-  }
-  
+    }
+  ],
+  "resourceType": "Bundle",
+  "type": "searchset"
+}

tests/test_sync/external_patient_search.json

@@ -1,13 +1,15 @@
 {
   "entry": [
     {
-      "birthDate": "1977-01-12",
-      "gender": "male",
-      "name": {
-        "family": "skywalker",
-        "given": ["luke"]
-      },
-      "resourceType": "Patient"
+      "resource": {
+        "birthDate": "1977-01-12",
+        "gender": "male",
+        "name": {
+          "family": "skywalker",
+          "given": ["luke"]
+        },
+        "resourceType": "Patient"
+      }
     }
   ],
   "resourceType": "Bundle",