Include replica_type in JSONL manifest

src/azul/service/manifest_service.py

@@ -2067,7 +2067,7 @@ def _all_replicas(self) -> Iterable[JSON]:
                 replica_id = replica.meta.id
                 if replica_id not in emitted_replica_ids:
                     num_new_replicas += 1
-                    yield replica.contents.to_dict()
+                    yield replica.to_dict()
                     # Note that this will be zero for replicas that use implicit
                     # hubs, in which case there are actually many hubs
                     explicit_hub_count = len(replica.hub_ids)
@@ -2113,6 +2113,10 @@ def create_file(self) -> tuple[str, Optional[str]]:
         os.close(fd)
         with open(path, 'w') as f:
             for replica in self._all_replicas():
-                json.dump(replica, f)
+                entry = {
+                    'contents': replica['contents'],
+                    'type': replica['replica_type']
+                }
+                json.dump(entry, f)
                 f.write('\n')
         return path, None

test/service/test_manifest.py

@@ -1306,7 +1306,10 @@ def test_verbatim_jsonl_manifest(self):
         ]
         response = self._get_manifest(ManifestFormat.verbatim_jsonl, {})
         self.assertEqual(200, response.status_code)
-        response = list(map(json.loads, response.content.decode().splitlines()))
+        response = [
+            json.loads(row)['contents']
+            for row in response.content.decode().splitlines()
+        ]
 
         def sort_key(hca_doc: JSON) -> str:
             return hca_doc['provenance']['document_id']
@@ -2041,7 +2044,7 @@ def test_jsonl_manifest(self):
         response = self._get_manifest(ManifestFormat.verbatim_jsonl, filters={})
         self.assertEqual(200, response.status_code)
         manifest = [
-            json.loads(row)
+            json.loads(row)['contents']
             for row in response.content.decode().splitlines()
         ]
         expected = [