fix tests failed

src/mds/agg_mds/adapters.py

@@ -418,6 +418,8 @@ def getRemoteDataAsJson(self, **kwargs) -> Dict:
                     logger.error(
                         f"An error occurred while requesting {mds_url} {exc}. Skipping {id}"
                     )
+        print("Results: ")
+        print(results)
 
         return results
 
@@ -507,14 +509,20 @@ def getRemoteDataAsJson(self, **kwargs) -> Dict:
 
         mds_url = kwargs.get("mds_url", None)
         if mds_url is None:
+            print("Clinical result with mds_url is None: ")
+            print(results)
             return results
 
         if "filters" not in kwargs or kwargs["filters"] is None:
+            print("Clinical result with filters is None: ")
+            print(results)
             return results
 
         term = kwargs["filters"].get("term", None)
 
         if term == None:
+            print("Clinical result with term is None: ")
+            print(results)
             return results
 
         term = term.replace(" ", "+")
@@ -552,6 +560,8 @@ def getRemoteDataAsJson(self, **kwargs) -> Dict:
                 numReturned = data["FullStudiesResponse"]["NStudiesReturned"]
                 results["results"].extend(data["FullStudiesResponse"]["FullStudies"])
                 if maxItems is not None and len(results["results"]) >= maxItems:
+                    print("Clinical result with maxItems is not None and result more than maxItems: ")
+                    print(results)
                     return results
                 remaining = remaining - numReturned
                 offset += numReturned
@@ -575,7 +585,8 @@ def getRemoteDataAsJson(self, **kwargs) -> Dict:
                     f"An error occurred while requesting {mds_url} {exc}. Returning {len(results['results'])} results."
                 )
                 break
-
+        print("Clinical result: ")
+        print(results)
         return results
 
     @staticmethod
@@ -1592,6 +1603,8 @@ def gather_metadata(
             globalFieldFilters=globalFieldFilters,
             schema=schema,
         )
+        print("Result after normalizing: ")
+        print(results)
         return results
     except ValueError as exc:
         logger.error(f"Exception occurred: {exc}. Returning no results")

src/mds/agg_mds/datastore/elasticsearch_dao.py

@@ -198,7 +198,6 @@ async def update_metadata(
     index_to_update = AGG_MDS_INFO_INDEX_TEMP if use_temp_index else AGG_MDS_INFO_INDEX
     elastic_search_client.index(
         index=index_to_update,
-        doc_type=AGG_MDS_INFO_TYPE,
         id=name,
         body=info,
     )
@@ -223,9 +222,7 @@ async def update_metadata(
 
 async def update_global_info(key, doc, use_temp_index: bool = False) -> None:
     index_to_update = AGG_MDS_INFO_INDEX_TEMP if use_temp_index else AGG_MDS_INFO_INDEX
-    elastic_search_client.index(
-        index=index_to_update, doc_type=AGG_MDS_INFO_TYPE, id=key, body=doc
-    )
+    elastic_search_client.index(index=index_to_update, id=key, body=doc)
 
 
 async def update_config_info(doc, use_temp_index: bool = False) -> None:
@@ -234,7 +231,6 @@ async def update_config_info(doc, use_temp_index: bool = False) -> None:
     )
     elastic_search_client.index(
         index=index_to_update,
-        doc_type="_doc",
         id=AGG_MDS_INDEX,
         body=doc,
     )
@@ -517,7 +513,6 @@ async def get_by_guid(guid):
     try:
         data = elastic_search_client.get(
             index=AGG_MDS_INDEX,
-            doc_type=AGG_MDS_TYPE,
             id=guid,
         )
         return data["_source"]

tests/test_agg_mds_clinicaltrials_adapter.py

@@ -1042,7 +1042,7 @@ def test_get_metadata_clinicaltrials():
     ).mock(
         return_value=httpx.Response(
             status_code=404,
-            content={},
+            content="{}",
         )
     )
 

tests/test_agg_mds_elasticsearch_dao.py

@@ -225,7 +225,6 @@ async def test_update_metadata():
         [
             call(
                 body={},
-                doc_type="commons-info",
                 id="my_commons",
                 index=AGG_MDS_INFO_INDEX,
             ),
@@ -237,7 +236,6 @@ async def test_update_metadata():
                         "sites": "",
                     }
                 },
-                doc_type="commons",
                 id="my_id",
                 index=AGG_MDS_INDEX,
             ),
@@ -274,7 +272,6 @@ async def test_update_metadata_to_temp_index():
         [
             call(
                 body={},
-                doc_type="commons-info",
                 id="my_commons",
                 index=AGG_MDS_INFO_INDEX_TEMP,
             ),
@@ -286,7 +283,6 @@ async def test_update_metadata_to_temp_index():
                         "sites": "",
                     }
                 },
-                doc_type="commons",
                 id="my_id",
                 index=AGG_MDS_INDEX_TEMP,
             ),
@@ -303,9 +299,7 @@ async def test_update_global_info():
     ) as mock_client:
         await elasticsearch_dao.update_global_info(key="123", doc={})
 
-    mock_client.index.assert_called_with(
-        index=AGG_MDS_INFO_INDEX, doc_type=AGG_MDS_INFO_TYPE, id="123", body={}
-    )
+    mock_client.index.assert_called_with(index=AGG_MDS_INFO_INDEX, id="123", body={})
 
 
 @pytest.mark.asyncio
@@ -319,7 +313,7 @@ async def test_update_global_info_to_temp_index():
         )
 
     mock_client.index.assert_called_with(
-        index=AGG_MDS_INFO_INDEX_TEMP, doc_type=AGG_MDS_INFO_TYPE, id="123", body={}
+        index=AGG_MDS_INFO_INDEX_TEMP, id="123", body={}
     )
 
 
@@ -332,7 +326,7 @@ async def test_update_config_info():
         await elasticsearch_dao.update_config_info(doc={})
 
     mock_client.index.assert_called_with(
-        index=AGG_MDS_CONFIG_INDEX, doc_type="_doc", id=AGG_MDS_INDEX, body={}
+        index=AGG_MDS_CONFIG_INDEX, id=AGG_MDS_INDEX, body={}
     )
 
 
@@ -345,7 +339,7 @@ async def test_update_config_info_to_temp_index():
         await elasticsearch_dao.update_config_info(doc={}, use_temp_index=True)
 
     mock_client.index.assert_called_with(
-        index=AGG_MDS_CONFIG_INDEX_TEMP, doc_type="_doc", id=AGG_MDS_INDEX, body={}
+        index=AGG_MDS_CONFIG_INDEX_TEMP, id=AGG_MDS_INDEX, body={}
     )
 
 
@@ -585,7 +579,6 @@ async def test_get_by_guid():
         await elasticsearch_dao.get_by_guid("my-commons")
         mock_client.get.assert_called_with(
             index=AGG_MDS_INDEX,
-            doc_type="commons",
             id="my-commons",
         )
 

tests/test_agg_mds_icpsr_adapter.py

@@ -231,7 +231,7 @@ def test_get_metadata_icpsr():
     respx.get("http://test/ok?verb=GetRecord&metadataPrefix=oai_dc&identifier=64").mock(
         return_value=httpx.Response(
             status_code=404,
-            content={},
+            content="{}",
         )
     )