Merge pull request #378 from EGA-archive/develop

Removed introspection

beacon/api_version.yml

@@ -1 +1 @@
-api_version: v2.0-19c610e
+api_version: v2.0-8917c2a

beacon/db/filters.py

@@ -19,13 +19,11 @@
 
 def cross_query(query: dict, scope: str, collection: str, request_parameters: dict):
     if scope == 'genomicVariation' and collection == 'g_variants' or scope == collection[0:-1]:
-        LOG.debug(query)
-        LOG.debug(request_parameters)
         subquery={}
         subquery["$or"]=[]
         if request_parameters != {}:
             biosample_ids = client.beacon.genomicVariations.find(request_parameters, {"caseLevelData.biosampleId": 1, "_id": 0})
-            final_id='id'
+            final_id='caseLevelData.biosampleId'
             original_id="biosampleId"
             def_list=[]
             for iditem in biosample_ids:
@@ -36,30 +34,16 @@ def cross_query(query: dict, scope: str, collection: str, request_parameters: di
                                 new_id={}
                                 new_id[final_id] = id_item[original_id]
                                 try:
-                                    #LOG.debug(new_id)
                                     subquery['$or'].append(new_id)
-                                except Exception:
+                                except Exception:# pragma: no cover
                                     def_list.append(new_id)
-
-            LOG.debug(subquery)
-            mongo_collection=client.beacon.biosamples
-            original_id="individualId"
-            join_ids2=list(join_query(mongo_collection, subquery, original_id))
-            def_list=[]
-            final_id="id"
-            for id_item in join_ids2:
-                new_id={}
-                new_id[final_id] = id_item.pop(original_id)
-                def_list.append(new_id)
-            subquery={}
-            subquery['$or']=def_list
+                                    subquery={}
+                                    subquery['$or']=def_list
             try:
-                LOG.debug(query)
                 query["$and"] = []
                 query["$and"].append(subquery)
             except Exception:
-                LOG.debug(query)
-        LOG.debug(query)
+                pass
     else:
         def_list=[]                
         if scope == 'individual' and collection == 'g_variants':

permissions/auth.py

@@ -102,6 +102,7 @@ async def get_user_info(access_token):
     LOG.error(user_info)
     user = None
 
+    '''
     async with ClientSession() as session:
         async with session.post(idp_introspection,
                                 auth=BasicAuth(idp_client_id, password=idp_client_secret),
@@ -117,6 +118,7 @@ async def get_user_info(access_token):
                 LOG.error('Invalid token')
                 user = 'public'
                 return user, list_visa_datasets
+    '''
 
     async with ClientSession(trust_env=True) as session:
         headers = { 'Accept': 'application/json', 'Authorization': 'Bearer ' + access_token }
@@ -125,6 +127,7 @@ async def get_user_info(access_token):
             LOG.error('Response %s', resp)
             if resp.status == 200:
                 user = await resp.json()
+                LOG.error(user)
                 try:
                     visa_datasets = user['ga4gh_passport_v1']
                     if visa_datasets is not None:
@@ -165,6 +168,7 @@ async def decorated(request):
         # We make a round-trip to the userinfo. We might not have a JWT token.
         try:
             user, list_visa_datasets = await get_user_info(access_token)
+            LOG.error(user)
         except Exception:
             user = 'public'
         LOG.info('The user is: %r', user)
@@ -174,7 +178,7 @@ async def decorated(request):
             username = 'public'
         else:
             username = user.get('preferred_username')
-        LOG.debug('username: %s', username)
+        LOG.error('username: %s', username)
 
         return await func(request, username, list_visa_datasets)
     return decorated