fixed caseLevelData empty

EGA-archive · Mar 26, 2024 · 267b10a · 267b10a
1 parent e45fc18
commit 267b10a
Showing 1 changed file with 32 additions and 28 deletions.
diff --git a/beacon/db/filters.py b/beacon/db/filters.py
@@ -31,13 +31,14 @@ def cross_query(query: dict, scope: str, collection: str, request_parameters: di
             for iditem in biosample_ids:
                 if isinstance(iditem, dict):
                     if iditem != {}:
-                        new_id={}
-                        new_id[final_id] = iditem['caseLevelData'][original_id]
-                        try:
-                            #LOG.debug(new_id)
-                            subquery['$or'].append(new_id)
-                        except Exception:
-                            def_list.append(new_id)
+                        for id_item in iditem['caseLevelData']:
+                            new_id={}
+                            new_id[final_id] = id_item[original_id]
+                            try:
+                                #LOG.debug(new_id)
+                                subquery['$or'].append(new_id)
+                            except Exception:
+                                def_list.append(new_id)
 
             LOG.debug(subquery)
             mongo_collection=client.beacon.biosamples
@@ -101,13 +102,14 @@ def cross_query(query: dict, scope: str, collection: str, request_parameters: di
             for iditem in biosample_ids:
                 if isinstance(iditem, dict):
                     if iditem != {}:
-                        new_id={}
-                        new_id[final_id] = iditem['caseLevelData'][original_id]
-                        try:
-                            #LOG.debug(new_id)
-                            query['$or'].append(new_id)
-                        except Exception:
-                            def_list.append(new_id)
+                        for id_item in iditem['caseLevelData']:
+                            new_id={}
+                            new_id[final_id] = id_item[original_id]
+                            try:
+                                #LOG.debug(new_id)
+                                query['$or'].append(new_id)
+                            except Exception:
+                                def_list.append(new_id)
             if def_list != []:
                 try:
                     query['$or'].def_list
@@ -142,13 +144,14 @@ def cross_query(query: dict, scope: str, collection: str, request_parameters: di
             for iditem in biosample_ids:
                 if isinstance(iditem, dict):
                     if iditem != {}:
-                        new_id={}
-                        new_id[final_id] = iditem['caseLevelData'][original_id]
-                        try:
-                            #LOG.debug(new_id)
-                            query['$or'].append(new_id)
-                        except Exception:
-                            def_list.append(new_id)
+                        for id_item in iditem['caseLevelData']:
+                            new_id={}
+                            new_id[final_id] = id_item[original_id]
+                            try:
+                                #LOG.debug(new_id)
+                                query['$or'].append(new_id)
+                            except Exception:
+                                def_list.append(new_id)
             if def_list != []:
                 try:
                     query['$or'].def_list
@@ -332,13 +335,14 @@ def apply_filters(query: dict, filters: List[dict], collection: str, query_param
                 for iditem in biosample_ids:
                     if isinstance(iditem, dict):
                         if iditem != {}:
-                            new_id={}
-                            new_id[final_id] = iditem['caseLevelData'][original_id]
-                            try:
-                                #LOG.debug(new_id)
-                                partial_query['$or'].append(new_id)
-                            except Exception:
-                                def_list.append(new_id)
+                            for id_item in iditem['caseLevelData']:
+                                new_id={}
+                                new_id[final_id] = id_item[original_id]
+                                try:
+                                    #LOG.debug(new_id)
+                                    partial_query['$or'].append(new_id)
+                                except Exception:
+                                    def_list.append(new_id)
                 LOG.debug(partial_query)
 
                 mongo_collection=client.beacon.biosamples