From 8db90d44525c3bd53a616c4d986114d7d00086ba Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Oriol=20L=C3=B3pez-Doriga?= <orildsaga@gmail.com>
Date: Tue, 26 Mar 2024 18:47:50 +0100
Subject: [PATCH] bug fixed in biosample cross query

---
 beacon/db/filters.py | 76 +++++++++++++++++++++-----------------------
 1 file changed, 36 insertions(+), 40 deletions(-)

diff --git a/beacon/db/filters.py b/beacon/db/filters.py
index 3d843559..1ccb4bac 100644
--- a/beacon/db/filters.py
+++ b/beacon/db/filters.py
@@ -29,16 +29,15 @@ def cross_query(query: dict, scope: str, collection: str, request_parameters: di
             original_id="biosampleId"
             def_list=[]
             for iditem in biosample_ids:
-                for id_item in iditem['caseLevelData']:
-                    if isinstance(id_item, dict):
-                        if id_item != {}:
-                            new_id={}
-                            new_id[final_id] = id_item[original_id]
-                            try:
-                                #LOG.debug(new_id)
-                                subquery['$or'].append(new_id)
-                            except Exception:
-                                def_list.append(new_id)
+                if isinstance(iditem, dict):
+                    if iditem != {}:
+                        new_id={}
+                        new_id[final_id] = id_item['caseLevelData'][original_id]
+                        try:
+                            #LOG.debug(new_id)
+                            subquery['$or'].append(new_id)
+                        except Exception:
+                            def_list.append(new_id)
             
             LOG.debug(subquery)
             mongo_collection=client.beacon.biosamples
@@ -100,16 +99,15 @@ def cross_query(query: dict, scope: str, collection: str, request_parameters: di
             original_id="biosampleId"
             def_list=[]
             for iditem in biosample_ids:
-                for id_item in iditem['caseLevelData']:
-                    if isinstance(id_item, dict):
-                        if id_item != {}:
-                            new_id={}
-                            new_id[final_id] = id_item[original_id]
-                            try:
-                                #LOG.debug(new_id)
-                                query['$or'].append(new_id)
-                            except Exception:
-                                def_list.append(new_id)
+                if isinstance(iditem, dict):
+                    if iditem != {}:
+                        new_id={}
+                        new_id[final_id] = id_item['caseLevelData'][original_id]
+                        try:
+                            #LOG.debug(new_id)
+                            query['$or'].append(new_id)
+                        except Exception:
+                            def_list.append(new_id)
             if def_list != []:
                 try:
                     query['$or'].def_list
@@ -142,16 +140,15 @@ def cross_query(query: dict, scope: str, collection: str, request_parameters: di
             original_id="biosampleId"
             def_list=[]
             for iditem in biosample_ids:
-                for id_item in iditem['caseLevelData']:
-                    if isinstance(id_item, dict):
-                        if id_item != {}:
-                            new_id={}
-                            new_id[final_id] = id_item[original_id]
-                            try:
-                                #LOG.debug(new_id)
-                                query['$or'].append(new_id)
-                            except Exception:
-                                def_list.append(new_id)
+                if isinstance(iditem, dict):
+                    if iditem != {}:
+                        new_id={}
+                        new_id[final_id] = id_item['caseLevelData'][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
@@ -333,16 +330,15 @@ def apply_filters(query: dict, filters: List[dict], collection: str, query_param
                 def_list=[]
                 partial_query['$or']=[]
                 for iditem in biosample_ids:
-                    for id_item in iditem['caseLevelData']:
-                        if isinstance(id_item, dict):
-                            if id_item != {}:
-                                new_id={}
-                                new_id[final_id] = id_item[original_id]
-                                try:
-                                    #LOG.debug(new_id)
-                                    partial_query['$or'].append(new_id)
-                                except Exception:
-                                    def_list.append(new_id)
+                    if isinstance(iditem, dict):
+                        if iditem != {}:
+                            new_id={}
+                            new_id[final_id] = id_item['caseLevelData'][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