From 098e64d7a87ff4a8355fd52a3cbae72e085fff98 Mon Sep 17 00:00:00 2001 From: Oriol Lopez-Doriga Date: Sun, 29 Sep 2024 11:08:39 +0200 Subject: [PATCH] g_variants with parameters and filtering terms --- beacon/db/filters.py | 26 +++++--------------------- 1 file changed, 5 insertions(+), 21 deletions(-) diff --git a/beacon/db/filters.py b/beacon/db/filters.py index f0007c31..0bbb2c2d 100644 --- a/beacon/db/filters.py +++ b/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':