From 61702a4710bd9ae452070b17aa7f95c3fa96e76a Mon Sep 17 00:00:00 2001 From: costero-e Date: Thu, 21 Nov 2024 18:16:34 +0100 Subject: [PATCH] making filters work for entry types with biosamples and variants --- .gitignore | 4 +++- beacon/connections/mongo/g_variants.py | 14 +++++++------- 2 files changed, 10 insertions(+), 8 deletions(-) diff --git a/.gitignore b/.gitignore index 2fad0f7..7e38acf 100644 --- a/.gitignore +++ b/.gitignore @@ -5,4 +5,6 @@ logs.log beacon/connections/mongo/data/datasets beacon/connections/mongo/data/rarediseases beacon/connections/mongo/data/rd-connect -*.vcf.gz \ No newline at end of file +*.vcf.gz +beacon/connections/mongo/data/db/* +!beacon/connections/mongo/data/db/dir.txt \ No newline at end of file diff --git a/beacon/connections/mongo/g_variants.py b/beacon/connections/mongo/g_variants.py index c6fdb11..19ca95d 100644 --- a/beacon/connections/mongo/g_variants.py +++ b/beacon/connections/mongo/g_variants.py @@ -65,16 +65,16 @@ def get_biosamples_of_variant(self, entry_id: Optional[str], qparams: RequestPar query = {"$and": [{"variantInternalId": entry_id}]} query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset) if parameters_as_filters == True: - query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover + query, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset)# pragma: no cover query_parameters={}# pragma: no cover else: query=query_parameters - query = apply_filters(self, query, qparams.query.filters, collection,query_parameters, dataset) + collection='biosamples' HGVSIds = client.beacon.genomicVariations \ .find(query, {"identifiers.genomicHGVSId": 1, "datasetId": 1, "_id": 0}) HGVSDataset=HGVSIds[0]["datasetId"] if dataset != HGVSDataset: - schema = DefaultSchemas.INDIVIDUALS + schema = DefaultSchemas.BIOSAMPLES return schema, 0, 0, [], dataset HGVSIds=list(HGVSIds) HGVSId=HGVSIds[0]["identifiers"]["genomicHGVSId"] @@ -116,11 +116,11 @@ def get_runs_of_variant(self, entry_id: Optional[str], qparams: RequestParams, d query = {"$and": [{"variantInternalId": entry_id}]} query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset) if parameters_as_filters == True: - query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover + query, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset)# pragma: no cover query_parameters={}# pragma: no cover else: query=query_parameters - query = apply_filters(self, query, qparams.query.filters, collection,query_parameters, dataset) + collection='runs' HGVSIds = client.beacon.genomicVariations \ .find(query, {"identifiers.genomicHGVSId": 1, "datasetId": 1, "_id": 0}) HGVSDataset=HGVSIds[0]["datasetId"] @@ -166,11 +166,11 @@ def get_analyses_of_variant(self, entry_id: Optional[str], qparams: RequestParam query = {"$and": [{"variantInternalId": entry_id}]} query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset) if parameters_as_filters == True: - query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover + query, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset)# pragma: no cover query_parameters={}# pragma: no cover else: query=query_parameters - query = apply_filters(self, query, qparams.query.filters, collection,query_parameters, dataset) + collection='analyses' HGVSIds = client.beacon.genomicVariations \ .find(query, {"identifiers.genomicHGVSId": 1, "datasetId": 1, "_id": 0}) HGVSDataset=HGVSIds[0]["datasetId"]