spreading all types of resultset responses

EGA-archive · Oct 10, 2024 · d65a7c7 · d65a7c7
1 parent c79d6ea
commit d65a7c7
Show file tree

Hide file tree

Showing 11 changed files with 78 additions and 100 deletions.
diff --git a/beacon/connections/mongo/analyses.py b/beacon/connections/mongo/analyses.py
@@ -30,8 +30,6 @@ def get_analyses(self, entry_id: Optional[str], qparams: RequestParams, dataset:
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
@@ -49,8 +47,6 @@ def get_analysis_with_id(self, entry_id: Optional[str], qparams: RequestParams,
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -70,8 +66,6 @@ def get_variants_of_analysis(self, entry_id: Optional[str], qparams: RequestPara
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     idq="caseLevelData.biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
diff --git a/beacon/connections/mongo/biosamples.py b/beacon/connections/mongo/biosamples.py
@@ -30,8 +30,6 @@ def get_biosamples(self, entry_id: Optional[str], qparams: RequestParams, datase
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     idq="id"
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
@@ -49,8 +47,6 @@ def get_biosample_with_id(self, entry_id: Optional[str], qparams: RequestParams,
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="id"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -67,8 +63,6 @@ def get_variants_of_biosample(self, entry_id: Optional[str], qparams: RequestPar
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="caseLevelData.biosampleId"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -84,8 +78,6 @@ def get_analyses_of_biosample(self, entry_id: Optional[str], qparams: RequestPar
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
@@ -102,8 +94,6 @@ def get_runs_of_biosample(self, entry_id: Optional[str], qparams: RequestParams,
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     idq="biosampleId"
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
diff --git a/beacon/connections/mongo/cohorts.py b/beacon/connections/mongo/cohorts.py
@@ -65,8 +65,6 @@ def get_individuals_of_cohort(self, entry_id: Optional[str], qparams: RequestPar
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="id"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -88,8 +86,6 @@ def get_analyses_of_cohort(self, entry_id: Optional[str], qparams: RequestParams
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="biosampleId"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -127,8 +123,6 @@ def get_variants_of_cohort(self,entry_id: Optional[str], qparams: RequestParams,
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="caseLevelData.biosampleId"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -150,8 +144,6 @@ def get_runs_of_cohort(self, entry_id: Optional[str], qparams: RequestParams, da
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="biosampleId"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -173,7 +165,5 @@ def get_biosamples_of_cohort(self, entry_id: Optional[str], qparams: RequestPara
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="id"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
diff --git a/beacon/connections/mongo/datasets.py b/beacon/connections/mongo/datasets.py
@@ -98,8 +98,6 @@ def get_variants_of_dataset(self, entry_id: Optional[str], qparams: RequestParam
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -122,8 +120,6 @@ def get_biosamples_of_dataset(self, entry_id: Optional[str], qparams: RequestPar
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="id"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -146,8 +142,6 @@ def get_individuals_of_dataset(self, entry_id: Optional[str], qparams: RequestPa
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="id"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -170,8 +164,6 @@ def get_runs_of_dataset(self, entry_id: Optional[str], qparams: RequestParams, d
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="biosampleId"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     list_of_records = (
             [r for r in docs] if docs else []
@@ -197,7 +189,5 @@ def get_analyses_of_dataset(self, entry_id: Optional[str], qparams: RequestParam
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
diff --git a/beacon/connections/mongo/filters.py b/beacon/connections/mongo/filters.py
@@ -219,6 +219,8 @@ def cross_query(self, query: dict, scope: str, collection: str, request_paramete
 def apply_filters(self, query: dict, filters: List[dict], collection: str, query_parameters: dict) -> dict:
     request_parameters = query_parameters
     total_query={}
+    LOG.debug(filters)
+    LOG.debug(query_parameters)
     if len(filters) >= 1:
         total_query["$and"] = []
         if query != {} and request_parameters == {}:
@@ -385,6 +387,8 @@ def apply_filters(self, query: dict, filters: List[dict], collection: str, query
             if total_query["$and"] == [{'$or': []}] or total_query['$and'] == []:
                 total_query = {}
     if total_query == {} and query != {}:
+        LOG.debug('ene')
+        LOG.debug(query)
         total_query=query
     return total_query
 

diff --git a/beacon/connections/mongo/g_variants.py b/beacon/connections/mongo/g_variants.py
@@ -2,7 +2,7 @@
 from beacon.response.schemas import DefaultSchemas
 from beacon.connections.mongo.__init__ import client
 from beacon.connections.mongo.utils import get_docs_by_response_type
-from beacon.logs.logs import log_with_args
+from beacon.logs.logs import log_with_args, LOG
 from beacon.conf.conf import level
 from beacon.connections.mongo.filters import apply_filters
 from beacon.connections.mongo.request_parameters import apply_request_parameters
@@ -63,21 +63,24 @@ def get_biosamples_of_variant(self, entry_id: Optional[str], qparams: RequestPar
     collection = 'g_variants'
     mongo_collection = client.beacon.biosamples
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
     if parameters_as_filters == True:
         query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
     query = apply_filters(self, query, qparams.query.filters, collection,query_parameters)
     biosample_ids = client.beacon.genomicVariations \
-        .find_one(query, {"caseLevelData.biosampleId": 1, "_id": 0})
-    biosample_id=biosample_ids["caseLevelData"]
+        .find(query, {"caseLevelData.biosampleId": 1, "_id": 0})
+    biosample_ids=list(biosample_ids)
+    biosample_id=biosample_ids[0]["caseLevelData"]
     try:
-        finalid=biosample_id[0]["biosampleId"]
+        finalids=[]
+        for bioid in biosample_id:
+            finalids.append({"id": bioid})
     except Exception:# pragma: no cover
-        finalid=biosample_id["biosampleId"]
-    query = {"id": finalid}
+        finalids=[]
+    query = {"$and": [{"$or": finalids}]}
     query = apply_filters(self, query, qparams.query.filters, collection, {})
     schema = DefaultSchemas.BIOSAMPLES
     include = qparams.query.include_resultset_responses
@@ -94,21 +97,24 @@ def get_runs_of_variant(self, entry_id: Optional[str], qparams: RequestParams, d
     collection = 'g_variants'
     mongo_collection = client.beacon.runs
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
     if parameters_as_filters == True:
         query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
     query = apply_filters(self, query, qparams.query.filters, collection,query_parameters)
     biosample_ids = client.beacon.genomicVariations \
-        .find_one(query, {"caseLevelData.biosampleId": 1, "_id": 0})
-    biosample_id=biosample_ids["caseLevelData"]
+        .find(query, {"caseLevelData.biosampleId": 1, "_id": 0})
+    biosample_ids=list(biosample_ids)
+    biosample_id=biosample_ids[0]["caseLevelData"]
     try:
-        finalid=biosample_id[0]["biosampleId"]
+        finalids=[]
+        for bioid in biosample_id:
+            finalids.append(bioid)
     except Exception:# pragma: no cover
-        finalid=biosample_id["biosampleId"]
-    query = {"biosampleId": finalid}
+        finalids=[]
+    query = {"$and": [{"$or": finalids}]}
     query = apply_filters(self, query, qparams.query.filters, collection, {})
     schema = DefaultSchemas.RUNS
     include = qparams.query.include_resultset_responses
@@ -125,21 +131,24 @@ def get_analyses_of_variant(self, entry_id: Optional[str], qparams: RequestParam
     collection = 'g_variants'
     mongo_collection = client.beacon.analyses
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
     if parameters_as_filters == True:
         query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
     query = apply_filters(self, query, qparams.query.filters, collection,query_parameters)
     biosample_ids = client.beacon.genomicVariations \
-        .find_one(query, {"caseLevelData.biosampleId": 1, "_id": 0})
-    biosample_id=biosample_ids["caseLevelData"]
+        .find(query, {"caseLevelData.biosampleId": 1, "_id": 0})
+    biosample_ids=list(biosample_ids)
+    biosample_id=biosample_ids[0]["caseLevelData"]
     try:
-        finalid=biosample_id[0]["biosampleId"]
+        finalids=[]
+        for bioid in biosample_id:
+            finalids.append(bioid)
     except Exception:# pragma: no cover
-        finalid=biosample_id["biosampleId"]
-    query = {"biosampleId": finalid}
+        finalids=[]
+    query = {"$and": [{"$or": finalids}]}
     query = apply_filters(self, query, qparams.query.filters, collection, {})
     schema = DefaultSchemas.ANALYSES
     include = qparams.query.include_resultset_responses
@@ -156,26 +165,44 @@ def get_individuals_of_variant(self, entry_id: Optional[str], qparams: RequestPa
     collection = 'g_variants'
     mongo_collection = client.beacon.individuals
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
     if parameters_as_filters == True:
-        query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
+        query, parameters_as_filters = apply_request_parameters(self, query, qparams)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
     query = apply_filters(self, query, qparams.query.filters, collection,query_parameters)
     biosample_ids = client.beacon.genomicVariations \
-        .find_one(query, {"caseLevelData.biosampleId": 1, "_id": 0})
-    biosample_id=biosample_ids["caseLevelData"]
+        .find(query, {"caseLevelData.biosampleId": 1, "_id": 0})
+    biosample_ids=list(biosample_ids)
+    biosample_id=biosample_ids[0]["caseLevelData"]
     try:
-        finalid=biosample_id[0]["biosampleId"]
+        finalids=[]
+        for bioid in biosample_id:
+            finalids.append(bioid["biosampleId"])
     except Exception:# pragma: no cover
-        finalid=biosample_id["biosampleId"]
-    query = {"id": finalid}
+        finalids=[]
+    finalquery={}
+    finalquery["$or"]=[]
+    for finalid in finalids:
+        query = {"id": finalid}
+        finalquery["$or"].append(query)
     individual_id = client.beacon.biosamples \
-        .find_one(query, {"individualId": 1, "_id": 0})
-    finalid=individual_id["individualId"]
-    query = {"id": finalid}
-    query = apply_filters(self, query, qparams.query.filters, collection, {})
+        .find(finalquery, {"individualId": 1, "_id": 0})
+    try:
+        finalids=[]
+        for indid in individual_id:
+            finalids.append(indid["individualId"])
+    except Exception:# pragma: no cover
+        finalids=[]
+    finalquery={}
+    finalquery["$or"]=[]
+    for finalid in finalids:
+        query = {"id": finalid}
+        finalquery["$or"].append(query)
+    superfinalquery={}
+    superfinalquery["$and"]=[finalquery]
+    query = apply_filters(self, superfinalquery, qparams.query.filters, collection, {})
     schema = DefaultSchemas.INDIVIDUALS
     include = qparams.query.include_resultset_responses
     limit = qparams.query.pagination.limit

diff --git a/beacon/connections/mongo/individuals.py b/beacon/connections/mongo/individuals.py
@@ -31,8 +31,6 @@ def get_individuals(self, entry_id: Optional[str], qparams: RequestParams, datas
     if limit > 100 or limit == 0:
         limit = 100
     idq="id"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -50,8 +48,6 @@ def get_individual_with_id(self, entry_id: Optional[str], qparams: RequestParams
     skip = qparams.query.pagination.skip
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -73,8 +69,6 @@ def get_variants_of_individual(self, entry_id: Optional[str], qparams: RequestPa
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="caseLevelData.biosampleId"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset
 
@@ -92,7 +86,5 @@ def get_biosamples_of_individual(self, entry_id: Optional[str], qparams: Request
     if limit > 100 or limit == 0:
         limit = 100# pragma: no cover
     idq="id"
-    if include not in ['ALL', 'NONE']:
-        include = 'ALL'
     count, dataset_count, docs = get_docs_by_response_type(self, include, query, dataset, limit, skip, mongo_collection, idq)
     return schema, count, dataset_count, docs, dataset