dataset variable in request parameters

EGA-archive · Nov 2, 2024 · d9ff62a · d9ff62a
1 parent 4c6468f
commit d9ff62a
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Showing 8 changed files with 39 additions and 39 deletions.
diff --git a/beacon/conf/conf.py b/beacon/conf/conf.py
@@ -15,7 +15,7 @@
 beacon_id = 'org.ega-archive.beacon-ri-demo'  # ID of the Beacon
 beacon_name = 'Beacon Reference Implementation demo'  # Name of the Beacon service
 api_version = 'v2.0.0' # Version of the Beacon implementation
-uri = 'https://beacon-ri-demo.ega-archive.org/api/'
+uri = 'http://beaconprod:5050/api/'
 environment = 'test'
 description = r"This Beacon is based on synthetic data hosted at the <a href='https://ega-archive.org/datasets/EGAD00001003338'>EGA</a>. The dataset contains 2504 samples including genetic data based on 1K Genomes data, and 76 individual attributes and phenotypic data derived from UKBiobank."
 version = api_version_yaml['api_version']

diff --git a/beacon/connections/mongo/analyses.py b/beacon/connections/mongo/analyses.py
@@ -15,9 +15,9 @@ def get_analyses(self, entry_id: Optional[str], qparams: RequestParams, dataset:
     collection = 'analyses'
     mongo_collection = client.beacon.analyses
     parameters_as_filters=False
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
     if parameters_as_filters == True and query_parameters != {'$and': []}:# pragma: no cover
-        query, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
         query_parameters={}
     elif query_parameters != {'$and': []}:
         query=query_parameters

diff --git a/beacon/connections/mongo/biosamples.py b/beacon/connections/mongo/biosamples.py
@@ -14,9 +14,9 @@ def get_biosamples(self, entry_id: Optional[str], qparams: RequestParams, datase
     collection = 'biosamples'
     mongo_collection = client.beacon.biosamples
     parameters_as_filters=False
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
     if parameters_as_filters == True and query_parameters != {'$and': []}:# pragma: no cover
-        query, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
         query_parameters={}
     elif query_parameters != {'$and': []}:
         query=query_parameters

diff --git a/beacon/connections/mongo/datasets.py b/beacon/connections/mongo/datasets.py
@@ -56,9 +56,9 @@ def get_list_of_datasets(self):
 @log_with_args_mongo(level)
 def get_dataset_with_id(self, entry_id: Optional[str], qparams: RequestParams):
     limit = qparams.query.pagination.limit
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
     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, {}, qparams, dataset)# pragma: no cover
     else:
         query={}
     query = query_id(self, query, entry_id)

diff --git a/beacon/connections/mongo/g_variants.py b/beacon/connections/mongo/g_variants.py
@@ -14,9 +14,9 @@ def get_variants(self, entry_id: Optional[str], qparams: RequestParams, dataset:
     collection = 'g_variants'
     mongo_collection = client.beacon.genomicVariations
     parameters_as_filters=False
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
     if parameters_as_filters == True and query_parameters != {'$and': []}:
-        query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover
         query_parameters={}# pragma: no cover
     elif query_parameters != {'$and': []}:
         query=query_parameters
@@ -41,9 +41,9 @@ def get_variant_with_id(self, entry_id: Optional[str], qparams: RequestParams, d
     collection = 'g_variants'
     mongo_collection = client.beacon.genomicVariations
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset)
     if parameters_as_filters == True:
-        query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
@@ -63,9 +63,9 @@ def get_biosamples_of_variant(self, entry_id: Optional[str], qparams: RequestPar
     collection = 'g_variants'
     mongo_collection = client.beacon.biosamples
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
+    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)# pragma: no cover
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
@@ -110,9 +110,9 @@ def get_runs_of_variant(self, entry_id: Optional[str], qparams: RequestParams, d
     collection = 'g_variants'
     mongo_collection = client.beacon.runs
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset)
     if parameters_as_filters == True:
-        query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
@@ -156,9 +156,9 @@ def get_analyses_of_variant(self, entry_id: Optional[str], qparams: RequestParam
     collection = 'g_variants'
     mongo_collection = client.beacon.analyses
     query = {"$and": [{"variantInternalId": entry_id}]}
-    query_parameters, parameters_as_filters = apply_request_parameters(self, query, qparams)
+    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)# pragma: no cover
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query=query_parameters
@@ -202,9 +202,9 @@ 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, query, qparams)
+    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, query, qparams)# 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

diff --git a/beacon/connections/mongo/individuals.py b/beacon/connections/mongo/individuals.py
@@ -14,9 +14,9 @@ def get_individuals(self, entry_id: Optional[str], qparams: RequestParams, datas
     collection = 'individuals'
     mongo_collection = client.beacon.individuals
     parameters_as_filters=False
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
     if parameters_as_filters == True and query_parameters != {'$and': []}:
-        query, parameters_as_filters = apply_request_parameters(self, {}, qparams)# pragma: no cover
+        query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)# pragma: no cover
         query_parameters={}# pragma: no cover
     elif query_parameters != {'$and': []}:
         query=query_parameters
@@ -39,7 +39,7 @@ def get_individual_with_id(self, entry_id: Optional[str], qparams: RequestParams
     collection = 'individuals'
     idq="id"
     mongo_collection = client.beacon.individuals
-    query, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
     query = apply_filters(self, query, qparams.query.filters, collection, {}, dataset)
     query = query_id(self, query, entry_id)
     schema = DefaultSchemas.INDIVIDUALS
@@ -83,7 +83,7 @@ def get_variants_of_individual(self, entry_id: Optional[str], qparams: RequestPa
     queryHGVS["$in"]=listHGVS
     query["identifiers.genomicHGVSId"]=queryHGVS
     mongo_collection = client.beacon.genomicVariations
-    query, parameters_as_filters = apply_request_parameters(self, query, qparams)
+    query, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset)
     query = apply_filters(self, query, qparams.query.filters, collection, {}, dataset)
     schema = DefaultSchemas.GENOMICVARIATIONS
     include = qparams.query.include_resultset_responses
@@ -100,7 +100,7 @@ def get_biosamples_of_individual(self, entry_id: Optional[str], qparams: Request
     collection = 'biosamples'
     mongo_collection = client.beacon.biosamples
     query = {"individualId": entry_id}
-    query, parameters_as_filters = apply_request_parameters(self, query, qparams)
+    query, parameters_as_filters = apply_request_parameters(self, query, qparams, dataset)
     query = apply_filters(self, query, qparams.query.filters, collection, {}, dataset)
     schema = DefaultSchemas.BIOSAMPLES
     include = qparams.query.include_resultset_responses

diff --git a/beacon/connections/mongo/request_parameters.py b/beacon/connections/mongo/request_parameters.py
@@ -67,7 +67,7 @@ def generate_position_filter_end(self, key: str, value: List[int]) -> List[Alpha
     return filters
 
 @log_with_args(level)
-def apply_request_parameters(self, query: Dict[str, List[dict]], qparams: RequestParams):
+def apply_request_parameters(self, query: Dict[str, List[dict]], qparams: RequestParams, dataset: str):
     collection = 'g_variants'
     if len(qparams.query.request_parameters) > 0 and "$and" not in query:
         query["$and"] = []
@@ -85,45 +85,45 @@ def apply_request_parameters(self, query: Dict[str, List[dict]], qparams: Reques
                         v = v.split(',')
                     filters = generate_position_filter_start(self, k, v)
                     for filter in filters:
-                        subquery["$and"].append(apply_alphanumeric_filter({}, filter, collection))
+                        subquery["$and"].append(apply_alphanumeric_filter({}, filter, collection, dataset))
                 elif k == "end":
                     if isinstance(v, str):
                         v = v.split(',')
                     filters = generate_position_filter_end(self, k, v)
                     for filter in filters:
-                        subquery["$and"].append(apply_alphanumeric_filter({}, filter, collection))
+                        subquery["$and"].append(apply_alphanumeric_filter({}, filter, collection, dataset))
                 elif k == "datasets":
                     pass
                 elif k == "variantMinLength":
                     try:
                         subquery["$and"].append(apply_alphanumeric_filter({}, AlphanumericFilter(
                             id=VARIANTS_PROPERTY_MAP[k],
                             value='min'+v
-                        ), collection))
+                        ), collection, dataset))
                     except KeyError:
                         raise web.HTTPNotFound
                 elif k == "variantMaxLength":
                     try:
                         subquery["$and"].append(apply_alphanumeric_filter({}, AlphanumericFilter(
                             id=VARIANTS_PROPERTY_MAP[k],
                             value='max'+v
-                        ), collection))
+                        ), collection, dataset))
                     except KeyError:
                         raise web.HTTPNotFound    
                 elif k == "mateName" or k == 'referenceName':
                     try:
                         subqueryor["$or"].append(apply_alphanumeric_filter({}, AlphanumericFilter(
                             id=VARIANTS_PROPERTY_MAP[k],
                             value='max'+v
-                        ), collection))
+                        ), collection, dataset))
                     except KeyError:
                         raise web.HTTPNotFound    
                 elif k != 'filters':
                     try:
                         subquery["$and"].append(apply_alphanumeric_filter({}, AlphanumericFilter(
                             id=VARIANTS_PROPERTY_MAP[k],
                             value=v
-                        ), collection))
+                        ), collection, dataset))
                     except KeyError:
                         raise web.HTTPNotFound
 
@@ -155,45 +155,45 @@ def apply_request_parameters(self, query: Dict[str, List[dict]], qparams: Reques
                     v = v.split(',')
                 filters = generate_position_filter_start(self, k, v)
                 for filter in filters:
-                    query["$and"].append(apply_alphanumeric_filter(self, {}, filter, collection))
+                    query["$and"].append(apply_alphanumeric_filter(self, {}, filter, collection, dataset))
             elif k == "end":
                 if isinstance(v, str):
                     v = v.split(',')
                 filters = generate_position_filter_end(self, k, v)
                 for filter in filters:
-                    query["$and"].append(apply_alphanumeric_filter(self, {}, filter, collection))
+                    query["$and"].append(apply_alphanumeric_filter(self, {}, filter, collection, dataset))
             elif k == "datasets":
                 pass
             elif k == "variantMinLength":
                 try:
                     query["$and"].append(apply_alphanumeric_filter(self, {}, AlphanumericFilter(
                         id=VARIANTS_PROPERTY_MAP[k],
                         value='min'+v
-                    ), collection))
+                    ), collection, dataset))
                 except KeyError:# pragma: no cover
                     raise web.HTTPNotFound
             elif k == "variantMaxLength":
                 try:
                     query["$and"].append(apply_alphanumeric_filter(self, {}, AlphanumericFilter(
                         id=VARIANTS_PROPERTY_MAP[k],
                         value='max'+v
-                    ), collection))
+                    ), collection, dataset))
                 except KeyError:# pragma: no cover
                     raise web.HTTPNotFound    
             elif k == "mateName" or k == 'referenceName':
                 try:
                     subqueryor["$or"].append(apply_alphanumeric_filter(self, {}, AlphanumericFilter(
                         id=VARIANTS_PROPERTY_MAP[k],
                         value=v
-                    ), collection))
+                    ), collection, dataset))
                 except KeyError:# pragma: no cover
                     raise web.HTTPNotFound
             elif k != 'filters':
                 try:
                     query["$and"].append(apply_alphanumeric_filter(self, {}, AlphanumericFilter(
                         id=VARIANTS_PROPERTY_MAP[k],
                         value=v
-                    ), collection))
+                    ), collection, dataset))
                 except KeyError:# pragma: no cover
                     raise web.HTTPNotFound
 

diff --git a/beacon/connections/mongo/runs.py b/beacon/connections/mongo/runs.py
@@ -14,9 +14,9 @@ def get_runs(self, entry_id: Optional[str], qparams: RequestParams, dataset: str
     collection = 'runs'
     mongo_collection = client.beacon.runs
     parameters_as_filters=False
-    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams)
+    query_parameters, parameters_as_filters = apply_request_parameters(self, {}, qparams, dataset)
     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, {}, qparams, dataset)# pragma: no cover
         query_parameters={}# pragma: no cover
     else:
         query={}