Merge pull request #15 from EGA-archive/testMode

Adding Test mode and fixing case insensitive searches for filtering terms

beacon/connections/mongo/filters.py

@@ -595,6 +595,7 @@ def apply_ontology_filter(self, query: dict, filter: OntologyFilter, collection:
             dict_regex={}
             try:
                 dict_regex['$regex']=label
+                dict_regex['$options']='i'
             except Exception:
                 dict_regex['$regex']=''
             dict_id={}
@@ -668,6 +669,7 @@ def apply_ontology_filter(self, query: dict, filter: OntologyFilter, collection:
         dict_regex={}
         try:
             dict_regex['$regex']=label
+            dict_regex['$options']='i'
         except Exception:# pragma: no cover
             dict_regex['$regex']=''
         dict_id={}
@@ -696,7 +698,6 @@ def apply_ontology_filter(self, query: dict, filter: OntologyFilter, collection:
                 query_id[query_term]=simil
                 new_query['$or'].append(query_id)
             query = new_query
-
         query=cross_query(self, query, scope, collection, request_parameters, dataset)
 
 
@@ -723,6 +724,7 @@ def apply_ontology_filter(self, query: dict, filter: OntologyFilter, collection:
         query_filtering['$and'].append(dict_scope)
         dict_regex={}
         dict_regex['$regex']=label
+        dict_regex['$options']='i'
         dict_id={}
         dict_id['id']=dict_regex
         query_filtering['$and'].append(dict_id)
@@ -1000,6 +1002,7 @@ def apply_alphanumeric_filter(self, query: dict, filter: AlphanumericFilter, col
             dict_id={}
             dict_regex={}
             dict_regex['$regex']=filter.id
+            dict_regex['$options']='i'
             dict_type['type']='custom'
             dict_id['id']=dict_regex
             query_filtering['$and'].append(dict_type)

beacon/request/parameters.py

@@ -216,6 +216,17 @@ def from_request(self, request: Request) -> Self:
                     self.query.request_parameters[k] = html.escape(v)
                 elif k == 'filters':
                     self.query.request_parameters[k] = html.escape(v)
+                elif k == 'testMode':
+                    v = html.escape(v)
+                    if v.lower() == 'true':
+                        v = True
+                    elif v.lower() == 'false':
+                        v = False
+                    else:
+                        err = 'testMode parameter can only be either true or false value'
+                        errcode=400
+                        raise_exception(err, errcode)
+                    self.query.test_mode = v
                 elif k in ["start", "end", "assemblyId", "referenceName", "referenceBases", "alternateBases", "variantType","variantMinLength","variantMaxLength","geneId","genomicAlleleShortForm","aminoacidChange","clinicalRelevance", "mateName"]:
                     try:
                         if ',' in v:# pragma: no cover

beacon/response/builder.py

@@ -35,6 +35,9 @@ async def builder(self, request: Request, datasets, qparams, entry_type, entry_i
         complete_module='beacon.connections.'+source+'.executor'
         import importlib
         module = importlib.import_module(complete_module, package=None)
+        testMode = qparams.query.test_mode
+        if testMode == True:
+            datasets = ['test']
         datasets_docs, datasets_count, count, entity_schema, include, datasets = await module.execute_function(self, entry_type, datasets, qparams, entry_id)
         if include != 'NONE' and granularity == Granularity.RECORD and default_beacon_granularity == 'record':
             response = build_beacon_record_response_by_dataset(self, datasets, datasets_docs, datasets_count, count, qparams, entity_schema)