From d9bc3fc9c745dc36fc626afd62770de9ff2bcb01 Mon Sep 17 00:00:00 2001
From: costero-e <orildsaga@gmail.com>
Date: Fri, 22 Nov 2024 15:25:39 +0100
Subject: [PATCH 1/3] creating datasets array with test dataset

---
 beacon/response/builder.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/beacon/response/builder.py b/beacon/response/builder.py
index 9c7389c..635ad84 100644
--- a/beacon/response/builder.py
+++ b/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.testMode
+        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)

From eaabfcfc996c8bfe15b9b6fb1cb124aad4feefd7 Mon Sep 17 00:00:00 2001
From: costero-e <orildsaga@gmail.com>
Date: Fri, 22 Nov 2024 16:15:53 +0100
Subject: [PATCH 2/3] added response for test dataset if testMode is true

---
 beacon/request/parameters.py | 11 +++++++++++
 beacon/response/builder.py   |  2 +-
 2 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/beacon/request/parameters.py b/beacon/request/parameters.py
index d159402..b1f604b 100644
--- a/beacon/request/parameters.py
+++ b/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
diff --git a/beacon/response/builder.py b/beacon/response/builder.py
index 635ad84..eb4a33f 100644
--- a/beacon/response/builder.py
+++ b/beacon/response/builder.py
@@ -35,7 +35,7 @@ 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.testMode
+        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)

From a5225bdbb47328a9fe0856db7e67faec02eb8bb7 Mon Sep 17 00:00:00 2001
From: costero-e <orildsaga@gmail.com>
Date: Fri, 22 Nov 2024 19:13:18 +0100
Subject: [PATCH 3/3] fixing case insensitive for filtering terms

---
 beacon/connections/mongo/filters.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/beacon/connections/mongo/filters.py b/beacon/connections/mongo/filters.py
index 276dab3..b4b8f91 100644
--- a/beacon/connections/mongo/filters.py
+++ b/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)