Merge pull request #36 from EGA-archive/ritools

Adding unit tests
EGA-archive · Jan 24, 2025 · 495e58f · 495e58f
2 parents a60c51d + 94b0250
commit 495e58f
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Showing 18 changed files with 1,068 additions and 185 deletions.
diff --git a/beacon/auth/tests.py b/beacon/auth/tests.py
@@ -7,7 +7,7 @@
 from dotenv import load_dotenv
 
 # for keycloak, create aud in mappers, with custom, aud and beacon for audience
-mock_access_token = ''
+mock_access_token = 'eyJhbGciOiJSUzI1NiIsInR5cCIgOiAiSldUIiwia2lkIiA6ICJreS1tUXNxZ0ZYeHdSUVRfRUhuQlJJUGpmbVhfRXZuUTVEbzZWUTJCazdZIn0.eyJleHAiOjE3Mzc3MjA0NDAsImlhdCI6MTczNzcyMDE0MCwianRpIjoiMTllODFkMTQtNDEzZS00ZGU0LWIwNzUtZDJlMjUzNGM1MDZjIiwiaXNzIjoiaHR0cDovL2xvY2FsaG9zdDo4MDgwL2F1dGgvcmVhbG1zL0JlYWNvbiIsImF1ZCI6ImJlYWNvbiIsInN1YiI6IjQ3ZWZmMWIxLTc2MjEtNDU3MC1hMGJiLTAxYTcxOWZiYTBhMiIsInR5cCI6IkJlYXJlciIsImF6cCI6ImJlYWNvbiIsInNlc3Npb25fc3RhdGUiOiI4ZDkwMGU1OS0xNmE1LTQzYzktYjgwNC05ZTFkMmY1ODNiOTYiLCJhY3IiOiIxIiwic2NvcGUiOiJvcGVuaWQgcHJvZmlsZSBlbWFpbCBtaWNyb3Byb2ZpbGUtand0Iiwic2lkIjoiOGQ5MDBlNTktMTZhNS00M2M5LWI4MDQtOWUxZDJmNTgzYjk2IiwidXBuIjoiamFuZSIsImVtYWlsX3ZlcmlmaWVkIjpmYWxzZSwibmFtZSI6IkphbmUgU21pdGgiLCJncm91cHMiOlsib2ZmbGluZV9hY2Nlc3MiLCJ1bWFfYXV0aG9yaXphdGlvbiIsIm9mZmxpbmVfYWNjZXNzIiwidW1hX2F1dGhvcml6YXRpb24iXSwicHJlZmVycmVkX3VzZXJuYW1lIjoiamFuZSIsImdpdmVuX25hbWUiOiJKYW5lIiwiZmFtaWx5X25hbWUiOiJTbWl0aCIsImVtYWlsIjoiamFuZS5zbWl0aEBiZWFjb24uZ2E0Z2gifQ.gOt5RgqH-OQG9mnjybrX_fJes9pPolrkXVMbwtImD4FpFP4cxKa-iZjLUoTCufYzFRAO0qj1rslY_50Q_pRlkr7rFwyzdbofKZ_ZCTCSIiV-rrnjE6fxQNdRKMpL9tZ-6wwGhB016cu4_YcznYdoTwahfRGRV9oiknucidSOd2jEfzfiaL89irFlzsrKYCYUY5iM4Ct21m6un7iQtxVs78RRFunzlKu4WwkKy-xtTBITZtSrLpOL7XI6EJ_P98KDGM5z_0XTTukYos7JqfSApDRMJuaap1A8zCZB4j5yjQUgY-Xb9gKUc2Ro7cNao_NuGmSzlSR788ukIh2XdTxtxQ'
 mock_access_token_false = 'public'
 #dummy test anonymous
 #dummy test login
@@ -103,7 +103,7 @@ async def test_fetch_user_info():
                 IDP_JWKS_URL = os.getenv('JWKS_URL')
                 list_visa_datasets=[]
                 user, list_visa_datasets = await fetch_user_info(self, mock_access_token, IDP_USER_INFO, IDP_ISSUER, list_visa_datasets)
-                assert user.get('preferred_username') == 'costero-e'
+                assert user.get('preferred_username') == 'jane'
             loop.run_until_complete(test_fetch_user_info())
             loop.run_until_complete(client.close())
     def test_auth_authentication(self):
@@ -113,7 +113,7 @@ def test_auth_authentication(self):
             loop.run_until_complete(client.start_server())
             async def test_authentication():
                 user, list_visa_datasets = await authentication(self, mock_access_token)
-                assert user.get('preferred_username') == 'costero-e'
+                assert user.get('preferred_username') == 'jane'
             loop.run_until_complete(test_authentication())
             loop.run_until_complete(client.close())
     def test_auth_authentication_false(self):

diff --git a/beacon/conf/api_version.yml b/beacon/conf/api_version.yml
@@ -1 +1 @@
-api_version: v2.0-ed7de15
+api_version: v2.0-a60c51d
diff --git a/beacon/connections/mongo/__init__.py b/beacon/connections/mongo/__init__.py
@@ -1,7 +1,7 @@
 from pymongo.mongo_client import MongoClient
 from beacon.connections.mongo import conf
 
-if conf.database_cluster:
+if conf.database_cluster:# pragma: no cover
     uri = "mongodb+srv://{}:{}@{}/?tls=true&authMechanism=SCRAM-SHA-256&retrywrites=false&maxIdleTimeMS=120000".format(
         conf.database_user,
         conf.database_password,
@@ -17,7 +17,7 @@
         conf.database_auth_source
     )
 
-if conf.database_certificate != '' and conf.database_cafile != '':
+if conf.database_certificate != '' and conf.database_cafile != '':# pragma: no cover
     uri += '&tls=true&tlsCertificateKeyFile={}&tlsCAFile={}'.format(conf.database_certificate, conf.database_cafile)
 
 client = MongoClient(uri)
diff --git a/beacon/connections/mongo/analyses.py b/beacon/connections/mongo/analyses.py
@@ -66,24 +66,12 @@ def get_variants_of_analysis(self, entry_id: Optional[str], qparams: RequestPara
     for bioid in bioids:
         if bioid == analysis_ids["biosampleId"]:
             break
-        position+=1
-    if position == len(bioids):
+        position+=1# pragma: no cover
+    if position == len(bioids):# pragma: no cover
         schema = DefaultSchemas.GENOMICVARIATIONS
         return schema, 0, -1, None, dataset
     position=str(position)
-    filters=qparams.query.filters
-    if filters != []:
-        for filter in filters:
-            if filter['id']=='GENO:GENO_0000458':
-                query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
-                qparams.query.filters.remove(filter)
-            elif filter['id']=='GENO:GENO_0000136':
-                query_cl={"$or": [{ position: "11", "datasetId": dataset}]}
-                qparams.query.filters.remove(filter)
-            else:
-                query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
-    else:
-        query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+    query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
     string_of_ids = client.beacon.caseLevelData \
         .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip)
     HGVSIds=list(string_of_ids)

diff --git a/beacon/connections/mongo/biosamples.py b/beacon/connections/mongo/biosamples.py
@@ -62,23 +62,11 @@ def get_variants_of_biosample(self, entry_id: Optional[str], qparams: RequestPar
         if bioid == entry_id:
             break
         position+=1
-    if position == len(bioids):
+    if position == len(bioids):# pragma: no cover
         schema = DefaultSchemas.GENOMICVARIATIONS
         return schema, 0, -1, None, dataset
     position=str(position)
-    filters=qparams.query.filters
-    if filters != []:
-        for filter in filters:
-            if filter['id']=='GENO:GENO_0000458':
-                query_cl={"$or": [{ position: "10", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
-                qparams.query.filters.remove(filter)
-            elif filter['id']=='GENO:GENO_0000136':
-                query_cl={"$or": [{ position: "11", "datasetId": dataset}]}
-                qparams.query.filters.remove(filter)
-            else:
-                query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
-    else:
-        query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
+    query_cl={"$or": [{ position: "10", "datasetId": dataset},{ position: "11", "datasetId": dataset}, { position: "01", "datasetId": dataset}]}
     string_of_ids = client.beacon.caseLevelData \
         .find(query_cl, {"id": 1, "_id": 0}).limit(qparams.query.pagination.limit).skip(qparams.query.pagination.skip)
     HGVSIds=list(string_of_ids)

diff --git a/beacon/connections/mongo/executor.py b/beacon/connections/mongo/executor.py
@@ -102,16 +102,16 @@ async def execute_function(self, entry_type: str, datasets: list, qparams: Reque
                     datasets_docs[dataset]=records
                     datasets_count[dataset]=dataset_count
                 else:
-                    datasets.remove(dataset)
+                    datasets.remove(dataset)# pragma: no cover
             elif include == 'HIT':
                 if dataset_count != -1 and dataset_count != 0:
                     new_count+=dataset_count
                     datasets_docs[dataset]=records
                     datasets_count[dataset]=dataset_count
                 else:
                     datasets.remove(dataset) 
-            else:  
-                if dataset_count == 0:
+            else:
+                if dataset_count == 0:# pragma: no cover
                     new_count+=dataset_count
                     datasets_docs[dataset]=records
                     datasets_count[dataset]=dataset_count
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		api_version: v2.0-ed7de15
		api_version: v2.0-a60c51d