fix typing based on tests

missconfigured some types and checking tests helped

Author: blankdots

beacon_api/permissions/ga4gh.py

@@ -97,7 +97,7 @@
 
 
 async def check_ga4gh_token(decoded_data: JWTClaims,
-                            token: str,
+                            token: Dict,
                             bona_fide_status: bool,
                             dataset_permissions: set) -> Tuple[set, bool]:
     """Check the token for GA4GH claims."""
@@ -145,7 +145,7 @@ async def decode_passport(encoded_passport: str) -> List[Dict]:
     return decoded_data
 
 
-async def get_ga4gh_permissions(token: str) -> tuple:
+async def get_ga4gh_permissions(token: Dict) -> tuple:
     """Retrieve GA4GH passports (JWTs) from ELIXIR AAI and process them into tangible permissions."""
     LOG.info('Handling permissions.')
 
@@ -182,7 +182,7 @@ async def get_ga4gh_permissions(token: str) -> tuple:
     return dataset_permissions, bona_fide_status
 
 
-async def retrieve_user_data(token: str) -> Optional[str]:
+async def retrieve_user_data(token: Dict) -> Optional[str]:
     """Retrieve GA4GH user data."""
     LOG.debug('Contacting ELIXIR AAI /userinfo.')
     headers = {"Authorization": f"Bearer {token}"}
@@ -211,7 +211,7 @@ async def get_jwk(url: str) -> Optional[Dict]:
         return None
 
 
-async def validate_passport(passport: List) -> JWTClaims:
+async def validate_passport(passport: Dict) -> JWTClaims:
     """Decode a passport and validate its contents."""
     LOG.debug('Validating passport.')
 

tests/test_basic.py

@@ -204,7 +204,7 @@ def test_access_resolution_controlled_registered(self):
         token = mock_token(True, ["5", "6"], True)
         host = 'localhost'
         result = access_resolution(request, token, host, ["1", "2"], ["3", "4"], ["5", "6"])
-        self.assertListEqual(result[0], ['PUBLIC', 'REGISTERED' ,'CONTROLLED'])
+        self.assertListEqual(result[0], ['PUBLIC', 'REGISTERED', 'CONTROLLED'])
         intermediate_list = result[1]
         intermediate_list.sort()
         self.assertListEqual(["1", "2", "3", "4", "5", "6"], intermediate_list)
@@ -434,7 +434,7 @@ async def test_get_ga4gh_permissions(self, m_userinfo, m_decode, m_controlled, m
         m_decode.return_value = header, payload
         m_controlled.return_value = set()
         m_bonafide.return_value = False
-        dataset_permissions, bona_fide_status = await get_ga4gh_permissions('token')
+        dataset_permissions, bona_fide_status = await get_ga4gh_permissions({})
         self.assertEqual(dataset_permissions, set())
         self.assertEqual(bona_fide_status, False)
         # Test: permissions
@@ -448,7 +448,7 @@ async def test_get_ga4gh_permissions(self, m_userinfo, m_decode, m_controlled, m
         m_decode.return_value = header, payload
         m_controlled.return_value = {'EGAD01'}
         m_bonafide.return_value = False
-        dataset_permissions, bona_fide_status = await get_ga4gh_permissions('token')
+        dataset_permissions, bona_fide_status = await get_ga4gh_permissions({})
         self.assertEqual(dataset_permissions, {'EGAD01'})
         self.assertEqual(bona_fide_status, False)
         # Test: bona fide
@@ -462,7 +462,7 @@ async def test_get_ga4gh_permissions(self, m_userinfo, m_decode, m_controlled, m
         m_decode.return_value = header, payload
         m_controlled.return_value = set()
         m_bonafide.return_value = True
-        dataset_permissions, bona_fide_status = await get_ga4gh_permissions('token')
+        dataset_permissions, bona_fide_status = await get_ga4gh_permissions({})
         self.assertEqual(dataset_permissions, set())
         self.assertEqual(bona_fide_status, True)
 

tests/test_mate_name.py

@@ -19,11 +19,10 @@ def tearDown(self):
     async def test_find_fusion(self, mock_filtered):
         """Test find datasets."""
         mock_filtered.return_value = []
-        token = dict()
-        token["bona_fide_status"] = False
-        result = await find_fusion(None, 'GRCh38', None, 'Y', 'T', 'C', [], token, "NONE")
+        access_type = list()
+        result = await find_fusion(None, 'GRCh38', (), 'Y', 'T', 'C', [], access_type, "NONE")
         self.assertEqual(result, [])
-        result_miss = await find_fusion(None, 'GRCh38', None, 'Y', 'T', 'C', [], token, "MISS")
+        result_miss = await find_fusion(None, 'GRCh38', (), 'Y', 'T', 'C', [], access_type, "MISS")
         self.assertEqual(result_miss, [])
 
     async def test_fetch_fusion_dataset_call(self):