Merge pull request #27 from NHS-NGS/pyCIPAPI_client

Update live 100K URL

pyCIPAPI/jellypy/pyCIPAPI/auth.py

@@ -101,7 +101,7 @@ def authenticate_ad(self, testing_on=False):
             self.auth_expires = datetime.fromtimestamp(int(auth_response['expires_on']))
         except KeyError:
             self.auth_time = False
-            raise Exception('Authentication Error')
+            raise Exception(f'Authentication Error: {auth_response}')
         except:
             raise
 

pyCIPAPI/jellypy/pyCIPAPI/config.py

@@ -10,5 +10,5 @@
 beta_testing_auth_url = 'https://login.microsoftonline.com/99515578-fda0-444c-8f5a-2005038880f2/oauth2/token'
 
 # CIP-API base URLs for live data and beta testing:
-live_100k_data_base_url = 'https://cipapi.gel.zone/api/2/'
+live_100k_data_base_url = 'https://cipapi.genomicsengland.nhs.uk/api/2/'
 beta_testing_base_url = 'https://cipapi-beta.genomicsengland.co.uk/api/2/'

pyCIPAPI/setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name='jellypy_pyCIPAPI',
-    version='0.2.2',
+    version='0.2.3',
     author="NHS Bioinformatics Group",
     author_email="[email protected]",
     description='Python client library the Genomics England CIPAPI',

pyCIPAPI/test/test_pyCIPAPI.py

@@ -1,9 +1,19 @@
 
 """
-Tests for jellypy-pyCIPAPI package
+Tests for jellypy-pyCIPAPI package. 
+
+Ensure you have installed jellypy-pyCIPAPI from the repository: 
+    $ pip install ./pyCIPAPI
 
 Usage:
-    pytest tierup/test/test_requests.py --jpconfig=tierup/test/config.ini
+    pytest pyCIPAPI/test/test_pyCIPAPI.py --jpconfig=config.ini
+
+Example config.ini format:
+    [pyCIPAPI]
+    client_id = YOUR_CLIENT_ID
+    client_secret = YOUR_CLIENT_SECRET
+    test_irid = VALID_INTERPRETATION_REQUEST_ID
+    test_irversion = VALID_INTERPRETATION_REQUEST_VERSION
 """
 import pytest
 
@@ -13,29 +23,38 @@
 
 
 def test_import():
-    """Objects in pyCIPAPI modules can be imported from the jellypy namespace."""
+    """Test jellypy-pyCIPAPI is installed and objects can be imported."""
     assert bool(config.live_100k_data_base_url)
 
 def test_config(jpconfig):
-    """A jellypy config.ini file has been parsed by pytest"""
+    """Test that a valid config.ini file has been parsed by pytest"""
     assert jpconfig is not None, \
         "ERROR: Jellypy tests require config file. Please pass --jpconfig <yourfile.ini>"
     try:
-        assert bool(jpconfig['pyCIPAPI']['username'])
-        assert bool(jpconfig['pyCIPAPI']['password'])
+        assert bool(jpconfig['pyCIPAPI']['client_id'])
+        assert bool(jpconfig['pyCIPAPI']['client_secret'])
     except KeyError:
         raise ValueError("ERROR: Could not read expected key from jpconfig. See example in docs.")
 
-def test_get_irjson(jpconfig):
-    """Interpretation requests json files can be downloaded from the CIPAPI"""
-    irid = jpconfig.get('pyCIPAPI', 'test_irid')
-    irversion = jpconfig.get('pyCIPAPI', 'test_irversion')
+@pytest.fixture()
+def authenticated_session(jpconfig):
+    """Create authenticated CIPAPI session using config details"""
     session = auth.AuthenticatedCIPAPISession(
             auth_credentials={
-            'username': jpconfig.get('pyCIPAPI', 'username'),
-            'password': jpconfig.get('pyCIPAPI', 'password')
+            'client_id': jpconfig.get('pyCIPAPI', 'client_id'),
+            'client_secret': jpconfig.get('pyCIPAPI', 'client_secret')
         }
     )
-    # Attempt to get a known interpretation request. This can be changed in the test config.
-    data = irs.get_interpretation_request_json(irid, irversion, reports_v6=True, session=session)
-    assert isinstance(data, dict)
+    return session
+
+def test_authentication(authenticated_session):
+    """Assert session fixture creates an authentaicated session from active directory login."""
+    assert authenticated_session.headers['Authorization']
+
+def test_get_irjson(jpconfig, authenticated_session):
+    """Test that the interpretation request in config can be pulled from the CIPAPI"""
+    irid = jpconfig.get('pyCIPAPI', 'test_irid')
+    irversion = jpconfig.get('pyCIPAPI', 'test_irversion')
+    """Interpretation request data can be downloaded from the CIPAPI with an authenticated session"""
+    data = irs.get_interpretation_request_json(irid, irversion, reports_v6=True, session=authenticated_session)
+    assert 'interpretation_request_id' in data.keys()

readme.md

@@ -25,3 +25,4 @@ To develop a new function or feature, please take a look at the issues raised. I
 * 0.2.0 - Update pyCIPAPI to work with GeL client token/secret GMS authentication
 * 0.2.1 - Support legacy authentication by allowing AD to be toggled on/off in config file
 * 0.2.2 - Add sub-heading to README changelog
+* 0.2.3 - Update live 100K url. Display response on API errors. Add tests for auth api calls.