Merge pull request #134 from CSCfi/feature/ga4gh-jwt-fixes

GA4GH JWT Standard 1.0 processing with Passports

Author: blankdots

beacon_api/api/exceptions.py

@@ -10,37 +10,35 @@
 from ..conf import CONFIG_INFO
 
 
-class BeaconError(Exception):
-    """BeaconError Exception specific class.
+def process_exception_data(request, host, error_code, error):
+    """Return request data as dictionary.
 
     Generates custom exception messages based on request parameters.
     """
-
-    def __init__(self, request, host, error_code, error):
-        """Return request data as dictionary."""
-        self.data = {'beaconId': '.'.join(reversed(host.split('.'))),
-                     "apiVersion": __apiVersion__,
-                     'exists': None,
-                     'error': {'errorCode': error_code,
-                               'errorMessage': error},
-                     'alleleRequest': {'referenceName': request.get("referenceName", None),
-                                       'referenceBases': request.get("referenceBases", None),
-                                       'includeDatasetResponses': request.get("includeDatasetResponses", "NONE"),
-                                       'assemblyId': request.get("assemblyId", None)},
-                     # showing empty datasetsAlleRsponse as no datasets found
-                     # A null/None would represent no data while empty array represents
-                     # none found or error and corresponds with exists null/None
-                     'datasetAlleleResponses': []}
-        # include datasetIds only if they are specified
-        # as per specification if they don't exist all datatsets will be queried
-        # Only one of `alternateBases` or `variantType` is required, validated by schema
-        oneof_fields = ["alternateBases", "variantType", "start", "end", "startMin", "startMax",
-                        "endMin", "endMax", "datasetIds"]
-        self.data['alleleRequest'].update({k: request.get(k) for k in oneof_fields if k in request})
-        return self.data
-
-
-class BeaconBadRequest(BeaconError):
+    data = {'beaconId': '.'.join(reversed(host.split('.'))),
+            "apiVersion": __apiVersion__,
+            'exists': None,
+            'error': {'errorCode': error_code,
+                      'errorMessage': error},
+            'alleleRequest': {'referenceName': request.get("referenceName", None),
+                              'referenceBases': request.get("referenceBases", None),
+                              'includeDatasetResponses': request.get("includeDatasetResponses", "NONE"),
+                              'assemblyId': request.get("assemblyId", None)},
+            # showing empty datasetsAlleRsponse as no datasets found
+            # A null/None would represent no data while empty array represents
+            # none found or error and corresponds with exists null/None
+            'datasetAlleleResponses': []}
+    # include datasetIds only if they are specified
+    # as per specification if they don't exist all datatsets will be queried
+    # Only one of `alternateBases` or `variantType` is required, validated by schema
+    oneof_fields = ["alternateBases", "variantType", "start", "end", "startMin", "startMax",
+                    "endMin", "endMax", "datasetIds"]
+    data['alleleRequest'].update({k: request.get(k) for k in oneof_fields if k in request})
+
+    return data
+
+
+class BeaconBadRequest(web.HTTPBadRequest):
     """Exception returns with 400 code and a custom error message.
 
     The method is called if one of the required parameters are missing or invalid.
@@ -49,13 +47,12 @@ class BeaconBadRequest(BeaconError):
 
     def __init__(self, request, host, error):
         """Return custom bad request exception."""
-        data = super().__init__(request, host, 400, error)
-
-        LOG.error(f'400 ERROR MESSAGE: {error}')
-        raise web.HTTPBadRequest(content_type="application/json", text=json.dumps(data))
+        data = process_exception_data(request, host, 400, error)
+        super().__init__(text=json.dumps(data), content_type="application/json")
+        LOG.error(f'401 ERROR MESSAGE: {error}')
 
 
-class BeaconUnauthorised(BeaconError):
+class BeaconUnauthorised(web.HTTPUnauthorized):
     """HTTP Exception returns with 401 code with a custom error message.
 
     The method is called if the user is not registered or if the token from the authentication has expired.
@@ -64,17 +61,17 @@ class BeaconUnauthorised(BeaconError):
 
     def __init__(self, request, host, error, error_message):
         """Return custom unauthorized exception."""
-        data = super().__init__(request, host, 401, error)
+        data = process_exception_data(request, host, 401, error)
         headers_401 = {"WWW-Authenticate": f"Bearer realm=\"{CONFIG_INFO.url}\"\n\
                          error=\"{error}\"\n\
                          error_description=\"{error_message}\""}
+        super().__init__(content_type="application/json", text=json.dumps(data),
+                         # we use auth scheme Bearer by default
+                         headers=headers_401)
         LOG.error(f'401 ERROR MESSAGE: {error}')
-        raise web.HTTPUnauthorized(content_type="application/json", text=json.dumps(data),
-                                   # we use auth scheme Bearer by default
-                                   headers=headers_401)
 
 
-class BeaconForbidden(BeaconError):
+class BeaconForbidden(web.HTTPForbidden):
     """HTTP Exception returns with 403 code with the error message.
 
     `'Resource not granted for authenticated user or resource protected for all users.'`.
@@ -84,13 +81,12 @@ class BeaconForbidden(BeaconError):
 
     def __init__(self, request, host, error):
         """Return custom forbidden exception."""
-        data = super().__init__(request, host, 403, error)
-
+        data = process_exception_data(request, host, 403, error)
+        super().__init__(content_type="application/json", text=json.dumps(data))
         LOG.error(f'403 ERROR MESSAGE: {error}')
-        raise web.HTTPForbidden(content_type="application/json", text=json.dumps(data))
 
 
-class BeaconServerError(BeaconError):
+class BeaconServerError(web.HTTPInternalServerError):
     """HTTP Exception returns with 500 code with the error message.
 
     The 500 error is not specified by the Beacon API, thus as simple error would do.
@@ -100,6 +96,5 @@ def __init__(self, error):
         """Return custom forbidden exception."""
         data = {'errorCode': 500,
                 'errorMessage': error}
-
+        super().__init__(content_type="application/json", text=json.dumps(data))
         LOG.error(f'500 ERROR MESSAGE: {error}')
-        raise web.HTTPInternalServerError(content_type="application/json", text=json.dumps(data))

beacon_api/conf/config.ini

@@ -7,7 +7,7 @@
 title=GA4GHBeacon at CSC
 
 # Version of the Beacon implementation
-version=1.4.1
+version=1.5.0
 
 # Author of this software
 author=CSC developers