Merge pull request #135 from CSCfi/dev

Release 1.5.0

Author: teemukataja

.coveragerc

@@ -14,6 +14,7 @@ omit =
 [report]
 # Regexes for lines to exclude from consideration
 exclude_lines =
+    pragma: no cover
     # Don't complain about missing debug-only code:
     def __repr__
     if self\.debug

Pipfile

@@ -13,7 +13,7 @@
 __license__ = CONFIG_INFO.license
 __copyright__ = CONFIG_INFO.copyright
 __docs_url__ = CONFIG_INFO.docs_url
-__handover_drs__ = CONFIG_INFO.handover_drs
+__handover_drs__ = CONFIG_INFO.handover_drs.rstrip("/")
 __handover_datasets__ = CONFIG_INFO.handover_datasets
 __handover_beacon__ = CONFIG_INFO.handover_beacon
 __handover_base__ = CONFIG_INFO.handover_base
@@ -26,7 +26,6 @@
 __createtime__ = CONFIG_INFO.createtime
 __updatetime__ = datetime.datetime.now().strftime('%Y-%m-%dT%H:%M:%SZ')  # Every restart of the application means an update to it
 
-
 __org_id__ = CONFIG_INFO.org_id
 __org_name__ = CONFIG_INFO.org_name
 __org_description__ = CONFIG_INFO.org_description
@@ -37,3 +36,7 @@
 __org_info__ = {'orgInfo': CONFIG_INFO.org_info}
 
 __sample_queries__ = SAMPLE_QUERIES
+
+# GA4GH Discovery
+__service_type__ = f'{CONFIG_INFO.service_type}:{__apiVersion__}'
+__service_env__ = CONFIG_INFO.environment

beacon_api/__init__.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/api/exceptions.py

@@ -9,7 +9,7 @@
 from .. import __apiVersion__, __title__, __version__, __description__, __url__, __alturl__, __handover_beacon__
 from .. import __createtime__, __updatetime__, __org_id__, __org_name__, __org_description__
 from .. import __org_address__, __org_logoUrl__, __org_welcomeUrl__, __org_info__, __org_contactUrl__
-from .. import __sample_queries__, __handover_drs__, __docs_url__
+from .. import __sample_queries__, __handover_drs__, __docs_url__, __service_type__, __service_env__
 from ..utils.data_query import fetch_dataset_metadata
 from ..extensions.handover import make_handover
 from aiocache import cached
@@ -26,13 +26,18 @@ async def ga4gh_info(host):
         # TO DO implement some fallback mechanism for ID
         'id': '.'.join(reversed(host.split('.'))),
         'name': __title__,
-        "type": "urn:ga4gh:beacon",
+        "type": __service_type__,
         'description': __description__,
-        'documentationUrl': __docs_url__,
-        "organization": __org_id__,
+        "organization": {
+            "name": __org_name__,
+            "url": __org_welcomeUrl__,
+        },
         'contactUrl': __org_contactUrl__,
-        'version': __version__,
-        "extension": {}
+        'documentationUrl': __docs_url__,
+        'createdAt': __createtime__,
+        'updatedAt': __updatetime__,
+        'environment': __service_env__,
+        'version': __version__
     }
     return beacon_info
 

beacon_api/api/info.py

@@ -82,7 +82,8 @@ async def initialize(app):
 
 async def destroy(app):
     """Upon server close, close the DB connection pool."""
-    await app['pool'].close()
+    # will defer this to asyncpg
+    await app['pool'].close()  # pragma: no cover
 
 
 def set_cors(server):

beacon_api/app.py

@@ -33,6 +33,8 @@ def parse_config_file(path):
         'url': config.get('beacon_api_info', 'url'),
         'alturl': config.get('beacon_api_info', 'alturl'),
         'createtime': config.get('beacon_api_info', 'createtime'),
+        'service_type': config.get('beacon_api_info', 'service_type'),
+        'environment': config.get('beacon_api_info', 'environment'),
         'org_id': config.get('organisation_info', 'org_id'),
         'org_name': config.get('organisation_info', 'org_name'),
         'org_description': config.get('organisation_info', 'org_description'),

beacon_api/conf/__init__.py

@@ -7,7 +7,7 @@
 title=GA4GHBeacon at CSC
 
 # Version of the Beacon implementation
-version=1.4.0
+version=1.5.0
 
 # Author of this software
 author=CSC developers
@@ -41,6 +41,13 @@ alturl=
 # Datetime when this Beacon was created
 createtime=2018-07-25T00:00:00Z
 
+# GA4GH Discovery type `groupId` and `artifactId`, joined in /service-info with apiVersion
+# See https://github.com/ga4gh-discovery/ga4gh-service-registry for more information and possible values
+service_type=org.ga4gh:beacon
+
+# GA4GH Discovery server environment, possible values: prod, dev, test
+environment=prod
+
 
 [organisation_info]
 # Globally unique identifier for organisation that hosts this Beacon service

beacon_api/conf/config.ini

@@ -22,7 +22,7 @@ def make_handover(paths, datasetIds, chr='', start=0, end=0, ref='', alt='', var
         for dataset in set(datasetIds):
             handovers.append({"handoverType": {"id": "CUSTOM", "label": label},
                               "description": desc,
-                              "url": __handover_drs__ + path.format(dataset=dataset, chr=chr, start=start,
-                                                                    end=end, ref=ref, alt=alt)})
+                              "url": __handover_drs__ + "/" + path.format(dataset=dataset, chr=chr, start=start,
+                                                                          end=end, ref=ref, alt=alt)})
 
     return handovers