Merge pull request #461 from NBISweden/develop

Relese v18

backend/auth.py

@@ -31,9 +31,9 @@ def get(self):
 
 
 class ElixirLoginHandler(BaseHandler, tornado.auth.OAuth2Mixin):
-    _OAUTH_AUTHORIZE_URL     = "https://perun.elixir-czech.cz/oidc/authorize"
-    _OAUTH_ACCESS_TOKEN_URL  = "https://perun.elixir-czech.cz/oidc/token"
-    _OAUTH_USERINFO_ENDPOINT = "https://perun.elixir-czech.cz/oidc/userinfo"
+    _OAUTH_AUTHORIZE_URL     = "https://login.elixir-czech.org/oidc/authorize"
+    _OAUTH_ACCESS_TOKEN_URL  = "https://login.elixir-czech.org/oidc/token"
+    _OAUTH_USERINFO_ENDPOINT = "https://login.elixir-czech.org/oidc/userinfo"
     _OAUTH_SETTINGS_KEY      = 'elixir_oauth'
 
     def _generate_state(self):

backend/beacon.py

@@ -91,27 +91,33 @@ def get(self):
                 ] #
             })
 
+def connect_mongo(dataset):
+    client = pymongo.MongoClient(host=settings.mongo_host, port=settings.mongo_port)
+
+    auth_db = client['exac-user']
+    auth_db.authenticate(settings.mongo_user, settings.mongo_password)
+
+    return client[dataset]
+
+
 def lookupAllele(chrom, pos, referenceAllele, allele, reference, dataset): #pylint: disable=too-many-arguments, unused-argument
     """CHeck if an allele is present in the database
     Args:
         chrom: The chromosome, format matches [1-22XY]
         pos: Coordinate within a chromosome. Position is a number and is 0-based
         allele: Any string of nucleotides A,C,T,G
         alternate: Any string of nucleotides A,C,T,G
-        reference: The human reference build that was used (currently unused)
+        reference: The human reference build that was used
         dataset: Dataset to look in (currently used to select Mongo database)
     Returns:
         The string 'true' if the allele was found, otherwise the string 'false'
     """
-    client = pymongo.MongoClient(host=settings.mongo_host, port=settings.mongo_port)
+    if reference == 'hg19':
+        reference = 'GRChg37'
 
-    # The name of the dataset in the database is exac as required by the
-    # exac browser we are using.
-    if dataset == 'SweGen':
-        dataset = 'exac'
+    dataset = "exac-{}-{}".format(dataset.lower(), reference)
 
-    mdb = client[dataset]
-    mdb.authenticate(settings.mongo_user, settings.mongo_password)
+    mdb = connect_mongo(dataset)
 
     # Beacon is 0-based, our database is 1-based in coords.
     pos += 1