black with line-length 120

polytope_server/common/auth.py

@@ -31,7 +31,6 @@
 
 
 class AuthHelper:
-
     """A helper to encapsulate checking user authentication and authorization"""
 
     def __init__(self, config):

polytope_server/common/authentication/authentication.py

@@ -77,7 +77,7 @@ def name(self) -> str:
     "plain": "PlainAuthentication",
     "keycloak": "KeycloakAuthentication",
     "federation": "FederationAuthentication",
-    "jwt" : "JWTAuthentication",
+    "jwt": "JWTAuthentication",
 }
 
 

polytope_server/common/authentication/jwt_authentication.py

@@ -53,9 +53,8 @@ def authenticate(self, credentials: str) -> User:
 
         try:
             certs = self.get_certs()
-            decoded_token = jwt.decode(token=credentials,
-                algorithms=jwt.get_unverified_header(credentials).get('alg'),
-                key=certs
+            decoded_token = jwt.decode(
+                token=credentials, algorithms=jwt.get_unverified_header(credentials).get("alg"), key=certs
             )
 
             user = User(decoded_token["sub"], self.realm())
@@ -67,6 +66,5 @@ def authenticate(self, credentials: str) -> User:
             raise ForbiddenRequest("Credentials could not be unpacked")
         return user
 
-
     def collect_metric_info(self):
         return {}

polytope_server/common/authentication/mongoapikey_authentication.py

@@ -29,7 +29,6 @@
 
 
 class ApiKeyMongoAuthentication(authentication.Authentication):
-
     """
     Authenticates a user using a polytope API key. A polytope API key is an alias to a user that was previously
     authenticated. It allows user to authenticate once, retrieve a key, and use that for future authentication.

polytope_server/common/authorization/ldap_authorization.py

@@ -48,7 +48,9 @@ def get_roles(self, user: User) -> list:
             )
         try:
             if self.username_attribute is None:
-                return retrieve_ldap_user_roles(user.username, self.filter, self.url, self.search_base, self.ldap_user, self.ldap_password)
+                return retrieve_ldap_user_roles(
+                    user.username, self.filter, self.url, self.search_base, self.ldap_user, self.ldap_password
+                )
             else:
                 return retrieve_ldap_user_roles(
                     user.attributes[self.username_attribute],
@@ -69,10 +71,12 @@ def collect_metric_info(self):
 #################################################
 
 
-def retrieve_ldap_user_roles(uid: str, filter: str, url: str, search_base: str, ldap_user: str, ldap_password: str) -> list:
+def retrieve_ldap_user_roles(
+    uid: str, filter: str, url: str, search_base: str, ldap_user: str, ldap_password: str
+) -> list:
     """
-        Takes an ECMWF UID and returns all roles matching
-        the provided filter 'filter'.
+    Takes an ECMWF UID and returns all roles matching
+    the provided filter 'filter'.
     """
 
     server = Server(url)
@@ -81,20 +85,20 @@ def retrieve_ldap_user_roles(uid: str, filter: str, url: str, search_base: str,
         server,
         user="CN={},OU=Connectors,OU=Service Accounts,DC=ecmwf,DC=int".format(ldap_user),
         password=ldap_password,
-        raise_exceptions=True
+        raise_exceptions=True,
     )
 
     with connection as conn:
         conn.search(
             search_base=search_base,
-            search_filter='(&(objectClass=person)(cn={}))'.format(uid),
+            search_filter="(&(objectClass=person)(cn={}))".format(uid),
             search_scope=SUBTREE,
-            attributes=['memberOf']
+            attributes=["memberOf"],
         )
         user_data = json.loads(conn.response_to_json())
-        if len(user_data['entries']) == 0:
-            raise KeyError('User {} not found in LDAP.'.format(uid))
-        roles = user_data['entries'][0]['attributes']['memberOf']
+        if len(user_data["entries"]) == 0:
+            raise KeyError("User {} not found in LDAP.".format(uid))
+        roles = user_data["entries"][0]["attributes"]["memberOf"]
 
     # Filter roles
     matches = []
@@ -104,7 +108,7 @@ def retrieve_ldap_user_roles(uid: str, filter: str, url: str, search_base: str,
 
     # Parse CN=x,OU=y,OU=z,... into dict and extract 'common name' (CN)
     for i, role in enumerate(matches):
-        d = dict(s.split('=') for s in role.split(','))
-        matches[i] = d['CN']
+        d = dict(s.split("=") for s in role.split(","))
+        matches[i] = d["CN"]
 
     return matches

polytope_server/common/datasource/mars.py

@@ -84,18 +84,17 @@ def match(self, request):
         r = yaml.safe_load(request.user_request) or {}
 
         for k, v in self.match_rules.items():
-            
+
             # An empty match rule means that the key must not be present
             if v is None or len(v) == 0:
                 if k in r:
                     raise Exception("Request containing key '{}' is not allowed".format(k))
                 else:
-                    continue # no more checks to do
-            
+                    continue  # no more checks to do
+
             # Check that all required keys exist
             if k not in r and not (v is None or len(v) == 0):
                 raise Exception("Request does not contain expected key '{}'".format(k))
-
 
             # Process date rules
             if k == "date":
@@ -196,7 +195,7 @@ def make_env(self, request):
                 "MARS_USER_EMAIL": mars_user,
                 "MARS_USER_TOKEN": mars_token,
                 "ECMWF_MARS_COMMAND": self.mars_binary,
-                "FDB5_CONFIG" : yaml.dump(self.fdb_config[0])
+                "FDB5_CONFIG": yaml.dump(self.fdb_config[0]),
             }
 
             if self.mars_config is not None:

polytope_server/common/datasource/polytope.py

@@ -71,19 +71,16 @@ def __init__(self, config):
 
         # Set up polytope feature extraction library
         self.polytope_options = {
-            "values": {
-                "mapper": {"type": "octahedral", "resolution": 1280, "axes": ["latitude", "longitude"]}
-            },
+            "values": {"mapper": {"type": "octahedral", "resolution": 1280, "axes": ["latitude", "longitude"]}},
             "date": {"merge": {"with": "time", "linkers": ["T", "00"]}},
             "step": {"type_change": "int"},
             "number": {"type_change": "int"},
-            "longitude" : {"cyclic": [0, 360]},
+            "longitude": {"cyclic": [0, 360]},
         }
 
         logging.info("Set up gribjump")
 
-
-    #todo: remove when we no longer need to set up a valid fdb to use gribjump
+    # todo: remove when we no longer need to set up a valid fdb to use gribjump
     def check_schema(self):
 
         schema = self.fdb_config.get("schema", None)
@@ -131,7 +128,7 @@ def git_download_schema(self, remote, branch, git_dir, git_file):
         logging.debug("Fetching FDB schema from git with call: {}".format(call))
         output = subprocess.check_output(call, shell=True)
         return output.decode("utf-8")
-    
+
     def get_type(self):
         return self.type
 
@@ -152,6 +149,7 @@ def retrieve(self, request):
         logging.info(self.polytope_config)
         logging.info(self.polytope_options)
         from polytope_mars.api import PolytopeMars
+
         p = PolytopeMars(self.polytope_config, self.polytope_options)
 
         self.output = p.extract(r)
@@ -177,7 +175,7 @@ def match(self, request):
 
             if r[k] not in v:
                 raise Exception("got {} : {}, but expected one of {}".format(k, r[k], v))
-            
+
             # Finally check that there is a feature specified in the request
             if "feature" not in r:
                 raise Exception("Request does not contain expected key 'feature'")

polytope_server/common/io/fifo.py

@@ -25,7 +25,6 @@
 
 
 class FIFO:
-
     """Creates a named pipe (FIFO) and reads data from it"""
 
     def __init__(self, name, dir=None):

polytope_server/common/metric.py

@@ -37,7 +37,6 @@ class MetricType(enum.Enum):
 
 
 class Metric:
-
     """A sealed class representing a metric"""
 
     __slots__ = ["uuid", "timestamp", "type"]

polytope_server/common/metric_collector/metric_collector.py

@@ -24,7 +24,6 @@
 
 
 class MetricCollector:
-
     """Interface to collect metrics from any component in Polytope
     for which a collector is implemented.
     """

polytope_server/common/metric_store/metric_store.py

@@ -27,7 +27,6 @@
 
 
 class MetricStore(ABC):
-
     """MetricStore is an interface for database-based storage for Metric objects"""
 
     def __init__(self):

polytope_server/common/request.py

@@ -41,7 +41,6 @@ class Verb(enum.Enum):
 
 
 class Request:
-
     """A sealed class representing a request"""
 
     __slots__ = [

polytope_server/common/request_store/request_store.py

@@ -27,7 +27,6 @@
 
 
 class RequestStore(ABC):
-
     """RequestStore is an interface for database-based storage for Request objects"""
 
     def __init__(self):

polytope_server/frontend/flask_handler.py

@@ -218,15 +218,15 @@ def uploads(request_id):
         @handler.route("/api/v1/collections", methods=["GET"])
         def list_collections():
             auth_header = get_auth_header(request)
-            collection_config =  authorized_collections = []
+            collection_config = authorized_collections = []
             for name, collection in collections.items():
                 try:
                     if auth.can_access_collection(auth_header, collection):
                         authorized_collections.append(name)
                 except ForbiddenRequest:
                     pass
             return RequestSucceeded(authorized_collections)
-        
+
         # New handler
         # @handler.route("/api/v1/collection/<collection>", methods=["GET"])
         # def describe_collection(collection):