Code cleaning and profile added to login builder

Author: ymarcon

datashield/interface.py

@@ -17,15 +17,15 @@ def is_completed(self) -> bool:
     wait for the completion, immediate response is expected. Once the result is
     identified as being completed, the raw result the operation can be get directly.
     """
-    raise NotImplementedError("DSResult function not available")
+    raise NotImplementedError('DSResult function not available')
 
   def fetch(self) -> any:
     """
     Wait for the result to be available and fetch the result from a previous assignment or aggregation operation that may have been
     run asynchronously, in which case it is a one-shot call. When the assignment or aggregation operation was not asynchronous,
     the result is wrapped in the object and can be fetched multiple times.
     """
-    raise NotImplementedError("DSResult function not available")
+    raise NotImplementedError('DSResult function not available')
 
 
 class DSConnection:
@@ -41,29 +41,29 @@ def list_tables(self) -> list:
     """
     List available table names from the data repository.
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def has_table(self, name: str) -> bool:
     """
     Check whether a table with provided name exists in the data repository.
 
     :param name: The name of the table to check
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def list_resources(self) -> list:
     """
     List available resource names from the data repository.
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def has_resource(self, name: str) -> bool:
     """
     Check whether a resource with provided name exists in the data repository.
 
     :param name: The name of the resource to check
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   #
   # Assign
@@ -79,7 +79,7 @@ def assign_table(self, symbol: str, table: str, variables: list = None,
     :param table: The name of the table to assign
     :param asynchronous: Whether the operation is asynchronous (if supported by the DataSHIELD server)
     """ 
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def assign_resource(self, symbol: str, resource: str, asynchronous: bool = True) -> DSResult:
     """
@@ -89,7 +89,7 @@ def assign_resource(self, symbol: str, resource: str, asynchronous: bool = True)
     :param resource: The name of the resource to assign
     :param asynchronous: Whether the operation is asynchronous (if supported by the DataSHIELD server)
     """ 
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def assign_expr(self, symbol: str, expr: str, asynchronous: bool = True) -> DSResult:
     """
@@ -99,7 +99,7 @@ def assign_expr(self, symbol: str, expr: str, asynchronous: bool = True) -> DSRe
     :param expr: The R expression to evaluate and which result will be assigned
     :param asynchronous: Whether the operation is asynchronous (if supported by the DataSHIELD server)
     """ 
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   #
   # Aggregate
@@ -113,7 +113,7 @@ def aggregate(self, expr: str, asynchronous: bool = True) -> DSResult:
     :param expr: The R expression to evaluate and which result will be returned
     :param asynchronous: Whether the operation is asynchronous (if supported by the DataSHIELD server)
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   #
   # Symbols
@@ -123,15 +123,15 @@ def list_symbols(self) -> list:
     """
     After assignments have been performed, some symbols live in the DataSHIELD R session on the server side.
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def rm_symbol(self, name: str) -> None:
     """
     After symbol removal, the data identified by the symbol will not be accessible in the DataSHIELD R session on the server side.
     
     :param name: The name of symbol to remove
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   #
   # DataSHIELD config
@@ -141,21 +141,21 @@ def list_profiles(self) -> list:
     """
     List available DataSHIELD profile names in the data repository.
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def list_methods(self, type: str = "aggregate") -> list:
     """
     Get the list of DataSHIELD methods that have been configured on the remote data repository.
 
     :param type: The type of method, either "aggregate" (default) or "assign"
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def list_packages(self) -> list:
     """
     Get the list of DataSHIELD packages with their version, that have been configured on the remote data repository.
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   #
   # Workspaces
@@ -165,15 +165,15 @@ def list_workspaces(self) -> list:
     """
     Get the list of DataSHIELD workspaces, that have been saved on the remote data repository.
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def save_workspace(self, name: str) -> list:
     """
     Save the DataSHIELD R session in a workspace on the remote data repository.
 
     :param name: The name of the workspace
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def restore_workspace(self, name: str) -> list:
     """
@@ -182,7 +182,7 @@ def restore_workspace(self, name: str) -> list:
 
     :param name: The name of the workspace
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def rm_workspace(self, name: str) -> list:
     """
@@ -191,7 +191,7 @@ def rm_workspace(self, name: str) -> list:
 
     :param name: The name of the workspace
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   #
   # Utils
@@ -205,21 +205,21 @@ def is_async(self) -> dict:
     aggregation operation ('aggregate'), table assignment operation ('assign_table'),
     resource assignment operation ('assign_resource') and expression assignment operation ('assign_expr').
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def keep_alive(self) -> None:
     """
     As the DataSHIELD sessions are working in parallel, this function helps at keeping
     idle connections alive while others are working. Any communication failure must
     be silently processed.
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   def disconnect(self) -> None:
     """
     This closes the connection, discards all pending work, and frees resources (e.g., memory, sockets).
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
 
 class DSDriver:
@@ -237,7 +237,7 @@ def new_connection(cls, name: str, args: dict, profile: str = "default", restore
     :param profile: The DataSHIELD profile name to be used
     :param restore: The workspace name to be restored
     """
-    raise NotImplementedError("DSConnection function not available")
+    raise NotImplementedError('DSConnection function not available')
 
   @classmethod
   def load_class(cls, name: str) -> any:
@@ -247,7 +247,7 @@ def load_class(cls, name: str) -> any:
     :param name: The driver class name
     :return The class of the driver on which the ``new_connection()`` function will be called 
     """
-    names = name.split(".")
+    names = name.split('.')
     className = names.pop()
-    moduleName = ".".join(names)
+    moduleName = '.'.join(names)
     return getattr(importlib.import_module(moduleName), className)

datashield/utils.py

@@ -10,13 +10,14 @@ class DSLoginBuilder:
     def __init__(self):
         self.items = list()
 
-    def add(self, name: str, url: str, user: str = None, password: str = None, token: str = None):
+    def add(self, name: str, url: str, user: str = None, password: str = None, token: str = None, profile: str = 'default'):
         self.items.append({
             'name': name,
             'url': url,
             'user': user,
             'password': password,
-            'token': token
+            'token': token,
+            'profile': profile
         })
         return self
 

tests/test_utils.py

@@ -1,14 +1,16 @@
 from datashield.utils import DSLoginBuilder
 
 def test_logins():
-    builder = DSLoginBuilder().add("server1", "https://opal-demo.obba.org", "dsuser", "P@ssw0rd").add("server2", "https://demo.datashield.org", token = "1234abcd")
+    builder = DSLoginBuilder().add('server1', 'https://opal-demo.obba.org', 'dsuser', 'P@ssw0rd').add('server2', 'https://demo.datashield.org', token = '1234abcd', profile = 'omics')
     logins = builder.build()
     assert len(logins) == 2
-    assert logins[0]["name"] == "server1"
-    assert logins[0]["user"] is not None
-    assert logins[0]["password"] is not None
-    assert logins[0]["token"] is None
-    assert logins[1]["name"] == "server2"
-    assert logins[1]["user"] is None
-    assert logins[1]["password"] is None
-    assert logins[1]["token"] is not None
+    assert logins[0]['name'] == 'server1'
+    assert logins[0]['user'] is not None
+    assert logins[0]['password'] is not None
+    assert logins[0]['token'] is None
+    assert logins[0]['profile'] == 'default'
+    assert logins[1]['name'] == 'server2'
+    assert logins[1]['user'] is None
+    assert logins[1]['password'] is None
+    assert logins[1]['token'] is not None
+    assert logins[1]['profile'] == 'omics'