switched update_to() and upload_to() to use named parameters and adde…

…d client named parameter. Fix for issues #80 and #81

ndex2/nice_cx_network.py

@@ -1474,66 +1474,142 @@ def to_cx_stream(self):
 
             return return_bytes
 
-    def upload_to(self, server, username, password,
-                  user_agent=''):
+    def upload_to(self, server=None, username=None, password=None,
+                  user_agent='', client=None):
         """
-        Upload this network as a new network to the specified
-        NDEx `server` using account credentials set via `username`
-        and `password.` Note, networks with duplicate names are allowed.
+        Upload this network as a new network on NDEx server.
+
+        .. versionchanged:: 3.4.0
+
+            This method was switched to named arguments and the server and account
+            credentials can be passed in one of two ways.
+
+        Option 1) Set **username** and **password** parameters.
+
+        Option 2) Set **client** parameter with valid :py:class:`~ndex2.client.Ndex2` object
+
+        .. note::
+
+            If **client** parameter is set, **username**, **password**, and **server**
+            parameters are ignored
 
         Example:
 
         .. code-block:: python
 
-            nice_cx.upload_to('public.ndexbio.org', username, password)
+            import ndex2
+            nice_cx = ndex2.nice_cx_network.NiceCXNetwork()
+            nice_cx.create_node('foo')
+
+            # using production NDEx server
+            nice_cx.update_to(username=user_var,
+                              password=password_var)
 
-        :param server: The NDEx server to upload the network to.
+            # if one needs to use alternate NDEx server
+            nice_cx.update_to(server='public.ndexbio.org',
+                              username=username_var,
+                              password=password_var)
+
+            # Option 2, create Ndex2 client object
+            ndex_client = ndex2.client.Ndex2(username=username_var,
+                                             password=password_var)
+
+            # using NDEx client object for connection
+            nice_cx.update_to(client=ndex_client)
+
+        :param server: The NDEx server to upload the network to. Leaving unset or `None` will use production
         :type server: str
         :param username: The username of the account to store the network.
         :type username: str
         :param password: The password for the account.
         :type password: str
         :param user_agent: String to append to User-Agent field sent to NDEx REST service
         :type user_agent: str
+        :param client: NDEx2 object with valid credentials. If set **server**, **username**, and **password**
+                       parameters will be ignored.
+        :type client: :py:class:`~ndex2.client.Ndex2`
         :return: The UUID of the network on NDEx.
         :rtype: str
         """
-        ndex = Ndex2(server, username, password, user_agent=user_agent)
+        if client is not None:
+            ndex = client
+        else:
+            ndex = Ndex2(server, username, password, user_agent=user_agent)
         return ndex.save_new_network(self.to_cx())
 
     def upload_new_network_stream(self, server, username, password):
         raise Exception('upload_new_network_stream() is no longer supported.  Please use upload_to()')
 
-    def update_to(self, uuid, server, username, password,
-                  user_agent=''):
+    def update_to(self, uuid, server=None, username=None, password=None,
+                  user_agent='', client=None):
         """
-        Replace the network on NDEx `server` with matching NDEx `uuid` with
-        this network using `username` and `password` account credentials
-        passed in.
+        Replace the network on NDEx server with matching NDEx `uuid` with
+        this network.
+
+        .. versionchanged:: 3.4.0
+
+            This method was switched to named arguments and the server and account
+            credentials can be passed in one of two ways.
+
+
+        Option 1) Set **username** and **password** parameters.
+
+        Option 2) Set **client** parameter with valid :py:class:`~ndex2.client.Ndex2` object
+
+        .. note::
+
+            If **client** parameter is set, **username**, **password**, and **server**
+            parameters are ignored.
 
         Example:
 
         .. code-block:: python
 
+            import ndex2
+            nice_cx = ndex2.nice_cx_network.NiceCXNetwork()
+            nice_cx.create_node('foo')
+
+            # using production NDEx server
             nice_cx.update_to('2ec87c51-c349-11e8-90ac-525400c25d22',
-                              'public.ndexbio.org', username, password)
+                              username=user_var,
+                              password=password_var)
+
+            # if one needs to use alternate NDEx server
+            nice_cx.update_to('2ec87c51-c349-11e8-90ac-525400c25d22',
+                              server='public.ndexbio.org',
+                              username=username_var,
+                              password=password_var)
+
+            # Option 2, create Ndex2 client object
+            ndex_client = ndex2.client.Ndex2(username=username_var,
+                                             password=password_var)
+
+            # using NDEx client object for connection
+            nice_cx.update_to('2ec87c51-c349-11e8-90ac-525400c25d22',
+                              client=ndex_client)
 
         :param uuid: UUID of the network on NDEx.
         :type uuid: str
-        :param server: The NDEx server to upload the network to.
+        :param server: The NDEx server to upload the network to. Leaving unset or `None` will use production.
         :type server: str
         :param username: The username of the account to store the network.
         :type username: str
         :param password: The password for the account.
         :type password: str
         :param user_agent: String to append to User-Agent field sent to NDEx REST service
         :type user_agent: str
+        :param client: NDEx2 object with valid credentials. If set **server**, **username**, and **password**
+                       parameters will be ignored.
+        :type client: :py:class:`~ndex2.client.Ndex2`
         :return: Empty string
         :rtype: str
 
         """
         cx = self.to_cx()
-        ndex = Ndex2(server, username, password, user_agent=user_agent)
+        if client is not None:
+            ndex = client
+        else:
+            ndex = Ndex2(server, username, password, user_agent=user_agent)
 
         if len(cx) > 0:
             if cx[len(cx) - 1] is not None:

tests/test_nice_cx_network.py

@@ -8,6 +8,7 @@
 import sys
 import warnings
 
+from unittest.mock import MagicMock, ANY
 import requests_mock
 from ndex2 import client
 from ndex2.nice_cx_network import NiceCXNetwork
@@ -445,6 +446,24 @@ def test__str__(self):
         net.create_edge(edge_source=0, edge_target=1)
         self.assertEqual('nodes: 3 \n edges: 1', str(net))
 
+    def test_upload_to_with_client_success(self):
+        mockclient = MagicMock()
+        fakeurl = 'http://foo/12345'
+        mockclient.save_new_network = MagicMock(return_value=fakeurl)
+        net = NiceCXNetwork()
+        res = net.upload_to(client=mockclient)
+        self.assertEqual(fakeurl, res)
+        mockclient.save_new_network.assert_called_with(net.to_cx())
+
+    def test_update_to_with_client_success(self):
+        mockclient = MagicMock()
+        mockclient.update_cx_network = MagicMock(return_value='')
+        net = NiceCXNetwork()
+        res = net.update_to('myuuid', client=mockclient)
+        self.assertEqual('', res)
+
+        mockclient.update_cx_network.assert_called_with(ANY, 'myuuid')
+
     def test_upload_to_success(self):
         with requests_mock.mock() as m:
             resurl = client.DEFAULT_SERVER + '/v2/network/asdf'