Merge pull request #26 from galaxy-genome-annotation/update_email

Improve user update method + add tests

Author: abretaud

README.rst

@@ -81,6 +81,9 @@ Or with the Arrow client:
 History
 -------
 
+- 4.2
+    - Improve user update method
+    - Add tests for user api
 - 4.1
     - Fix loading attributes from gff3
     - Better handling of genome sequence update, with or without the no_reload_sequences option

apollo/users/__init__.py

@@ -219,7 +219,7 @@ def delete_user(self, user):
         """
         return self.post('deleteUser', {'userToDelete': user})
 
-    def update_user(self, email, first_name, last_name, password, metadata={}):
+    def update_user(self, email, first_name, last_name, password=None, metadata={}, new_email=None):
         """
         Update an existing user
 
@@ -233,21 +233,37 @@ def update_user(self, email, first_name, last_name, password, metadata={}):
         :param last_name: User's last name
 
         :type password: str
-        :param password: User's password
+        :param password: User's password (omit to keep untouched)
 
         :type metadata: dict
         :param metadata: User metadata
 
+        :type new_email: str
+        :param new_email: User's new email (if you want to change it)
+
         :rtype: dict
         :return: a dictionary containing user information
         """
         data = {
             'email': email,
             'firstName': first_name,
             'lastName': last_name,
-            'newPassword': password,
             'metadata': metadata,
         }
+
+        if password:
+            data['newPassword'] = password
+
+        # If updating the email, we need to give apollo a userId
+        if new_email:
+            user = self.show_user(email)
+            if not isinstance(user, list):
+                user = [user]
+            user = self._assert_user(user)
+
+            data['email'] = new_email
+            data['userId'] = user['userId']
+
         response = self.post('updateUser', data)
         return self._handle_empty(email, response)
 

arrow/__init__.py

@@ -1 +1 @@
-__version__ = '4.1'
+__version__ = '4.2'

arrow/commands/users/update_user.py

@@ -7,20 +7,29 @@
 @click.argument("email", type=str)
 @click.argument("first_name", type=str)
 @click.argument("last_name", type=str)
-@click.argument("password", type=str)
+@click.option(
+    "--password",
+    help="User's password (omit to keep untouched)",
+    type=str
+)
 @click.option(
     "--metadata",
     help="User metadata",
     type=str
 )
+@click.option(
+    "--new_email",
+    help="User's new email (if you want to change it)",
+    type=str
+)
 @pass_context
 @custom_exception
 @dict_output
-def cli(ctx, email, first_name, last_name, password, metadata={}):
+def cli(ctx, email, first_name, last_name, password="", metadata={}, new_email=""):
     """Update an existing user
 
 Output:
 
     a dictionary containing user information
     """
-    return ctx.gi.users.update_user(email, first_name, last_name, password, metadata=metadata)
+    return ctx.gi.users.update_user(email, first_name, last_name, password=password, metadata=metadata, new_email=new_email)

docs/commands/users.rst

@@ -271,7 +271,7 @@ Update the permissions of a user on a specified organism
 
 **Usage**::
 
-    arrow users update_user [OPTIONS] EMAIL FIRST_NAME LAST_NAME PASSWORD
+    arrow users update_user [OPTIONS] EMAIL FIRST_NAME LAST_NAME
 
 **Help**
 
@@ -286,6 +286,8 @@ Update an existing user
 **Options**::
 
 
-      --metadata TEXT  User metadata
-      -h, --help       Show this message and exit.
+      --password TEXT   User's password (omit to keep untouched)
+      --metadata TEXT   User metadata
+      --new_email TEXT  User's new email (if you want to change it)
+      -h, --help        Show this message and exit.
     

requirements.txt

@@ -1,6 +1,6 @@
 requests
 biopython
-cachetools
+cachetools<4
 click>=6.7
 wrapt
 pyyaml

setup.py

@@ -16,7 +16,7 @@
 
 setup(
     name="apollo",
-    version='4.1',
+    version='4.2',
     description="Apollo API library",
     long_description=readme,
     author="Helena Rasche;Anthony Bretaudeau",

test/__init__.py

@@ -17,9 +17,11 @@ def waitOrgDeleted(self, org_id):
         """
 
         org_info = wa.organisms.show_organism(org_id)
-        if 'directory' in org_info:
+        tries = 1
+        while 'directory' in org_info and tries < 10:
             time.sleep(1)
             org_info = wa.organisms.show_organism(org_id)
+            tries += 1
 
         return org_info
 
@@ -29,8 +31,38 @@ def waitOrgCreated(self, org_id):
         """
 
         org_info = wa.organisms.show_organism(org_id)
-        if 'directory' not in org_info:
+        tries = 1
+        while 'directory' not in org_info and tries < 10:
             time.sleep(1)
             org_info = wa.organisms.show_organism(org_id)
+            tries += 1
 
         return org_info
+
+    def waitUserDeleted(self, user_id):
+        """
+        Wait for an user to be really deleted from Apollo
+        """
+
+        user_info = wa.users.show_user(user_id)
+        tries = 1
+        while 'userId' in user_info and tries < 10:
+            time.sleep(1)
+            user_info = wa.users.show_user(user_id)
+            tries += 1
+
+        return user_info
+
+    def waitUserCreated(self, user_id):
+        """
+        Wait for an user to be really created from Apollo
+        """
+
+        user_info = wa.users.show_user(user_id)
+        tries = 1
+        while 'userId' not in user_info and tries < 10:
+            time.sleep(1)
+            user_info = wa.users.show_user(user_id)
+            tries += 1
+
+        return user_info

test/user_test.py

@@ -0,0 +1,132 @@
+import time
+
+from . import ApolloTestCase, wa
+
+
+class UserTest(ApolloTestCase):
+
+    def test_get_users(self):
+
+        users = wa.users.get_users()
+
+        # We at least have admin + junior + temp from setup
+        assert len(users) >= 3
+
+        first_user = users[0]
+
+        assert 'firstName' in first_user
+        assert 'lastName' in first_user
+        assert 'inactive' in first_user
+        assert 'role' in first_user
+        assert 'availableGroups' in first_user
+        assert 'userCount' in first_user
+        assert 'searchName' in first_user
+        assert 'groups' in first_user
+        assert 'userId' in first_user
+        assert 'organismPermissions' in first_user
+        assert 'username' in first_user
+
+    def test_show_user(self):
+
+        users = wa.users.get_users()
+
+        user_id = users[0]['userId']
+
+        user_info = wa.users.show_user(user_id)
+
+        # userCount changes depending on what was requested to Apollo
+        del user_info['userCount']
+        del users[0]['userCount']
+
+        assert user_info == users[0]
+
+    def test_create_user(self):
+
+        meta = {"bla": "bli"}
+        res = wa.users.create_user("trash@bx.psu.edu", 'Poutrelle', 'Lapinou', 'superpassword', role="user", metadata=meta)
+        self.waitUserCreated(res['userId'])
+
+        res = wa.users.show_user('trash@bx.psu.edu')
+
+        assert res['username'] == 'trash@bx.psu.edu'
+        assert res['firstName'] == 'Poutrelle'
+        assert res['lastName'] == 'Lapinou'
+        assert res['role'] == 'USER'
+
+    def test_delete_user(self):
+
+        user_info = wa.users.create_user("trash@bx.psu.edu", 'Tempxx', 'oraryxx', 'coolpasswordxx', role="user")
+        self.waitUserCreated(user_info['userId'])
+
+        wa.users.delete_user(user_info['username'])
+        self.waitUserDeleted(user_info['userId'])
+
+        users = wa.users.get_users()
+
+        for user in users:
+            assert user['username'] != 'trash@bx.psu.edu'
+
+    def test_update_user(self):
+
+        user_info = wa.users.create_user("trash@bx.psu.edu", 'Tempxx', 'oraryxx', 'coolpasswordxx', role="user")
+        self.waitUserCreated(user_info['userId'])
+
+        wa.users.update_user(user_info['username'], 'firstname2', 'lastname2')
+
+        time.sleep(3)
+        res = wa.users.show_user('trash@bx.psu.edu')
+
+        assert res['username'] == 'trash@bx.psu.edu'
+        assert res['firstName'] == 'firstname2'
+        assert res['lastName'] == 'lastname2'
+        assert res['role'] == 'USER'
+
+    def test_update_user_email(self):
+
+        user_info = wa.users.create_user("trash@bx.psu.edu", 'Tempxx', 'oraryxx', 'coolpasswordxx', role="user")
+        self.waitUserCreated(user_info['userId'])
+
+        wa.users.update_user(user_info['username'], 'firstname2', 'lastname2', new_email='updated@bx.psu.edu')
+
+        time.sleep(3)
+        res = wa.users.show_user('updated@bx.psu.edu')
+
+        assert res['username'] == 'updated@bx.psu.edu'
+        assert res['firstName'] == 'firstname2'
+        assert res['lastName'] == 'lastname2'
+        assert res['role'] == 'USER'
+
+    def setUp(self):
+        # Make sure the user is not already there
+        temp_user_info = wa.users.show_user('test_temp@bx.psu.edu')
+        if 'username' in temp_user_info:
+            wa.users.delete_user(temp_user_info['username'])
+            self.waitUserDeleted(temp_user_info['userId'])
+
+        temp_user_info = wa.users.show_user('trash@bx.psu.edu')
+        if 'username' in temp_user_info:
+            wa.users.delete_user(temp_user_info['username'])
+            self.waitUserDeleted(temp_user_info['userId'])
+
+        temp_user_info = wa.users.show_user('updated@bx.psu.edu')
+        if 'username' in temp_user_info:
+            wa.users.delete_user(temp_user_info['username'])
+            self.waitUserDeleted(temp_user_info['userId'])
+
+        wa.users.create_user("test_temp@bx.psu.edu", 'Temp', 'orary', 'coolpassword', role="user")
+
+    def tearDown(self):
+        temp_user_info = wa.users.show_user('test_temp@bx.psu.edu')
+        if temp_user_info and 'username' in temp_user_info:
+            wa.users.delete_user(temp_user_info['username'])
+            self.waitUserDeleted(temp_user_info['userId'])
+
+        temp_user_info = wa.users.show_user('trash@bx.psu.edu')
+        if 'username' in temp_user_info:
+            wa.users.delete_user(temp_user_info['username'])
+            self.waitUserDeleted(temp_user_info['userId'])
+
+        temp_user_info = wa.users.show_user('updated@bx.psu.edu')
+        if 'username' in temp_user_info:
+            wa.users.delete_user(temp_user_info['username'])
+            self.waitUserDeleted(temp_user_info['userId'])