Merge branch '20-modify-the-command-line-to-use-the-personal-authentication-token' into 'master'

Resolve "Modify the command line to use the personal authentication token"

Closes #20

See merge request !18

pyiricdata/Client.py

@@ -26,36 +26,39 @@ class Client:
     api_datafiles_meta = 'api/v1/datafiles/json/metadata'
     api_datafiles_annotation = 'api/v1/datafiles/json/annotation'
     api_my_datasets = 'api/v1/my-datasets/list/json/'
-    
+
     """ python client to IRICdata API"""
     def __init__(self, username, password=None, token=None,
                  url='https://thepond.bioinfo.iric.ca'):
         self.url = url
         self.user = username
-        self.pwd = password 
+        self.pwd = password
         self.token = token
-        
+
         if self.token is None and self.pwd is None:
             self.pwd = getpass()
 
         session = requests.session()
-        
+
         if self.token is not None:
+            if self.pwd is not None:
+                sys.stderr.write('WARNING: Ambiguous authentification, ignoring ' +
+                        'password in favor of PAT\n')
             self.token = self.token.strip()
             session.headers.update({'Iric-Auth-Token': F'{self.token}'})
 
         elif self.user and self.pwd:
-            login = os.path.join(self.url, 'login/')
-            session.get(login)
+            login_url = os.path.join(self.url, 'login/')
+            session.get(login_url)
             csrftoken = session.cookies['csrftoken']
             cookies = {'csrftoken': csrftoken}
             payload = {
                 'username': self.user, 'password': self.pwd,
                 'csrfmiddlewaretoken': csrftoken, 'next': ''
             }
-            headers = {'Referer': login}
+            headers = {'Referer': login_url}
 
-            login = session.post(login, cookies=cookies, data=payload,
+            login = session.post(login_url, cookies=cookies, data=payload,
                              headers=headers)
 
             if login.status_code == 200:
@@ -69,9 +72,9 @@ class Client:
                 raise IricDataConnectionError('Could not initiate connexion ' +
                                           'with IRIC-Data')
         else:
-            raise IricDataConnectionError('Could not initiate connexion ' +
-                                          'with IRIC-Data')
-            
+            raise IricDataConnectionError('Connexion failed -- please verify ' +
+                                          'that you submitted a token or a ' +
+                                          'username/password combination')
 
         self.session = session
 
@@ -80,7 +83,7 @@ class Client:
         except:
             self.labs = None
             print('get_available_labs() method is not implemented in api/v1 of IRIC-Data')
-        
+
         self.datasets = self.get_available_datasets()
         #self.datafiles = self.get_available_datafiles()
 
@@ -115,7 +118,7 @@ class Client:
     """
     def get_datafiles_list(self, key_anno=None, value_anno=None,
                            dataset_id=None):
-        
+
         if key_anno is None and value_anno is None and dataset_id is None:
             sys.stderr.write("WARNING: return all files is not implemented\n")
             return(None)

pyiricdata/__main__.py

@@ -9,15 +9,23 @@ def main():
     parser = argparse.ArgumentParser()
     parser.add_argument("-u", "--username", help="Username", type=str, required=True)
     parser.add_argument("-p", "--password", help="Password", type=str, default=None)
+    parser.add_argument("-t", "--token-file-path", type=str, default=None,
+            help="File containg Personal Authentication Token (PAT)")
     parser.add_argument("--url", help="URL", type=str, default='https://thepond.bioinfo.iric.ca')
     parser.add_argument("--dataset-id", help="Dataset ID", type=str, default=None)
     parser.add_argument("--datafile-id", help="Datafile ID", type=str, default=None)
     parser.add_argument("-D", "--download", help="Download", action='store_true')
     parser.add_argument("-U", "--upload", help="Upload", action='store_true')
     parser.add_argument("-P", "--update", help="Update", action='store_true')
+
     args = parser.parse_args().__dict__
 
-    client = Client(args['username'], args['password'], args['url'])
+    if args['token_file_path'] is not None:
+        token = open(args['token_file_path'], 'r').read().strip()
+    else:
+        token = None
+
+    client = Client(username=args['username'], password=args['password'], token=token, url=args['url'])
 
     if args['download']:
         dsid = args['dataset_id']