access_token logic changed

libraries/sing/sing/operations/publish/__init__.py

@@ -2,6 +2,7 @@
 from ...operation_types.SingOperationType import Singoperationtype
 import requests
 import os
+import json
 
 class Publish(Singoperationtype):
 
@@ -14,18 +15,18 @@ def description():
         return "Publish an analysis"
 
     def _parser(self, main_parser):
-        main_parser.add_argument('access_token_variable', help="Access token global variable name")
+        main_parser.add_argument('access_token', help="Access token variable")
         main_parser.add_argument('study', help="ICGC study ID")
         main_parser.add_argument('analysis_id', help="Analysis ID")
         return
 
     def _run(self):
-        access_token = os.environ.get(self.args.access_token_variable)
+        access_token = self.args.access_token
         response = requests.put('%s/studies/%s/analysis/publish/%s' % (self.song_server,self.args.study,self.args.analysis_id),headers={'Authorization':'Bearer '+access_token,'Content-Type':'application/json','Accept':'application/json'})
 
         if not response.status_code == 201:
             raise Exception(response.json().get('message'))
 
-        print(response.json())
+        print(json.dump(response.json()))
 
         return response.json()

libraries/sing/sing/operations/save/__init__.py

@@ -2,6 +2,7 @@
 from ...operation_types.SingOperationType import Singoperationtype
 import requests
 import os
+import json
 
 class Save(Singoperationtype):
 
@@ -14,15 +15,15 @@ def description():
         return "Save a SONG upload ID."
 
     def _parser(self, main_parser):
-        main_parser.add_argument('access_token_variable', help="Access token global variable name")
+        main_parser.add_argument('access_token', help="SONG access token")
         main_parser.add_argument('study', help="ICGC study ID")
         main_parser.add_argument('upload_id', help="Upload ID")
         return
 
     def _run(self):
-        access_token = os.environ.get(self.args.access_token_variable)
+        access_token = self.args.access_token
         response = requests.post('%s/upload/%s/save/%s' % (self.song_server, self.args.study,self.args.upload_id),headers={'Authorization':'Bearer '+access_token})
         if not response.status_code >= 200 and not response.status_code <=204:
             raise Exception(response.text)
-        print(response.json())
+        print(json.dumps(response.json()))
         return response.json()

libraries/sing/sing/operations/upload/__init__.py

@@ -17,26 +17,20 @@ def description():
         return "Upload json payload to song"
 
     def _parser(self, main_parser):
-        main_parser.add_argument('access_token_variable', help="Access token global variable name")
+        main_parser.add_argument('access_token', help="SONG access token")
         main_parser.add_argument('study', help="ICGC study ID")
         main_parser.add_argument('payload', type=argparse.FileType('r'), help="Path to payload.json")
         return
 
-    def _before_start(self):
-        super(Upload,self)._before_start()
-        if not os.environ.get(self.args.access_token_variable):
-            raise Exception("Your environment does not contain variable: %s" % (self.args.access_token_variable))
-        return True
-
     def _run(self):
-        access_token = os.environ.get(self.args.access_token_variable)
+        access_token = self.args.access_token
         headers={'Authorization':'Bearer '+access_token,'Content-Type':'application/json','Accept':'application/json'}
         payload = json.dumps(json.load(self.args.payload))
 
         response = requests.post('%s/upload/%s' % (self.args.song_server,self.args.study),data=payload,headers=headers)
 
         if response.status_code == 200:
-            print(response.json())
+            print(json.dumps(response.json()))
             return response.json()
         else:
             raise Exception(response.json().get('message'))