Use auth more, don't fail if output has status but is not asynchronous, like /metagenome

Author: Will Trimble

mglib/mglib.py

@@ -123,28 +123,31 @@ def async_rest_api(url, auth=None, data=None, debug=False, delay=60):
     submit = obj_from_url(url, auth=auth, data=data, debug=debug)
 # If "status" is nor present, or if "status" is somehow not "submitted" 
 # assume this is not an asynchronous call and it's done.
-    if ('status' in submit) and (submit['status'] == 'done') and ('data' in submit):
+    if ('status' in submit) and (submit['status'] != 'submitted') and ('data' in submit):
         return submit['data']
 #    if not (('status' in submit) and (submit['status'] == 'submitted') and ('url' in submit)):
 #        return submit  # No status, no url and no submitted
-    result = obj_from_url(submit['url'], debug=debug)
+    result = obj_from_url(submit['url'], auth=auth, debug=debug)
     try:
-        while result['status'] != 'done':
+        while result['status'] == 'submitted':
             if debug:
                 print("waiting %d seconds ..."%delay)
             time.sleep(delay)
-            result = obj_from_url(submit['url'], debug=debug)
+            result = obj_from_url(submit['url'], auth=auth, debug=debug)
     except KeyError:
         print("Error in response to "+url, file=sys.stderr)
         print("Does not contain 'status' field, likely API syntax error", file=sys.stderr)
         print(json.dumps(result), file=sys.stderr)
         sys.exit(1)
     except TypeError:  # result isn't json, return it anyway
         return(result.decode("utf8"))
-    if 'ERROR' in result['data']:
-        sys.stderr.write("ERROR: %s\n" %result['data']['ERROR'])
-        print(json.dumps(result), file=sys.stderr)
-        sys.exit(1)
+    try: 
+        if 'ERROR' in result['data']:
+            sys.stderr.write("ERROR: %s\n" %result['data']['ERROR'])
+            print(json.dumps(result), file=sys.stderr)
+            sys.exit(1)
+    except KeyError:  # result doesn't have "data"
+        return result    
     return result['data']
 
 # POST file to MG-RAST or Shock
@@ -412,7 +415,7 @@ def kbids_to_mgids(kbids):
 def kbid_lookup(ids, reverse=False):
     request = 'mg2kb' if reverse else 'kb2mg'
     post = json.dumps({'ids': ids}, separators=(',',':'))
-    data = obj_from_url(API_URL+'/job/'+request, data=post)
+    data = obj_from_url(API_URL+'/job/'+request, auth=auth, data=post)
     return data['data']
 
 def get_auth_token(opts=None):

scripts/mg-query.py

@@ -13,14 +13,15 @@
 if __name__ == '__main__':
     usage = "usage: %prog [options]  URI"
     parser = ArgumentParser(usage)
-#    parser.add_argument("-v", "--verbose", dest="verbose", action="store_true")
+    parser.add_argument("-v", "--verbose", dest="verbose", action="store_true")
     parser.add_argument("-k", "--token", dest="token", type=str,
                       help="Auth token")
     parser.add_argument("URI", type=str, help="URI to query")
 
     opts = parser.parse_args()
     key = get_auth_token(opts)
-
+    if opts.verbose:
+        print("KEY = {}".format(key), file=sys.stderr)   
 # assign parameters
     URI = opts.URI