I am trying to connect to an AppEngine instance with the remote API with something like this:
os.environ['GOOGLE_APPLICATION_CREDENTIALS'] = ".../path/to/key"
remote_api_stub.ConfigureRemoteApiForOAuth(
    server.encode('ascii'), path, secure=True
)
Where the path/to/key points to a JSON file created in the Google Cloud (Beta), API Manager -> Credentials -> Add Credentials -> Service Account.  The service account "Can edit" per the Permissions panel.
When I run this I get an error like this on the console, corresponding to a 401 (as reported in the App Engine log viewer):
  File "/usr/local/share/app-engine-python/google/appengine/ext/remote_api/remote_api_stub.py", line 768, in ConfigureRemoteApiForOAuth
    rpc_server_factory=rpc_server_factory)
  File "/usr/local/share/app-engine-python/google/appengine/ext/remote_api/remote_api_stub.py", line 835, in ConfigureRemoteApi
    app_id = GetRemoteAppIdFromServer(server, path, rtok)
  File "/usr/local/share/app-engine-python/google/appengine/ext/remote_api/remote_api_stub.py", line 569, in GetRemoteAppIdFromServer
    response = server.Send(path, payload=None, **urlargs)
  File "/usr/local/share/app-engine-python/google/appengine/tools/appengine_rpc_httplib2.py", line 258, in Send
    NeedAuth()
  File "/usr/local/share/app-engine-python/google/appengine/tools/appengine_rpc_httplib2.py", line 234, in NeedAuth
    RaiseHttpError(url, response_info, response, 'Too many auth attempts.')
  File "/usr/local/share/app-engine-python/google/appengine/tools/appengine_rpc_httplib2.py", line 85, in RaiseHttpError
    raise urllib2.HTTPError(url, response_info.status, msg, response_info, stream)
urllib2.HTTPError: HTTP Error 401: Unauthorized Too many auth attempts.
I checked and the correct credentials seem to be set in /google/appengine/ext/remote_api/remote_api_stub.py:760 and should be passed to the remote api.
The app.yaml has the basic setting - remote_api: on under builtins.
This setup works for the local dev_appserver.py, so I am led to believe the problem is on the Google server/cloud settings.
I have tried both authentication schemes in App Engine -> Settings -> Application settings (Google Accounts API and Google Apps domain).
I followed the Google Application Default Credentials as fit as I could, but maybe I missed something?
It is probably also worth noting that from the command line:
$ GOOGLE_APPLICATION_CREDENTIALS=~/path-to-key
    remote_api_shell.py -s APPID.appspot.com --secure APPID
also gives the same 401 exception.
Just encountered this issue and nothing here resolved it.
The only thing that worked for me is adding the --secure option to the remote shell command
$APPENGINE/remote_api_shell.py  --secure -s my-app.appspot.com
                        Ok, so what seemed to be necessary was:
remote_api_stub.ConfigureRemoteApiFromServerConfigureRemoteApiForOAuth works fine.At least after performing the above access works as expected.
I hope others similarly situated find this helpful.
For people using the remote api from the command line (bulkloader.py, remote_api_shell.py etc.), a 401 error might also happen if your appengine cookies are expired.
Try deleting them and authenticating again:
rm ~/.appcfg*
gcloud auth login
This could happen in cases where changes made to a Google account force logging out (e.g: enabling 2 factor authentication).
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