Scout: How to set up Simple login

[andreaswallberg]

Dear all,

I can not find the documentation or example config.py that specifies how to arrange a "simple login". For our teaching scenario, this is the preferred login method.

The docs over at:
http://www.clinicalgenomics.se/scout/admin-guide/login-system/#simple-login-with-userid-and-password

Just say:
Basic login with userid and password is the login system available whenever no advanced login system (either Google or LDAP) is specified in the Scout config file.

It is not clear if it is already specified in some file sitting around on disk, or if it should be specified here by the admin.

Can you please provide the means for arranging a simple login?

[andreaswallberg]

Answering myself here: commenting out the Google OAuth part of the main config file pulls up the simple login instead.

Next challenge: figuring out how to whitelist a user.

[dnil]

Good! We should just leave you at it and you will have it figured in notime! Sorry if there were still references to whitelisting: I thought we had them all gone? Please let us know if it for some reason doesn't work with a plain user load (adding a user, that is) as in the admin guide. Or if you wish, just use a mongo db client to edit users like the demo ones; MongoDB Compass is pretty handy.

[dnil]

Dont forget institutes! 😸

[andreaswallberg]

Even after creating institutes, users and assigning institutes and roles to them, I keep triggering the issue upon simple login:
User not whitelisted

No idea what I am doing wrong. Maybe you have all used Google OAth for so long there is some bitrot in there for simple logins (outside the demo session?)? ;-)

[andreaswallberg]

I believe it triggers the error at line 84 of views.py , but I can not understand why.

[dnil]

I think you are right: this likely happens when you nowadays add non-demo users that have email and user_id that differ. Once upon a time they were the same. Let’s fix that tomorrow. Sleep tight! 😴

[northwestwitch]

Hi! If you want to create a simple login user please omit the -id parameter when you create it from the command line. The command would be for instance:
scout (--demo) load user -i cust000 -u "Your Name" -m [email protected]

Then you use the email for logging in.

It's not really a bug, but we should definitely document the process better!

[dnil]

Thanks @northwestwitch! Sorry @andreaswallberg - we may have been a bit tired yesterday. I can't reproduce your issue now. Could you provide some commands / db snapshot - or better yet try again and find it working? Both with and without a forced _id work for me. See below, but drop --demo obviously - or substitute for your db connection preferences if you need it.

´´´
scout --demo load user -i cust000 -u "Barry Allen" -m "[email protected]" -id "inaflash"
scout --demo load user -i cust000 -u "Funker Ejder" -m "[email protected]"
´´´

[andreaswallberg]

I tried both Barry Allen and Funker Ejder but I get the same problem. I can see the attempted login in the Scout server log, and there is not error message there (in multiple web browsers).

scout view users confirms they are all there:

name email roles institutes

Clark Kent clark.[email protected] admin cust000
Barry Allen inaflash cust000
Funker Ejder [email protected] cust000
Your Name [email protected] cust000

For the record, I am not running a demo site, but initiated scout as scout setup database. I have confirmed the presence of them in the database with Compass and can see that users created without id gets the email for id as well.

[andreaswallberg]

If I press login without providing any email, I get this error in the server log:

scout.adapter.mongo.user[138357] WARNING No key provided to fetch user

That does not happen when I provide emails.

If I comment out this in views.py:

    if user_obj is None:
        flash("User not whitelisted", "warning")
        return redirect(url_for("public.index"))

I get a server error on the web page, so my best guess is whatever user_object store.user was meant to collect on the line before, it did indeed fail.

[andreaswallberg]

Must a user be assigned roles or cases or something else before it can log in?

[northwestwitch]

Must a user be assigned roles or cases or something else before it can log in?

No, it should work anyway. Does the institute associated to the user exist in the database?

[dnil]

Nope, not needed. Also works for me on a local non-demo instance. Your user table looks good. And you are typing the email, not user id in the cases where they differ.

[dnil]

I updated the docs slightly in #2042, but lets get this working before merging. 😄

[andreaswallberg]

Yes it exists. It is default one created by scout setup database

_id internal_id display_name sanger_recipients created_at updated_at coverage_cutoff frequency_cutoff
cust000 cust000 cust000 ['clark.[email protected]'] 2020-08-24 23:22:04.050000 2020-08-24 23:22:04.050000 10 0.01

I have tried both emails and ids at the login :-)

Btw, is it expected that Clark Kent should be created also when running scout setup database (so not the demo)?

[northwestwitch]

Btw, is it expected that Clark Kent should be created also when running scout setup database (so not the demo)?

Nope

[northwestwitch]

Trying to reproduce your error @andreaswallberg.

I've been running:

1. scout setup database
2. scout load user -u "Diana Prince" -m [email protected] -i cust000
3. scout serve
4. Logging in with email [email protected]

It works

[andreaswallberg]

Do you have Clark Kent among the users?

[northwestwitch]

Do you have Clark Kent among the users?

Yes I do, then it is created by that command after all..

[andreaswallberg]

I will start over now.

scout wipe --yes
scout --demo wipe --yes

In the case of the second wipe, I did not have the demo database in mongodb but I did it anyway :-D
I verified the deletion from mongodb with Compass.

Can you please post your startup scout config.py so that I can compare to mine?

[northwestwitch]

I'm not using any specific scout config. If you don't specify one it should be using the database named scout on localhost.

[dnil]

Btw, is it expected that Clark Kent should be created also when running scout setup database (so not the demo)?

Well, one user will be created, but you can override the name of your hero with
[-n | --user-name] (defaults to Clark Kent)

[dnil]

You seem to be able to connect to the db fine, since e.g. the wipe commands, user view etc is working. Also the error from empty email login is as expected. I wonder what we do differently for the existing email?! Gotta be something. Unicode for @???

[dnil]

What do you get for an error on the terminal when you try logging in as an existing user? Something like
Validating user None against Scout database?

[andreaswallberg]

One step closer.

It works when using @northwestwitch instructions, but only when using scout serve for localhost:5000 and in my case scout serve -h 0.0.0.0 -p XXXXX to bring it up for external login on my custom port.

The error occurs when I switch to gunicorn. It brings up the site, but does not accept the login. This happens regardless of me using HTTP or HTTPS with my own key and cert. So the issue seems to be the behavior when starting the server with gunicorn.

[dnil]

And how do you provide your scout Flask config path when running through gunicorn? As an environment variable SCOUT_CONFIG?

[andreaswallberg]

Got it.

My scout config, copied over from the online instructions, which was only loaded when using gunicorn, had the line:

MONGO_DBNAME = 'scoutTest'

It should of course be:

MONGO_DBNAME = 'scout'

After changing this, it works :-D

[dnil]

Same here, docs updated a bit in #2042 and #2046. Good luck with the course - looking forward to hear more about your experiences - or issues getting there!

[andreaswallberg]

I would just like to add an addendum here. Our course lab worked well in 2020 and we are running it again in fall 2021.

I have been too scared to break things, so for now so I am still at the very same release of Scout that I used last year ;-)

[northwestwitch]

Our course lab worked well in 2020 and we are running it again in fall 2021.

Nice to hear it! We are about to release a new version of Scout on these days, of course it could happen that something needs fixing, but the current version is stable and shouldn't give you major problems. You could give it a try, we have added a lot of nice features in the last year! :)