ldap authentication with latest version

[kforner]

Hi,

So on one of my server I can run tmapp. It works with the default Config.groovy. If I try to put the LDAP related bits from my current working config with the old instance, it does not seem to be taken into account (i.e. I can not login with the LDAP credentials).

If I just replace the Config.groovy with the old one, tmapp crashes. I can see these types of messages in the logs:

transmart.log:11-05-2017 17:48:21,118 ERROR GrailsContextLoader - Error initializing Grails: No bean named 'ldapAuthProvider' is defined
transmart.log:org.springframework.beans.factory.NoSuchBeanDefinitionException: No bean named 'ldapAuthProvider' is defined

So my question: do you have any information about how to setup LDAP authentication with this version, and if some thing has changed regarding the configuration ?

Thanks.
Karl

[dennyverbeeck]

Hi Karl,

The 'latest' branch is built from the code in the Transmart foundation's github repo. LDAP is an eTRIKS specific plugin and as far as i know it is not available in the foundation's version of Transmart. In a week or two we will have a brand new eTRIKS release. If possible for you i would suggest to wait until that release, as it will include all the latest developments from the Transmart Foundation's branch as well.

I'll drop a comment in this thread once the new release is up.

Thanks!
Denny

[kforner]

Ok. I also think it's best to wait then.
Are you using the LDAP plugin yourself, or testing it ?

[dennyverbeeck]

Ok, at the moment i'm not supporting any projects using it, nor am i using it myself. But if there are any issues we'll reach out to someone else within eTRIKS who has more knowledge on the LDAP plugin, and solve it together :)

[kforner]

cool !

[dennyverbeeck]

Hi Karl,

eTRIKS v4 has been released and i have built the new docker images. The master branch now contains this release. Keep in mind that, when logging in, you have to click the "Federated login" link below the login form to be redirected to your custom login service.
Looking forward to hear from you how it goes!

Denny

[kforner]

Great,
I'll test it ASAP, and don't worry you'll probably hear from me ;)
Thanks,
Karl

[hcountou]

Hello, great work !

Did you solved the Rserve issue that was not starting ?
I still get : "transmartdocker_tmrserve_1 exited with code 132", when composing with the new docker-compose you've provide. Any clue ?

If anyone has a successful procedure for setting the LDAP configuration right we are looking forward to it.

Hector

[dennyverbeeck]

Hi Hector,

Could you please provide the output of docker logs transmartdocker_tmrserve_1? I don't have an issue with Rserve on my system (Ubuntu 16.04).

Thanks!
Denny

[kforner]

same problem here:

> docker-compose up tmrserve
Creating network "transmartdocker_default" with the default driver
Creating transmartdocker_tmrserve_1
Attaching to transmartdocker_tmrserve_1
transmartdocker_tmrserve_1 exited with code 132

no logs:

docker logs transmartdocker_tmrserve_1

[hcountou]

docker logs transmartdocker_tmrserve_1 won't give me any logs if it isn't started...
We had to replace in previous version you tmrserve in order to make it work.

A collegue of mine did it. He made a new Dockerfile i'll ask him if i can forward it to you.

[dennyverbeeck]

Interesting, i can confirm on an ubuntu 14.04 the same issue. I know Karl is running that, is that what you are running as well Hector?

I see from the dockerfile you are getting the 16.1 version of transmart-data. It might be the case that having an older version will not install all required R packages (don't have time to check right now). This would impact things like SmartR and the advanced analysis workflows.

In any case, building on a 14.04 system with the original Dockerfile also results in an image that runs on both 14.04 and 16.04, while the original image, built on a 16.04 system, does not run on 14.04. My best guess is that since there is a difference in kernel versions, there might be a difference in library versions being linked to when compiling R.

The new image is now pushed to dockerhub. You should be able to pull it by just doing a docker pull dennyverbeeck/transmart-rserve:etriks-v4.0. Then the regular docker-compose up should pick up the newly pulled image 👍

[hcountou]

Yes we are still on Ubuntu 14.04. I'll test your new version right away. And tell you the conclusion.

Thanks.

[kforner]

not better:

> docker pull dennyverbeeck/transmart-rserve:etriks-v4.0
etriks-v4.0: Pulling from dennyverbeeck/transmart-rserve
Digest: sha256:d3771e83915b7da509e87ebcabb62f00ddb92c8a657c8921c9c71e2af15f648b
Status: Image is up to date for dennyverbeeck/transmart-rserve:etriks-v4.0

> docker-compose  up tmrserve
Creating network "transmartdocker_default" with the default driver
Creating transmartdocker_tmrserve_1
Attaching to transmartdocker_tmrserve_1
transmartdocker_tmrserve_1 exited with code 132

[hcountou]

Same here. Still got the error.

[dennyverbeeck]

Strange, could you give me the output of docker version and docker-compose version? In the meantime, probably the safest way to move forward for is for you to build the image yourself locally. You can just run docker build -t dennyverbeeck/transmart-rserve:etriks-v4.0 . in the transmart-rserve directory to build it and overwrite the image from dockerhub. Alternatively, you can provide your own image tag after the -t flag but then you need to update your docker-compose.yml file so that the same tag is used there as well.