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    simisimi
    @iamatsundere
    Have you run kubectl apply -f . -n vinlab ? Because I think you run with the default namespace in somewhere
    Matvey Ezhov
    @ematvey
    Nope, I ran kubectl apply -f . following the instructions
    simisimi
    @iamatsundere
    Oh, please follow the instruction from README.md file in vindr-lab-deployment repo. It is the latest version.
    simisimi
    @iamatsundere
    hey @ematvey, how is your deployment, does it work?
    Jan Witowski
    @jwitos
    Hi, just wanted to add a note of interest for 3D annotation tools. Contrary to @ematvey I love 3D Slicer but for personal annotation, not "MLops" / engaging new people to do segmentation. I think simple tools like a brush is sufficient for many use cases. Even something as simple as https://www.medseg.ai/ would work. Thanks for contributing, I've also worked for some time on a similar project when I was at Harvard for a few months (markit.mgh.harvard.edu) so I understand how difficult this can be.
    Jakob Thrane
    @jakthra
    Hello! having some issues uploading DICOM files. I've added an issue to the uploader API endpoint (error not handled). However, if trying to upload a DICOM with the DICM tag, I get hit by the following error
    2021-04-20 07:31:36.613 | ERROR    | middleware.authenticate:get_authentication:60 - error when get info
    2021-04-20 07:31:36.847 | ERROR    | middleware.authenticate:get_authentication:56 - Token is missing the "aud" claim
    simisimi
    @iamatsundere
    @jakthra do you use Docker or Kubernetes?
    Jakob Thrane
    @jakthra
    @iamatsundere Kubernetes
    simisimi
    @iamatsundere
    ok, please login to the Keycloak admin console, go to Clients/vinlab-frontend
    image.png
    and tell me do you see any thing like these
    Jakob Thrane
    @jakthra
    image.png
    Did I miss something in the setup guide?
    simisimi
    @iamatsundere
    No, I think it's my bad, I will update it in the Keycloak document
    But I will support you to get it done now
    pleas click the Add Builtin button
    Jakob Thrane
    @jakthra
    Thanks a lot :)
    simisimi
    @iamatsundere
    and looking for something like audience resolve
    Jakob Thrane
    @jakthra
    I have nothing under "Builtin" with that name. I do however have it under "Create"
    simisimi
    @iamatsundere
    ok, so please click the Create button then setup like this
    image.png
    if you completed it, you should re-login
    Jakob Thrane
    @jakthra
    Ok, thanks, will try :-D
    simisimi
    @iamatsundere
    Ok, notice me if you have any issues or just finish this :)
    21 replies
    guigautier
    @guigautier
    Hi, I m trying to run the application with kubernetes, I met the same problem (vinbigdata-medical/vindr-lab-deployment#5), when I try to create a new project. I think, I miss something during the keycloak installation, but I don’t know what. Any ideas ? Thank tou
    1 reply
    guigautier
    @guigautier
    Everything works fine. Keycloak configuration files are working well. Thanks a lot
    1 reply
    guigautier
    @guigautier
    Hi, I tested your system, the workflow process and the UI are really nice. However I did not succeed to see my labeling annotations after completed it in task mode. (saved labeling annotation are not visible) Maybe I ommitted to do something. I have also a question, how can I retrieve the stored data and associated annotations from the json file ? Thanks
    5 replies
    guigautier
    @guigautier
    Hi, I retested on an other computer with the same configuration, and I got the same issue. I can’t review done annotation.
    Otherwise the app is really nice. Missing some tools for 3D annotations. I saw it’s Work in progress. I will be interested to help you to define the 3D brush tools.
    3 replies
    Rasmus Bonnevie
    @Bonnevie
    Hi, this seems related to the issue mentioned by guigautier. I am using the Kubernetes deployment on Ubuntu 20.04 with the keycloak files you've supplied, and I can access the UI just fine. When annotating, though, (in the medical-view subdomain) it happens that when I press "Save", all my annotations immediately disappear. Is this a lacking permission of some kind?
    6 replies
    Nghia
    @Lego1st
    Hi everyone, after weeks of being busy. We have fixed the saving issues on Github. Please check it out and let me know if everything is ok. :-D
    markcorsi
    @markcorsi
    Hi All - I finished the setup instructions at: https://github.com/vinbigdata-medical/vindr-lab-deployment/blob/master/KEYCLOAK.md At the end of the document says: "And here we go!....." And then nothing. I am sorry. But where do I go? I can login to the account user info, but how do I actually start the software and upload my first study?
    markcorsi
    @markcorsi
    By the way, I noticed one issue with my install that I don't see covered in the documentation. I am trying to install this on a real webserver (e.g. running it from a fqdn not localhost). Is this my problem?
    markcorsi
    @markcorsi
    Hi again! That was exactly the issue. I installed everything on a local vagrant box running ubuntu and everything worked perfectly for 'localhost'. However, I cannot seem to find where I change localhost to a FQDN inside the settings for deploying on the internet. I found four places in the clients 'vinlab-frontend' and 'vinlab-backend' where localhost is part of the URL configurations but changing those to my fqdn still doesn't stop the redirect to localhost when I try to log into the system. Any help will be greatly appreciated! (Oh, and thanks for writing this application! It looks great!!)
    Nghia
    @Lego1st
    Sorry for late reply. How are you doing? Did you mean that you cannot expose to the Internet with a domain name?
    markcorsi
    @markcorsi
    I mean I have installed everything on a vagrant box on my localhost and everything works correctly. However, when I install it on a aws server with a fully qualified domain name and then go to that domain: "http://ai-vinlab.totalcloudpacs.com:8080/" some sort of loopback occurs and it attempts to go to localhost: "http://localhost:8080/auth/realms/vinlab/protocol/openid-connect/auth?client_id=vinlab-frontend&response_type=code&state=7zrxwtar04a&scope=profile&redirect_uri=http://localhost:8080/dashboard"
    simisimi
    @iamatsundere
    Oh, sorry for that, are you using Docker or Kubernetes?
    markcorsi
    @markcorsi
    Kubernetes
    markcorsi
    @markcorsi
    Any idea what the issue is?
    simisimi
    @iamatsundere
    Yeah, I know it's complicated and 'dummy' in someway, but there is a solution for this. By deploying on cloud environment, you should replace the phrase http://localhost:8080 by your domain https://your.domain.
    Because of just thinking about demo cases when writing the documents so we focused on local deployment. We will update the document shortly!
    simisimi
    @iamatsundere

    Yeah, I know it's complicated and 'dummy' in someway, but there is a solution for this. By deploying on cloud environment, you should replace the phrase http://localhost:8080 by your domain https://your.domain.

    ...in viewer and dashboard deployment file

    markcorsi
    @markcorsi
    I changed all the 'localhost' to 'ai-vinlab.totalcloudpacs.com' in 'vinlab-viewer.deployment.yml' and in 'vinlab-dashboard.deployment.yml'. I rebooting the server. The server came up very slowly, but finally got there (might have been an unrelated network issue). I can still get to: http://ai-vinlab.totalcloudpacs.com:8080/auth/ (which allows me to get into the keycloak admin area. But when I go to http://ai-vinlab.totalcloudpacs.com:8080 it redirects to http://ai-vinlab.totalcloudpacs.com:8080/dashboard/ which gives me an nginx 'bad gateway' error. It seems like we are getting closer. Any further ideas?
    Sorry, but when I hit refresh on http://ai-vinlab.totalcloudpacs.com:8080/dashboard/ it went back to the localhost redirect originally detailed in this thread. Did I not edit the correct files?
    simisimi
    @iamatsundere
    Hmmm, it seems like you are in the correct way. Have you tried to re-apply these 2 deployment files by the command kubectl -n vinlab apply -f <yml-file-name>?
    markcorsi
    @markcorsi
    No - I hadn't tried that command. I first tried restarting k3s (which didn't work) and then I tried rebooting the whole server (which didn't work). I tried running the command you gave me twice (once for each file) and it also has not worked. I do notice that I now have two dashboard and two viewer kubernetes pods though:
    root@ip-172-31-73-161:/home/markcorsi/git/vindr-lab-deployment/kubernetes# kubectl -n vinlab get pod
    NAME READY STATUS RESTARTS AGE
    vinlab-dashboard-deployment-df449f65-8sgjq 0/1 Running 0 16m
    vinlab-viewer-deployment-69c76f4ff9-spd6s 0/1 Running 0 16m
    es-deployment-779db4985d-vgv2m 1/1 Running 2 13d
    keycloak-deployment-68b78d9b67-gnfqv 1/1 Running 3 13d
    vinlab-dashboard-deployment-b65cd4db5-shhf8 1/1 Running 2 13d
    apigateway-deployment-d6dcc5d8f-8zt4d 1/1 Running 3 13d
    vinlab-uploader-deployment-785449b44f-xlkn4 1/1 Running 2 13d
    redis-deployment-756b4b8956-55p5v 1/1 Running 2 13d
    id-generator-deployment-7454b7bf6d-qrmh7 2/2 Running 4 13d
    minio-deployment-556459976d-6sxvk 1/1 Running 2 13d
    svclb-vinlab-lb-hrdsk 1/1 Running 2 13d
    vinlab-viewer-deployment-6cf845cf5-dt45t 1/1 Running 2 13d
    vinlab-api-deployment-d4fbc5c5f-whcs7 1/1 Running 13 13d
    I am new to kubernetes and also to your software. Can you please walk me through, step by step, how I can best fix this issue?
    markcorsi
    @markcorsi
    By the way - It has been 30 minutes since I ran those commands and the machine is currently 'locked up'. It will not accept new ssh requests and will not take new commands from the shell I had open. I will keep you posted, but I have a feeling that even though kubernetes is a bit of a resource hog, this behavior is not expected.
    markcorsi
    @markcorsi
    After locking up the machine for nearly an hour, kubernetes finally came up. There are now only one pod for each of the yaml files I modified. However, the problem still exists. It still loops back to localhost. Here are the pods:
    root@ip-172-31-73-161:~# kubectl -n vinlab get pod
    NAME READY STATUS RESTARTS AGE
    redis-deployment-756b4b8956-55p5v 1/1 Running 2 13d
    id-generator-deployment-7454b7bf6d-qrmh7 2/2 Running 4 13d
    minio-deployment-556459976d-6sxvk 1/1 Running 2 13d
    svclb-vinlab-lb-hrdsk 1/1 Running 2 13d
    vinlab-api-deployment-d4fbc5c5f-whcs7 1/1 Running 13 13d
    orthanc-deployment-fb799595-2zqqb 1/1 Running 2 13d
    vinlab-uploader-deployment-785449b44f-xlkn4 1/1 Running 2 13d
    apigateway-deployment-d6dcc5d8f-8zt4d 1/1 Running 3 13d
    es-deployment-779db4985d-vgv2m 1/1 Running 2 13d
    vinlab-dashboard-deployment-df449f65-8sgjq 1/1 Running 0 80m
    vinlab-viewer-deployment-69c76f4ff9-spd6s 1/1 Running 0 80m
    keycloak-deployment-68b78d9b67-gnfqv 1/1 Running 3 13d