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    simisimi
    @iamatsundere
    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
    And here is the loopback url:
    http://localhost:8080/auth/realms/vinlab/protocol/openid-connect/auth?client_id=vinlab-frontend&response_type=code&state=43j0i7es159&scope=profile&redirect_uri=http://localhost:8080/dashboard
    You should be able to see this process yourself by going to:
    http://ai-vinlab.totalcloudpacs.com:8080/
    Thanks for all the help up till now. Any other ideas?
    simisimi
    @iamatsundere
    Hm, I think there is an issue somewhere
    Maybe you can go to the Keycloak url, choose vinlab-frontend and change all the URL fields to *
    But I think it is not the root cause
    markcorsi
    @markcorsi
    Hi - I think there was something weird with Kubernetes and the acceptance of the new yaml files. Last night, the machine locked up entirely and we were forced to reboot it from the AWS console. When It came up, everything is now working! Thanks for the help!!
    markcorsi
    @markcorsi
    Now that I am into the setup screens, I have found some issues that I don't understand and I can't find the explanations in the documentation. I set up a project and went into the 'data' screen. The 'import data' button is greyed out. How do I import the first studies into the project? Also, on the settings tab in the workflow section. The project owner is listed but there are no reviewers nor annotators. I have three users all of whom have reviewer and annotator roles but when I click the search box under reviewer, the pop up box says 'no data'. When I try to save the settings, the reviewer box is hilighted in red with a 'Please select users' message. Under the 'Tasks' tab, I do not see any way of setting up new tasks. I think some of the above issues are interrelated. Can you please walk me through them? I have been through the instructions at: https://vinbigdata-medical.github.io/vindr-lab/user-guide/project/ but was unable to find solutions to these issues. Is there any place else I should look? Thanks again!
    simisimi
    @iamatsundere
    Thanks for replying, it is good to see it works normally, at least in the services-to-services interface
    About your issue, just re-confirm that your user have role: Project Owner in the Keycloak
    About the Import data button, please send us some screenshot
    simisimi
    @iamatsundere
    About getting users in the Settings tab, I think you've changed the password of the Keycloak's master account. If it's true, you will have to change the password of Keycloak account in the setting of vindr-lab-api too.
    Hope it'll help you.
    Nghia
    @Lego1st
    About the way of setting up new tasks, please refer to the following section https://vinbigdata-medical.github.io/vindr-lab/user-guide/project/#assignment
    markcorsi
    @markcorsi
    Regarding your second comment above. I assume you mean: vinlab-api.deployment.yaml
    markcorsi
    @markcorsi
    Another question is, once I make a change to the yaml files, how do I force kubernetes to accept those new parameters? The only way I have found so far is a hard reboot from the AWS console and that is equivalent to hitting the power button so not super desirable. Soft reboots leave behind the old configuration 'pod' for some reason.
    simisimi
    @iamatsundere
    Normally, you just use kubectl -n vinlab apply -f vinlab-viewer.deployment.yaml, then check it again by kubectl -n vinlab get pod
    simisimi
    @iamatsundere

    Regarding your second comment above. I assume you mean: vinlab-api.deployment.yaml

    Sure it is