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    Matvey Ezhov
    @ematvey
    I'll try that thanks
    simisimi
    @iamatsundere
    @ematvey yeah, ping us if it works (or you need any support) :))
    Matvey Ezhov
    @ematvey
    Great, thanks!
    Can you share your estimates for when 3D annotation will be released?
    I get that it'll be done when it's done) but what do you think? We only need 3D annotation...
    Matvey Ezhov
    @ematvey
    Seems to be a typo in k8s doc: vinbigdata-medical/vindr-lab#1
    Matvey Ezhov
    @ematvey
    Nope, something's not right with the namespaces still.
    Events:
      Type     Reason       Age                  From               Message
      ----     ------       ----                 ----               -------
      Normal   Scheduled    19m                  default-scheduler  Successfully assigned default/apigateway-deployment-d6dcc5d8f-kngb6 to minikube
      Warning  FailedMount  8m43s (x2 over 13m)  kubelet            Unable to attach or mount volumes: unmounted volumes=[apigateway-configmap], unattached volumes=[default-token-vq7vz apigateway-configmap]: timed out waiting for the condition
      Warning  FailedMount  118s (x6 over 17m)   kubelet            Unable to attach or mount volumes: unmounted volumes=[apigateway-configmap], unattached volumes=[apigateway-configmap default-token-vq7vz]: timed out waiting for the condition
      Warning  FailedMount  86s (x17 over 19m)   kubelet            MountVolume.SetUp failed for volume "apigateway-configmap" : configmap "apigateway-configmap" not found
    Events:
      Type     Reason       Age                  From               Message
      ----     ------       ----                 ----               -------
      Normal   Scheduled    20m                  default-scheduler  Successfully assigned default/vinlab-api-deployment-d4fbc5c5f-w72xk to minikube
      Warning  FailedMount  4m54s (x2 over 16m)  kubelet            Unable to attach or mount volumes: unmounted volumes=[backend-configmap], unattached volumes=[default-token-vq7vz backend-configmap]: timed out waiting for the condition
      Warning  FailedMount  25s (x7 over 18m)    kubelet            Unable to attach or mount volumes: unmounted volumes=[backend-configmap], unattached volumes=[backend-configmap default-token-vq7vz]: timed out waiting for the condition
      Warning  FailedMount  8s (x18 over 20m)    kubelet            MountVolume.SetUp failed for volume "backend-configmap" : configmap "backend-configmap" not found
    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?