Migration from Version v0.1.3 to v0.2.2

Follow these steps if Kaapana in Version 0.1.3 is currently running on the server and there is data on the platform which should be migrated to the new version. Beware that Kaapana is not a storage solution but an analysis platform, a backup of all data send to Kaapana is strongly advised. The platform does not provide any guarantees regarding data integrity especially if the migration between version fails. In such a case it would be needed to start with a fresh Kaapana installation and resend all the data. With these words of caution here the necessary steps:

What this migration guide presevers

  • Images in PACS

  • Minio Storage

Requirements

  • Script deploy_platform_0.2.2.sh to deploy new Kaapana version.

Instructions

  1. Copy the server_installation_0.2.2.sh as well as the deploy_platform_0.2.2.sh onto the server.

  2. Undeploy the old platform using the old install_platform.sh script by executing it and choosing option 2) Uninstall.

    https://codebase.helmholtz.cloud/-/project/2521/uploads/8e2116c651e01efd555b589d5aee1df7/image.png

  3. When the platform is undeployed uninstall the older server initialization using the old server_installation.sh script by executing: sudo ./server_installation.sh --uninstall

  4. Reboot the machine

  5. Follow the Server Installation Guide to initialize the server. (The server_installation.sh is the provided server_installation_0.2.2.sh)

  6. Add the container registry username and password in the according Line 15 & 16 in the deploy_platform_0.2.2.sh script.

  7. Move data from the old installation to a temporary folder by executing mv /home/kaapana /home/kaapana_0.1.3. Make sure that the directories for the new version (e.g. default /home/kaapana) does not exist when the new version of the platform is booted up for the first time, so that the new platform does not boot using the old data (which would fail and leave an invalid state).

  8. Follow the Platform Deployment Guide using the deploy_platform_0.2.2.sh script with the preconfigured private registry.

  9. Optional: If TLS certificates are installed reinstall them in the updated instance by following the FAQ in the KAAPANA

  10. After the new version of the platform is successfully deployed with the initial file structure created in the fresh data directory the platform must be undeployed again by using the deploy_plaform_0.2.2.sh script and choosing option 2) Undeploy. Wait till the platform is undeployed.

  11. Move the data from PACS and MINIO from the old installation over to the new installation be executing the following commands (if the data directories have been customized in the previous installation replace /home/kaapana_0.1.3 with the path of the old installation and /home/kaapana with the path for the new installation):

    sudo rm -rf /home/kaapana/dcm4che
sudo rm -rf /home/kaapana/postgres-dcm4che
sudo rm -rf /home/kaapana/minio
sudo cp -r /home/kaapana_0.1.3/dcm4che /home/kaapana/dcm4che
sudo cp -r /home/kaapana_0.1.3/postgres-dcm4che /home/kaapana/postgres-dcm4che
sudo cp -r /home/kaapana_0.1.3/minio /home/kaapana/minio

  12. Ensure that the permissions for dcm4chee are correct by executing sudo chown -R 1023:1023 /home/kaapana/dcm4che/server_data/

  13. Deploy the Platform again as done in step 8

  14. Login to the platform and check that Store > Minio lists the files from the previous installation and that Store > OHIF shows the studies of the old version of the platform.

  15. To populate the meta-index which is used by the Workflows > Datasets View as well as by all Dashboards under Meta, go to System > Airflow and click the play Button next to the service-re-index-dicom-data DAG. In the Popup menu select the “Trigger DAG” Option.

  16. Await the successful completion of the service-re-index-dicom-data DAG as well as any service-extract-metadata DAGs. When finished none of this DAGs should have operators in the running or queued state.

  17. Generate the thumbnails (used as preview images in the Datasets view):

    1. Open the code-server from the Extensions view.

    2. In file mounted/workflows/dags/dag_service_segmentation_thumbnail.py set ui_visible from False to True. This change may take 2-3 minutes to be visible in the frontend.

      https://codebase.helmholtz.cloud/-/project/2521/uploads/58bc36bb3215c0efe5856e5155cb242a/image.png

    3. In the Workflows > Dataset view click on RTSTRUCT and SEG in the Dashboard on the right side to add both to the filters, then click the SEARCH button so that all RTSTRUCT and SEG objects are selected.

    4. Click the Play button and select the service-segmentation-thumbnail workflow and trigger it.

    5. After the service-segmentation-thumbnail is completed and the thumbnails have been generated reset the ui_visible of the service-segmentation-thumbnail from False to True again.

  18. When everything works in the new version the old data can be deleted using: sudo rm -rf /home/kaapana_0.1.3