Skip to content

Latest commit

 

History

History
119 lines (77 loc) · 4.23 KB

Orthanc.md

File metadata and controls

119 lines (77 loc) · 4.23 KB

Orthanc

free and open-source, lightweight DICOM server for medical imaging from Belgium.

GitHub

Migration

Start the application:

get Docker Compose from Orthanc Team


git clone https://github.com/orthanc-server/orthanc-setup-samples.git
cd orthanc-setup-samples/docker/postgresql

Modify the following in the Docker Compose file:

  • Add yb to the host list to connect to the YugabyteDB database when we stop the PostgreSQL one and start PostgreSQL (orthanc-index) and Orthanc (orthanc);
sed -e '/depends_on/s/^/#/'                -i docker-compose.yml
sed -e '/Host/s/orthanc-index/&,yb/'       -i docker-compose.yml
git diff
docker compose up -d orthanc-index
docker compose up -d orthanc

Test the application:

Run the application (Orthanc Explorer 2) on http://localhost:8042/ui/app/index.html#/

Upload some DICOM files. You can get some 💀 from in https://medimodel.com/wp-content/uploads/2021/03/2_skull_ct.zip (unzip and upload the DICOM directory)

image

Stop the application


docker compose stop orthanc

Start YugabyteDB

Add YugabyteDB service to docker compose:


  yb:
    image: yugabytedb/yugabyte:2.25.0.0-b489
    command: bash -c 'rm -rf /tmp/.yb.* ; yugabyted start --ysql_port=5432 --enable_pg_parity_early_access --background=false --tserver_flags=ysql_colocate_database_by_default=true'
    ports:
      - 15433:15433

Start YugabyteDB

Use the same database name, user and password, and also the same port 5432 so that there's no confict to change except the host name


docker compose up -d yb

Migrate with YugabyteDB Voyager

Start a container with the YugabyteDB voyager image and run the migration steps (the database is installed in the default database postgres)


docker run -it --rm --name ybv --network postgresql_default --link postgresql-orthanc-index-1:pg --link postgresql-yb-1:yb \
 yugabytedb/yb-voyager:1.8.9.1 \
 bash -xc '
yb-voyager assess-migration --export-dir /var/tmp --start-clean=true --source-db-host pg --source-db-user postgres --source-db-password postgres --source-db-name postgres --source-db-schema public --source-db-type postgresql --iops-capture-interval 0 <<<Y
cat /var/tmp/assessment/reports/migration_assessment_report.json
yb-voyager export schema    --export-dir /var/tmp --start-clean=true --source-db-host pg --source-db-user postgres --source-db-password postgres --source-db-name postgres --source-db-schema public --source-db-type postgresql
yb-voyager analyze-schema   --export-dir /var/tmp
cat /var/tmp/reports/schema_analysis_report.json
yb-voyager import schema    --export-dir /var/tmp                    --target-db-host yb --target-db-user postgres --target-db-password postgres --target-db-name postgres --target-db-port=5432 --target-db-schema public <<<Y 
yb-voyager export data      --export-dir /var/tmp --start-clean=true --source-db-host pg --source-db-user postgres --source-db-password postgres --source-db-name postgres --source-db-schema public --source-db-type postgresql
yb-voyager import data      --export-dir /var/tmp                    --target-db-host yb --target-db-user postgres --target-db-password postgres --target-db-name postgres --target-db-port=5432
PGPASSWORD=password psql -h yb -p 5432 -U postgres -c 'analyze' postgres      
'

Stop PostgreSQL and start the application with YugabyteDB


# Stop PostgreSQL
docker compose stop orthanc-index 

# Start Orthanc
docker compose start orthanc

docker compose logs orthanc

It fails with:

postgresql-orthanc-1  | W0830 20:27:45.380556             MAIN PluginsManager.cpp:158] An SQL transaction failed and
will likely be retried: ERROR:  advisory locks are not yet implemented
postgresql-orthanc-1  | HINT:  See https://github.com/yugabyte/yugabyte-db/issues/3642. React with thumbs up to raise its priority

Note the config file (/tmp/orthanc.json) already has "Lock": false (doc)

As the advisory lock prevents multiple Orthanc instances on the same database, it is safe to add ysql_suppress_unsupported_error=true in the tserver_flags comma-separated list.