HAPI FHIR Data

FHIR messages Backup & Restore.

Validated messages from HAPI FHIR will be stored in PostgreSQL database.

The following content will detail the backup and restore process of this data.

Backups

This section assumes Postgres backups are made using pg_basebackup

Postgres (Hapi-FHIR)

To start up HAPI FHIR and ensure that the backups can be made, ensure that you have created the HAPI FHIR bind mount directory (eg./backup)

Disaster Recovery

NB! DO NOT UNTAR OR EDIT THE FILE PERMISSIONS OF THE POSTGRES BACKUP FILE

Postgres (HAPI FHIR)

Preliminary steps:

1. Do a destroy of fhir-datastore-hapi-fhir using the CLI binary (./platform-linux for linux)

2. Make sure the Postgres volumes on nodes other than the swarm leader have been removed as well! You will need to ssh into each server and manually remove them.

3. Do an init of fhir-datastore-hapi-fhir using the CLI binary

After running the preliminary steps, run the following commands on the node hosting the Postgres leader:

NOTE: The value of the REPMGR_PRIMARY_HOST variable in your .env file indicates the Postgres leader

1. Retrieve the Postgres leader's container-ID using: docker ps -a. Hereafter called postgres_leader_container_id

2. Run the following command: docker exec -t <postgres_leader_container_id> pg_ctl stop -D /bitnami/postgresql/data

3. Wait for the Postgres leader container to die and start up again. You can monitor this using: docker ps -a

4. Run the following command: docker rm <postgres_leader_container_id>

5. Retrieve the new Postgres leader's container-ID using docker ps -a, be weary to not use the old postgres_leader_container_id

6. Retrieve the Postgres backup file's name as an absolute path (/backups/postgresql_xxx). Hereafter called backup_file

7. Run the following commands in the order listed :

   # Stop the server running in the container
   docker exec -t <postgres_leader_container_id> pg_ctl stop -D /bitnami/postgresql/data
   
   # Clear the contents of /bitnami/postgresql/data
   docker exec -t --user root <postgres_leader_container_id> sh -c 'cd /bitnami/postgresql/data && rm -rf $(ls)'
   
   # Copy over the base.tar file
   sudo docker cp <backup_file>/base.tar <postgres_leader_container_id>:/bitnami/postgresql
   
   # Extract the base.tar file
   docker exec -t --user root <postgres_leader_container_id> sh -c 'tar -xf /bitnami/postgresql/base.tar --directory=/bitnami/postgresql/data'
   
   # Copy over the pg_wal.tar file
   sudo docker cp <backup_file>/pg_wal.tar <postgres_leader_container_id>:/bitnami/postgresql
   
   # Extract pg_wal.tar
   docker exec -t --user root <postgres_leader_container_id> sh -c 'tar -xf /bitnami/postgresql/pg_wal.tar --directory=/bitnami/postgresql/data/pg_wal'
   
   # Copy conf dir over
   docker exec -t --user root <postgres_leader_container_id> sh -c 'cp -r /bitnami/postgresql/conf/. /bitnami/postgresql/data'
   
   # Set pg_wal.tar permissions
   docker exec -t --user root <postgres_leader_container_id> sh -c 'cd /bitnami/postgresql/data/pg_wal && chown -v 1001 $(ls)'
   
   # Start the server
   docker exec -t <postgres_leader_container_id> pg_ctl start -D /bitnami/postgresql/data

8. Do a down of fhir-datastore-hapi-fhir using the CLI binary Example: ./instant-linux package down -n=fhir-datastore-hapi-fhir --env-file=.env.*

9. Wait for the down operation to complete

10. Do an init of fhir-datastore-hapi-fhir using the CLI binary Example: ./instant-linux package init -n=fhir-datastore-hapi-fhir --env-file=.env.*

Postgres should now be recovered

Note: After performing the data recovery, it is possible to get an error from HAPI FHIR (500 internal server error) while the data is still being replicated across the cluster. Wait a minute and try again.