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FHIR BLOBs

Hapi-fhir-jpaserver is used alongside OpenELIS to provide FHIR support. Older versions of the project made extensive use of the Postgres BLOB data type. This data type cannot be handled in the same way as "normal" Postgres data types. Because of this, upgrading a large DB with many BLOBs takes a long time, is very memory intensive, and is prone to failing if enough memory isn't available. Due to these reasons, it is recommended to upgrade your hapi-fhir-jpaserver to at least 6.6.0 before upgrading your DB, so you can run the reindex command which moves all resources (smaller than a configurable limit) into the normal table structure.

Instructions for updating FHIR BLOBs

  1. Stop the existing containers besides the database

    1. sudo docker stop openelisglobal-webapp autoheal-oe external-fhir-api
  2. Collect metrics around the data to see what you're working with

    1. sudo docker exec -it openelisglobal-database psql -Uclinlims

    2. SELECT COUNT(*) FROM clinlims.hfj_res_ver;

    3. SELECT pg_table_size('pg_largeobject');

  3. Run the script for upgrading hapi-fhir-jpaserver data structure in the database

    1. wget https://github.com/hapifhir/hapi-fhir/releases/download/v6.2.0/hapi-fhir-6.2.0-cli.tar.bz2

    2. bzip2 -d hapi-fhir-6.2.0-cli.tar.bz2

    3. tar xf hapi-fhir-6.2.0-cli.tar

    4. ./hapi-fhir-cli migrate-database -d POSTGRES_9_4 -u "jdbc:postgresql://localhost:15432/clinlims currentSchema=clinlims" -n "clinlims" --no-column-shrink -p <password>

  4. Collect metrics around the data to see that data loss has not occurred

    1. sudo docker exec -it openelisglobal-database psql -Uclinlims

    2. SELECT COUNT(*) FROM clinlims.hfj_res_ver;

    3. SELECT pg_table_size('pg_largeobject');

  5. Run 2.7 OE installer

    1. wget <online-path-to-2.7-installer>

    2. tar -xzf <installer-tar.gz>

    3. cd <installer-dir>

    4. sudo python3 OpenELIS.py

    5. No to logical db backup, docker cleans, and backup script

  6. Modify the docker-compose.yml

    1. Change db container image from 14.4 to 9.5
  7. Start the containers. From this point until the db migration is started, these commands can be run in the background while normal use of the application(s) goes ahead

    1. sudo docker-compose up -d
  8. Create files to submit to the updated FHIR store to trigger a reindex of the various data types from BLOBs to regular column data. Resource types that are commonly used, leading to the bulk of the BLOBs are: Task, Patient, ServiceRequest, DiagnosticReport, Observation, Specimen, Practitioner, Organization, Location, QuestionnaireResponse

    { "resourceType": "Parameters", "parameter": [ { "name": "url", "valueString": "<ResourceType>?" }, { "name": "optimizeStorage", "valueString": "ALL_VERSIONS" } ] }

  9. Send each optimize request as a POST request to the FHIR server (detailed instructions for making POST requests to the FHIR server can be found here)

    1. sudo curl -X POST -H "Content-Type: application/json" -d '@task-optimize.json' --cert /etc/openelis-global/cert.pem --key /etc/openelis-global/key.pem -k 'https://localhost:8444/fhir/$reindex'
  10. Wait for the reindexes to succeed (checking the logs of the FHIR container should give some indication that they are running or not)

  11. Run the vacuum lob command to clean up the database (first run is a test)

    1. sudo docker exec -it openelisglobal-database vacuumlo -Uclinlims --dry-run

    2. sudo docker exec -it openelisglobal-database vacuumlo -Uclinlims

  12. Collect metrics around the data to see that data loss has not occurred. The pg_largeobject should be MUCH smaller, but hfj_res_ver should be similar to before.

    1. sudo docker exec -it openelisglobal-database psql -Uclinlims

    2. SELECT COUNT(*) FROM clinlims.hfj_res_ver;

    3. SELECT pg_table_size('pg_largeobject');

  13. Run the pg_upgrade as in the "Migrate with pg_upgrade" section below

  14. Collect metrics around the data to see that data loss has not occurred.

    1. sudo docker exec -it openelisglobal-database psql -Uclinlims

    2. SELECT COUNT(*) FROM clinlims.hfj_res_ver;

    3. SELECT pg_table_size('pg_largeobject');

Migrate with pg_upgrade

Much faster method of upgrading postgres dbs

If you are running these commands on a remote server, it is recommended to use a recoverable script session. For example, running screen. If you disconnect, just reconnect and run screen -x to recover active session.

NOTES:

  1. It is paramount that data backups are up to date and recovery is tested before attempting a database migration.

  2. This can be a very memory intensive process. It is recommended to increase memory on the server that this is running on to 128 GB or more. This can be accomplished without too much of a performance hit by adding an SSD as a swap drive.

  3. This process doesn't delete the old database files until the new database is up, running, and tested. Ensure that OE is running properly and the data is there BEFORE deleting the old machine.

  4. Because of point number 3, you will require room on the server for a copy of all the database files located at /var/lib/openelis-global/data

Migrating OE 9.5 database to 14.4 database in dockerized environments

  1. stop containers so no changes happen while migration is occurring

    1. sudo docker stop autoheal-oe external-fhir-api openelisglobal-webapp openelisglobal-database
  2. remove db container so auto restart doesn’t occur

    1. sudo docker rm openelisglobal-database1.
  3. create folders for first step db migration to take place (this can be done on a separate machine with docker installed if the main server lacks resources to run the upgrade).

    1. sudo mkdir /var/lib/openelis-global/db

    2. sudo mkdir /var/lib/openelis-global/db/9.5

    3. sudo mkdir /var/lib/openelis-global/db/14

    4. sudo mkdir /var/lib/openelis-global/db/14/data

  4. copy current db to the upgrade location (copy will preserve the old data so that we can more easily revert if something goes wrong)

    1. If you are performing the upgrade on the machine where the database is installed:

      1. sudo cp -r /var/lib/openelis-global/data /var/lib/openelis-global/db/9.5/data
    2. If you are performing the upgrade on another machine where the database is not installed:

      1. sudo tar cf /var/lib/openelis-global/data.tar.gz -C /var/lib/openelis-global/ data

      2. sudo scp /var/lib/openelis-global/data.tar.gz username@destination:/var/lib/openelis-global/db/9.5/data.tar.gz

      3. ssh username@destination

      4. tar xzf /var/lib/openelis-global/db/9.5/data.tar.gz -C /var/lib/openelis-global/db/9.5/

  5. run the 9.5 to 14 migration

    1. sudo docker pull ctsteele/postgres-migration:9.5-14

    2. sudo docker run -it --rm -v /var/lib/openelis-global/db/:/var/lib/postgresql/ ctsteele/postgres-migration:9.5-14 --link

  6. replace old db with new db

    1. sudo mv /var/lib/openelis-global/data /var/lib/openelis-global/data2

    2. sudo mv /var/lib/openelis-global/db/14/data /var/lib/openelis-global/data

  7. ensure file permissions and db access permissions are correct

    1. sudo chown -R tomcat2:tomcat2 /var/lib/openelis-global/data

    2. edit /var/lib/openelis-global/data/pg_hba.conf to include all the same entries that are in /var/lib/openelis-global/data2/pg_hba.conf

  8. run the setup script for the new version with updated db, ignoring db backup couldn’t occur step

    1. sudo python3 setup_OpenELIS.py
  9. ensure systems start up and that data is present

  10. optionally delete old db (or move to a secure backup server)

    1. sudo rm /var/lib/openelis-global/db /var/lib/openelis-global/data2

Migrating OE 9.5 database to 14.4 database in non dockerized environment into dockerized environment (untested)

  1. stop containers so no changes happen while migration is occurring

    1. sudo docker stop autoheal-oe external-fhir-api openelisglobal-webapp
  2. stop postgres instance

    1. sudo -upostgres /usr/lib/postgresql/9/bin/pg_ctl -D /var/lib/postgresql/9/data -l logfile stop
  3. check that upgrade can occur

    1. time /usr/lib/postgresql/14/bin/pg_upgrade --old-bindir /usr/lib/postgresql/9/bin --new-bindir /usr/lib/postgresql/14/bin --old-datadir /var/lib/postgresql/9/data --new-datadir /var/lib/openelis-global/data --link --check
  4. run the upgrade

    1. time /usr/lib/postgresql/14/bin/pg_upgrade --old-bindir /usr/lib/postgresql/9/bin --new-bindir /usr/lib/postgresql/14/bin --old-datadir /var/lib/postgresql/9/data --new-datadir /var/lib/openelis-global/data --link
  5. run the setup script for the new version with updated db, ignoring db backup couldn’t occur step

    1. sudo setup_OpenELIS.py
  6. ensure systems start up and that data is present

Migrate with pg_dump

This approach is mentioned as being the preferred option in postgres docs, but is VERY slow when restoring BLOBs

Migrating OE 9.5 database to 14.4 database in dockerized environments

  1. Run the following commands to create the backup for restoring into OE 14, and the backup for 9.5 in case something goes wrong

    1. sudo docker exec openelisglobal-database pg_dump -j 8 -d clinlims --verbose -U admin -F c -f /backups/95db.backup

    2. sudo docker kill openelisglobal-database && sudo mv /var/lib/openelis-global/data /var/lib/openelis-global/data2

  2. install new OE with setup script - ignore db missing when prompted

  3. Run the following to pause non-db connections and restore the backup before bringing the containers up again (must run in OE installer directory). Restoring a db can take a long time for large dbs. To avoid a long downtime, this can be done in a separate container

    1. sudo docker kill external-fhir-api openelisglobal-webapp && sudo docker rm external-fhir-api openelisglobal-webapp

    2. sudo docker exec openelisglobal-database pg_restore -j 8 -d clinlims -U postgres -v -Fc -c /backups/95db.backup

    3. sudo docker-compose up -d

  4. confirm that OpenELIS is working and that the data is there by accessing the front end

  5. optionally, delete old data

    1. rm /var/lib/openelis-global/data2

    2. rm /var/lib/openelis-global/backups/95db.backup

Migrating OE 9.5 database to 14.4 database in non dockerized environment into dockerized environment (untested)

  1. Run the following commands to create the backup for restoring into OE 14

    1. pg_dump -d clinlims -h localhost -p 5432 –verbose -U clinlims -F c -f /var/lib/openelis-global/backups/95db.backup

    2. [enter password for clinlims]

  2. Modify setup.ini to have docker db on port other than 5432 and use docker db

    1. sudo vi /etc/openelis-global/setup.ini
  3. install new OE with setup script

  4. Run the following to pause non-db connections and restore the backup before bringing the containers up again (must run in OE installer directory)

    1. sudo docker kill external-fhir-api openelisglobal-webapp && sudo docker rm external-fhir-api openelisglobal-webapp

    2. sudo docker exec openelisglobal-database pg_restore -d clinlims -U postgres -v -Fc -c /backups/95db.backup

    3. sudo docker-compose up -d

  5. confirm that OpenELIS is working and that the data is there by accessing the front end

  6. optionally, delete old data

    1. sudo rm /var/lib/openelis-global/backups/95db.backup
  7. uninstall native postgres if you want to move the docker db onto port 5432