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Updating a SORMAS Server

SORMAS releases starting from 1.21.0 contain a script that automatically updates and deploys the server. If you are using an older version and therefore need to do a manual server update, please download the 1.21.0 release files and use the commands specified in the server-update.sh script.

Preparations

  • Get the latest release files (deploy.zip) from https://github.com/sormas-foundation/SORMAS-Project/releases/latest
  • Unzip the archive and copy/upload its contents to /root/deploy/sormas/$(date +%F) 
    cd /root/deploy/sormas
SORMAS_VERSION=1.y.z
wget https://github.com/sormas-foundation/SORMAS-Project/releases/download/v${SORMAS_VERSION}/sormas_${SORMAS_VERSION}.zip
unzip sormas_${SORMAS_VERSION}.zip
mv deploy/ $(date +%F)
rm sormas_${SORMAS_VERSION}.zip

Breaking Updates

The following is a list of version that have breaking changes in the update. You only have to consider this if you are coming from an earlier version. For fresh installs, this is not relevant.

1.67.0

Coming from 1.66.4 or earlier, you have to update the payara server, as explained in the Payara migration.

1.73.0

Deploying this release will clear the userrolesconfig and userrole_userrights tables and overwrite them with the default user role configurations of SORMAS. If you added entries to these tables in order to customize the user roles on your system, please run the following queries before deploying this release in order to prevent data loss:

-- Retrieve all customized roles
SELECT * FROM userrolesconfig;
 
-- Overridden rights for roles
SELECT c.userrole, ur.userright FROM userroles_userrights ur LEFT JOIN userrolesconfig c (ON c.id = ur.userrole_id);

After deploying the new version, the information retrieved from these queries can be used to alter the new user role configurations accordingly.

1.81.0

The temporal tables extension is replaced during the deployment of the backend. As a preparation the following SQL needs to be executed on the SORMAS database using the postgres user.

-- versioning function will be replaced during server backend startup
ALTER FUNCTION public.versioning() OWNER TO sormas_user;

After the successful deployment, you need to run the following SQL to get rid of the no longer used extension - otherwise the versioning function will not correctly be part of backups.

-- needed because `ALTER FUNCTION ... NO DEPENDS ON EXTENSION` is not possible in Postgres 10 and below
DELETE FROM pg_depend
WHERE deptype = 'e'
  AND refobjid = (SELECT oid FROM pg_extension WHERE extname = 'temporal_tables')
  and objid = (SELECT oid FROM pg_proc WHERE proname = 'versioning');

DROP EXTENSION IF EXISTS temporal_tables;

1.85.0

Payara is updated from 5.2021.10 to 5.2022.5. If you are not using SORMAS-Docker, please follow the Payara migration guide.

Automatic Server Update

  • Navigate to the folder containing the unzipped deploy files: cd /root/deploy/sormas/$(date +%F)
  • Make the update script executable: chmod +x server-update.sh
  • Optional: Open server-update.sh in a text editor to customize the values for e.g. the domain path or the database name. You only need to do this if you used custom values while setting up the server.
  • Execute the update script and follow the instructions: ./server-update.sh
  • If anything goes wrong, open the latest update log file (by default located in the "update-logs" folder in the domain directory) and check it for errors.

Restoring the Database

If anything goes wrong during the automatic database update process when deploying the server, you can use the following command to restore the data:

pg_restore --clean -U postgres -Fc -d sormas_db sormas_db_....dump

Default Logins

These are the default users for most user roles, intended to be used on development or demo systems. In all cases except the admin user, the username and password are identical. Make sure to deactivate them or change the passwords on productive systems.

Admin

Username: admin Password: sadmin

Web users

Surveillance Supervisor: SurvSup Case Supervisor: CaseSup Contact Supervisor: ContSup Point of Entry Supervisor: PoeSup Laboratory Officer: LabOff Event Officer: EveOff National User: NatUser National Clinician: NatClin

Mobile app users

Surveillance Officer: SurvOff Hospital Informant: HospInf Point of Entry Informant: PoeInf

Updating Keycloak

Standalone installation

Follow the official Keycloak upgrade guide.

To update follow this steps:

  1. Prerequisites
  • Backup the DB
  • Backup the current Keycloak configuration
  • Download the 18.0.1 zip from https://www.keycloak.org/downloads
  • Extract everything from the archive somewhere on your disk (will call this KEYCLOAK_HOME_NEW)
  1. From you current installation (will call this KEYCLOAK_HOME_OLD) directory copy the following into the new installation
  • Copy directory KEYCLOAK_HOME_OLD/themes/sormas over to KEYCLOAK_HOME_NEW/themes
  • Copy KEYCLOAK_HOME_OLD/providers/sormas-keycloak-service-provider-*.jar over to KEYCLOAK_HOME_16/providers
  1. Setup Keycloak to use the Database
  2. Start Keycloak
  • Database will be migrated automatically

Docker installation

The docker installation is automatically upgraded to the latest version specified in the Dockerfile.

Prerequisites: Make sure the DB is backed up, because once the upgrade is done the new DB won't be usable with the old version of Keycloak.

For more info see the Keycloak Docker Documentation.

How to migrate to new Payara Server

Step 1: Shutdown and backup existing domain

# Stop domain
service payara-sormas stop

# Move (backup) existing domain
DOMAIN_PATH=/opt/domains
DOMAIN_NAME="sormas"
DOMAIN_BACKUP_NAME="sormas_backup"
mv $DOMAIN_PATH/$DOMAIN_NAME $DOMAIN_PATH/$DOMAIN_BACKUP_NAME

Step 2: Setup Payara domain

Please follow the server setup: Create the payara domain under the same path as before, use the same directory paths and the same database settings.

Step 3: Apply your config file changes

Transfer your settings from sormas.properties, logback.xml or changes in the domain setup. Use the new provided files and copy your changes in, don't reuse old files!

Step 4: Install new SORMAS version

To install the new SORMAS version in the Payara domain, proceed with the automatic update or for developers: Deploy SORMAS via the IDE as usual.

Alternative for development systems

For minor updates of the payara version, you will most often be able to keep the existing domain and only replace the payara server.

  1. Download the needed version of Payara server.
  2. Undeploy all sormas modules from the payara domain and stop the domain.
  3. Replace your payara server in /opt/payara5 (default path) with the downloaded one. Remove the default domain in opt/payara5/glassfish/domains as it is not needed.
  4. Replace the application server in your IDE with the new server. See IDE setup guide
  5. If you are facing any problems, restart your IDE and clean all generated files from the sormas domain.