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SERVER_UPDATE.md

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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

Note: At some versions it is mandatory to switch to a new Payara Server. If your version bump does apply to the listing below, please proceed with Payara migration.

  • Switching from <=v1.66.4 to v1.67.0 or newer

Note: You can skip this step if you've just set up your SORMAS server and have already downloaded the latest release.

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

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

Upgrading from Keycloak 12 to 16 following the steps from here https://www.keycloak.org/docs/16.1/upgrading/#_upgrading

16.1.0 doesn't provide a way to upgrade host based installations as there were a lot of changes due to the Wildfly update https://www.keycloak.org/docs/16.1/upgrading/#migrating-to-16-0-0

To update follow this steps:

  1. Prerequisites
  • Backup the DB
  • Backup the current Keycloak configuration
  • Download 16.1.0 zip from https://www.keycloak.org/downloads
  • Extract everything from the archive somewhere on your disk (will call this KEYCLOAK_HOME_16)
  1. From you current installation (will call this KEYCLOAK_HOME_12) directory copy the following into the new installation
  • Copy directory KEYCLOAK_HOME_12/themes/sormas over to KEYCLOAK_HOME_16/themes
  • Copy directory KEYCLOAK_HOME_12/modules/system/layers/keycloak/org/postgresql over into KEYCLOAK_HOME_16/modules/system/layers/keycloak/org
  • Copy KEYCLOAK_HOME_12/standalone/deployments/sormas-keycloak-service-provider-*.jar over to KEYCLOAK_HOME_16/standalone/deployments
  1. Edit the KEYCLOAK_HOME_16/standalone/configuration/standalone.xml
  • Search for java:jboss/datasources/KeycloakDS and you should find something like this
<datasource jndi-name="java:jboss/datasources/KeycloakDS" pool-name="KeycloakDS" enabled="true" use-java-context="true" statistics-enabled="${wildfly.datasources.statistics-enabled:${wildfly.statistics-enabled:false}}">
  • Replace it's content with the content from KEYCLOAK_HOME_12/standalone/configuration/standalone.xml and you should end up with something like this
<datasource jndi-name="java:jboss/datasources/KeycloakDS" pool-name="KeycloakDS" enabled="true" use-java-context="true" statistics-enabled="${wildfly.datasources.statistics-enabled:${wildfly.statistics-enabled:false}}">
    <connection-url>jdbc:postgresql://host:5432/keycloak-db-name</connection-url>
    <driver>postgresql</driver>
     <pool>
         <max-pool-size>20</max-pool-size>
     </pool>
     <security>
          <user-name>keycloak-db-username</user-name>
          <password>keycloak-db-password</password>
      </security>
 </datasource>
  • Make sure that you replace keycloak-db-name, keycloak-db-username and keycloak-db-password with your actual values
  • In the section <drivers> bellow, add also this option
<driver name="postgresql" module="org.postgresql">
    <xa-datasource-class>org.postgresql.xa.PGXADataSource</xa-datasource-class>
</driver>
  • You should end up with something like this
<drivers>
    <driver name="postgresql" module="org.postgresql">
        <xa-datasource-class>org.postgresql.xa.PGXADataSource</xa-datasource-class>
    </driver>
    <driver name="h2" module="com.h2database.h2">
        <xa-datasource-class>org.h2.jdbcx.JdbcDataSource</xa-datasource-class>
    </driver>
</drivers>
  1. Start Keycloak
  • Database will be migrated automatically

Upgrading from Keycloak 11 to 12 following the steps from here https://www.keycloak.org/docs/12.0/upgrading/#_upgrading

  1. Stop the old server and make sure to remove any open connections to the DB
  2. Backup the DB (once the upgrade is done the old version cannot be used with the new DB version)
  3. Backup the old installation
  4. Remove ${OLD_KEYCLOAK_HOME}/standalone/data/tx-object-store/
  5. Download the new Keycloak installation from https://www.keycloak.org/downloads
  6. Copy the ${NEW_KEYCLOAK_HOME}/standalone/ directory from the previous installation over the directory in the new installation
  7. Copy the postgres module from ${OLD_KEYCLOAK_HOME}/modules/system/layers/keycloak/org/ over to the new installation directory
  8. Copy the SORMAS themes from {OLD_KEYCLOAK_HOME}/themes/ over to the new installation directory
  9. While the new installation is stopped, run ${NEW_KEYCLOAK_HOME}/bin/jboss-cli.sh ----file=${NEW_KEYCLOAK_HOME}/bin/migrate-standalone.cli (.bat for Windows)
  10. Start the new Keycloak installation from ${NEW_KEYCLOAK_HOME}/bin/standalone.sh (.bat for Windows)

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 existing domain

# Stop domain
service payara-sormas stop

# Move 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.