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Installing a SORMAS Server

Note: This guide explains how to set up a SORMAS server on Linux and Windows systems, the latter only being intended for usage on development systems. Please also note that certain parts of the setup script will not be executed on Windows.

Content

Related

Prerequisites

Java 11

Download and install the Java 11 JDK (not JRE) for your operating system. We suggest using the Zulu OpenJDK.

Linux

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xB1998361219BD9C9
sudo apt-add-repository 'deb https://repos.azul.com/zulu/deb/ stable main'
sudo apt-get update
sudo apt-get install zulu11

Windows

For testing and development environments we suggest to download and run the installer of the Java 11 JDK for 32 or 64 bit client systems (depending on your system). You can check your Java version from the shell/command-line using: java -version.

Postgres Database

  • Install PostgreSQL (currently 14 to 15) on your system (manuals for all OS can be found here: https://www.postgresql.org/download)
  • Set max_connections = 288 and max_prepared_transactions = 256 (at least, sum of all connection pools) in postgresql.conf (e.g. /etc/postgresql/14.0/main/postgresql.conf; C:/Program Files/PostgreSQL/14.0/data) - make sure the property is uncommented and restart the service to apply the changes.
  • Install the "temporal tables" extension for Postgres (https://github.com/arkhipov/temporal_tables)
    • Windows: Download the latest version for your Postgres version:
    • Linux (see https://github.com/arkhipov/temporal_tables#installation) 
      sudo apt-get install libpq-dev
sudo apt-get install postgresql-server-dev-all
sudo apt install pgxnclient
#Check for GCC:
gcc --version # and install if missing
sudo pgxn install temporal_tables
# The packages can be removed afterward
      • Add the PostgreSQL path (/etc/PostgreSQL/10/bin) to Environment Variables

SORMAS Server

Get the latest SORMAS build by downloading the ZIP archive from the latest release on GitHub: https://github.com/sormas-foundation/SORMAS-Project/releases/latest

Install on Linux

Unzip the archive, copy/upload its contents to /root/deploy/sormas/$(date +%F) and make the setup script executable (as root user).

sudo su
mkdir -p /root/deploy/sormas
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
chmod +x $(date +%F)/server-setup.sh

Install on Windows

  • Download & install Git for Windows. This will provide a bash emulation that you can use to run the setup script: https://gitforwindows.org/
  • Unzip the ZIP archive (e.g. into you download directory)
  • Open Git Bash and navigate to the setup sub-directory

Auditing

You can configure the audit logger of SORMAS by providing a Logback configuration file and setting the audit.logger.config property accordingly. An example is provided in sormas-base/setup/audit-logback.xml. Not specifying a value for the property will effectively disable the audit log.

Sormas installation

  • Optional: Open server-setup.sh in a text editor to customize the install paths, database access and ports for the server. The default ports are 6080 (HTTP), 6081 (HTTPS) and 6048 (admin). Important: Do not change the name of the database user. The predefined name is used in the statements executed in the database.
  • Set up the database and a Payara domain for SORMAS by executing the setup script: sudo -s ./server-setup.sh Press enter whenever asked for it
  • IMPORTANT: Make sure the script executed successfully. If anything goes wrong you need to fix the problem (or ask for help), then delete the created domain directory and re-execute the script.
  • IMPORTANT: Adjust the SORMAS configuration for your country in /opt/domains/sormas/sormas.properties
  • Adjust the logging configuration in /opt/domains/sormas/config/logback.xml based on your needs (e.g. configure and activate email appender)
  • Linux: Update the SORMAS domain

Keycloak Server

Note: SORMAS also comes with a basic auth mechanism using an JEE authentication realm. This authentication mechanism should only be used for development environments. For production environments always use the keycloak authentication mechansim. See Authentication & Authorization.

Keycloak can be set up in two ways:

  • as a Docker container (for just using Keycloak approach)
  • as a Standalone installation (for doing development in Keycloak like themes, SPIs)

Keycloak as a Docker container

To be done only in the situation when SORMAS is already installed on the machine as a standalone installation.

For complete Docker setup see the SORMAS-Docker repository.

Prerequisites

  • SORMAS Server is installed
  • PostgreSQL is installed
  • Docker is installed
  • Open and edit sormas-base/setup/keycloak/keycloak-setup.sh with your system's actual values (on Windows use Git Bash).

Setup

  • Run sormas-base/setup/keycloak/keycloak-setup.sh
  • Update sormas.properties file in the SORMAS domain with the property authentication.provider=KEYCLOAK

Keycloak as a standalone installation

Prerequisites

  • SORMAS Server is installed
  • PostgreSQL is installed

Setup

Setting Keycloak up as a standalone installation as described in the Getting started section of the official guide

  • Make sure to configure Keycloak with PostgreSQL Database
  • Set up an Admin User
  • Copy the themes folder content to ${KEYCLOAK_HOME}/themes as described here
  • Deploy the sormas-keycloak-service-provider as described here
  • Update the sormas-base/setup/keycloak/SORMAS.json file by replacing the following placeholders: ${SORMAS_SERVER_URL}, ${KEYCLOAK_SORMAS_UI_SECRET}, ${KEYCLOAK_SORMAS_BACKEND_SECRET}, ${KEYCLOAK_SORMAS_REST_SECRET}
  • Create the SORMAS Realm by importing sormas-base/setup/keycloak/SORMAS.json see Create a New Realm
  • Update the sormas-* clients by generating new secrets for them
  • Update the realm's email settings to allow sending emails to users

To update the SORMAS Server run the following commands:

${ASADMIN} set-config-property --propertyName=payara.security.openid.clientSecret --propertyValue=${KEYCLOAK_SORMAS_UI_SECRET} --source=domain
${ASADMIN} set-config-property --propertyName=payara.security.openid.clientId --propertyValue=sormas-ui --source=domain
${ASADMIN} set-config-property --propertyName=payara.security.openid.scope --propertyValue=openid --source=domain
${ASADMIN} set-config-property --propertyName=payara.security.openid.providerURI --propertyValue=http://localhost:${KEYCLOAK_PORT}/keycloak/auth/realms/SORMAS --source=domain
${ASADMIN} set-config-property --propertyName=sormas.rest.security.oidc.json \
        --propertyValue="{\"realm\":\"SORMAS\",\"auth-server-url\":\"http://localhost:${KEYCLOAK_PORT}/auth\",\"ssl-required\":\"external\",\"resource\":\"sormas-rest\",\"credentials\":{\"secret\":\"${KEYCLOAK_SORMAS_REST_SECRET}\"},\"confidential-port\":0,\"principal-attribute\":\"preferred_username\",\"enable-basic-auth\":true}" \
        --source=domain
${ASADMIN} set-config-property --propertyName=sormas.backend.security.oidc.json --propertyValue="{\"realm\":\"SORMAS\",\"auth-server-url\":\"http://localhost:${KEYCLOAK_PORT}/auth/\",\"ssl-required\":\"external\",\"resource\":\"sormas-backend\",\"credentials\":{\"secret\":\"${KEYCLOAK_SORMAS_BACKEND_SECRET}\"},\"confidential-port\":0}" --source=domain

where:

  • ${ASADMIN} - represents the location to ${PAYARA_HOME}\bin\asadmin
  • ${KEYCLOAK_PORT} - the port on which keycloak will run
  • ${KEYCLOAK_SORMAS_UI_SECRET} - is the secret generated in Keycloak for the sormas-ui client
  • ${KEYCLOAK_SORMAS_REST_SECRET} - is the secret generated in Keycloak for the sormas-rest client
  • ${KEYCLOAK_SORMAS_BACKEND_SECRET} - is the secret generated in Keycloak for the sormas-backend client

Then update sormas.properties file in the SORMAS domain with the property authentication.provider=KEYCLOAK

Connect Keycloak to an already running instance of SORMAS

after setting up Keycloak as one of the described options above

In case Keycloak is set up alongside an already running instance of SORMAS, these are the steps to follow to make sure already existing users can access the system:

  1. Manually create an admin user in Keycloak for the SORMAS realm Creating a user (username has to be the same as admin's username in SORMAS)
  2. If your server is not using SSL (e.g. because it's a development environment), you need to update the Root URL of the sormas-ui client in the SORMAS realm to use http instead of https
  3. Login to SORMAS and trigger the Sync Users button from the Users page
  4. This will sync users to Keycloak keeping their original password - see SORMAS Keycloak Service Provider for more information about this

Keycloak configuration

More about the default configuration and how to customize can be found here Keycloak

Web Server Setup

Apache Web Server

Note: This is not necessary for development systems. When you are using SORMAS in a production environment you should use a http server like Apache 2 instead of putting the Payara server in the first line. Here are some things that you should do to configure the Apache server as a proxy:

Activate all needed modules:

a2enmod ssl
a2enmod rewrite
a2enmod proxy
a2enmod proxy_http
a2enmod headers

Create a new site /etc/apache2/sites-available/your.sormas.server.url.conf (e.g. sormas.org.conf).

Force SSL secured connections: redirect from http to https:

<VirtualHost *:80>
        ServerName your.sormas.server.url
        RewriteEngine On
        RewriteCond %{HTTPS} !=on
        RewriteRule ^/(.*) https://your.sormas.server.url/$1 [R,L]
</VirtualHost>
<IfModule mod_ssl.c>
<VirtualHost *:443>
        ServerName your.sormas.server.url
        ...
</VirtualHost>
</IfModule>

Configure logging:

ErrorLog /var/log/apache2/error.log
LogLevel warn
LogFormat "%h %l %u %t \"%r\" %>s %b _%D_ \"%{User}i\"  \"%{Connection}i\"  \"%{Referer}i\" \"%{User-agent}i\"" combined_ext
CustomLog /var/log/apache2/access.log combined_ext

SSL key config:

SSLEngine on
SSLCertificateFile    /etc/ssl/certs/your.sormas.server.url.crt
SSLCertificateKeyFile /etc/ssl/private/your.sormas.server.url.key
SSLCertificateChainFile /etc/ssl/certs/your.sormas.server.url.ca-bundle

# disable weak ciphers and old TLS/SSL
SSLProtocol all -SSLv3 -TLSv1 -TLSv1.1
SSLCipherSuite ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256:ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:DHE$
SSLHonorCipherOrder off

Add a proxy pass to the local port:

ProxyRequests Off
ProxyPass /sormas-ui http://localhost:6080/sormas-ui
ProxyPassReverse /sormas-ui http://localhost:6080/sormas-ui
ProxyPass /sormas-rest http://localhost:6080/sormas-rest
ProxyPassReverse /sormas-rest http://localhost:6080/sormas-rest

Configure security settings:

Header always set X-Content-Type-Options "nosniff"
Header always set X-Xss-Protection "1; mode=block"
# Disable Caching
Header always set Cache-Control "no-cache, no-store, must-revalidate, private"
Header always set Pragma "no-cache"

Header always set Content-Security-Policy \
        "default-src 'none'; \
        object-src 'self'; \
        script-src 'self' 'unsafe-inline' 'unsafe-eval'; \
        connect-src https://fonts.googleapis.com https://fonts.gstatic.com 'self'; \
        img-src *; \
        style-src 'self' https://fonts.googleapis.com 'unsafe-inline'; \
        font-src https://fonts.gstatic.com 'self'; \
        frame-src 'self'; \
        worker-src 'self'; \
        manifest-src 'self'; \
        frame-ancestors 'self'

# The Content-Type header was either missing or empty.
# Ensure each page is setting the specific and appropriate content-type value for the content being delivered.
AddType application/vnd.ms-fontobject    .eot
AddType application/x-font-opentype      .otf
AddType image/svg+xml                    .svg
AddType application/x-font-ttf           .ttf
AddType application/font-woff            .woff

Activate output compression (very important!):

<IfModule mod_deflate.c>
        AddOutputFilterByType DEFLATE text/plain text/html text/xml
        AddOutputFilterByType DEFLATE text/css text/javascript
        AddOutputFilterByType DEFLATE application/json
        AddOutputFilterByType DEFLATE application/xml application/xhtml+xml
        AddOutputFilterByType DEFLATE application/javascript application/x-javascript
        DeflateCompressionLevel 1
</IfModule>

Provide the Android apk:

Options -Indexes
AliasMatch "/downloads/sormas-(.*)" "/var/www/sormas/downloads/sormas-$1"

For the Apache 2 security configuration we suggest the following settings (/etc/apache2/conf-available/security.conf):

ServerTokens Prod
ServerSignature Off
TraceEnable Off

Header always set Strict-Transport-Security "max-age=15768000; includeSubDomains; preload"
Header unset X-Frame-Options
Header always set X-Frame-Options SAMEORIGIN
Header unset Referrer-Policy
Header always set Referrer-Policy "same-origin"
Header edit Set-Cookie "(?i)^((?:(?!;\s?HttpOnly).)+)$" "$1;HttpOnly"
Header edit Set-Cookie "(?i)^((?:(?!;\s?Secure).)+)$" "$1;Secure"

Header unset X-Powered-By
Header unset Server
  • In case you need to update the site config while the server is running, use the following command to publish the changes without the need for a reload:
apache2ctl graceful

Firewall

  • The server should only publish the ports that are needed. For SORMAS this is port 80 (HTTP) and 443 (HTTPS). In addition you will need the SSH port to access the server for admin purposes.
  • We suggest to use UFW (Uncomplicated Firewall) which provides a simple interface to iptables:
sudo apt-get install ufw
sudo ufw default deny incoming
sudo ufw default allow outgoing
sudo ufw allow ssh
sudo ufw allow http
sudo ufw allow https
sudo ufw enable

Postfix Mail Server

Install postfix and mailutils

apt install aptitude
aptitude install postfix
-> choose "satelite system"
apt install mailutils

Configure your system

nano /etc/aliases
-> add "root: enter-your@support-email-here.com"
nano /opt/domains/sormas/config/logback.xml
-> make sure "EMAIL_ERROR" appender is active and sends out to your email address

Testing the Server Setup

Use SSL Labs to test your server security config: https://www.ssllabs.com/ssltest

R Software Environment

In order to enable disease network diagrams in the contact dashboard, R and several extension packages are required. Then the Rscript executable has to be configured in the sormas.properties file. This can be conveniently accomplished by executing the R setup script from the SORMAS ZIP archive (see SORMAS Server):

  • If the SORMAS installation has been customized, r-setup.sh the install paths may have to be adjusted accordingly with a text editor.
  • Execute R setup script and follow its instructions.
chmod +x r-setup.sh
./r-setup.sh

SORMAS to SORMAS Certificate Setup

To be able to communicate with other SORMAS instances, there are some additional steps which need to be taken, in order to set up the certificate and the truststore. Please see the related guide for detailed instructions regarding SORMAS to SORMAS setup.

Troubleshooting

Problem: Login fails

Check that the users table does have a corresponding entry. If not, the database initialization that is done when deploying sormas-ear.ear probably had an error.

Problem: Server is out of memory

Old servers were set up with a memory size of less than 2048MB. You can change this using the following commands:

/opt/payara-172/glassfish/bin/asadmin --port 6048 delete-jvm-options -Xmx512m
/opt/payara-172/glassfish/bin/asadmin --port 6048 delete-jvm-options -Xmx1024m
/opt/payara-172/glassfish/bin/asadmin --port 6048 create-jvm-options -Xmx2048m

Alternative: You can edit the settings directly in the domain.xml in the config directory of the SORMAS domain. Just search for Xmx - there should be two entries that need to be changed.