Main Configuration File

The file OPAL_HOME/conf/ is to be edited to match your server needs.

HTTP Server Configuration

Opal web services and web application user interface can be accessed through HTTP or secured HTTP requests. The HTTP(S) connection ports can be configured.

Property Description
org.obiba.opal.http.port The port to use for listening for HTTP connections. Default value is 8080, -1 to disable.
org.obiba.opal.https.port The port to use for listening for HTTPS connections. Default value is 8443, -1 to disable.
org.obiba.opal.maxIdleTime The maximum time a single read/write HTTP operation can take in millis (default is 30000). See idleTimeout Jetty configuration.
org.obiba.opal.ssl.excludedProtocols Specify the SSL/TLS protocols to be excluded. Usually SSLv3 will be excluded. Use commas for separating multiple protocol names. Default is no protocol is excluded (for legacy reason). See JSSE Provider documentation.
org.obiba.opal.ssl.includedCipherSuites Specify which Cipher Suites to be included. Use commas for separating multiple cipher suites names. Default is all that is available. See JSSE Provider documentation.

The HTTPS server requires a certificate. If none can be found Opal creates a default one to ensure that HTTPS is always available. It should be configured afterward, following the procedure described in HTTPS Configuration.

SSH Server Configuration

Opal is accessible using SSH clients: SFTP is available through SSH connections. The SSH connection port can be configured.

Property Description
org.obiba.opal.ssh.port The port to use for listening for SSH connections. Default value is 8022.

SMTP Server Configuration

Opal is able to send emails to notify that a rapport has been produced. To allow this, it is required to configuration to a SMTP server.

Property Description The SMTP server host name.
org.obiba.opal.smtp.port The SMTP server port number.
org.obiba.opal.smtp.from The “From” email address when sending emails.
org.obiba.opal.smtp.auth A flag to indicated if authentication against SMTP server is required. Allowed values are: true/false. Default is false (usually not required when server is in the same intranet).
org.obiba.opal.smtp.username The SMTP user name to be authenticate (if authentication is activated).
org.obiba.opal.smtp.password The SMTP user password (if authentication is activated).

Apps Configuration

External applications can be discovered or can self-register. The following settings the apps management defaults.

Property Description
apps.registration.token Apps self-registration default token. Default is empty (self-registration not allowed). When configured from Apps administration page, this value is overridden.
apps.registration.include White list rule to accept an app self-registration: (java) regular expression applied to app’s server address. If not defined (default) all apps are filtered-in.
apps.registration.exclude Black list rule to accept an app self-registration: (java) regular expression applied to app’s server address. If not defined (default) no app is filtered-out.
apps.discovery.interval Apps discovery scheduling in milliseconds. Default is 10000.
apps.discovery.rock.hosts Comma separated list of Rock R server URLs to discover on start up. Default is localhost:8085. See also R Server Configuration.

R Server Configuration

Opal is able to perform R queries by talking with a running R server. See the R Server documentation. The properties for connecting to the default Rock R server(s) are the following:

Property Description
rock.default.administrator.username Rock administrator user name. Default is administrator.
rock.default.administrator.password Rock administrator user password. Default is password.
rock.default.manager.username Rock manager user name.
rock.default.manager.password Rock manager user password.
rock.default.user.username Rock regular user name.
rock.default.user.password Rock regular user password.
org.obiba.opal.r.endpoint Enable/disable the plain R web service. When disabled, even the system administrator cannot interact directly with a plain R session. Use of the DataSHIELD web service is recommended instead. Default is true (enabled).
org.obiba.opal.r.sessionTimeout Time in minutes after which an active R session will be automatically terminated (default is 4 hours).
org.obiba.opal.r.repos The list of CRAN repositories from which R packages can be downloaded, comma separated. Default value is,

DataSHIELD Configuration

Some minimal default DataSHIELD infrastructure settings can be defined.

Property Description
datashield.r.parser DataSHIELD R parser version: v1 or v2 See DataSHIELD4J library documentation. Default is the latest.

Login Policy Configuration

To prevent brute force password guessing, a user can be temporarily banned after too many login failures.

Property Description Number of failed login attempts before being banned (default is 3). Time span in which the maximum of retry count should happen before starting a ban period, in seconds (default is 300). No time limit if not positive. Ban time after max retry, within the retry time span, was reached, in seconds (default is 300). No ban if not positive. Time in days after which a personal access token is automatically removed. Default is -1 (i.e. tokens never expire). Time in days since last access after which a personal access token is marked as being inactive. This state can be reverted by user. Default is 60 (2 months).

Agate Server Configuration

Opal user lookup can include the Agate’s user realm. Default configuration enables connection to a Agate server.

Property Description
org.obiba.realm.url Address to connect to Agate server. Default is https://localhost:8444. To disable Agate connection, specify an empty value for this property.
org.obiba.realm.publicUrl Public address to create a link from Opal’s user profile page to the Agate’s one where personal information, password and two-factor authentication can be managed. Default is empty. Application name of this Opal instance in Agate. Default is opal.
org.obiba.realm.service.key Application key of this Opal instance in Agate. Default is changeit.

System Identifiers Generation Configuration

When importing data and selecting a identifiers mapping, if an imported identifier does not exist for the selected mapping and the strategy that was chosen is to generate a system identifier, then the following default settings apply for system identifiers generation:

Property Description
org.obiba.opal.identifiers.length Length of the numerical part of the identifier (i.e. not including the prefix length). Default is 10.
org.obiba.opal.identifiers.zeros Allow leading zeros in the numerical part of the identifiers. Default is false.
org.obiba.opal.identifiers.prefix Character prefix to be applied. Default is none.
org.obiba.opal.identifiers.checksum Add a checksum digit so that the generated identifier can be validated regarding the Luhn algorithm. Default is false.

Cross Site Resource Forgery (CSRF)

CSRF attacks can be mitigated by a built-in interceptor. Default behavior allows connections (http or https) from localhost and Requests from pages served by Opal should be allowed as well (https only), unless network settings or proxies modify or do not report the referer URL.

Property Description
csrf.allowed Comma separated list of client host:port explicitly allowed to connect to Opal server. Use * as a wildcard. Default is empty.

Miscelaneous Configuration

Advanced settings.

Property Description
org.obiba.opal.keys.entityType Type of entities to store in the identifiers table.
org.obiba.opal.keys.tableReference Fully-qualified name of the identifiers table
org.obiba.opal.taxonomies Comma separated list of URIs to taxonomy files in YAML format. Note that file URI schema is supported (allows to read locally defined taxonomy). The URL to the plugins repository (default is A plugin repository is not just a list of files, meta-data information about plugins are expected to be provided by a plugins.json file.
org.obiba.opal.maxFormContentSize Maximum body size of a HTTP(S) form post request. Default value is 200000 bytes. Limit of the Protobuf message size. Default value is 524288000 bytes (500MB).
org.obiba.magma.entityIdNames Specify the column name per entity type to be used for the entity identifier when exporting data to a file (CSV, SAS, SPSS, Stata). If empty for the considered entity type, the default column name will apply. The format to be used is a comma-separated key-value list, for instance: org.obiba.magma.entityIdNames=Participant=Idepic,Biomarker=Biom_Id
org.obiba.magma.entityIdName Specify the default column name to be used for the entity identifier when exporting data to a file (CSV, SAS, SPSS, Stata). If empty, this name depends on the file format.
org.obiba.magma.readDataPointsCount Maximum number of data points (number of rows per number of variables) when batches of values are read from a table. Default value is 100000. Allow user to login from different realms with the same username. Note that the user is always logged in one realm at a time (no addition of the privileges). Default value is true. When connecting to MongoDB using SSL and when remote certificate is self-signed, the certificate check can be deactivated (not recommended, default is false).
org.obiba.opal.jdbc.maxPoolSize Maximum size of the pool of JDBC connections, for each SQL database. Default value is 100.
productionMode When set to false the CSRF check is disabled and plugin jars conflict checks are skipped. Default value is true.

Advanced Configuration File

The file OPAL_HOME/data/opal-config.xml can be edited to match some of your server needs.

File System Root

Opal offers a “file system” in which users may manipulate files without having a user defined in the OS running Opal. That is, all interactions with the underlying file-system go through a unique system-user: the one that runs the Opal server.

The Opal file system root is set by default to be OPAL_HOME/fs. To change it, modify the following statement:

<!-- Windows example -->

Several types of file root names are recognized:

  • Absolute URI. These must start with a scheme, such as ‘file:’, followed by a scheme dependent file name. For example:

  • Absolute local file name. For example, /home/someuser/somedir or c:dirsomedir. Elements in the name can be separated using any of the following characters: /, , or the native file separator character. For example, the following file names are the same:

    c:dirsomedir c:/dir/somedir

User Directories

The security framework that is used by Opal for authentication, authorization etc. is Shiro. Configuring Shiro for Opal is done via the file OPAL_HOME/conf/shiro.ini. See also Shiro ini file documentation.


Default configuration is a static user ‘administrator’ with password ‘password’ (or the one provided while installing Opal Debian/RPM package).

By default Opal server has several built-in user directories (in the world of Shiro, a user directory is called a realm):

  • a file-based user directory (shiro.ini file),
  • the internal Opal user directory,
  • the user directory provided by Agate.

In the world of Shiro, a user directory is called a realm.

File Based User Directory

The file-based user directory configuration file OPAL_HOME/conf/shiro.ini.


It is not recommended to use this file-based user directory. It is mainly dedicated to define a default system super-user.

For a better security, user passwords are encrypted with a one way hash such as sha256.

The example shiro.ini file below demonstrates how encryption is configured.

# =======================
# Shiro INI configuration
# =======================

# Objects and their properties are defined here,
# Such as the securityManager, Realms and anything else needed to build the SecurityManager

# The 'users' section is for simple deployments
# when you only need a small number of statically-defined set of User accounts.
# Password here must be encrypted!
# Use shiro-hasher tools to encrypt your passwords:
#     cd /usr/share/opal/tools && ./shiro-hasher -p
#   UNIX:
#     cd <OPAL_DIST_HOME>/tools && ./shiro-hasher -p
#     cd <OPAL_DIST_HOME>/tools && shiro-hasher.bat -p
# Format is:
# username=password[,role]*
administrator = $shiro1$SHA-256$500000$dxucP0IgyO99rdL0Ltj1Qg==$qssS60kTC7TqE61/JFrX/OEk0jsZbYXjiGhR7/t+XNY=,admin

# The 'roles' section is for simple deployments
# when you only need a small number of statically-defined roles.
# Format is:
# role=permission[,permission]*
opal-administrator = *

Passwords must be encrypted using shiro-hasher tools (included in Opal tools directory):

cd /usr/share/opal/tools
./shiro-hasher -p

LDAP and Active Directory Authentication

Opal can authenticate users by using an existing LDAP or Active Directory server. This is done by adding the proper configuration section in the shiro.ini file:

ldapRealm = org.apache.shiro.realm.ldap.JndiLdapRealm
ldapRealm.contextFactory.url = ldap://ldap.hostname.or.ip:389
ldapRealm.userDnTemplate = uid={0},ou=users,dc=mycompany,dc=com

The userDnTemplate should be modified to match your LDAP schema. The {0} will be replaced by the username provided at login. Authentication will use the user’s credentials to try to bind to LDAP; if binding succeeds, the credentials are considered valid and authentication will succeed.

There is currently no support to extract a user’s groups from LDAP. This will be added in a future release.

With Active Directory you can specify a mapping between AD groups and roles in Shiro. Example configuration for Active Directory authentication:

adRealm = org.apache.shiro.realm.activedirectory.ActiveDirectoryRealm
adRealm.url = ldap://ad.hostname.or.ip:389
adRealm.systemUsername = usernameToConnectToAD
adRealm.systemPassword = passwordToConnectToAD
adRealm.searchBase = "CN=Users,DC=myorg"
adRealm.groupRolesMap = "CN=shiroGroup,CN=Users,DC=myorg":"myrole"
#adRealm.principalSuffix =

Atlassian Crowd User Directory

Atlassian Crowd is not supported any more because the connector was based on libraries with security issues. OpenID Connect is to be preferred for authentication delegation. For more information see section Identity Providers.

Other Settings

Shiro’s default session timeout is 1800s (half an hour). The session timeout can be set explicitly in the shiro.ini file, in the [main] section:

# =======================
# Shiro INI configuration
# =======================

# Objects and their properties are defined here,
# Such as the securityManager, Realms and anything else needed to build the SecurityManager
# 3,600,000 milliseconds = 1 hour
securityManager.sessionManager.globalSessionTimeout = 3600000

# ...

The session timeout is in milliseconds and allowed values are:

  • a negative value means sessions never expire.
  • a non-negative value (0 or greater) means session timeout will occur as expected.

Reverse Proxy Configuration

Opal server can be accessed through a reverse proxy server.


Example of Apache directives that:

  • redirects HTTP connection on port 80 to HTTPS connection on port 443,
  • specifies acceptable protocols and cipher suites,
  • refines organization’s specific certificate and private key.
<VirtualHost *:80>
    ProxyRequests Off
    ProxyPreserveHost On
    <Proxy *>
        Order deny,allow
        Allow from all
    RewriteEngine on
    ReWriteCond %{SERVER_PORT} !^443$
    RewriteRule ^/(.*)$1 [NC,R,L]
<VirtualHost *:443>
    SSLProxyEngine on
    SSLEngine on
    SSLProtocol All -SSLv2 -SSLv3
    SSLHonorCipherOrder on
    # Prefer PFS, allow TLS, avoid SSL, for IE8 on XP still allow 3DES
    # Prevent CRIME/BREACH compression attacks
    SSLCompression Off
    SSLCertificateFile /etc/apache2/ssl/cert/
    SSLCertificateKeyFile /etc/apache2/ssl/private/
    ProxyRequests Off
    ProxyPreserveHost On
    ProxyPass / https://localhost:8443/
    ProxyPassReverse / https://localhost:8443/

For performance, you can also activate Apache’s compression module (requires deflate module) with the following settings (note the json content type setting) in file /etc/apache2/mods-available/deflate.conf:

<IfModule mod_deflate.c>
  <IfModule mod_filter.c>
      # these are known to be safe with MSIE 6
      AddOutputFilterByType DEFLATE text/html text/plain text/xml
      # everything else may cause problems with MSIE 6
      AddOutputFilterByType DEFLATE text/css
      AddOutputFilterByType DEFLATE application/x-javascript application/javascript application/ecmascript
      AddOutputFilterByType DEFLATE application/rss+xml
      AddOutputFilterByType DEFLATE application/xml
      AddOutputFilterByType DEFLATE application/json

Recommended security headers are (to be added to the apache2.conf file, requires headers module):

# Security Headers, see
Header set Strict-Transport-Security "max-age=63072000"
Header set X-Frame-Options DENY
Header set X-XSS-Protection 1;mode=block
Header set X-Content-Type-Options nosniff
Header set Content-Security-Policy "frame-ancestors 'none'"
Header set Referrer-Policy "same-origin"
Header set Permissions-Policy "fullscreen=(self)"
Header onsuccess edit Set-Cookie ^(.+)$ "$1;HttpOnly;Secure;SameSite=Strict"

Proxy Configuration

Outbound connections may go through a proxy, depending on the host institution’s network setup. It is possible to declare the proxy settings by modifying the JAVA_OPTS environment variable. As an example:

# without authentication
JAVA_OPTS=-Dhttp.proxyHost= -Dhttp.proxyPort=3020 -Xms1G -Xmx8G

# or with authentication
JAVA_OPTS=-Dhttp.proxyHost= -Dhttp.proxyPort=3020 -Dhttp.proxyUser=opal -Dhttp.proxyPassword=xxxxxx -Xms1G -Xmx8G