Configuration¶

Main Configuration File¶

The file OPAL_HOME/conf/opal-config.properties 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.
`org.obiba.opal.server.context-path`	The context path when server is accessed at a subdirectory (for instance in `http://example.org/opal` the context path is `/opal`). Default is empty.

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
`org.obiba.opal.smtp.host`	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 inactive R session will be automatically terminated (default is 4 hours).
`org.obiba.opal.r.sessionTimeout.R`	Time in minutes after which an inactive R session with R context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.sessionTimeout.DataSHIELD`	Time in minutes after which an inactive R session with DataSHIELD context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.sessionTimeout.Import`	Time in minutes after which an inactive R session with Import context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.sessionTimeout.Export`	Time in minutes after which an inactive R session with Export context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.sessionTimeout.Report`	Time in minutes after which an inactive R session with Report context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.sessionTimeout.SQL`	Time in minutes after which an inactive R session with SQL context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.sessionTimeout.Analyse`	Time in minutes after which an inactive R session with Analyse context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.sessionTimeout.View`	Time in minutes after which an inactive R session with View context will be automatically terminated (default is to fallback to `org.obiba.opal.r.sessionTimeout`).
`org.obiba.opal.r.repos`	The list of CRAN repositories from which R packages can be downloaded, comma separated. Default value is `https://cloud.r-project.org,https://cran.obiba.org`.
`org.obiba.opal.r.workspaces.expires`	The number of days since last modification date after which a saved R/DataSHIELD workspace is removed. Default value is `365` (one year).

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
`org.obiba.opal.security.login.maxRetry`	Number of failed login attempts before being banned (default is `3`).
`org.obiba.opal.security.login.retryTime`	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.
`org.obiba.opal.security.login.banTime`	Ban time after max retry, within the retry time span, was reached, in seconds (default is `300`). No ban if not positive.
`org.obiba.opal.security.login.pat.expiresIn`	Time in days after which a personal access token is automatically removed. Default is `-1` (i.e. tokens never expire).
`org.obiba.opal.security.login.pat.activityTimeout`	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.
`org.obiba.realm.service.name`	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 127.0.0.1. 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).
`org.obiba.opal.plugins.site`	The URL to the plugins repository (default is https://plugins.obiba.org). 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.
`org.obiba.opal.ws.messageSizeLimit`	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`.
`org.obiba.opal.security.multiProfile`	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`.
`org.obiba.opal.security.ssl.allowInvalidCertificates`	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 -->
<fileSystemRoot>C:/opal-filesystem</fileSystemRoot>

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:

file:/c:/dir/somedir
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.

Note

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.

Note

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
# =======================

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


[users]
# 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:
#   DEBIAN:
#     cd /usr/share/opal/tools && ./shiro-hasher -p
#   UNIX:
#     cd <OPAL_DIST_HOME>/tools && ./shiro-hasher -p
#   WINDOWS:
#     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

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

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:

[main]
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:

[main]
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
# =======================

[main]
# 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.

Apache

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>
    ServerName opal.your-organization.org
    ProxyRequests Off
    ProxyPreserveHost On
    <Proxy *>
        Order deny,allow
        Allow from all
    </Proxy>
    RewriteEngine on
    ReWriteCond %{SERVER_PORT} !^443$
    RewriteRule ^/(.*) https://opal.your-organization.org:443/$1 [NC,R,L]
</VirtualHost>
<VirtualHost *:443>
    ServerName opal.your-organization.org
    SSLProxyEngine on
    SSLEngine on
    SSLProtocol All -SSLv2 -SSLv3
    SSLHonorCipherOrder on
    # Prefer PFS, allow TLS, avoid SSL, for IE8 on XP still allow 3DES
    SSLCipherSuite "EECDH+ECDSA+AESGCM EECDH+aRSA+AESGCM EECDH+ECDSA+SHA384 EECDH+ECDSA+SHA256 EECDH+aRSA+SHA384 EECDH+aRSA+SHA256 EECDH+AESG CM EECDH EDH+AESGCM EDH+aRSA HIGH !MEDIUM !LOW !aNULL !eNULL !LOW !RC4 !MD5 !EXP !PSK !SRP !DSS"
    # Prevent CRIME/BREACH compression attacks
    SSLCompression Off
    SSLCertificateFile /etc/apache2/ssl/cert/your-organization.org.crt
    SSLCertificateKeyFile /etc/apache2/ssl/private/your-organization.org.key
    ProxyRequests Off
    ProxyPreserveHost On
    ProxyPass / https://localhost:8443/
    ProxyPassReverse / https://localhost:8443/
</VirtualHost>

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
  </IfModule>
</IfModule>

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

# Security Headers, see https://securityheaders.com/
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=127.0.0.1 -Dhttp.proxyPort=3020 -Xms1G -Xmx8G

# or with authentication
JAVA_OPTS=-Dhttp.proxyHost=127.0.0.1 -Dhttp.proxyPort=3020 -Dhttp.proxyUser=opal -Dhttp.proxyPassword=xxxxxx -Xms1G -Xmx8G