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The file MICA_HOME/conf/application.yml is to be edited to match your server needs. This file is written in YAML format allowing to specify a hierarchy within the configuration keys. The YAML format uses indentations to express the different levels of this hierarchy. The file is already pre-filled with default values (to be modified to match your configuration), just be aware that you should not modify the indentations. In the following documentation, the configuration keys will be presented using the dot-notation (levels are separated by dots) for readability.

HTTP Server Configuration

Mica server is a web application and as such, you need to specify on which ports the web server should listen to incoming requests.

Property Description
server.port HTTP port number. Generally speaking this port should not be exposed to the web. Use the https port instead. Web server host name.
server.context-path The URL's context path, starting with a /. For instance when setting /repo, the base URL will be
https.port HTTPS port number.

MongoDB Server Configuration

Mica server will store its data (system configuration, networks, studies, datasets, etc.) in a MongoDB database. You must specify how to connect to this database.

Property Description MongoDB URI. Read Standard Connection String Format to learn more.

By default MongoDB does not require any user name, it is highly recommended to configure the database with a user. This can be done by enabling the Client Access Control procedure.

Follow these steps to enable the Client Access Control on your server:

  • create a user with the proper roles on the target databases
  • restart the MongoDB service with Client Access Control enabled


Once the MongoDB service runs with Client Access Control enabled, all database connections require authentication.

MongoDB User Creation Example

The example below creates the micaadmin user for mica database:

use admin

db.createUser( {
  user: "micaadmin", pwd: "micaadmin",
  roles: [
       { "role" : "readWrite", "db" : "mica" },
       { "role" : "dbAdmin", "db" : "mica" },
       { "role" : "readAnyDatabase", "db": "admin" }

Here is the required configuration snippet in /etc/mica/application.yml for the above user:

      uri: mongodb://micaadmin:micaadmin@localhost:27017/mica?authSource=admin


Mica requires either clusterMonitor or readAnyDatabase role on the admin database for validation operations. The first role is useful for a cluster setup and the latter if your MongoDB is on a single server.

Opal Server Configuration

Mica server uses Opal to retrieve data dictionaries, data summaries and variable taxonomies. This server is sometimes referred as the Opal primary server (secondary servers can be defined at study level). If you want to publish datasets, the following Opal connection details needs to be configured.

Property Description
opal.url Opal server URL. It is highly recommended to use https protocol.
opal.username User name for connection to Opal server.
opal.password User password for connection to Opal server.
opal.token Opal personal access token for connection to Opal server. If defined it has the priority over the username/password credentials.

Mica server should connect to Opal and access to some selected tables only with the lowest level of permissions (View dictionary and summary, i.e. no access to individual data). Please refer to the Opal Table Documentation for more details about the permissions that can be applied on a table.

Agate Server Configuration

Mica server uses Agate as a user directory and as a notification emails service. From the Agate point of view, Mica is not a user: it is an application. Each time Mica needs a service from Agate, it will provide the information necessary to its identification. The application credentials registered in Mica are to be specified in this section. If you want to specify advanced permissions or allow users to submit data access requests, the following Mica connection details needs to be configured.

Property Description
agate.url Agate server URL. It is highly recommended to use https protocol. Mica application ID for connection to Agate server.
agate.application.key Mica application key for connection to Agate server.

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 Mica 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.

Shiro Configuration

Shiro is the authentication and authorization framework used by Mica. There is a minimum advanced configuration that can be applied to specify how Shiro will hash the password. In practice this only applies to the users defined in the shiro.ini file. Default configuration is usually enough.

Property Description
shiro.password.nbHashIterations Number of re-hash operations.
shiro.password.salt Salt to be applied to the hash.

Elasticsearch Configuration

Mica server embeds Elasticsearch as its search engine. Elasticsearch is a key functionality of Mica as the process of publication consist in indexing documents (networks, studies, variables etc.) in the search engine. Advanced queries can be applied on the published documents. Elasticsearch is embeded, i.e. it is not an external application. Mica's Elasticsearch can be part of a cluster of Elasticsearch cluster. The configuration of the Elasticsearch node and how it should connect to the other nodes of the cluster can be specified in this section. Default configuration is usually enough.

Property Description
elasticsearch.dataNode Boolean to specify if this node has data or if it is just a proxy to other nodes in a cluster.
elasticsearch.clusterName Cluster identifier.
elasticsearch.shards Number of shards.
elasticsearch.replicas Number of replicas.
elasticsearch.settings A string in JSON or YAML format to define other elasticsearch settings. See Elasticsearch Documentation for advanced settings.
elasticsearch.transportClient Boolean to indicate to use the Transport Client instead of creating an elasticsearch Node.
elasticsearch.transportAddress Elasticsearch service IP address and port when using the Transport Client, defaults to the localhost at port 9300.
elasticsearch.transportSniff Boolean to indicate the Transport Client to collect IP addresses from nodes in an elasticsearch cluster.
elasticsearch.maxConcurrentJoinQueries Maximum count of ES queries that can be executed concurrently. Default value is 4.
elasticsearch.concurrentJoinQueriesWaitTimeout Wait timeout when executing concurrent ES queries in millis. Default value is 30000 milliseconds.

Elasticsearch Cluster

Mica can be set to join or connect to an Elasticsearch cluster. You need to set elasticsearch.clusterName to the name of the cluster you want to join. There are different possible cluster topologies, each of which has different resource utilization profiles in terms or memory and CPU.


To avoid API incompatibility issues, the recommended version of Elasticsearch server is 2.4.

An example of a configuration to join an elasticsearch cluster using a Client Node:

  clusterName: mycluster
  dataNode: false
  settings: '{"node.master": false, "node.local": false}'

An example of a configuration using the transport client:

  clusterName: mycluster
  transportClient: true
  transportAddress: "myhost:9300"

Elasticsearch Server Configuration

Mica uses the scripting capabilities of Elasticsearch. All the machines in the Elasticsearch cluster should have the scripting module enabled by setting the following values in the elasticsearch.yml configuration file (location of this file depends on how your elasticsearch service is installed):

  inline: true
  indexed: true

Miscelaneous Configuration

Advanced settings.

Property Description
dar.reminder.cron Schedule (cron syntax) of the email reminder for Data Access report. Default value is 0 0 0 * * ? (every day at midnight).
sets.cleanup.cron Schedule (cron syntax) of the expired cart/sets cleanup. Default value is 0 0 * * * ? (every hour).

User Directories

The security framework that is used by Mica for authentication, authorization etc. is Shiro. Configuring Shiro for Mica is done via the file MICA_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 Mica Debian/RPM package).

By default Mica 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 user directory provided by Agate.

Although it is possible to register some additional user directories, this practice is not recommended as Agate provides more than a service of authentication (user profile, notification emails etc.).

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

File Based User Directory

The file-based user directory configuration file MICA_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 and a password for the anonymous 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/mica2/tools && ./shiro-hasher -p
#   UNIX:
#     cd <MICA_DIST_HOME>/tools && ./shiro-hasher -p
#     cd <MICA_DIST_HOME>/tools && shiro-hasher.bat -p
# Format is:
# username=password[,role]*
administrator = $shiro1$SHA-256$500000$dxucP0IgyO99rdL0Ltj1Qg==$qssS60kTC7TqE61/JFrX/OEk0jsZbYXjiGhR7/t+XNY=,mica-administrator
anonymous = $shiro1$SHA-256$500000$dxucP0IgyO99rdL0Ltj1Qg==$qssS60kTC7TqE61/JFrX/OEk0jsZbYXjiGhR7/t+XNY=

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

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

cd /usr/share/mica2/tools
./shiro-hasher -p

Reverse Proxy Configuration

Mica 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:8445/
    ProxyPassReverse / https://localhost:8445/

For performance, you can also activate Apache's compression module (mod_deflate) 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"