System Requirements

Table 1. Requirements for users

Browser

Chrome or Safari

Table 2. Requirements to run the standalone version

Java Runtime Environment

version 8 or higher

Table 3. Requirements run a WebAnno server

Java Runtime Environment

version 8 or higher

Apache Tomcat

version 8.5 or higher (Servlet API 3.1.0)

MySQL Server

version 5 or higher

Installation

Prerequisites

  • This guide assumes Debian 9.1 (Stretch). It may also work on Ubuntu with some modifications, but we do not test this. Instructions for other Linux distributions likely deviate significantly.

  • It is further assumed that the user "www-data" already exists on the system and that it shall be used to run WebAnno.

  • All commands assume that you are logged in as the root user.

If you cannot log in as root but have to use sudo to become root, then the recommended way to do that is using the command sudo su -.

Install Java 8

You can install an Oracle Java 8 JDK using the following commands.

$ apt-get update
$ apt-get install dirmngr
$ echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee /etc/apt/sources.list.d/webupd8team-java.list
$ echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu trusty main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list
$ apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886
$ apt-get update
$ apt-get install oracle-java8-installer
$ apt-get install oracle-java8-set-default

Prepare database

For production use of WebAnno, it is highly recommended to use a MySQL database. In this section, we briefly describe how to install a MySQL server and how to prepare it for use with WebAnno.

  • Install MySQL

    $ apt-get install mysql-server
  • make sure your MySQL server is configured for UTF-8. Check the following line is present in /etc/mysql/mariadb.conf.d/50-server.cnf (this is specific to Debian 9; on other systems the relevant file may be /etc/mysql/my.cnf):

    character-set-server = utf8
    collation-server     = utf8_bin
  • also ensure the default settings for client connections to are UTF-8 in /etc/mysql/mariadb.conf.d/50-server.cnf (again Debian 9; likely in /etc/mysql/my.cnf on other systems)

    default-character-set = utf8
  • login to MySQL

    $ mysql -u root -p
  • create a database

    mysql> CREATE DATABASE webanno DEFAULT CHARACTER SET utf8 COLLATE utf8_bin ;
  • create a database user called webanno with the password t0t4llYSecreT which is later used by the application to access the database (instructions for settings.properties file below).

    mysql> CREATE USER 'webanno'@'localhost' IDENTIFIED BY 't0t4llYSecreT';
    mysql> GRANT ALL PRIVILEGES ON webanno.* TO 'webanno'@'localhost';
    mysql> FLUSH PRIVILEGES;
For production use, make sure you choose a different, secret, and secure password.

Setting up the WebAnno home folder

The WebAnno home folder is the place where WebAnno’s configuration file settings.properties resides and where WebAnno stores its data. Mind that if you are using a MySQL database server (recommended), then WebAnno also stores some data in the MySQL database. This is important when you plan to perform a backup, as both the home folder and the database content need to be included in the backup.

Now, let’s go through the steps of setting up a home folder for WebAnno and creating a configuration file instructing WebAnno to access the previously prepared MySQL database.

  • Create WebAnno home folder. This is the directory where WebAnno settings files and projects (documents, annotations, etc.) are stored

    $ mkdir /srv/webanno
  • Edit /srv/webanno/settings.properties to define the database connection as well as internal backup properties:

    database.dialect=org.hibernate.dialect.MySQL5InnoDBDialect
    database.driver=com.mysql.jdbc.Driver
    database.url=jdbc:mysql://localhost:3306/webanno?useSSL=false
    database.username=webanno
    database.password=t0t4llYSecreT
    
    # 60 * 60 * 24 * 30 = 30 days
    backup.keep.time=2592000
    
    # 60 * 5 = 5 minutes
    backup.interval=300
    
    backup.keep.number=10
  • Fix permissions in WebAnno home folder

    $ chown -R www-data /srv/webanno

Running via embedded Tomcat

The WebAnno standalone JAR with an embedded Tomcat server and can be easily set up as a UNIX service. This is the recommended way of running WebAnno on a server.

Installing WebAnno as a service

To set it up as a service, you can do the following steps. For the following example, I assume that you install WebAnno in /srv/webanno:

  • Copy the standalone JAR file webanno-standalone-{revnumber}.jar to /srv/webanno/webanno.jar. Note the change of the filename to webanno.jar.

  • Create the file /srv/webanno/webanno.conf with the following content

    JAVA_OPTS="-Djava.awt.headless=true -Dwebanno.home=/srv/webanno"
  • In the previous step, you have already created the /srv/webanno/settings.properties file. You may optionally configure the Tomcat port using the following line

    server.port=18080

    If you need to do additional configurations of the embedded Tomcat, best refer to the documentation of Spring Boot itself.

  • Make sure that the file /srv/webanno/webanno.conf is owned by the root user. If this is not the case, WebAnno will ignore it and any settings made there will not have any effect. If you start WebAnno and intead of using the MySQL database, it is using an embedded database, then you should double-check that /srv/webanno/webanno.conf is owned by the root user.

    $ chown root:root /srv/webanno/webanno.conf
  • Change the owner/group of /srv/webanno/webanno.jar to www-data. When the service is started, it will run with the privileges of the user that owns the JAR file, i.e. in this case WebAnno will run as under the www-data user. Do NOT run WebAnno as root.

    $ chown www-data:www-data /srv/webanno/webanno.jar
  • Create a symlink from /etc/init.d to the /srv/webanno/webanno.jar:

    $ ln -s /srv/webanno/webanno.jar /etc/init.d/webanno
  • Enable the WebAnno service using

    $ systemctl enable webanno
  • Start WebAnno using

    $ service webanno start
  • Stop WebAnno using

    $ service webanno stop

Running the standalone behind HTTPD

These are optional instructions if you want to run WebAnno behind an Apache web-server instead of accessing it directly. This assumes that you already have the following packages installed:

  • Apache Web Server

  • mod_proxy

  • mod_proxy_ajp

  • Add the following lines to /srv/webanno/settings.properties:

    tomcat.ajp.port=18009
    server.contextPath=/webanno
    server.use-forward-headers=true
  • Edit /etc/apache2/conf.d/webanno.local.conf

    ProxyPreserveHost On
    
    <Proxy ajp://localhost/webanno >
      Order Deny,Allow
      Deny from none
      Allow from all
    </Proxy>
    
    <Location /webanno >
      ProxyPass ajp://localhost:18009/webanno timeout=1200
      ProxyPassReverse http://localhost/webanno
    </Location>
  • Restart Apache web server

    $ service apache2 restart

Running via separate Tomcat

Instead of using the WebAnno standalone JAR (recommended) which comes with an embedded Tomcat, you can also deploy the WebAnno WAR archive into a separately installed Tomcat instance.

Installing Tomcat

  • Install package to install user-instances of Tomcat.

    $ apt-get install tomcat8-user authbind
  • Create new instance

    $ cd /opt
    $ tomcat8-instance-create -p 18080 -c 18005 webanno
    $ chown -R www-data /opt/webanno
If WebAnno is the only application you install on your server, then you can also have WebAnno running on port 80 or port 443. In that case, substitute all instances of port 18080 in these guidelines with the respective port. Mind that running via SSL on port 443 requires additional steps that we have not yet documented. Ports lower than 1024 are privileged and the WebAnno init script will automatically use a tool called authbind to allow WebAnno to operate on these ports as the unprivileged www-data user.
  • Configure the startup script. Edit /etc/init.d/webanno and add the following contents or just download the file from here and place it in /etc/init.d.

    #!/bin/sh
    
    # Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
    
    # kFreeBSD do not accept scripts as interpreters, using #!/bin/sh and sourcing.
    if [ true != "$INIT_D_SCRIPT_SOURCED" ] ; then
        set "$0" "$@"; INIT_D_SCRIPT_SOURCED=true . /lib/init/init-d-script
    fi
    ### BEGIN INIT INFO
    # Provides:          webanno
    # Required-Start:    $remote_fs $syslog
    # Required-Stop:     $remote_fs $syslog
    # Default-Start:     2 3 4 5
    # Default-Stop:      0 1 6
    # Short-Description: WebAnno init script
    # Description:       This file should be placed in /etc/init.d. It
    #                    allows starting/stopping WebAnno using the
    #                    "service" command and ensures that WebAnno starts
    #                    when the system is booted.
    ### END INIT INFO
    
    # Author: Richard Eckart de Castilho
    
    NAME="WebAnno"
    DAEMON=none
    WEBANNO_HOME="/srv/webanno"
    WEBANNO_PORT="18080"
    WEBANNO_USER="www-data"
    CATALINA_BASE="/opt/webanno"
    AUTHBIND=""
    JAVA_OPTS="-Djava.awt.headless=true -Xmx750m -XX:+UseConcMarkSweepGC -Dwebanno.home=$WEBANNO_HOME"
    
    setup_authbind() {
      # log_action_msg "Setting up authbind configuration for $DESC on port $WEBANNO_PORT"
      touch /etc/authbind/byport/$WEBANNO_PORT
      chmod 500 /etc/authbind/byport/$WEBANNO_PORT
      chown $WEBANNO_USER /etc/authbind/byport/$WEBANNO_PORT
      AUTHBIND="authbind --deep"
    }
    
    tomcat_pid() {
      echo `ps -fe | grep -- "-Dcatalina.base=$CATALINA_BASE" | grep -v grep | tr -s " "|cut -d" " -f2`
    }
    
    do_start_cmd_override() {
      if [ $WEBANNO_PORT -lt 1024 ]
      then
        setup_authbind
      fi
    
      su - www-data -s "/bin/bash" -c "JAVA_OPTS=\"$JAVA_OPTS\" $AUTHBIND $CATALINA_BASE/bin/startup.sh" > /dev/null 2>&1
    }
    
    do_stop_cmd_override() {
      su - www-data -s "/bin/bash" -c "$CATALINA_BASE/bin/shutdown.sh" > /dev/null 2>&1
    }
    
    do_status() {
      local pid
      pid=$(tomcat_pid)
      if [ -n "$pid" ]
      then
        log_action_msg "Status $DESC: running"
        return 0
      else
        log_action_msg "Status $DESC: stopped"
        return 1
      fi
    }
  • Make the script executable and register it to run during system start:

    $ chmod +x /etc/init.d/webanno
    $ update-rc.d webanno defaults
If you deploy WebAnno on a Linux machine that is short on entropy, you can significantly decrease startup time by adding -Djava.security.egd=file:/dev/urandom to the JAVA_OPTS variable in the init script.

Now we have a dedicated Apache Tomcat instance for WebAnno installed at /opt/webanno/ that automatically starts when the system boots and that can be managed through the usual service commands.

Deploying the WAR file

  • Place the WebAnno WAR into the Tomcat webapps folder:

    $ cp webanno-webapp-3.4.5.war /opt/webanno/webapps/webanno.war
    Mind that the copy command above renames the WAR file to webanno.war! This is important so that WebAnno is accessible at the URL noted later in the present guidelines.
  • Start WebAnno

    $ service webanno start
  • Open it with your browser at http://localhost:18080/webanno. If you chose to run WebAnno behind the Apache web-server use http://localhost/webanno. The first time, it will create a username admin with password admin. Log in with this username and proceed.

Running the WAR behind Apache HTTPD

These are optional instructions if you want to run WebAnno behind an Apache web-server instead of accessing it directly. This assumes that you already have the following packages installed:

  • Apache Web Server

  • mod_proxy

  • mod_proxy_ajp

  • Edit /opt/webanno/conf/server.xml and enable AJP Connector on localhost (comment in, add address, and change port

    <Connector port="18009" protocol="AJP/1.3" redirectPort="8443" address="127.0.0.1"/>
  • Disable HTTP Connector (just comment it out)

    <!--Connector port="8080" protocol="HTTP/1.1".
               connectionTimeout="20000".
               URIEncoding="UTF-8"
               redirectPort="8443" /-->
  • Edit /etc/apache2/conf.d/webanno.local.conf

    ProxyPreserveHost On
    
    <Proxy ajp://localhost/webanno >
      Order Deny,Allow
      Deny from none
      Allow from all
    </Proxy>
    
    <Location /webanno >
      ProxyPass ajp://localhost:18009/webanno timeout=1200
      ProxyPassReverse http://localhost/webanno
    </Location>
  • Restart Apache web server

    $ service apache2 restart

Database

WebAnno uses an SQL database to store project and user data.

We test MySQL using a MySQL server. WebAnno uses by default an embedded HSQLDB database. However, we recommend using the embedded database only for testing purposes. For production use, we recommend using a MySQL server. The reason for this is, that:

  • we do more testing on the MySQL server and

  • in the past, we had cases where we described in-place upgrade procedures that required performing SQL commands to change the data model as part of the upgrade. We promise to try avoiding this in the future. However, in case we offer advice on fixing anything directly in the database, this advice will refer to a MySQL database.

We try to keep the data model simple, so there should be no significant requirements to the database being used. Theoretically, it should be possible to use any JDBC-compatible database after adding a corresponding driver to the classpath and configuring WebAnno to use the driver in the settings.properties file.

If you plan to use UTF-8 encoding for project name and tagset/tag name, make sure either of the following settings for MySQL databse a) in the settings.properties file, make sure that database.url includes

useUnicode=true&characterEncoding=UTF-8

b) change the my.conf MySQL databse configuration file to include the following line

character-set-server = utf8

Using HSQLDB in production

WebAnno displays a warning in the user interface when an embedded database is being used. In case that you really want to run WebAnno with an embedded database in production, you probably want to disable this warning. To do so, please add the following entry to the settings.properties file:

warnings.embeddedDatabase=false

Upgrade

Exporting/importing

  • Log into WebAnno and export all the projects that you wish to migrate using the Export pane in the project settings

  • Move your WebAnno home folder to a safe location so that WebAnno and create a new home folder in the old location

  • Copy the settings.properties and formats.properties (if present) back from your moved folder

  • Start the new WebAnno version to initialize the database

  • Recreate the users

    • If you are using MySQL

      • create a new database for the new WebAnno version and update the settings.properties accordingly

      • use mysqldump to dump the tables users and authorities from the old database and load it back into the new database

    • If you are not using MySQL, you have to recreate the users manually

  • When upgrading to WebAnno 2.x from a pre 2.x version, remove the format.properties file from the WebAnno home folder

  • Restart WebAnno and import the previously exported projects

In-place update

This method should work when updating only a bugfix version, e.g. from 2.0.9 to 2.0.10. When performing a minor or major update, better use the exporting/importing method above.

Backup your data

  • Make a copy of your WebAnno home folder

  • If you are using MySQL, make a backup of your WebAnno database, e.g. using the mysqldump command.

Standalone service

  • Stop the WebAnno service

  • Replace the webanno.jar file with the new version

  • Ensure that the file has the right owner/group (usually www-data)

  • Start the WebAnno service again

Separate Tomcat

  • While Tomcat is running, delete the old WAR from your webapps folder

  • Wait until Tomcat has automatically deleted the WebAnno folder

  • Stop Tomcat

  • Place the new WAR file into your webapps folder

  • Start Tomcat

Upgrading Tomcat 7 to Tomcat 8

If you have been using our installation instructions to install WebAnno on Linux, you are probably running an instance of Tomcat 6. WebAnno 3.3.0 is no longer compatible with Tomcat 6 and requires at least Tomcat 8.

To upgrade your existing instance, you can try the following procedure (adapt the procedure as necessary if you have deviated from our installation instructions):

  • Stop the current WebAnno Tomcat 7 instance

$ service webanno stop
  • Move your old Tomcat instance out of the way

$ mv /opt/webanno /opt/webanno-tomcat7
  • Install tomcat8-user package (this will automatically uninstall Tomcat 7)

$ apt-get install tomcat8-user
  • Create new instance

$ cd /opt
$ tomcat8-instance-create -p 18080 -c 18005 webanno
$ chown -R www-data /opt/webanno
  • Copy the WAR file over to the new instance

$ mv /opt/webanno-tomcat7/webapps/webanno.war /opt/webanno/webapps/webanno.war
  • Stop the new WebAnno Tomcat 8 instance

$ service webanno start
If you have made additional changes to the Tomcat 7 configuration files, e.g. changed conf/server.xml, please make sure to redo them in the new Tomcat 8 instance.

Version 3.2.x to 3.3.0

  • When upgrading from 3.2.x or earlier to 3.3.0 or later, Automation projects break.

Version 2.3.1 to 3.0.0

  • The access permissions of the super admin have changed. Super admins can no longer access annotation, curation, and monitoring pages for all projects. They can only access them if they are annotators, admins, or curators in the respective projects. However, they still have full access to the project settings of all projects and can simply give themselves the missing permissions. After an upgrade to 3.0.0, all super admins who require project permissions on existing projects should assign these permissions to themselves. This also applies when importing old projects. For new projects, the creator of the project always starts with annotator, curator, and project admin permissions. If these permissions are not required by the project creator, they should be removed after project creation.

System Properties

Setting Description Default Example

webanno.home

WebAnno home folder

~/.webanno

/srv/webanno

javamelody.disabled

Disable JavaMelody

true

false

Settings

Setting Description Default Example

auth.mode

Authentication mode

 database

preauth

auth.preauth.header.principal

Principal header

 remote_user

some other header

auth.preauth.newuser.roles

Default roles for new users (comma separated)

 <none>

ROLE_PROJECT_CREATOR

auth.user.<username>.roles

Extra roles for user (comma separated)

 <none>

ROLE_ADMIN

database.dialect

Database dialect

 org.hibernate.dialect.HSQLDialect

org.hibernate.dialect.MySQL5InnoDBDialect

database.driver

Database driver

org.hsqldb.jdbc.JDBCDriver

com.mysql.jdbc.Driver

database.url

JDBC connection string

location in WebAnno home

jdbc:mysql://localhost:3306/weblab?useUnicode=true&characterEncoding=UTF-8

database.username

Database username

 sa

user

database.password

Database password

 unset

pass

database.initial-pool-size

Initial database connection pool size

4

database.min-pool-size

Minimum database connection pool size

4

database.max-pool-size

Maximum database connection pool size

10

backup.interval

Time between backups (seconds)

0

300 (60 * 5 = 5 minutes)

backup.keep.number

Maximum number of backups to keep

0

5

backup.keep.time

Maximum age of backups to keep (seconds)

0

2592000 (60 * 60 * 24 * 30 = 30 days)

ui.brat.autoScroll

Whether to scroll the annotation being edited into the center of the page

true

ui.brat.pageSize

The number of sentences to display per page

5

ui.brat.singleClickSelection

Whether to select annotations with a single click

false

style.logo

Logo image displayed in the upper-right corner

unset

path to an image file

style.header.icon…​

Icons/links to display in the page header. For details, see below.

unset

warnings.embeddedDatabase

Warn about using an embedded database

true

false

warnings.unsupportedBrowser

Warn about unsupported browser

true

false

debug.showExceptionPage

Show a page with a stack trace instead of an "Internal error" page. Do not use in production!

false

true

login.message

Custom message to appear on the login page, such as project web-site, annotation guideline link, …​ The message can be an HTML content.

unset

<span style="color:red; font-size: 200%;">Use are your own risk.</span>

user.profile.accessible

Whether regular users can access their own profile to change their password and other profile information. This setting has no effect if WebAnno is running in pre-authentication mode.

false

true

Configure database via environment variables

The database connection details can also be configured via environment variables. When these environment variables are present, they are preferred over the settings.properties file. The following environment variables can be used:

Setting Description Default Example

WEBANNO_DB_DIALECT

Database dialect

 org.hibernate.dialect.HSQLDialect

org.hibernate.dialect.MySQL5InnoDBDialect

WEBANNO_DB_DRIVER

Database driver

org.hsqldb.jdbc.JDBCDriver

com.mysql.jdbc.Driver

WEBANNO_DB_URL

JDBC connection string

location in WebAnno home

jdbc:mysql://localhost:3306/weblab?useUnicode=true&characterEncoding=UTF-8

WEBANNO_DB_USERNAME

Database username

 sa

user

WEBANNO_DB_PASSWORD

Database password

 unset

pass

Custom header icons

WebAnno allows adding custom icons to the page header. You can declare such custom icons in the WebAnno settings file as shown in the example below. Each declaration begins with the prefix style.header.icon. followed by an identifier (here myOrganization and mySupport). The suffixes .linkUrl and .imageUrl indicate the URL of the target page and of the icon image respectively. Images are automatically resized via CSS. However, to keep loading times low, you should point to a reasonably small image.

The order of the icons is controlled by the ID, not by the order in the configuration file!

Example: Custom header icon
style.header.icon.myOrganization.linkUrl=http://my.org
style.header.icon.myOrganization.imageUrl=http://my.org/logo.png
style.header.icon.mySupport.linkUrl=http://my.org/support
style.header.icon.mySupport.imageUrl=http://my.org/help.png

Internal backups

WebAnno stores its annotations internally in files. Whenever a user performs an action on a document, the file is updated. It is possible to configure WebAnno to keep internal backups of these files, e.g. to safeguard against crashes or bugs.

The internal backups are controlled through three properties:

Setting Description Default

backup.interval

Time between backups (seconds)

0 (disabled)

backup.keep.number

Maximum number of backups to keep

0 (unlimited)

backup.keep.time

Maximum age of backups to keep (seconds)

0 (unlimited)

By default, backups are disabled (backup.interval is set to 0). Changing this properties to any positive number enables internal backups. The interval controls the minimum time between changes to a document that needs to have elapsed in order for a new backup to be created.

When backups are enabled, either or both of the properties backup.keep.number and backup.keep.time should be changed as well, because their default values will cause the backups to be stored indefinitely and they will eventually fill up the disk.

The properties backup.keep.number and backup.keep.time control how long backups are keep and the maximal number of backups to keep. These settings are effective simultaneously.

Example: Make backups every 5 minutes and keep 10 backups irrespective of age
backup.interval    = 300
backup.keep.number = 10
backup.keep.time   = 0
Example: Make backups every 5 minutes and all not older than 7 days (60 * 60 * 24 * 7 seconds)
backup.interval    = 300
backup.keep.number = 0
backup.keep.time   = 604800
Example: Make backups every 5 minutes and keep at most 10 backups that are not older than 7 days
backup.interval    = 300
backup.keep.number = 10
backup.keep.time   = 604800

External pre-authentication

WebAnno can be used in conjunction with header-based external per-authentication. In this mode, WebAnno looks for a special HTTP header (by default remote_user) and if that header exists, it is taken for granted that this user has been authenticated. WebAnno will check its internal database if a user by the given name exists, otherwise it will create the user.

Pre-authentication can be enabled by setting the property auth.mode to preauth. When enabling pre-authentication mode, the default roles for new users can be controlled using the auth.preauth.newuser.roles property. The ROLE_USER is always added, even if not specified explicitly. Adding also the role ROLE_PROEJCT_CREATOR allows all auto-created users also to create their own projects.

Since the default administrator user is not created in pre-authentication, it is useful to also declare at least one user as an administrator. This is done through the property auth.user.<username>.roles where <username> must be replaced with the name of the user. The example below shows how the user Franz is given administrator permissions.

Example: Authenticate using the remote_user header, new users can create projects, user Franz is always admin.
auth.mode                     = preauth
auth.preauth.header.principal = remote_user
auth.preauth.newuser.roles    = ROLE_PROJECT_CREATOR
auth.user.Franz.roles         = ROLE_ADMIN
The roles specified through auth.preauth.newuser.roles are saved in the database when a user logs in for the first time and can be changed after creation through the user interface.
The roles added through auth.user.<username>.roles properties are not saved in the database and cannot be edited through the user interface.