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README.md

README.md

WebAnno

WebAnno Server Installation Guide (Version 3.2.2)

The following installation is based on Debian Operating System (Jessie 8.4.4) and the installation commands are executed as a root user.

First of all, Login as the root user using the following command:
sudo su -

You're now logged in as the root user. Run the following commands:

  1. Add the repository source:
    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

  2. verify it with the keys:
    apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys EEA14886

  3. Update the apt-get package manager:
    apt-get update

  4. Install the java8 package:
    apt-get install oracle-java8-installer
    apt-get install oracle-java8-set-default

  5. Check whether the installation is successful using the following command:
    java -version

  6. Create a user for the tomcat Server (before we install the Tomcat server):
    sudo adduser --system --shell /bin/bash --gecos 'Tomcat Java Servlet and JSP engine' --group --disabled-password --home /home/tomcat tomcat

  7. Create a directory called tmp:
    mkdir -p ~/tmp

  8. Choose the directory:
    cd ~/tmp

  9. Download the Apache Tomcat Server from a mirror:
    wget http://muug.ca/mirror/apache-dist/tomcat/tomcat-8/v8.5.20/bin/apache-tomcat-8.5.20.tar.gz

  10. unzip the tar contents:
    tar xvzf ./apache-tomcat-8.5.20.tar.gz

  11. Once you unzip the contents, you can delete the gzip file:
    rm ./apache-tomcat-8.5.20.tar.gz

  12. Move the Apache Tomcat directory to /usr/share :
    sudo mv ./apache-tomcat-8.5.20/ /usr/share/

  13. remove the older tomcat directory(if you have any) to make sure you are using the newest version:
    sudo rm -f /usr/share/tomcat

  14. Provide the soft link to Apache tomcat directory:
    sudo ln -s /usr/share/apache-tomcat-8.5.5 /usr/share/tomcat

  15. Install the apache server:
    apt-get install apache2

  16. Load and source the environment configurations of apache2 server:
    source /etc/apache2/envvars

  17. Start the Apache server:
    /etc/init.d/apache2 start

  18. To print the process info of apache server:
    ps -ef | grep apache

  19. Install the MySql server:
    sudo apt-get install mysql-server

  20. Now we will need to add the character-set-server=utf8 line to the my.cnf file(read the next step)

  21. Open the my.cnf file in nano file editor using nano /etc/mysql/my.cnf and add this line character-set-server=utf8 at the end of the file
    (You can exit the nano editor with Ctrl+x , then type y at the prompt and hit Enter)

  22. Login to MySQL:
    mysql -u root -p
    Enter your password at the prompt

  23. Execute following commands in Mysql interpreter:

    Create a database user called webanno with your password 'enter_your_password' which is later used by the application to access the database (instructions for settings.properties file below).

    mysql> CREATE DATABASE webanno DEFAULT CHARACTER SET utf8 COLLATE utf8_bin ;

    mysql> CREATE USER 'webanno'@'localhost' IDENTIFIED BY 'enter_your_password';

    mysql> GRANT ALL PRIVILEGES ON webanno.* TO 'webanno'@'localhost';

    mysql> exit

  24. Install aptitude package manager with following command:
    aptitude install tomcat8-user authbind

  25. Create a directory called /opt:
    cd /opt/

  26. Create a new Tomcat Instance:
    tomcat8-instance-create -p 18080 -c 18005 webanno

  27. Change the permissions of /opt/webanno:
    chown -R www-data /opt/webanno

  28. Open the webanno configuration file in nano editor using:
    nano /etc/init.d/webanno

  29. Paste the following script in the file:

    #!/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
    }

You can exit the nano editor with Ctrl+x , then type y at the prompt and hit Enter

  1. Change the permissions of the above script file to an executable:
    chmod +x /etc/init.d/webanno

  2. Update the boot script to include webanno while starting system:
    update-rc.d webanno defaults

  3. Download the Webanno Web archive(.WAR) file:
    wget https://github.com/webanno/webanno/releases/download/webanno-3.2.2/webanno-webapp-3.2.2.war

  4. Moving the .WAR file to /opt/webanno/webapps:
    cp webanno-webapp-3.2.2.war /opt/webanno/webapps/webanno.war

  5. Create a directory /srv/webanno using following command:
    mkdir /srv/webanno

  6. Open the file settings.properties in the nano editor:
    nano /srv/webanno/settings.properties

  7. Paste the following properties definition:

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=1000000

# 60 * 5 = 5 minutes
backup.interval=1000

backup.keep.number=10

ui.brat.sentences.number = 5
You can exit the nano editor with `Ctrl`+`x` , then type `y` at the prompt and hit `Enter`
  1. Change the permissions of webanno home directory:
    chown -R www-data /srv/webanno

  2. Finally, Start WebAnno!

    service webanno start

    WebAnno will be up and running at http://localhost:18080/webanno

  3. Following commands will display all the active ports with the service name:
    netstat -lp


Following are the commands to run ngrok. (No need to run the following commands if we are exposing the Port on web using the instance IP)
40. wget https://bin.equinox.io/c/4VmDzA7iaHb/ngrok-stable-linux-amd64.zip
41. unzip ngrok-stable-linux-amd64.zip
42. apt-get install unzip
43. unzip ngrok-stable-linux-amd64.zip
45. ./ngrok authtoken
46. ./ngrok http 18080
47. nano /root/.ngrok2/ngrok.yml
48. nohup ./ngrok http 18080
49. nano nohup.out
50. ngrok -log=stdout 18080 > ngrok.log &
51. ps -ef | grep ngrok

Reference:

Official WebAnno Installation guide Installation steps are available on this link but it's not up-to-date and it assumes you have server installed with a user called www-data.

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