Please read [[Docker HowTo Install]] before installing i2b2

== Prerequisites if required

'''Step 1 - Install Docker'''

[[Docker HowTo Install]]

'''Step 2 - Install Git''' 

    {{{$ sudo apt-get update }}}

    {{{$ sudo apt-get install git }}}

== Install using Docker

This will install i2b2 1.7.08

1. On the host machine go to directory

    {{{/local/docker/<USER>/}}}

2. Go to this directory and checkout from git docker_i2b2_1708_fresh

    {{{sudo git clone https://github.com/LCBRU/docker_i2b2_1708_fresh.git}}}

    {{{sudo chmod -R 777 docker_i2b2_1708_fresh/}}}

A README.md file is available here.

This will create a directory /local/docker/<USER>/docker_i2b2_1708_fresh

3. Go to the folder 'scripts' and view the file CreateDatabase.sql

Run these on your Microsoft sql database only if you are creating a new i2b2 install.

4. The main configuration files are :

   {{{i2b2-1.7.08-install-procedures/config/config.properties}}} 

   {{{i2b2-1.7.08-install-procedures/config/defaults.sh}}} 

   {{{i2b2-1.7.08-install-procedures/bin/compositions/install-all.sh}}} 

5. In the file install-all.sh, make sure that you comment out the line :

   {{{# $I2B2_INSTALL_PROCS_HOME/bin/installs/6-data-install.sh $JOB_NAME}}} 

   also look at files in the folder :

   {{{docker_i2b2_1708_fresh/i2b2-1.7.08-install-procedures/merge-files/sqlserver/data/sql}}}

If you have a fresh database uncomment it.

6. Modify the following files :

   {{{docker_i2b2_1708_fresh/www/admin/i2b2_config_data.js}}}

   {{{docker_i2b2_1708_fresh/www/main/i2b2_config_data.js}}}

   {{{docker_i2b2_1708_fresh/www/webclient/i2b2_config_data.js}}}

Make sure urlCellPM contains the correct server i.e. "http://uhlbriccsapp03.xuhl-tr.nhs.uk

7. Build Docker container

   {{{sudo docker build -t lcbruit/i2b2:v1.7.08 .}}}

8. Run container

   {{{sudo docker run -v /share:/share -itd -p 80:80 -p 8080:8080 -p 9990:9990 -p 9090:9090 lcbruit/i2b2:v1.7.08}}}

9. Open URL

   {{{http://<HOST>.xuhl-tr.nhs.uk/admin}}}

   {{{http://<HOST>.xuhl-tr.nhs.uk/main}}}

   {{{http://<HOST>.xuhl-tr.nhs.uk/webclient}}}

10. Use the following to connect to server :

   {{{sudo docker ps -a}}}

   {{{sudo docker exec -i -t [CONTAINER ID] /bin/bash}}}

11. To stop and start tomcat use :

   {{{/i2b2/jboss/bin/jboss-cli.sh --connect command=:shutdown}}}

   {{{/i2b2/jboss/bin/standalone.sh -b 0.0.0.0}}}


Useful locations

https://github.com/LCBRU/docker_i2b2_1708_fresh/tree/master/datasources

https://github.com/LCBRU/docker_i2b2_1708_fresh/tree/master/i2b2-1.7.08-install-procedures/merge-files/sqlserver/data/sql