i2b2 Installation Guide i2b2 Server and Clients

This is a long (300 page) document - reference at end of this article. Selected sections are included to direct searches here.

1 Installation Process

Installation Overview

It is critical that you follow this guide in the order that the steps are written. Some steps have to occur before others. For instance the PM Cell has to be installed before any other cells.  The chapters are organized in the order in which the installation has to occur.

For instance, Chapter 5 addresses the installation of the PM Cell; Chapter 6 address the installation of the Web Client and Chapter 7 address the installation of the Ontology Cell. The reason the Web Client is chapter 5 is because you need the Admin module, which is part of the web client installed before you can finish installing the PM Cell. The reason you can’t install the web client first is because the PM Cell needs to be deployed first. It is for this reason we highly recommend you follow the chapters in the order in which they are written.

Order of Installation

The following is a high level overview of the order that will be taken during this installation process. As stated earlier it is important that you don't jump around. It is also recommended that you review each chapter as there are steps within the chapters that need to be followed.

Step 1:   Software and System Requirements

Step 2:   Data Installation

Step 3:   i2b2 Server-Common Install

Step 4:   Project Management (PM) Cell Install

Step 5:   i2b2 Administration Module Install

Step 6:   i2b2 Web Client Install

Step 7:   i2b2 Workbench Install

Step 8:   Ontology Management (ONT) Cell Install

Step 9:   Data Repository (CRC) Cell Install

Step 10:   Workplace Framework (WORK) Cell Install

Step 11:   File Repository (FR) Cell Install

Step 12:   Identity Management (IM) Cell Install (Optional)

Step 13:   Initial Setup of i2b2 in Admin

Next Steps

The next step is to proceed to the Software Requirements chapter where you will be setting up your environment with the necessary software from third parties such as JBoss and Apache Ant.

2 Software and System Requirements

The i2b2 has a number of software and system requirements which have been outlined in this chapter for you to review. Some of the requirements involve the installation of additional software from various third parties and when appropriate we have outlined the steps to install and configure it to work in your i2b2 environment.

2.2 Database Requirements

The i2b2 data is stored in a relational database in a star schema format. Currently, the i2b2 supports three different database management systems (DBMS); Only one of them is required to store your i2b2 data.

1. Oracle
2. PostgreSQL
3. SQL Server

The DBMS you choose to use is dependent on what works best for your institution. At this point in the installation all that we require is that you have a DBMS setup in your environment.

If you do not have a DBMS currently setup then you will need to do so at this point in the installation. The setup of the DBMS is specific to the version you are installing, therefore we recommend you follow the installation procedures documented by the vendor providing the software. The following table provides the links to the websites for each DBMS.

DBMS	Website
Oracle	http://www.oracle.com/us/downloads/index.html
PostgreSQL	http://www.postgresql.org/download/
SQL Server	http://www.microsoft.com/en-us/sql-server/

2.3 Browser Requirements

A web browser is required to use the i2b2 Web Client and Administration Module. The following three browsers are currently supported:

Firefox

Microsoft Internet Explorer (I.E.) Safari

Important JavaScript must be enabled in your web browser.

i2b2 Server Requirements

  Install Java JDK 7.0 on your i2b2 Server.

  Install JBoss 7.1.1 Application Server on your i2b2 Server.

  Install Apache Ant 1.8.2 on your i2b2 Server.

  Install Apache Axis2 1.6.2 on your i2b2 Server.

  Set your system environment variables on your i2b2 Server.

Web Server Requirements

  Install IIS on your web server Windows machine only.

  Installe Curl on your web server Linux machine only.

  Install Php: Hypertext Preprocessor on your web server.

 i2b2 Software Requirements

  Download the i2b2 data installation scripts.

  Download the i2b2 core source code.

  Download the i2b2 Web Client code.

  Download the i2b2 Workbench application for Windows or Macintosh.

  Download the VMWare image of the i2b2 Core Server. Optional

3 Data Installation

Extract the i2b2 data package

Create database user accounts for i2b2 schemas

Create the tables and loaded the data for the following:

• Crcdata
• Hivedata
• Imdata
• Metadata
• Pmdata
• Workdata

4 i2b2 Server-Common Install

Extract the i2b2 source code to a directory of your choice (YOUR_I2B2_SRC_DIR)

Stop JBoss Services

Deploy edu.harvard.i2b2.server-common

5 Project Management (PM) Cell Install

Stop JBoss services

Configure the build properties

Configure the data sources

Deploy edu.harvard.i2b2.pm

Start JBoss services

Verify installation

• PM Web Services are running

6 i2b2 Administration Module Install

Copy Admin files to web server directory

Configure Admin for the your domain (i2b2demo)

Verify the installation

7 i2b2 Web Client Install

Copy Web Client files to web server directory

Configure Web Client for your domain

Verify installation

8 i2b2 Workbench Install

Extract the i2b2 Workbench files

Configure the Workbench properties

Update the Workbench properties file with the hive location

Update physical memory (Windows only and optional step)

Verify installation

9 Ontology Management (ONT) Cell Install

Stop JBoss services

Configure the build properties

Configure the application directory properties

Configure the Ontology properties

Set the Metadata Schema Name (location of hivedata tables)

Set the PM cell properties

Set the FR cell properties

Set the CRC cell properties

Set the metadata delimiter property

Deploy edu.harvard.i2b2.ontology

Start JBoss services

Verify installation

10 Data Repository (CRC) Cell Install

Stop JBoss services

Configure the build properties

Configure the application directory properties

Configure the CRC Loader properties

Configure FR cell properties

Configure PM cell properties

Configure data source lookup (schema name for hivedata tables)

Configure the CRC properties

Configure PM cell properties

Configure data source lookup (schema name for hivedata tables)

Configure ONT cell properties

Configure CRC service account properties

Configure the optional “performance” properties

Configure the data sources

Deploy edu.harvard.i2b2.crc

Start JBoss services

Verify installation

11 Workplace (WORK) Cell Install

Stop JBoss services

Configure the build properties

Configure the application directory properties

Configure the Workplace properties

Set the Metadata Schema Name (location of hivedata tables)

Set the PM cell properties

Configure the data sources

Deploy edu.harvard.i2b2.workplace

Start JBoss services

Verify installation

12 File Repository (FR) Cell Install

Stop JBoss services

Configure the build properties

Configure the application directory properties

Configure the FR Properties: Defined the PM cell

Deploy edu.harvard.i2b2.fr

Start JBoss services

Verify installation

13 Identity Management (IM) Cell Install

Stop JBoss services

Configure the build properties

Configure the application directory properties

Configure the IM properties

Set the Schema Name (location of hivedata tables)

Set the PM cell properties

Set the properties for a third party EMPI service Optional

Configure the data sources

Deploy edu.harvard.i2b2.im

Start JBoss services

Verify installation

14 Initial Setup of i2b2 in Admin

Hive Data Management

• Edit Hive Data
• Add, Edit and Delete Hive Parameters

Cell Data Management

• Add, Edit and Delete Cell Data
• Add, Edit and Delete Cell Parameters

User Data Management

• Add, Edit and Delete User Data
• Add, Edit and Delete User Parameters

Project Data Management

• Add, Edit and Delete Project Data
• Add, Edit and Delete Project Parameters
• Add and Remove Users to/from a Project
• Add and Edit User Role(s)
• Add, Edit and Delete Project User Parameters

Authentication in i2b2

• Active Directory Authentication
• LDAP Authentication

Optional Parameters

• Unit Conversion for Numerical Observations
• Enable Process Timing

15 Troubleshooting Installation Errors

16 Licenses

The i2b2 source code is licensed under the i2b2 Software License 2.1. This includes but is not limited to all code in the edu.harvard.i2b2.* package namespace.

The i2b2 Web Client uses three open source JavaScript Libraries:

1. Yahoo! User Interface (YUI)
2. Prototype
3. Firebug

The code and respective license agreements for the above libraries can be found in the js-ext directory.

 

References

1. June 2014 (i2b2 v1.7) Original document https://www.i2b2.org/software/files/PDF/current/i2b2Workbench_Installation_Guide.pdf