This checklist is designed to assist you in the installation of the i2b2 Server and Clients. It is organized to coincide with the installation chapters. The items appear in the checklist in the order in which they need to occur during the installation.

Note

This checklist is not a replacement for the i2b2 Installation Guide. The guide itself contains detailed information, important notes and warnings as well as helpful tips.

Installation Overview

Environment:	Demo / Test / Production / Other	Version of i2b2:
Domain ID:		Domain Name:
Setup Date:		Setup By:

Installation Order and Resources

Installation Order	Checklist Name	Install Guide Resource
1. System and Software Requirements	Requirements Checklist	Chapter 2. Requirements
2. Data Installation	Data Checklist	Chapter 3. Data Installation
3. Deploying the server-common	Server-Common Checklist	Chapter 4. i2b2 Server-Common Install
4. PM Cell Installation	PM Checklist	Chapter 5. Project Management (PM) Cell Install
5. i2b2 Admin Installation	i2b2 Admin Checklist	Chapter 6. i2b2 Administration Module Install
6. i2b2 Web Client Installation	i2b2 Web Client Checklist	Chapter 7. i2b2 Web Client Install
7. i2b2 Workbench Installation	i2b2 Workbench Checklist	Chapter 8. i2b2 Workbench Install
8. ONT Cell Installation	ONT Checklist	Chapter 9. Ontology Management (ONT) Cell Install
9. CRC Cell Installation	CRC Checklist	Chapter 10. Data Repository (CRC) Cell Install
10. WORK Cell Installation	WORK Checklist	Chapter 11. Workplace (WORK) Cell Install
11. FR Cell Installation	FR Checklist	Chapter 12. File Repository (FR) Cell Install
12. IM Cell Installation	IM Checklist	Chapter 13. Identity Management (IM) Cell Install
13. Setting up i2b2	Initial i2b2 Setup Checklist	Chapter 14. Initial Setup of i2b2 in Admin

Things To Keep In Mind

For the most part the installation of the different i2b2 Core Cells involves steps that are very similar. For instance, they all have a build.properties file where you will need to set the jboss.home and axis2.war.name properties for the cell you will be deploying.

Based on feedback provided by our users, a common area for confusion and errors seems to be around the configuration of the data sources for each cell. Here are some things to keep in mind that will hopefully eliminate or at least minimize any confusion around defining your datasources.

1. The PM, ONT, CRC, WORK, and IM cells each have a ds.xml file that needs to be updated before deploying the cell. (pm-ds.xml, ont-ds.xml, crc-ds.xml, work-ds.xml, and im-ds.xml)

2. At least two datasources have to be defined in the ds.xml files for the ONT, CRC, WORK, and IM Cells.

The BootstrapDS datasource points to the DB_LOOKUP tables that are part of the Hivedata tables.
The DemoDS datasource points to the tables for the cell you are configuring.

3. The PM Cell has only one datasource (PMBootsrapDS) defined and it points to the location of the Pmdata tables.

Note

Depending on how you have setup your database environment the Pmdata tables may or may not be in the same location as your Hivedata tables.

4. The <connection-url> for every <datasource> defined in each ds.xml file needs to be updated with information that is specific to your environment.

Update the <connection-url> with the correct JDBC information for your type of database.
The address in the URL needs to point to either the location of your hivedata tables (BootstratpDS) or the tables for your cell (DemoDS).

5. The <driver-class> and <driver> for each <datasource> needs to be defined correctly for the type of database you are connecting to.

Important

Depending on your environment, the default of localhost may not be appropriate for you. Some systems require the I.P. address instead of the alias name.

6. The <username> and <password> for each <datasource> needs to match the database users you setup during the data installation.

The following table shows the usernames and passwords for the i2b2 demo environment.

Data Package	Cell Owner	Database / Schema Name	User Name	Password
Crcdata	Data Repository (CRC)	i2b2demodata	i2b2demodata	demouser
Hivedata	Project Management (PM)	i2b2hive	i2b2hive	demouser
Imdata	Identity Management (IM)	i2b2imdata	i2b2imdata	demouser
Metadata	Ontology Management (ONT)	i2b2metadata	i2b2metadata	demouser
Pmdata	Project Management (PM)	i2b2pm	i2b2pm	demouser
Workdata	Workplace (WORK)	i2b2workdata	i2b2workdata	demouser

Tip

Obviously the passwords and possible the usernames will be different for those databases that contain your real patient data. The Install Worksheet (Appendix A) can be used to document and organize the settings for your environment. The worksheet is particularly useful if you are setting up multiple environments and need to keep track of the settings for each environment.

7. Multiple projects with different data sources.

Need to add an additional <datasource> section for each project data source.
In addition to updating the connection-url, drivers and database user information you also need to update both the jndi-name and pool-name to reflect the name of the other projects.

Important

Any changes made to a cell's ds.xml file after it has been deployed will require you to re-deploy the cell in order for the changes to take effect.

In addition to the ds.xml files, several cells have additional "data configurations" defined in their property files. These additional data configurations are typically defining the schema / database name and location of your Hivedata tables so the cells can lookup relevant information.

Installation Checklists

Requirements Checklist

Step	File Name or Comment	Completed
*Database Requirements*
Installed a Database Management System supported by i2b2	Oracle / PostgreSQL / SQLServer
*Browser Requirements*
Installed a web browser supported by i2b2	Firefox / Internet Explorer / Safari
*i2b2 Server Requirements*
Installed Java JDK 8.0 on your i2b2 Server
Installed WildFly 17.0.0 Application Server on your i2b2 Server
Set WildFly logging level to INFO
Documented WildFly port; if other than 9090 then install scripts have to be updated
Setup WildFly to run as either a Linux or Windows service
Installed Apache Ant 1.9.6 on your i2b2 Server
Installed Apache Axis2 1.6.2 on your i2b2 Server
Set your system environment variables on your i2b2 Server
*Web Server Requirements*
Installed/Configured cURL on your web server	Only required for Linux Machines
Installed IIS on your web server	Only required for Windows Machines
Installed Php: Hypertext Preprocessor on your web server	Required for both Linux and Windows Machines
*i2b2 Software Requirements*	Downloaded zip files from i2b2.org
i2b2 data installation scripts
i2b2 core source code
i2b2 Web Client code
i2b2 Workbench application for Macintosh or Windows
i2b2 VMWare image of the i2b2 Core Server	Optional

Data Checklist

Step	File Name or Comment	Completed
Extracted the i2b2 data package to a directory of your choice	YOUR_I2B2_DATA_DIR
Created database user accounts for all the i2b2 schemas
*Crcdata*
Set the database properties	db.properties
Created the Crcdata tables
Created the stored procedures
Loaded the data into the Crcdata tables	*Type of data loaded:* i2b2 demo data or your local data
*Hivedata*
Set the database properties	db.properties
Created the Hivedata tables
Loaded the data into the Hivedata tables	*Type of data loaded:* i2b2 demo data or your local data
*Imdata*	*Optional Cell*
Set the database properties	db.properties
Created the Imdata tables
Loaded the data into the Imdata tables	*Type of data loaded:* i2b2 demo data or your local data
*Metadata*
Set the database properties	db.properties
Created the Metadata tables
Loaded the data into the Metadata tables	*Type of data loaded:* i2b2 demo data or your local data
*Pmdata*
Set the database properties	db.properties
Created the Pmdata tables
Created the PM triggers
Loaded the data into the Pmdata tables	*Type of data loaded:* i2b2 demo data or your local data
*Workdata*
Set the database properties	db.properties
Created the Workdata tables
Loaded the data into the Workdata tables	*Type of data loaded:* i2b2 demo data or your local data

Server-Common Checklist

Step

File Name or Comment

Completed

Extracted the i2b2 source code to a directory of your choice

YOUR_I2B2_SRC_DIR

Configured the build properties

build.properties

Deployed edu.harvard.i2b2.server-common

PM Checklist

Step	File Name or Comment	Completed
Configured the PM build properties	build.properties
Configured the datasources for the PM Cell	pm-ds.xml
Deployed edu.harvard.i2b2.pm
Verified the installation of the PM Cell

i2b2 Admin Checklist

Warning

The Admin Module and the Web Client each have their own folder that contains the necessary files to run the respective application. Both the admin and webclient folders contain files with similar names which can be a source of confusion. Therefore it is important to make sure you are editing the files in the admin folder and not the ones that reside in the webclient folder.

In addition to the above, you also want to make sure you are editing the admin files in your webserver directory and not the ones that reside in YOUR_I2B2_SRC_DIR.

Step	File Name or Comment	Completed
Copied Admin files to your web server directory
Configured the Domain information for your Admin Module	See note at end of this table
Commented out or removed the pre-configured domain of i2b2demo	See note at end of this table
Added the domain information for your environment	i.e. test and production
Verified the installation of the i2b2 Admin

Note

The i2b2 Admin is pre-configured with the following domain information:

The domain is i2b2demo

The URL points to the local PM in your i2b2 demo environment

If you comment out or remove this domain then i2b2 will not work in your demo environment.

i2b2 Web Client Checklist

Warning

The Admin Module and the Web Client each have their own folder that contains the necessary files to run the respective application. Both the admin and webclient folders contain files with similar names which can be a source of confusion. Therefore it is important to make sure you are editing the files in the webclient folder and not the ones that reside in the admin folder.

In addition to the above, you also want to make sure you are editing the web client files in your webserver directory and not the ones that reside in YOUR_I2B2_WC_DIR.

Step	File Name or Comment	Completed
Extracted the i2b2 Web Client code to a directory of your choice	YOUR_I2B2_WC_DIR
Copied Web Client files to your web server directory
Configured the Proxy information for your environment
Using the default PHP proxy file that is included with the i2b2 Software
Update security configurations in the PHP proxy
Verified the correct proxy is defined in the Web Client's config file (i2b2_config_data.js)
Not using the default PHP proxy file that is included with the i2b2 Software
Write your own proxy file
Update the urlProxy in the Web Client's config file to reflect the correct proxy (i2b2_config_data.js)
Configured the Domain information for your Web Client	See note at end of this table
Commented out, or removed the default domain of HarvardDemo	Optional
Added the i2b2demo domain for your i2b2 demo environment
Added the domain information for your environment	i.e. test and production
Verified the installation of the i2b2 Web Client

Note

The i2b2 Web Client is pre-configured with the following domain information:

The domain is HarvardDemo

The URL points to the public i2b2 in your i2b2.org site

If you comment out or remove this domain then i2b2 Web Client will not be able to connect to the public i2b2 site.

i2b2 Workbench Checklist

Step

File Name or Comment

Completed

Extracted the i2b2 Workbench files to a directory of your choice

YOUR_I2B2_WB_DIR

Configured the Workbench properties with the location of your hive

i2b2workbench.properties

Verified the installation of the i2b2 Workbench

ONT Checklist

Step

File Name or Comment

Completed

Configured the Ontology build properties

build.properties

Configured the Ontology application directory properties

ontology_application_directory.properties

Configured the following Ontology properties

ontology.properties

Set the Metadata Schema Name

Location of the Hivedata tables

Set the Project Management Cell Integration Properties

Settings to locate and communicate with the PM Cell

Set the File Management Cell Properties

Settings to locate and communicate with the FRC Cell

Set the CRC Cell Properties

Settings to locate and communicate with the CRC Cell

Set the Ontology Service Account Properties

Set the metadata delimiter property

Configured the data sources for the Ontology Cell

ont-ds.xml

Deployed edu.harvard.i2b2.ontology

Updated the ONT Cell Data in the i2b Admin Module

Verified the installation of the Ontology Cell

CRC Checklist

Step	File Name or Comment	Completed
Configured the CRC build properties	build.properties
Configured the CRC application directory properties	crc_application_directory.properties
Configured the following CRC Loader properties	edu.harvard.i2b2.crc.loader.properties
Set the File Management Cell Properties	Settings to locate and communicate with the FRC cell
Set the Project Management Cell Properties	Settings to locate and communicate with the PM Cell
Configured the datasource lookups for the CRC Loader	CRCLoaderApplicationContext.xml edu.harvard.i2b2.crc.loader.properties
Configured the following CRC properties	crc.properties
Set the Project Management Cell Properties	Settings to locate and communicate with the PM Cell
Set the CRC Datasource Lookup Properties	Location of your hivedata tables and the type of database
Set the Ontology Cell Properties	Settings to locate and communicate with the ONT Cell
Set the CRC Service Account Properties
Set the PDO paging properties	Optional performance property
Set the Analysis plug-in: Queue properties	Optional performance property
Set the Setfinder query: Timeout properties	Optional performance property
Set the Setfinder query: Lockout properties	Optional performance property
Set the Setfinder query: Temp table properties	Optional performance property
Configured the data sources for the CRC Cell	crc-ds.xml
Deployed edu.harvard.i2b2.crc
Updated the CRC Cell Data in the i2b Admin Module
Updated the metadata key in the CRC Tables	QT_BREAKDOWN_PATH table
Verified the installation of the CRC Cell

WORK Checklist

Step	File Name or Comment	Completed
Configured the Workplace build properties	build.properties
Configured the Workplace application directory properties	workplace_application_directory.properties
Configured the following Workplace properties	workplace.properties
Set the Metadata Schema Name	Location of the Hivedata tables
Set the Project Management Cell Integration Properties	Settings to locate and communicate with the PM Cell
Configured the data sources for the Workplace Cell	work-ds.xml
Deployed edu.harvard.i2b2.workplace
Updated the WORK Cell Data in the i2b Admin Module
Verified the installation of the Workplace Cell

FR Checklist

Step	File Name or Comment	Completed
Configured the File Repository build properties	build.properties
Configured the File Repository application directory properties	fr_application_directory.properties
Configured the following File Repository properties	edu.harvard.i2b2.fr.properties
Set the Project Management Cell Integration Properties	Settings to locate and communicate with the PM Cell
Deployed edu.harvard.i2b2.fr
Updated the FRC Cell Data in the i2b Admin Module

IM Checklist

Step	File Name or Comment	Completed
Configured the IM build properties	build.properties
Configured the IM application directory properties	im_application_directory.properties
Configured the following IM properties	ontology.properties
Set the Metadata Schema Name	Location of the Hivedata tables
Set the Project Management Cell Properties	Settings to locate and communicate with the PM Cell
Set the Patient in Project Property
Set the EMPI Service Properties	Optional 3rd party EMPI Service
Configured the data sources for the IM Cell	im-ds.xml
Deployed edu.harvard.i2b2.im
Updated the IM Cell Data in the i2b Admin Module

Initial i2b2 Setup Checklist

Step

File Name or Comment

Completed

Hive Data Management

Updated the Help URL for your environment

Optional

Verified Domain Name is entered correctly in i2b2 Admin

Defined the type of environment

Cell Data Management

Verified the information for each of your cells is entered correctly; particularly the cell id and cell url

Defined any cell specific parameters

User Management

Entered at least one i2b2 user in i2b2 Admin

Defined any user specific parameters

Project Management

Entered at least one project in i2b2 Admin

Defined any project specific parameters

i.e. Unit Conversion for Numerical Observations or Enable Process Timing

At least one user given access to the project and defined their level of access

Defined any project-user parameters

Setup i2b2 Authentication Method of Active Directory

Optional

Added parameter for authentication method

Added parameter for PDC Domain of your NT domain

Added parameter for the connection URL of your NT domain

Setup i2b2 Authentication Method of LDAP

Optional

Added parameter for authentication method

Added parameter for the connection URL of your LDAP server

Added parameter for search base

Added parameter for distinguished name

Added parameter for security authentication

Added parameter for ssl

Added parameter for security layer

Added parameter for privacy strength

Added parameter for max buffer

Installation Overview

Installation Order and Resources

Things To Keep In Mind

Installation Checklists

Requirements Checklist

Data Checklist

Server-Common Checklist

PM Checklist

i2b2 Admin Checklist

i2b2 Web Client Checklist

i2b2 Workbench Checklist

ONT Checklist

CRC Checklist

WORK Checklist

FR Checklist

IM Checklist

Initial i2b2 Setup Checklist

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Appendix B - i2b2 Installation Checklist

Installation Overview

Installation Order and Resources

Things To Keep In Mind

Installation Checklists

Requirements Checklist

Data Checklist

Server-Common Checklist

PM Checklist

i2b2 Admin Checklist

i2b2 Web Client Checklist

i2b2 Workbench Checklist

ONT Checklist

CRC Checklist

WORK Checklist

FR Checklist

IM Checklist

Initial i2b2 Setup Checklist

Pages

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