Developers Getting Started With i2b2
Space shortcuts
Space Tools
Skip to end of metadata
Go to start of metadata

Printable version of this worksheet



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 7.0 on your i2b2 Server


Installed JBoss 7.1.1 Application Server on your i2b2 Server


Set JBoss logging level to INFO


Documented JBoss port; if other than 9090 then install scripts have to be updated


Setup JBoss to run as either a Linux or Windows service


Installed Apache Ant 1.8.2 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 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


$body

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