Developers Getting Started With i2b2
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Printable version of this worksheet



One of the benefits of the i2b2 software is its flexibility in that it is completely customizable to meet the needs of your institution. This flexibility means there are a number of configurable settings that need to be modified with your site specific information. This worksheet is designed to assist you with keeping track of the various directories, ports, hosts and database settings that are specific to your environment. These variables are referenced in the i2b2 Installation document and the values will be needed when configuring your i2b2 database(s) and software for installation.

 

Tip

You may want to use this worksheet in conjunction with Appendix B - i2b2 Installation Checklist.

 

Location of Software Directories


During the installation you will be downloading and extracting software that will be used during the installation process. The following table will help you keep track of where this software is located in your environment.

 

Software

Reference in i2b2 Document  

Root Directory Path                     

JAVA (JDK)

YOUR_JAVA_HOME_DIR

 

JBoss 7

YOUR_JBOSS_HOME_DIR

 

Apache Ant

YOUR_ANT_HOME_DIR

 

i2b2 Database Scripts

YOUR_I2B2_DATA_DIR

 

i2b2 Source Code

YOUR_I2B2_SRC_DIR

 

i2b2 Web Client Directory (Source Code)  

YOUR_I2B2_WC_DIR

 

i2b2 Workbench

YOUR_I2B2_WB_DIR

 

 

Example Locations


The following table contains the location examples provided in the installation documentation.

 

Software

Reference in i2b2 Document  

Root Directory Path (Linux)  

Root Directory Path (Windows)

JAVA (JDK)

YOUR_JAVA_HOME_DIR

/opt/java/jdk1.7.0_51/

C:\Program Files\Java\jdk1.7.0_51\  

JBoss 7

YOUR_JBOSS_HOME_DIR

/opt/jboss-as-7.1.1.Final/

C:\opt\jboss-as-7.1.1.Final\

Apache Ant

YOUR_ANT_HOME_DIR

/opt/apache-ant-1.8.4/

C:\opt\apache-at-1.8.4\

i2b2 Database Scripts

YOUR_I2B2_DATA_DIR

/opt/data/

C:\opt\data\

i2b2 Source Code

YOUR_I2B2_SRC_DIR

/opt/i2b2/

C:\opt\i2b2\

i2b2 Web Client Directory (Source Code)  

YOUR_I2B2_WC_DIR

/opt/webclient/

C:\opt\webclient\

i2b2 Workbench

YOUR_I2B2_WB_DIR

/applications/

C:\Program Files\

 

JBoss Port Settings


The following table can be used to keep track of the ports in your environment.

Name  

JBoss Default Port  

i2b2 Default Port  

Your Port       

ajp

8008

9009

 

http

8080

9090

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Host and Domain Settings


The following table can be used to keep track of your host and domain information for the i2b2 Administration Module and Web Client.

 

Client   

IP Address / Hostname  

Domain   

i2b2 Host (name)  

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

i2b2 Pre-configured (Default) Host and Domain Settings

 

Client

IP Address / Hostname

Domain

i2b2 Host (name)  

i2b2 Admin

127.0.0.1

i2b2demo  

i2b2demo

i2b2 Web Client  

services.i2b2.org
127.0.0.1

i2b2demo
i2b2demo

HarvardDemo
i2b2demo (1.7)

 

Cell Locations


The i2b2 cells can be installed on different machines in your environment. The location of the cells are needed when configuring the different property files as well as setting up your cells in i2b2 Admin. You can use the following table to keep track of where these cells are installed in your network.

 


Name


Cell ID   

Default Cell Location
    (Hostname:Port)

Your Cell Location
   (Hostname:Port)     

Data Repository Cell

CRC

localhost:9090

 

File Repository Cell

FRC

localhost:9090

 

Identity Management Cell

IM

localhost:9090

 

Ontology Management Cell

ONT

localhost:9090

 

Project Management Cell

PM

localhost:9090

 

Workplace Cell

WORK

localhost:9090

 

 

Database Drivers


Incorrect driver information in a configuration file is often the source of database connection errors. The following table is a guide for you to reference when setting your database properties and configuring you data sources.

 

Type of Database

JDBC (URL)

Driver-Class

Driver

Oracle

oracle:thin

oracle.jdbc.driver.OracleDriver

ojdbc6.jar

PostgreSQL

postgresql

org.postgresql.Driver

postgresql-9.2-1002.jdbc4.jar

SQL Server

sqlserver

com.microsoft.sqlserver.jdbc.SQLServerDriver

sqljdbc4.jar

 

Database Location / Configuration / Users


Each cell has a set of tables that are created and loaded with data during the Data Installation chapter. The location of these tables, the name of the database / schema as well as the user information is captured when configuring each cell for installation. The following table will help you keep track of the database / schema names, their locations and the database user for each grouping of i2b2 Data Tables.

 

Note

i2b2 is fairly flexible in that it does not require all your data tables to reside in the same location. For instance, you may want to install the PM data tables in a different location than those for the Ontology Cell. If this is the case then the following table can help you keep track of the different tables are installed.


i2b2 Data Tables  


Database / Schema Name  

Database Location
    (Host:Port)

Database
Username  

Database
Password  


Project  

Crcdata

 

 

 

 

 

Hivedata

 

 

 

 

 

Imdata

 

 

 

 

 

Metadata

 

 

 

 

 

Pmdata

 

 

 

 

 

Workdata

 

 

 

 

 

 

i2b2 Demo Data Default Configuration


The following table outlines the default configurations that are delivered with the i2b2 software. It is configured for the i2b2 demo domain as a local host.

 


i2b2 Data Tables  


Database / Schema Name  

Database Location
    (Host:Port)

Database
Username  

Database
Password  


Project  

Crcdata

i2b2demodata

localhost:1521

i2bdemodata

demouser

demo

Hivedata

i2b2hive

localhost:1521

i2b2hive

demouser

 

Imdata

i2b2imdata

localhost:1521

i2b2imdata

demouser

demo

Metadata

i2b2metadata

localhost:1521

i2b2metadata

demouser

demo

Pmdata

i2b2pm

localhost:1521

i2b2pm

demouser

 

Workdata

i2b2workdata

localhost:1521

i2b2workdata

demouser

demo