i2b2 WorkBench Developers Guide: Eclipse Neon & i2b2 Source Code 

About this guide

Informatics for Integrating Biology and the Bedside (i2b2) began as one of the sponsored initiatives of the NIH Roadmap National Centers for Biomedical Computing (http://www.bisti.nih.gov/ncbc/).

One of the goals of i2b2 is to provide clinical investigators with the software tools necessary to collect and manage project-related clinical research data in the genomics age as a cohesive entity; a software suite to construct and manage the modern clinical research chart.

This guide is designed to provide an overview of installing and configuring the i2b2 Workbench within the Eclipse IDE. 

Document management

Prerequisites

There are a few requirements that need to be met before you can continue with the developer’s guide for the i2b2 Workbench. Mainly, you need to make sure the third-party software listed below has been downloaded and installed on the same machine that you will be running the i2b2 source code on. You will also need to download the 

Third-Party Software

There are a few requirements that need to be met before you can continue with the developer’s guide for the i2b2 Workbench. The next couple of sections outline these requirements.

Java JDK

There are two things to know about the i2b2 Workbench and Java JDK / JRE:

1. The i2b2 Workbench Application / Executable requires JRE to be installed on the same machine. If it is missing then a user will receive an error when trying to log into the i2b2 Workbench.
2. To build your Workbench plugins in Eclipse, JDK / JRE must be installed on the same machine as your Eclipse application. Otherwise you will receive errors and will not be able export the workbench application or build custom JAR files.

Eclipse

The i2b2 Workbench is a series of components that are designed as an Eclipse-based plugin and therefore the Eclipse SDK is an integral piece of software when developing new plugins for the i2b2 Workbench. 

The latest version of the i2b2 Workbench (2.0.01) has been upgraded to work with Eclipse (Neon). The second prerequisite is to download and install version 4.x of the Eclipse SDK (Neon) from the Eclipse website by going to:  https://www.eclipse.org/neon/

Further information regarding the eclipse product can be found on their website (http://www.eclipse.org/documentation/)

i2b2 Software i2b2 Workbench Source Code

The latest version of the source code for the i2b2 Workbench needs to be downloaded. For your convenience, we have created a zip file that contains all the i2b2 Workbench plugins plus the required xml plugin and have made it available on the i2b2 Community Wiki. Here are some basic steps you can take to access this file and to download it to your local environment.

1. Go to Software Release 2.0.01 page in the Workbench Space on the i2b2 Community Wiki.

(https://community.i2b2.org/wiki/display/WB/Software+Release+2.0.01)

2. Scroll to the Source Code section

3. In the Download Link column, click on the name of the file you want to download.
4. The download process will begin.
5. If prompted, answer any questions regarding the i2b2 license to continue.

Install

i2b2 Workbench Project Files

The project software is contained in the Eclipse “Archive” file called i2b2Workbench-src-xxx.zip, which you downloaded in the previous section. 

The above file name has been modified slightly in that the numbers that would normally appear have been replaced with an ‘x’. In actuality, these ‘x’s would be the version of software in the zip file. Example: i2b2 Workbench-src-2001.zip means the zip file contains version 2.0.01 of the i2b2 Workbench.

The zip for the i2b2 Workbench source code contains the following Eclipse projects:

1. BuildAssist
2. harvard.i2b2.common
3. harvard.i2b2.eclipse
4. harvard.i2b2.eclipse.plugins.adminTool
5. harvard.i2b2.eclipse.plugins.analysis
6. harvard.i2b2.eclipse.plugins.commons_apache
7. harvard.i2b2.eclipse.plugins.crcxmljaxb
8. harvard.i2b2.eclipse.plugins.createTables
9. harvard.i2b2.eclipse.plugins.explorer
10. harvard.i2b2.eclipse.plugins.jdnc_support
11. harvard.i2b2.eclipse.plugins.log
12. harvard.i2b2.eclipse.plugins.ontology
13. harvard.i2b2.eclipse.plugins.patientMapping
14. harvard.i2b2.eclipse.plugins.patientSet
15. harvard.i2b2.eclipse.plugins.previousQuery
16. harvard.i2b2.eclipse.plugins.query
17. harvard.i2b2.eclipse.plugins.querytool
18. harvard.i2b2.eclipse.plugins.webservicesAxis2
19. harvard.i2b2.eclipse.plugins.workplace
20. harvard.i2b2.eclipse.plugins.xml_support_jaxb
21. harvard.i2b2.eclipse.plugins.xml_support_jdom
22. harvard.i2b2.xml

For further information, see the original document - reference at end of this article.

References

1. Oct 2017 Original document https://www.i2b2.org/software/files/PDF/current/i2b2Workbench_Developers_Guide.pdf