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.
Operating Systems The i2b2 Workbench does run on Microsoft Windows (“Windows”) and Apple’s Macintosh (“Mac”) operating systems. However, there is a problem with the i2b2 Workbench not running correctly on newer apple machines. Since the problem is with a third-party software and out of the hands of the i2b2 community we have decided to create two new virtual machines (VM) that mac users can download and use in their environment. The Workbench VM Guide explains how to use the VM and can be used in combination with this guide to understand how to use the i2b2 Workbench source code within Eclipse. |
Document management
Revision Number |
Date |
Author |
Description of Change |
2.0.01-0001 |
10/01/2017 |
Janice Donahoe |
Created initial version of the developer’s guide for the i2b2 Workbench 2.0.01 Software. |
2.0.01-0002 |
10/17/2017 |
Janice Donahoe |
Fixed link to Software Release page. |
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:
- 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.
- 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.
i2b2 Resource: Download & Install Java JDK |
Chapter 2.4.1 Java JDK of the i2b2 Installation Guide provides links to download JDK for Linux or Windows and how to install it in your environment. |
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.
- 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)
- Scroll to the Source Code section
- In the Download Link column, click on the name of the file you want to download.
- The download process will begin.
- 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:
- BuildAssist
- harvard.i2b2.common
- harvard.i2b2.eclipse
- harvard.i2b2.eclipse.plugins.adminTool
- harvard.i2b2.eclipse.plugins.analysis
- harvard.i2b2.eclipse.plugins.commons_apache
- harvard.i2b2.eclipse.plugins.crcxmljaxb
- harvard.i2b2.eclipse.plugins.createTables
- harvard.i2b2.eclipse.plugins.explorer
- harvard.i2b2.eclipse.plugins.jdnc_support
- harvard.i2b2.eclipse.plugins.log
- harvard.i2b2.eclipse.plugins.ontology
- harvard.i2b2.eclipse.plugins.patientMapping
- harvard.i2b2.eclipse.plugins.patientSet
- harvard.i2b2.eclipse.plugins.previousQuery
- harvard.i2b2.eclipse.plugins.query
- harvard.i2b2.eclipse.plugins.querytool
- harvard.i2b2.eclipse.plugins.webservicesAxis2
- harvard.i2b2.eclipse.plugins.workplace
- harvard.i2b2.eclipse.plugins.xml_support_jaxb
- harvard.i2b2.eclipse.plugins.xml_support_jdom
- harvard.i2b2.xml
For further information, see the original document - reference at end of this article.
Note For additional information on the above projects please see the section called Package Structure. |
References
- Oct 2017 Original document https://www.i2b2.org/software/files/PDF/current/i2b2Workbench_Developers_Guide.pdf
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