Install Guide. Version 1.0 Demonstration. Copyright 2007 MGH

Transcription

1 Install Guide Version 1.0 Demonstration Copyright 2007 MGH

2 Table of Contents About this Guide iii Prerequisites 1 Downloads and Installation 1 Install & Configure 3 Setting up the cell and hive within Eclipse 3.2: 3 Set up and run the PFT cell: 5 Run the PFT hive within the Eclipse IDE 7 Package Structure 8 License 9 ii

3 About this Guide Informatics for Integrating Biology and the Bedside (i2b2) is one of the sponsored initiatives of the NIH Roadmap National Centers for Biomedical Computing ( One of the goals of i2b2 is to provide clinical investigators broadly with the software tools necessary to collect and manage projectrelated 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 with the provided source code will help you to learn about the developing and understand the requirements for creating i2b2 cells. iii

4 1 Prerequisites Downloads and Installation a. Java JDK Make sure that you have Java 1.5 or higher installed. If you need to get and install the 1.5 JDK, go to Run the installer. b. Eclipse You will need to use version 3.2 or higher of the Eclipse SDK, available at If you install a new version of Eclipse, be sure to install it in an area separate from any previous Eclipse installations. To install, extract the zip file into a directory such as C:\ c. Tomcat 5.5 Tomcat is a servlet container, which is based off the Reference Implementation provided by Sun Microsystems for both Servlet and Java Server Pages. Retrieve version of the Core binary distribution found at To install, extract the zip file into a directory such as C:\ d. Tomcat Plug-in for Eclipse 3.2 The Tomcat plug-in allows for debugging and deployment of your web applications. It can be retrieved at Extract the zip file into eclipse/plugins directory, which was created during the installation of eclipse. If Eclipse was running, restart Eclipse after installing the Tomcat plugin. 1

5 e. Axis2 Axis2 version 1.1 is the only version that has been certified to work with i2b2 Workbench version 1.0 Demonstration. Version is known to not be compatible. Retrieve the WAR file at Copy the WAR into the apache-tomcat-5.5.x/webapps directory, which was created during the installation of tomcat. 2

6 2 Install & Configure Setting up the cell and hive within Eclipse 3.2: If launching eclipse for the first time, via either the eclipse application shortcut or eclipse.exe, you will be greeted by a Welcome page. Click on the arrow labeled Workbench to startup the eclipse SDK. Importing the i2b2 Workbench projects The project software is contained in the Eclipse Archive file called workspacepft.zip, which can be downloaded from In this file are the Eclipse projects: 1) edu.harvard.i2b2.eclipse 2) edu.harvard.i2b2.eclipse.plugins.commons_apache 3) edu.harvard.i2b2.eclipse.plugins.log 4) edu.harvard.i2b2.eclipse.plugins.pft 5) edu.harvard.i2b2.eclipse.plugins.webservicesaxis2 6) edu.harvard.i2b2.eclipse.plugins.xml_support_jaxb 7) edu.harvard.i2b2.pft 8) edu.harvard.i2b2.xml 9) edu.harvard.i2b2.common 3

7 To import them into the EclipseSDK, use: File->Import->General->Existing Projects into Workspace and select the archive file workspacepft.zip: 4

8 Set up and run the PFT cell: Configure tomcat within Eclipse: Window->Preferences ->Tomcat Select Version 5.x and also enter the directory that contains the root tomcat installation Open the edu.harvard.i2b2.pft project and double click on build.properties and go to the build.properties tab. Change the tomcat.home to point to your tomcat installation, the java perspective will need to be active. Next, double click on the master_build.xml file (also in the edu.harvard.i2b2.pft project). In the outline section on the right side, right click on the tomcat-deploy and select Run As -> 1 Ant Build 5

9 Once the build is complete, start Tomcat by either clicking on the icon of the cat, or in the menu select Tomcat->Start Tomcat. On successful startup, you will see the message INFO: Server startup in xxxx ms in the Console window. If you are running Windows XP SP2 than allow Unblock Windows Firewall if asked. 6

10 Run the PFT hive within the Eclipse IDE Right click the edu.harvard.i2b2.eclipse project -> Run As -> Run Create a new Eclipse Application Configuration by double-clicking on Eclipse Application. Give the configuration a meaningful name: e.g. i2b2. Select Run a product: edu.harvard.i2b2.eclipse.product Go to the Arguments tab. In Working directory: select Other and click on Workspace... button. Select edu.harvard.i2b2.eclipse and click OK Go to the plug-ins tab. You can configure any combination of workspace plug-ins and target platform plug-ins as your IDE configuration. Default is that all of the workspace and target platform plug-ins are selected. Select Apply; Run You are now running the i2b2 Workbench and PFT cell under control of the Eclipse IDE. 7

11 3 Package Structure The archive file contains the following projects, within the edu.harvard.ui2b2.eclipse directory contains the properties files and configuration files. The pft.properties file contains the location of the pft server. Directory Description edu.harvard.i2b2.eclipse The base plug-in for our development (namely the UI for the top panel) edu.harvard.i2b2.eclipse.plugins.commons_apache Third party jars needed for common functions edu.harvard.i2b2.eclipse.plugins.log Third party jars needed for logging edu.harvard.i2b2.eclipse.plugins.pft UI for the PFT view edu.harvard.i2b2.eclipse.plugins.webservicesaxis2 Third party jars needed for web service support edu.harvard.i2b2.eclipse.plugins.xml_support_jaxb Third party jars needed for jaxb/message processing edu.harvard.i2b2.pft Axis2-based PFT web service edu.harvard.i2b2.xml edu.harvard.i2b2.common XSD for the hive Common core exception, jaxb, and utilities used by i2b2 hive 8

12 4 License The i2b2 source code is licensed under the i2b2 Software License Software. This includes but not limited to all code in the edu.harvard.mgh.i2b2.* package namespace. 9