s15: how to make an i2b2 cell: mike mendis
DESCRIPTION
M. Mendis, PartnersTRANSCRIPT
ARTNERP STM
H E A L T H C A R E S Y S T E M
1. i2b2 cell 2. Vmware 3. Applica2ons 4. Technologies 5. Server Code 6. Client Code
How to make an
I2b2 cell
By Mike
ARTNERP STM
H E A L T H C A R E S Y S T E M
Loosely Coupled
No Assump2ons about proximity
Connected by web services
Ac2vity can be directed manually or automa2cally
Default package names
Emphasize using open protocols
Leverage exis2ng soKware
ARTNERP STM
H E A L T H C A R E S Y S T E M
Run mul2ple opera2on systems on a single machine
Available for Windows, Linux and Macintosh
Divide System resources within virtual machines
X86 Architecture
ARTNERP STM
H E A L T H C A R E S Y S T E M
ARTNERP STM
H E A L T H C A R E S Y S T E M
I2b2 VM
Java development within the Eclipse environment
JDeveloper provides a clean Interface into Oracle XE
Complete i2b2 1.4 server with demo patient set of 133 patients
Client testing with Firefox
Deploy finished project to Production servers.
ARTNERP STM
H E A L T H C A R E S Y S T E M
The Standard for java Enterprise Applica2ons
ARTNERP STM
H E A L T H C A R E S Y S T E M
ARTNERP STM
H E A L T H C A R E S Y S T E M
" Java Management Extensions (JMX) for server management and deployment
" JMX Services deployed in xxx-service.xml files
" Relevant Directories " bin Startup and shutdown scripts " client Client-‐side JARs " docs/dtd J2EE and JBoss deployment descriptors " docs/examples/jca Datasource configura2on examples " lib Core JBoss libraries " server/default/conf Configura2on files for default configura2on " server/default/deploy Deployment directory for default " server/default/lib Libraries specific to default " server/default/log Server and web access logs for default
ARTNERP STM
H E A L T H C A R E S Y S T E M
Package javax.xml.bind
Implementa5on of
javax.xml.bind
Interfaces And Object Factory
Implementa5on Classes
Applica5on Code
Binding Customiza5ons
(op5onal)
Binding Compiler
marshall
unmarshall
Applica5on
XML Input
Document
XML Output
Document
XML Schema
" Speed " Low memory
" Hot Deployment
" Stability " WSDL Support
ARTNERP STM
H E A L T H C A R E S Y S T E M
Apache Axis2 is a core engine for web services. It supports SOAP 1.1, 1.2 and REST and adds support to web applica2ons
ARTNERP STM
H E A L T H C A R E S Y S T E M
Workspace
Help
Team
Workbench
JFace
SWT
Java Development
Tools (JDT)
Your Plugin
i2b2 Client
Another Tool
Plug-‐in Development Environment
(PDE)
Eclipse PlaRorm
Debug
PlaRorm Run5me
ARTNERP STM
H E A L T H C A R E S Y S T E M
Username Password
Opera5on System root demouser
demo demouser
Oracle Database sys demouser
system demouser
i2b2 Server i2b2 demouser
demo demouser
ARTNERP STM
H E A L T H C A R E S Y S T E M
" ExecutorRunnable.java " JAXBConstant.java " MessageFactory.java
" Pa2entDataMessage.java
" TutorialHelper.java " TutorialService.java " TutorialServiceRESTTest.java
ARTNERP STM
H E A L T H C A R E S Y S T E M
" Object that executes a Runnable task " Completed flag
" Input/Output string
ARTNERP STM
H E A L T H C A R E S Y S T E M
" Define JAXB Constants " Default package names
ARTNERP STM
H E A L T H C A R E S Y S T E M
" Creates Request/Response objects " Observa2on Fact " i2b2 header and body " Error response
ARTNERP STM
H E A L T H C A R E S Y S T E M
" JAXB unmarshalling
" Observa2on Fact
ARTNERP STM
H E A L T H C A R E S Y S T E M
" Calls Pa2entDataMessage
" Get blob from observa2on fact
" Runs regex on content in blob
ARTNERP STM
H E A L T H C A R E S Y S T E M
" Main webservice interface
" Calls ExecutorRunnable " Executes from client waibmems
ARTNERP STM
H E A L T H C A R E S Y S T E M
" URL of service " Read and convert request XML
" Change request.xml for tes2ng
ARTNERP STM
H E A L T H C A R E S Y S T E M
ARTNERP STM
H E A L T H C A R E S Y S T E M
A Q &