s15: how to make an i2b2 cell: mike mendis

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1.  i2b2  cell  2.  Vmware  3.  Applica2ons  4.  Technologies  5.  Server  Code  6.  Client  Code  

How to make an

I2b2 cell

By Mike

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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  

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Run  mul2ple  opera2on  systems  on  a  single  machine  

Available  for  Windows,  Linux  and  Macintosh  

Divide  System  resources  within  virtual  machines  

X86  Architecture  

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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.

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The  Standard  for  java  Enterprise  Applica2ons  

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"    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  

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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  

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Apache  Axis2  is  a  core  engine  for  web  services.    It  supports  SOAP  1.1,  1.2  and  REST  and  adds  support  to  web  applica2ons  

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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  

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Username   Password  

Opera5on  System   root   demouser  

demo   demouser  

Oracle  Database   sys   demouser  

system   demouser  

i2b2  Server   i2b2   demouser  

demo   demouser  

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"  ExecutorRunnable.java  "  JAXBConstant.java  "  MessageFactory.java  

"  Pa2entDataMessage.java  

"  TutorialHelper.java  "  TutorialService.java  "  TutorialServiceRESTTest.java  

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"    Object  that  executes  a  Runnable  task  "    Completed  flag  

"    Input/Output  string  

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"    Define  JAXB  Constants  "    Default  package  names  

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"    Creates  Request/Response  objects  "    Observa2on  Fact  "    i2b2  header  and  body  "    Error  response  

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"    JAXB  unmarshalling  

"    Observa2on  Fact  

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"    Calls  Pa2entDataMessage  

"    Get  blob  from  observa2on  fact  

"    Runs  regex  on  content  in  blob  

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"    Main  webservice  interface  

"    Calls  ExecutorRunnable  "    Executes  from  client  waibmems  

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"    URL  of  service  "    Read  and  convert  request  XML  

"    Change  request.xml  for  tes2ng  

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A Q &