randonode it conference sept 17, 2008. 9/17/08 randonode it conference 2 development environment...

RandoNode IT Conference

Sept 17, 2008

9/17/08 RandoNode IT Conference 2

Development Environment Setup• System Environment Windows OS

– JAVA_HOME - where the SUN jdk(development and runtime is installed).


Cont– CTSU_HOME – where the

meta data files are installed.


CTSU Provided Classes• The interface classes

• The framework classes

• The ODM classes that represent meta data and clinical data

• The domain classes and xml files for persisting using hibernate

• The hibernate persist classes

• The web service classes


Group Implementation Classes• A main class that inherits from RanodeNodeApp. This

class is called from the CTSU provided web service class to obtain a object to handle the OPEN requests.

• Class(es) that inherit(s) from RegistrationCore which contains the business logic for the web services provided by the groups’ RandoNode.


Install RandoNode Starter Kit• Unzip the files

• Create project from Eclipse

• Build

• Deploy


Install Project to Eclipse Workspace


Create Project Using build.xml


Cont


Build Project Using build.xml


Deploy RandoNode War• The war from the build file is created in deploy directory

C:/SandBox/EclipseWorkspace3.3/RandoNode/deploy/RandoNode.war

• Copy RandoNode.war to your server deployment directory.

• Using Jboss as an example, the war is copied to C:\Servers\jboss-4.0.5.GA\server\default\deploy where c:\Servers/jboss-4.0.5.GA is the jboss home directory.

• Using tomcat as an example, the war is copied to C:\Servers\apache-tomcat-5.5.20\webapps where c:\Servers\apache-tomcat-5.5.20 is the tomcat home directory.


isAvailable Interface• Input

– OpenRequest

• Output– OpenResponse

• OpenResponse.responseCode

– READY

– NOT_READY• OpenResponse.responseText : please fill in the reason if

RandoNode is not NOT_READY to accept request


Example to call isAvailable• Modify the IsAvailable.java located in

c:/SandBox/EclipseWorkspace3.3/RandoNode/src/com/westat/ctsu/open/node/example– Change to your IP address at line 74

• Modify the return value in c:/SandBox/EclipseWorkspace3.3/RandoNode/src/com/westat/ctsu/open/node/RandoNode.java.– Change OpenResponse.setResponseCode between READY

and NOT_READY

• Build

• Deploy

• Test


RandoNode Logging• The log files are located in

CTSU_HOME/RandoNode/logs


CDISC ODM..• Standard for interchange of data collected during the

course of clinical trials.

• Handles– study meta data.– study administrative data– study clinical data.


ODM XSD Metadata Diagram


ODM XSD Clinical Data Diagram


ODM XSD/Study Metadata MappingODM Metadata Element Study

Study Protocol Number

GlobalVariables.StudyName Protocol Number

GlobalVariables.StudyDescription Protocol Title

MetaDataVersion.StudyEventDef Study Event

MetaDataVersion.FormDef Form

MetaDataVersion.ItemGroupDef Module

MetaDataVersion.ItemDef Question

MetaDataVersion.CodeList Question’s valid values


Study Form E1505


Study Form Translated Into ODM Metadata


ODM XSD/Study Data MappingODM Clinical Element Study Data

AdminData.User Administrative user for this study event.

AdminData.Location Location of the user or the sites associated with this study event.

ClinicalData.SubjectData Key information for a subject data (patient).

ClinicalData.FormData Study Form data

ClinicalData.ItemGroupData Modules data

ClinicalData.ItemData Question data.


Fill In Study Using OPEN


Study Data Translated Into ODM


RandoNode Metadata Diagram


RandoNode ClinicalData Diagram


RandoNode Configuration • Setup system environment variable CTSU_HOME

• Create repository for meta data file under CTSU_HOME/RandoNode/meta

• Install Application.xml under CTSU_HOME/RandoNode/config


Setup CTSU_HOME on Windows

Application.xml Example• <Applications>

• 

• <Application Name="RandoNode" Package="com.westat.ctsu.open.node">

• 

• <GroupRandoNodeApp>RandoNodeECOG</GroupRandoNodeApp>

• 

• <GroupRandoNodePackage>com.ECOG.ctsu.open.node</GroupRandoNodePackage>

• </Application>

• </Applications>


Example Code To Read Application.xmlKAppConfig kAppConfig =

KAppConfig.getInstance("RandoNode");

String groupRandoClass = kAppConfig.get("GroupRandoNodeApp",

"RandoNodeECOG");

String groupRandoPackage = kAppConfig.get("GroupRandoNodePackage", "com.ECOG.ctsu.open.node");


Extract Metadata Options• Get all the questions within a form

– MetaDataUtil.itemMap

• Get question based on question’s CDE public – MetaDataUtil.getItem(String cdePublicId)

• Get all modules within a form– MetaDataUtil.itemGroupMap

• Get question’s valid value– Item.codeListMap

• Get all the valid values within a form– MetaDataUtil. codeListMap


Example To Extract Metadata• Run MetadataExtract.java within Eclipse

• Console output the extraction result with different options.

• Modify MetadataExtract.java (Exercise time )


Extract Clinical Data Options• Get administrative users

– ClinicalDataUtil.userMap– ClinicalDataUtil.getUser(String userCtepId)

• Get administrative locations– ClinicalDataUtil.locationMap– ClinicalDataUtil.getLocation(String locationCtepId)

• Get all the form response data– ClinicalDataUtil.itemDataMap

• Get response data based on question’s cde public id– ClinicalDataUtil.getItemData(String cdePublicId)

• Get response data based on question’s long name– ClinicalDataUtil.getItemDataByName(String longName)

• Get the override approval list– ClinicalDataUtil.overrideApprovalList


Example To Extract Clinical Data• Run ClinicaldataExtract.java

• Extraction output with different options.

• Modify ClinicalDataExtract.java.


doCredential• Call

– Credit group is the protocol lead group– AND

– When the protocol lead group does not maintain person roster and/or site roster within RSS

– AND– Lead group requests the call from OPEN before the registrar fills

in the EC form


doCredential Interface• Input

– OpenRequest– OpenRegistration

• Output– RegistrationResponse

• OpenResponse.responseCode

– PROCESSED

– EXCEPTION• OpenResponse.responseText : optional, but highly recommended• OpenRegistration.status

– SUCCESS

– FAILURE


doValidate• Ravi please fill in.


doRegister • Call

– EC is filled and response passed the validation check


doRegister Interface• Input

– OpenRequest– OpenRegistration– OdmData

• Output– RegistrationResponse

• OpenRegistration.status • OpenRegistration.eligibility• OpenRegistration.treatmentAssignment • OpenRegistration. ineligibilityReason

• What about the groupRegistration


Metadata Update • Assumption: an active protocol form is modified to add in

a new question– The form is updated with a new version date– The form’s meta data is generated and saved to OPEN DB– RandoNode requests the meta data from CEWS when a

registration request is sent using the new form.

• RandoNode starter kit software is not affected.

• May need to update your business logic.


WSDL changes• Install the new RandoNode.jar to your lib directory.

• Jar is versioned with MANIFEST.MF

• Example:– Add an attribute(associate) to OpenRegistration class– The wsdl is updated with a new version number.– To use the added attribute, OpenRegistration.associate to get

the value of this attribute.

• How to check the jar version– Read manifest.mf within the jar– Deploy the war with the new RandoNode.jar, read manifest.mf

under DEPLOY/RandoNode/WEB-INF/classes


WSDL Migration Exercise• Replace your RandoNode.jar with the updated

RandoNode.jar. Note: the jar version is different.

• Rebuild the RandoNode project

• Run DoRegister with previously WSDL data file and current WSDL data file.


Questions?


Contacts• Ravi Rajaram – OPEN Development Manager

– [email protected]– (301) 294-2045

• Lucille Patrichuk – Transition Manager– [email protected]– (240) 314-2572

• Jerry Wernimont – CTSU Associate Director - IT– [email protected]– (240) 314-2396

• Steve Riordan – CTSU Project Director– [email protected]– (301) 517-4045

randonode it conference sept 17, 2008. 9/17/08 randonode it conference 2 development environment...

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