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).

9/17/08 RandoNode IT Conference 3 Cont –CTSU_HOME – where the meta data files are installed.

9/17/08 RandoNode IT Conference 4 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

9/17/08 RandoNode IT Conference 5 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.

9/17/08 RandoNode IT Conference 6 Install RandoNode Starter Kit Unzip the files Create project from Eclipse Build Deploy

9/17/08 RandoNode IT Conference 7 Install Project to Eclipse Workspace

9/17/08 RandoNode IT Conference 8 Create Project Using build.xml

9/17/08 RandoNode IT Conference 9 Cont

9/17/08 RandoNode IT Conference 10 Build Project Using build.xml

9/17/08 RandoNode IT Conference 11 Deploy RandoNode War The war from the build file is created in deploy directory C:/SandBox/EclipseWorkspace3.3/RandoNode/deploy/R andoNode.war Copy RandoNode.war to your server deployment directory. Using Jboss as an example, the war is copied to C:\Servers\jboss GA\server\default\deploy where c:\Servers/jboss GA is the jboss home directory. Using tomcat as an example, the war is copied to C:\Servers\apache-tomcat \webapps where c:\Servers\apache-tomcat is the tomcat home directory.

9/17/08 RandoNode IT Conference 12 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

9/17/08 RandoNode IT Conference 13 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

9/17/08 RandoNode IT Conference 14 RandoNode Logging The log files are located in CTSU_HOME/RandoNode/logs

9/17/08 RandoNode IT Conference 15 CDISC ODM.. Standard for interchange of data collected during the course of clinical trials. Handles –study meta data. –study administrative data –study clinical data.

9/17/08 RandoNode IT Conference 16 ODM XSD Metadata Diagram

9/17/08 RandoNode IT Conference 17 ODM XSD Clinical Data Diagram

9/17/08 RandoNode IT Conference 18 ODM XSD/Study Metadata Mapping ODM Metadata ElementStudy Protocol Number GlobalVariables.StudyNameProtocol Number GlobalVariables.StudyDescriptionProtocol Title MetaDataVersion.StudyEventDefStudy Event MetaDataVersion.FormDefForm MetaDataVersion.ItemGroupDefModule MetaDataVersion.ItemDefQuestion MetaDataVersion.CodeListQuestion’s valid values

9/17/08 RandoNode IT Conference 19 Study Form E1505

9/17/08 RandoNode IT Conference 20 Study Form Translated Into ODM Metadata

9/17/08 RandoNode IT Conference 21 ODM XSD/Study Data Mapping ODM Clinical ElementStudy Data AdminData.UserAdministrative user for this study event. AdminData.LocationLocation of the user or the sites associated with this study event. ClinicalData.SubjectDataKey information for a subject data (patient). ClinicalData.FormDataStudy Form data ClinicalData.ItemGroupDataModules data ClinicalData.ItemDataQuestion data.

9/17/08 RandoNode IT Conference 22 Fill In Study Using OPEN

9/17/08 RandoNode IT Conference 23 Study Data Translated Into ODM

9/17/08 RandoNode IT Conference 24 RandoNode Metadata Diagram

9/17/08 RandoNode IT Conference 25 RandoNode ClinicalData Diagram

9/17/08 RandoNode IT Conference 26 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

9/17/08 RandoNode IT Conference 27 Setup CTSU_HOME on Windows

9/17/08 RandoNode IT Conference 28 Application.xml Example RandoNodeECOG com.ECOG.ctsu.open.node

9/17/08 RandoNode IT Conference 29 Example Code To Read Application.xml KAppConfig kAppConfig = KAppConfig.getInstance("RandoNode"); String groupRandoClass = kAppConfig.get("GroupRandoNodeApp", "RandoNodeECOG"); String groupRandoPackage = kAppConfig.get("GroupRandoNodePackage", "com.ECOG.ctsu.open.node");

9/17/08 RandoNode IT Conference 30 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

9/17/08 RandoNode IT Conference 31 Example To Extract Metadata Run MetadataExtract.java within Eclipse Console output the extraction result with different options. Modify MetadataExtract.java (Exercise time )

9/17/08 RandoNode IT Conference 32 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

9/17/08 RandoNode IT Conference 33 Example To Extract Clinical Data Run ClinicaldataExtract.java Extraction output with different options. Modify ClinicalDataExtract.java.

9/17/08 RandoNode IT Conference 34 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

9/17/08 RandoNode IT Conference 35 doCredential Interface Input –OpenRequest –OpenRegistration Output –RegistrationResponse OpenResponse.responseCode –PROCESSED –EXCEPTION OpenResponse.responseText : optional, but highly recommended OpenRegistration.status –SUCCESS –FAILURE

9/17/08 RandoNode IT Conference 36 doValidate Ravi please fill in.

9/17/08 RandoNode IT Conference 37 doRegister Call –EC is filled and response passed the validation check

9/17/08 RandoNode IT Conference 38 doRegister Interface Input –OpenRequest –OpenRegistration –OdmData Output –RegistrationResponse OpenRegistration.status OpenRegistration.eligibility OpenRegistration.treatmentAssignment OpenRegistration. ineligibilityReason What about the groupRegistration

9/17/08 RandoNode IT Conference 39 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.

9/17/08 RandoNode IT Conference 40 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

9/17/08 RandoNode IT Conference 41 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.

9/17/08 RandoNode IT Conference 42 Questions?

9/17/08 RandoNode IT Conference 43 Contacts Ravi Rajaram – OPEN Development Manager –(301) Lucille Patrichuk – Transition Manager –(240) Jerry Wernimont – CTSU Associate Director - IT –(240) Steve Riordan – CTSU Project Director –(301)