Clinical and Meta Data Extraction Tasks 2a and 2b OPEN Development Conference September 17, 2008 Phoebe Whitefield Senior Systems Analyst

9/17/08 Data Extraction – Task 2 2 Set up for exercises No database connection Everything works within the local desktop Metadata.xml and OpenrequestObjects.xml are available in appropriate directories Implementation methods are in RegistrationNSABPB42.java

9/17/08 Data Extraction – Task 2 3 OPENPortalProxy Simple file that acts as proxy for OPEN Portal Reads the OpenRequestObjects.xml from \EclipseWorkspace3.3\RandoNode directory Serializes the data from the OpenRequestObjects.xml into three objects openRequest, openRegistration and odmData Invokes the RandoNodeNSABP’s doRegister method using these three objects Gets the response object registrationResponse back from the RandoNodeNSABP

9/17/08 Data Extraction – Task 2 4 Task -2 Open the OpenRequestObjects.xml from c:\openconference\java\task2. Make sure that the file contains data for three objects. Copy the OpenRequestObjects.xml to \EclipseWorkspace3.3\RandoNode directory Copy the metadata file NSABP-B- 42_ _080410_step0_meta.xml from c:\openconference\java\task2 to C:\CTSU\Applications\RandoNode\meta Set up the run environment in Eclipse Run the OpenPortalproxy.java in Eclipse

9/17/08 Data Extraction – Task 2 5 Source Metadata file

9/17/08 Data Extraction – Task 2 6 Copy Metadata to Target directory Target folder

9/17/08 Data Extraction – Task 2 7 OpenRequestObjects file

9/17/08 Data Extraction – Task 2 8 Target location for Open requestObjects Target folder

9/17/08 Data Extraction – Task 2 9 Setup for OpenPortalProxy

9/17/08 Data Extraction – Task 2 10 Setup for OpenPortalProxy Cont’d

9/17/08 Data Extraction – Task 2 11 Setup for OpenPortalProxy Cont’d

9/17/08 Data Extraction – Task 2 12 Setup for OpenPortalProxy Cont’d

9/17/08 Data Extraction – Task 2 13 Run OpenPortalProxy

9/17/08 Data Extraction – Task 2 14 Results from OpenPortalProxy

9/17/08 Data Extraction – Task 2 15 Data Extraction End of Task 2a

9/17/08 Data Extraction – Task 2 16 Application.xml Main properties are set outside of the application Easy to configure for any group

9/17/08 Data Extraction – Task 2 17 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 Data Extraction – Task 2 18 MetaDatautil Utility class to extract metadata from ODM objects 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 Data Extraction – Task 2 19 ClinicalDataUtil 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 Data Extraction – Task 2 20 Steps for Task 2b Open RegistrationNSABPB42.java Review the code that extracts data for simple questions Modify the code to extract data for –Ethnicity –Date of Most Recent Mammogram –Did this patient receive any tamoxifen? Set the OpenResponse.status, OpenResponse.statusText, OpenRegistration.patientId, OpenRegistration.eligibility, OpenRegistration.status, OpenRegistration.statusText, OpenRegistration.statusDetailText, OpenRegistration.statusDetailText Add code to output result to the console Run OPENPortalProxy.java to verify the data extracted correctly

9/17/08 Data Extraction – Task 2 21 Data Extraction End of Task 2b