running opencdisc in sas

Running OpenCDISC in SAS

Kevin Lee

Any views or opinions presented in this presentation are solely those of the author and do not necessarily represent those of the company.

Disclaimer

11/26/2013 Cytel Inc. 2

1. Introduction of OpenCDISC Validator2. The Current Process of CDISC Compliance 

Check3. The New Process of CDISC Compliance Check4. How to run OpenCDISC validator in SAS5. Conclusion & Questions

Agenda

11/26/2013 Cytel Inc. 3

• a CDISC Compliance Check Software• An Open‐Source Software• The most recent version – 1.4, released in 

March 14th, 2013

Introduction of OpenCDISC Validator

11/26/2013 Cytel Inc. 4

Functionality of OpenCDISC Validator

11/26/2013 Cytel Inc. 5

• CDISC compliance validation• SDTM• ADaM• Send• Define.xml

• Creation of Define.xml

OpenCDISC Validator Batch File

11/26/2013 Cytel Inc. 6

START /B javaw ‐Xms256m ‐Xmx1024m ‐jar lib/validator‐gui‐1.3.jar

Validator-gui-1.3.jar

11/26/2013 Cytel Inc. 7

OpenCDISC Validator Interface

11/26/2013 Cytel Inc. 8

OpenCDISC Validator Report

11/26/2013 Cytel Inc. 9

Current Process of CDISC Compliance Checks using OpenCDISC

11/26/2013 Cytel Inc. 10

SDTM DM SAS 

Programdm.xpt OpenCDISC

Validator

CDISC Compliant dm.xpt

New Process of CDISC Compliance Checks

11/26/2013 Cytel Inc. 11

SDTM DM SAS Program with OpenCDISCValidator

CDISC Compliant dm.xpt

OpenCDISC Validator Program Interface

11/26/2013 Cytel Inc. 12

coregui cli api

****opening OpenCDISC Validator Interface;x java ‐jar "C:\zother\industry\CDISC\opencdiec\opencdisc‐validator 1.3\lib\validator‐gui‐1.3.jar";

Call gui in SAS

11/26/2013 Cytel Inc. 13

C:\zother\industry\CDISC\opencdisc\opencdisc‐validator 1.3\lib>java –jar validator‐cli‐1.3.jar –help

General Parameters‐task               Validate|Generate (Validate)‐type               SDTM|Define|Custom (SDTM)

Source Data Parameters‐source              <path>‐source:type SAS|Delimited (SAS)‐source:delimiter <delimiter> (,)‐source:qualifier <qualifier> (“)

Use cli(Command Line Interpreter) (1)

11/26/2013 Cytel Inc. 14

C:\zother\industry\CDISC\opencdisc\opencdisc‐validator 1.3\lib>java –jar validator‐cli‐1.3.jar –help

General Parameters‐task               Validate|Generate (Validate)‐type               SDTM|Define|Custom (SDTM)

Source Data Parameters‐source              <path>‐source:type SAS|Delimited (SAS)‐source:delimiter <delimiter> (,)‐source:qualifier <qualifier> (“)

Use cli(Command Line Interpreter) (1)

11/26/2013 Cytel Inc. 15

C:\zother\industry\CDISC\opencdisc\opencdisc‐validator 1.3\lib>java –jar validator‐cli‐1.3.jar –help

General Parameters‐task               Validate|Generate (Validate)‐type               SDTM|Define|Custom (SDTM)

Source Data Parameters‐source              <path>‐source:type SAS|Delimited (SAS)‐source:delimiter <delimiter> (,)‐source:qualifier <qualifier> (“)

Use cli(Command Line Interpreter) (1)

11/26/2013 Cytel Inc. 16

C:\zother\industry\CDISC\opencdisc\opencdisc‐validator 1.3\lib>java –jar validator‐cli‐1.3.jar –help

General Parameters‐task               Validate|Generate (Validate)‐type               SDTM|Define|Custom (SDTM)

Source Data Parameters‐source              <path>‐source:type SAS|Delimited (SAS)‐source:delimiter <delimiter> (,)‐source:qualifier <qualifier> (“)

Use cli(Command Line Interpreter) (1)

11/26/2013 Cytel Inc. 17

C:\zother\industry\CDISC\opencdisc\opencdisc‐validator 1.3\lib>java –jar validator‐cli‐1.3.jar –help

General Parameters‐task               Validate|Generate (Validate)‐type               SDTM|Define|Custom (SDTM)

Source Data Parameters‐source              <path>‐source:type SAS|Delimited (SAS)‐source:delimiter <delimiter> (,)‐source:qualifier <qualifier> (“)

Use cli(Command Line Interpreter) (1)

11/26/2013 Cytel Inc. 18

• pass parameters to core(main java program)• Type of works – Compliance check on data or generation of Define.xml

• Location and format of source data• Location of configuration file• Location of Define.xml• Report format• Name and location of OpenCDISC Validator Report

Use cli(Command Line Interpreter) (3)

11/26/2013 Cytel Inc. 19

Running OpenCDISC Validator 1.3

11/26/2013 Cytel Inc. 20

x java ‐jar “C:\zother\industry\CDISC\opencdiec\opencdisc‐validator 1.3\lib\validator‐cli‐1.3.jar" 

‐task="validate" ‐type="sdtm" ‐source:type="sas" ‐source="C:\data\sdtm\dm.xpt" ‐config="C:\zother\industry\CDISC\opencdiec\opencdisc‐validator 1.3\config\config‐sdtm‐3.1.2.xml" 

‐report="C:\data\openCDISC_v1.3_DM.xls" ‐report:type="excel" –report:overwrite=”yes”;

Running OpenCDISC Validator 1.3

11/26/2013 Cytel Inc. 21

x java ‐jar “C:\zother\industry\CDISC\opencdiec\opencdisc‐validator 1.3\lib\validator‐cli‐1.3.jar" 

‐task="validate" ‐type="sdtm" ‐source:type="sas" ‐source="C:\data\sdtm\dm.xpt" ‐config="C:\zother\industry\CDISC\opencdiec\opencdisc‐validator 1.3\config\config‐sdtm‐3.1.2.xml" 

‐report="C:\data\openCDISC_v1.3_DM.xls" ‐report:type="excel" –report:overwrite=”yes”;

Running OpenCDISC Validator 1.4

11/26/2013 Cytel Inc. 22

x java ‐jar “C:\zother\industry\CDISC\opencdisc\opencdisc‐validator 

1.4\lib\validator‐cli‐1.4.jar" ‐task="validate" ‐type="sdtm" ‐source:type="sas" ‐source="C:\data\sdtm\dm.xpt" ‐config="C:\zother\industry\CDISC\opencdiec\opencdisc‐validator 

1.4\config\config‐sdtm‐3.1.3.xml" –config:cdisc=”2012‐12‐21” ‐report="C:\data\openCDISC_v1.4_DM.xls" ‐report:type="excel"  –report:overwrite=”yes”;

• Yes, we can run OpenCDISC validator in SAS• One Process ‐ both creation of CDISC datasets and compliance checks in a single process(SAS program)

• A control on the location of the OpenCDISCValidator Report.

Conclusion

11/26/2013 Cytel Inc. 23