running opencdisc in sas
TRANSCRIPT
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