Using OpenCDISC Validator CLI

Open a new command line shell
- Windows 7 or newer: press Start ,type cmd in the run box, hit enter
- Windows XP or older: press Start --> Run, type cmd and press OK.
- Linux - launch a new terminal window
- OS X - open Finder and navigate to Applications -> Utilities -> Terminal, then double click it.
As of version 2.0.1, java 1.7 32 and 64 bit for Windows and MAC OS come packaged. No need to worry about your java version anymore !
Navigate to the components/lib directory where you unzipped the OpenCDISC Validator .zip file. You will find validator-cli-2.0.1.jar.
Issue the first command below to view the help menu for a list of available parameters to use on the command line
- java -jar validator-cli-2.0.1.jar -help
- Values in parens ( ) are the default values if param not specified
- Values in brackets <> are descriptions and should be replaced by user
- Values spearated by a pipe | indicate the only acceptable values
- see parameter reference below for details of -help output
Specify Dictionaries: OpenCDISC validator-cli can be extended with older or newer versions of control terminology and MedDRA files. They must be placed in specific locations within the folder structure to be accessible to OpenCDISC validator-cli. Reviewing the folder structure under config/data will provide examples for where new items should be uploaded.
- CDISC CT
  - specify the version found at: components/config/data/CDISC/[Standard]/[version].
  - Example: components/config/data/CDISC/SDTM/2012-12-21. Therefore -config:cdisc=2012-12-21
  - Versions of CDISC CT can be found at NCI EVS CDISC
  - For more information, visit Configuring CDISC CT
- MedDRA
  - specify the version found at components/config/data/MedDRA/[version]. Ensure all .asc files are placed there
  - Example: components/config/data/MedDRA/14.0. Therefore -config:meddra=14.0
  - Current MedDRA Rules: SD0008,SD0008C, SD1114,SD1114C and SD2007 thru SD2016
  - For more information, visit Configuring MedDRA

Sample Commands

Running OpenCDISC Validator can require some very long command strings. Saving your commands and modifying them for future use can save you a great deal of typing time. The following are typical command strings:

Example 1: Validate SAS .xpt against SDTM using define.xml, controlled terminology, MedDRA and produce excel output

java -Xms256m -Xmx1024m -jar validator-cli-2.0.1 jar -type=SDTM -source=/home/user/opencdisc-validator/data/6073K1-006/*.XPT -source:type=SAS -config=/home/user/opencdisc-validator/config/config-sdtm-3.1.1.xml -config:define=/home/user/opencdisc-validator/data/6073K1-006/define.xml -config:cdisc=2012-12-21 -config:meddra=14.0 -report=/home/user/opencdisc-validator/reports/Drug-study-report1000.xls -report:type=Excel -report:cutoff=1000 report:overwrite=Yes

Parameter Reference

Parameter Type	Parameter	Valid Values	Default	Applicable Task Type	Description
	-type	SDTM,ADaM, SEND,Define,Custom	SDTM	Validate	Data Standard/Structure to validate

Source Data	-source	<path>		both	Path to the source data files
	-source:type	SAS\|Delimited	SAS	both	file format
	-source:delimiter	<delimiter>	,	both	field Delimeter if source:type = Delimited
	-source:qualifier	<qualifier>	"	both	field qualifier if source:type = Delimited

Configuration	-config	<path>		both	path the xml configuration document which lists rules to validate
	-config:define	<path>		Validate	path and name of define.xml for the study
	-config:cdisc	<version>		Validate	CDISC Controlled Terminology Version
	-config:meddra	<version>		Validate	MedDRA dictionary version

Report	-report	<path>		Validate	path and file name to where the report will be saved
	-report:type	Excel,CSV,XML	Excel	Validate	report format
	-report:cutoff	<#>	1000	Validate	Number of times a record detail is printed per distinct domain issue
	-report:overwrite	yes,no		Validate	indicates if report should be overwritten if same name provided

Want a demo?

Let’s Talk.

We're eager to share and ready to listen.

Request A Demo

* Required Field