Using OpenCDISC Validator CLI

  1. 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.
  2. 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