s Subin
on

 

Hi, consider me as an absolute beginner to this. I am trying to validate using SDTM through cli but getting an error. I have tried the exact file using the GUI and it has generated me the report. Details are below.

Engine
FDA (2304.3)


Standard
SDTM


Source Format
SAS® Transport (XPORT)


Configuration
SDTM-IG 3.2 (FDA)


Source Data

Define.xml


SDTM CT
2024-03-29


Trying to generate the report using the exact configuration using the cli. Below is the command I'm using 

java -jar "C:\Users\~\Documents\Pinnacle 21 Community\p21-client-1.0.8.jar" ^
--engine.version="FDA 2304.3" ^
--standard=sdtm ^
--standard.version=3.2 ^
--source.sdtm="C:\Users\~\Desktop\study-101\SDTM.xpt" ^
--cdisc.ct.sdtm.version=2024-03-29 ^
--report.type=Excel ^
--report="C:\Users\~\Documents\Pinnacle 21 Community\reports\hg.xlsx" 

I'm getting an error, part of the log is below.

2024-08-16 16:32:10 [main] INFO  n.p.oce.clients.BootstrapCli - Engine Version: 2304.3
2024-08-16 16:32:12 [main] INFO  n.p.oce.services.ValidationService - Engine folder: C:\Users\~\Documents\Pinnacle 21 Community\lib
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.jboss.modules.JDKSpecific$2 (file:/C:/Users/~/Documents/Pinnacle%2021%20Community/p21-client-1.0.8.jar) to method java.lang.ClassLoader.getPackage(java.lang.String)
WARNING: Please consider reporting this to the maintainers of org.jboss.modules.JDKSpecific$2
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The ItemDef IT.TS.TSVAL.FCNTRY contains a reference to the unknown codelist CL.COUNTRY
The ItemDef IT.QS.QSTEST.FCNTRY contains a reference to the unknown codelist CL.COUNTRY
The ItemDef IT.DA.DALOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.DD.DDLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.DO.DOLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.DU.DULOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.EG.EGLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.FA.FALOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.IE.IELOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.IS.ISLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.LB.LBLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.FINDINGS.__LOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.FINDINGSABOUT.__LOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.MB.MBLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.MI.MILOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.MO.MOLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.MO.MOTEST contains a reference to the unknown codelist CL.MOTEST
The ItemDef IT.MO.MOTESTCD contains a reference to the unknown codelist CL.MOTESTCD
The ItemDef IT.MS.MSLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.PC.PCLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.PE.PELOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.PP.PPLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.QS.QSLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.RP.RPLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.RS.RSLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.SC.SCLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.SR.SRLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.SS.SSLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.TR.TRLOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.TU.TULOINC contains a reference to the unknown codelist CL.LOINC
The ItemDef IT.VS.VSLOINC contains a reference to the unknown codelist CL.LOINC
2024-08-16 16:32:14 [ForkJoinPool.commonPool-worker-5] WARN  n.p.validator.settings.Template - Refusing to register rule DD0101 because rule type Schematron is invalid
2024-08-16 16:32:14 [ForkJoinPool.commonPool-worker-5] INFO  n.p.validator.engine.BlockValidator - Beginning validation tasks
2024-08-16 16:32:15 [main] INFO  net.bootstrap.api.iq.data.IQData - Start IQ check ...
Failed local validation process. packages=LocalDataPackage{dataPackage=DataPackage{standard=Input{value=StandardType{value=SDTM-IG, name=SDTMIG}, userProvided=true, empty=false}, standardVersion=StringInput{value=3.2, userProvided=true, empty=false}, meddraVersion=StringInput{value=, userProvided=false, empty=true}, sdtmCtVersion=StringInput{value=2024-03-29, userProvided=true, empty=false}, qrsCtVersion=StringInput{value=, userProvided=false, empty=true}, adamCtVersion=StringInput{value=, userProvided=false, empty=true}, sendCtVersion=StringInput{value=, userProvided=false, empty=true}, ndfrt=StringInput{value=, userProvided=false, empty=true}, unii=StringInput{value=, userProvided=false, empty=true}, loinc=StringInput{value=, userProvided=false, empty=true}, whodrug=StringInput{value=, userProvided=false, empty=true}, snomed=StringInput{value=, userProvided=false, empty=true}, projectName=StringInput{value=, userProvided=false, empty=true}, studyName=StringInput{value=, userProvided=false, empty=true}, groupName=StringInput{value=, userProvided=false, empty=true}, dataPackageName=StringInput{value=, userProvided=false, empty=true}, reportSource=DataSourceInfo{dataSource=FileDS{path=C:\Users\~\Documents\Pinnacle 21 Community\reports\hg.xlsx\pinnacle21-report-2024-08-16T16-32-10-217.xlsx, schema=FILE, cleanup=false, valid=false}, format=Input{value=EXCEL, userProvided=true, empty=false}, cutoff=1000, delimitedInfo=net.pinnacle21.oce.model.input.DelimitedInfo@2c822a91, remoteDataSource=null}, source=FileDS{path=C:\Users\~\Desktop\study-101\SDTM.xpt, schema=FILE, cleanup=false, valid=true}, standardFilter=Input{value=FDA, userProvided=false, empty=false}, sourceFormatType=Input{value=XPORT, userProvided=false, empty=false}, sourceDelimiter=StringInput{value=,, userProvided=false, empty=false}, sourceQualifier=StringInput{value=", userProvided=false, empty=false}, define=Empty{absolutePath=EMPTY}, createAlways=Input{value=true, userProvided=false, empty=true}, engineVersion=Input{value=2304.3, userProvided=true, empty=false}, encoding=Input{value=null, userProvided=false, empty=true}, engineFolder=determined, downloadConfig=Input{value=false, userProvided=true, empty=false}, defineVersion=Input{value=Define-XML 2.0, userProvided=true, empty=false}}, config=ConfigInfo{configSource=FileDS{path=C:\Users\~\Documents\Pinnacle 21 Community\configs\2304.3\SDTM-IG 3.2 (FDA).xml, schema=FILE, cleanup=false, valid=true}, standard=SDTM-IG, version=3.2}, threadCount=3}
2024-08-16 16:32:16 [main] ERROR n.p.oce.events.ExceptionEvent - Failed core process.
net.pinnacle21.oce.exceptions.CLIException: Failed local validation process. packages=LocalDataPackage{dataPackage=DataPackage{standard=Input{value=StandardType{value=SDTM-IG, name=SDTMIG}, userProvided=true, empty=false}, standardVersion=StringInput{value=3.2, userProvided=true, empty=false}, meddraVersion=StringInput{value=, userProvided=false, empty=true}, sdtmCtVersion=StringInput{value=2024-03-29, userProvided=true, empty=false}, qrsCtVersion=StringInput{value=, userProvided=false, empty=true}, adamCtVersion=StringInput{value=, userProvided=false, empty=true}, sendCtVersion=StringInput{value=, userProvided=false, empty=true}, ndfrt=StringInput{value=, userProvided=false, empty=true}, unii=StringInput{value=, userProvided=false, empty=true}, loinc=StringInput{value=, userProvided=false, empty=true}, whodrug=StringInput{value=, userProvided=false, empty=true}, snomed=StringInput{value=, userProvided=false, empty=true}, projectName=StringInput{value=, userProvided=false, empty=true}, studyName=StringInput{value=, userProvided=false, empty=true}, groupName=StringInput{value=, userProvided=false, empty=true}, dataPackageName=StringInput{value=, userProvided=false, empty=true}, reportSource=DataSourceInfo{dataSource=FileDS{path=C:\Users\~\Documents\Pinnacle 21 Community\reports\hg.xlsx\pinnacle21-report-2024-08-16T16-32-10-217.xlsx, schema=FILE, cleanup=false, valid=false}, format=Input{value=EXCEL, userProvided=true, empty=false}, cutoff=1000, delimitedInfo=net.pinnacle21.oce.model.input.DelimitedInfo@2c822a91, remoteDataSource=null}, source=FileDS{path=C:\Users\~\Desktop\study-101\SDTM.xpt, schema=FILE, cleanup=false, valid=true}, standardFilter=Input{value=FDA, userProvided=false, empty=false}, sourceFormatType=Input{value=XPORT, userProvided=false, empty=false}, sourceDelimiter=StringInput{value=,, userProvided=false, empty=false}, sourceQualifier=StringInput{value=", userProvided=false, empty=false}, define=Empty{absolutePath=EMPTY}, createAlways=Input{value=true, userProvided=false, empty=true}, engineVersion=Input{value=2304.3, userProvided=true, empty=false}, encoding=Input{value=null, userProvided=false, empty=true}, engineFolder=determined, downloadConfig=Input{value=false, userProvided=true, empty=false}, defineVersion=Input{value=Define-XML 2.0, userProvided=true, empty=false}}, config=ConfigInfo{configSource=FileDS{path=C:\Users\~\Documents\Pinnacle 21 Community\configs\2304.3\SDTM-IG 3.2 (FDA).xml, schema=FILE, cleanup=false, valid=true}, standard=SDTM-IG, version=3.2}, threadCount=3}
 

As I mentioned above, I'm a beginner testing and learning about pinnacle21. Please help.

Forums: SDTM

j Jozef
on August 17, 2024

A few questions back:
What flavor of Java are you using? What version? Is it Oracle-Java, OpenJDK? The logs say something about JBoss ...
Is your system a Windows system, or Linux (Redhat?), what version?

Regarding the messages "The ItemDef xxx contains a reference to the unknown codelist CL.LOINC",
do you have the codelist with OID "CL.LOINC" in your define.xml as an "ExternalCodeList" ?

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