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The open source release of SAS Clinical Standards Toolkit is a direct port of the last production release with minor modifications to adapt to a new deployment architecture.

License: Apache License 2.0

Java 0.83% XSLT 15.80% SAS 38.71% HTML 44.64% Groovy 0.02%

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clinical-standards-toolkit's Issues

Java Check continually fails

CST0202, JAVA CHECK, SYSERR=1012 DATA STEP Component Object failure. Aborted during the EXECUTION phase.

This happens continuously and I can't figure out why. Everything else seems to work fine.

Installing CST in SAS EG

Hello,
I'm trying to install the open source CST to use in SAS EG. I've installed Apache ANT and downloaded the v1.7.5 release package. In the config.properties file (C:\Program Files\SASHome\SASStudioSingleUser\3.8\war\config), I've added the following.

#---SAS Clinical Standards toolkit
SET CSTHOME C:Users\Y.D.Dang_pc\Documents\SAS CST\cstFrameworkLibrary
CSTGLOBALLIB C:Users\Y.D.Dang_pc\Documents\SAS CST\cstGlobalLibrary
CSTSAMPLELIB C:Users\Y.D.Dang_pc\Documents\SAS CST\cstSampleLibrary
insert sasautos '!CSTHOME/macros'
JREOPTIONS (-Dsas.app.class.dirs=!CSTHOME/jar)
SET CLASSPATH !CSTHOME/jar

I'm currently however unable to run any of the programs. E.g. if I run cstvalidate I'm getting the following message:
WARNING: Apparent symbolic reference _CST_RC not resolved.
ERROR: A character operand was found in the %EVAL function or %IF condition where a numeric operand is required. The condition was:
&_cst_rc
ERROR: The macro CSTVALIDATE will stop executing.

  1. Is the config file the correct one as I'm using SAS EG.
  2. If correct should I add a '-' before each line. E.g. -SET CSTHOME.... ( It is originally added in the txt file in sctFrameworklibrary)
  3. I'm not able to stop server. Is it automatically stopped if I close SAS EG? A local server on my machine is used.
  4. Any other points that I've missed that might cause these errors?

Thanks,
Yen

SDTM codelist issues

I'm having an odd issue when generating metadata for the 2.1 definexml. I've been using the generate from saslib sample program and the settings are:

%define_createsrcmetafromsaslib(
 _cstTrgStandard=&_cstTrgStandard,
 _cstTrgStandardVersion=&_cstTrgStandardVersion,
 _cstLang=en,
 _cstUseRefLib=Y,
 _cstKeepAllCodeLists=N
); 

I also tried the other variant:

%define_createsrcmetafromsaslib(
 _cstSASDataLib=srcdata,
 _cstStudyMetadata=work.studymetadata,
 _cstTrgStandard=&_cstTrgStandard,
 _cstTrgStandardVersion=&_cstTrgStandardVersion,
 _cstTrgStudyDS=trgmeta.source_study,
 _cstTrgTableDS=trgmeta.source_tables,
 _cstTrgColumnDS=trgmeta.source_columns,
 _cstTrgCodeListDS=trgmeta.source_codelists,
 _cstTrgValueDS=trgmeta.source_values,
 _cstTrgDocumentDS=trgmeta.source_documents,
 _cstTrgAnalysisResultDS=trgmeta.source_analysisresults,
 _cstLang=en,
 _cstUseRefLib=Y,
 _cstRefTableDS=refmeta.reference_tables,
 _cstRefColumnDS=refmeta.reference_columns,
 _cstClassTableDS=refmeta.class_tables,
 _cstClassColumnDS=refmeta.class_columns,
 _cstKeepAllCodeLists=Y,
 _cstFormatCatalogs=cstfmt.formats ncifmt.cterms,
 _cstNCICTerms=ncifmt.cterms
 );

The issue I get is the metadata source_codelist file shows every possible term for every variable, when I only want the terminology for the terms used within the study data. Everything else seems like it is working correctly and when I change _cstKeepAllCodeLists=N to _cstKeepAllCodeLists=Y, it does what I'd expect it to do and show every term regardless of what is in the data. The User Guide has not done much to help me here and I'm not sure what I need to change in order to get this to work the way I want it to. Any advice here would be appreciated.

Using SAS Clinical Standards Toolkit with Viya

Hi All,
I'm a part of SAS Techical Support. A customer hosting Viya 3.5 on SAS Cloud has asked whether SAS Clinical Standards Toolkit (openCST) can be used on Viya. My answer would be it is not supported in Viya when reading the prerequiste section saying "the installation scripts have NOT been validated on SAS Viya yet."

  • The customer asks what does it mean exaclty "the installation scripts have NOT been validated on SAS Viya yet "
  • They asks if they can connect to CST installed on Windows from Viya: will it work but it is not supported or it will never work?

CST compatibility with Viya has also been raised here #5 but no answer has been provided.

Thanks
Ira

define v2.1

Interested if this could be compatible with generation of define v2.1, happy to help anyway I can.

remove use of %sysevalf to check SAS version

The &sysver value in Viya is V.04.00. A number of CST macros check this value using %sysevalf(&sysver) to support backwards compatibility for SAS 9.3 and 9.4, but this produces an error when processing the Viya version.

This will need to be refactored when Viya is officially supported.

cstutilwriteresultsintro

When removing unnecessary sysver checks, too much was removed in the cstutilwriteresultsintro macro.
This results in LOG messages:
[CSTLOGMESSAGE.CSTUTILWRITERESULTSINTRO]: Program name could not be determined and has been set to Unspecified

The %else statement needs to be restored in the macro:

%if %nrbquote(%sysfunc(getoption(SYSIN))) EQ and &sysscp eq WIN
  %then %do;
       %if %sysfunc(sysexist(SAS_EXECFILENAME)) %then %let _cstProgram = %sysget(SAS_EXECFILENAME);
  %end;
  %else %let _cstProgram = %sysfunc(scan(%nrbquote(%sysfunc(getoption(SYSIN))),-1,\));  

Support for SAS Viya

I would like to utilize this toolkit with our existing SAS Viya infrastructure. Is there any known way (even not supported or partially supported) to leverage the toolkit in Viya?

Trying to recreate ADaM 2.1 data sets: which SDTM and Define XML metadata versions should be used?

In CSTSAMPLELIB, I'm trying to recreate the data sets in ADaM 2.1, but there are significant differences when using SDTM 3.1.3/3.2, and Define XML 2.0 does not include all of the columns in ADaM 2.1, including:

  • Define XML 2.0:
    -- ADSL.RANDDT
    -- ADSL.DSDECOD/DCDECOD
  • SDTM 3.1.3/3.2:
    -- ADSL/DM.ARM
    -- ADSL/DM.ARMCD
    -- ADSL/DM.AGE
    -- ADSL/DM.AGEU
    -- ADSL/DM.RACE
    -- ADSL.VISIT1DT/SV.SVSTDTC
    -- ADSL.TRTSDT/SV.SVSTDTC
    -- ADSL.TRTEDT/EX.EXENDTC
    -- ADSL.COMPLT2/SV.SVSTDTC
    -- ADSL.COMPLT4/SV.SVSTDTC
    -- ADSL.COMPLT6/SV.SVSTDTC

I want to use the recreation of the sample ADaM data sets as a training exercise for new clinical SAS programmers, but the lack of consistency is proving to be a major obstacle. Is this information documented anywhere?

............Phil Holland

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