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®
SAS Clinical Data Standards
Toolkit 1.3
Installation Qualification
The correct bibliographic citation for this manual is as follows: SAS Institute Inc. 2010.
SAS ® Clinical Data Standards Toolkit 1.3: Installation Qualification. Cary, NC: SAS
Institute Inc.
SAS® Clinical Data Standards Toolkit 1.3: Installation Qualification
Copyright © 2010, SAS Institute Inc., Cary, NC, USA
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iii
Contents
Chapter 1 Installation Qualification 1
Purpose 1
Notes and Assumptions 2
Test 1 – SAS Hot Fix for ISO 8601 Informats Has Been Installed 3
Steps 3
Sign-off 3
Test 2 –SDTM 3.1.1 Validation 3
Steps 3
Sign-off 5
Test 3 – SDTM 3.1.1 Report Process Results 5
Steps 6
Sign-off 6
Test 4 – SDTM 3.1.2 Validation 6
Steps 6
Sign-off 7
Test 5 – SDTM 3.1.2 Build Source Data 7
Steps 7
Sign-off 8
Test 6 – SDTM 3.1.2 Build Source Metadata 8
Steps 8
Sign-off 9
Test 7 – SDTM 3.1.2 Build SAS Formats 9
Steps 9
Sign-off 10
Test 8 – SDTM 3.1.2 Report Check Metadata 10
Steps 10
Sign-off 11
Test 9 – CRT-DDS Create 11
Steps 11
Sign-off 11
Test 10 – CRT-DDS Create Define.xml 11
Steps 12
Sign-off 13
Test 11 – ODM 1.3.0 Create SAS ODM from XML 13
Steps 13
Sign-off 14
Test 12 – Controlled Terminology 200810 14
iv
Contents
Steps 14
Sign-off 15
Test 13 – Controlled Terminology 201003 15
Steps 15
Sign-off 16
Final Sign-off 16
1
C H A P T E R
1
Installation Qualification
Installation Qualification 1
Purpose 1
Notes and Assumptions 2
Test 1 – SAS Hot Fix for ISO 8601 Informats Has Been Installed 3
Steps 3
Sign-off 3
Test 2 –SDTM 3.1.1 Validation 3
Steps 3
Sign-off 5
Test 3 – SDTM 3.1.1 Report Process Results 5
Steps 6
Sign-off 6
Test 4 – SDTM 3.1.2 Validation 6
Steps 6
Sign-off 7
Test 5 – SDTM 3.1.2 Build Source Data 7
Steps 7
Sign-off 8
Test 6 – SDTM 3.1.2 Build Source Metadata 8
Steps 8
Sign-off 9
Test 7 – SDTM 3.1.2 Build SAS Formats 9
Steps 9
Sign-off 10
Test 8 – SDTM 3.1.2 Report Check Metadata 10
Steps 10
Sign-off 11
Test 9 – CRT-DDS Create 11
Steps 11
Sign-off 11
Test 10 – CRT-DDS Create Define.xml 11
Steps 12
Sign-off 13
Test 11 – ODM 1.3.0 Create SAS ODM from XML 13
Steps 13
Sign-off 14
Test 12 – Controlled Terminology 200810 14
Steps 14
Sign-off 15
Test 13 – Controlled Terminology 201003 15
Steps 15
Sign-off 16
Final Sign-off 16
Purpose

This document explains how to verify that SAS Clinical Standards Toolkit 1.3 has
been installed correctly and is functioning properly. The installation is tested by
running a series of SAS programs. These tests must be run in the sequence that is
presented.
2
Notes and Assumptions
Chapter 1
Notes and Assumptions
The SAS System itself is assumed to be installed and functioning correctly. It is
not being tested.
 SAS Clinical Standards Toolkit 1.3 has been installed.
 The following code should be run to confirm that the post-installation step to
update the CDISC-SDTM 3.1.2 data set validation_master has been completed.

%cstutil_setcstgroot;
libname refcntl "&_cstGRoot./standards/cdisc-sdtm-3.1.21.3/validation/control";
data _null_;
set refcntl.validation_master (where=(checkid='SDTM0602'));
if columnscope='' then
put "Post-installation step verified.";
else
do;
put "Warning: It appears that the post-installation step has not been
completed.";
put "Warning: Review the installation instructions to ensure Toolkit
functions properly.";
end;
run;
The person running these tests is familiar with running SAS programs. This
includes being able to submit SAS programs using the Program Editor, review the
SAS log, and review the contents of SAS data sets.
 This document is used for both the UNIX and Windows environments. The
forward slash character ( / ) is used in file paths as the separator between path
components, which works on both OS environments. There is one table that
contains SAS output from a Windows environment that has a backslash in the file
paths.
 Within this document
 SASINSTALL is used to denote the SAS installation folder. This is the folder
into which all SAS products are installed.
 SASROOT is used to denote the root folder for the SAS system installation.
 The default value for SAS 9.1.3 is SASINSTALL/SAS 9.1.
 The default value for SAS 9.2 is SASINSTALL/SASFoundation/9.2.
 The tests refer to the following variables, which are defined relative to
SASINSTALL. When running the tests, you need to substitute the variable with
the following associated paths.
 CST_SDTM_311
SASINSTALL/SASClinicalStandardsToolkitSDTM311/1.3/sample/cdisc-sdtm3.1.1/sascstdemodata
 CST_SDTM_312
SASINSTALL/SASClinicalStandardsToolkitSDTM312/1.3/sample/cdisc-sdtm3.1.2/sascstdemodata
 CST_ODM
SASINSTALL/SASClinicalStandardsToolkitODM130/1.3/sample/cdisc-odm1.3.0
 CST_CRTDDS
SASINSTALL/SASClinicalStandardsToolkitCRTDDS10/1.3/sample/cdisccrtdds-1.0

Installation Qualification / /

Test 2 –SDTM 3.1.1 Validation
3
Some of the tests (Tests 3 and 8) generate a PDF file. In Windows, when the PDF
is generated, a browser window should automatically appear that contains the
PDF for viewing. On UNIX, if you have not set up the SAS configuration variable
SAS.helpBrowser, then you get a dialog box that states “The requested
information could not be displayed because the connection to the remote browser
server failed.” Click OK to continue. You should either configure your UNIX SAS
environment to support a browser that can display PDF files or you need to copy
the PDF file to an environment where you can examine it.
Test 1 – SAS Hot Fix for ISO 8601 Informats Has Been Installed
This test only needs to be run if you are running SAS Version 9.1.3. If you have
downloaded SAS Clinical Data Standards Toolkit 1.3 from the SAS hot-fix site, then you
should verify that the SAS hot fix for the ISO 8601 SAS Informats has installed.
The identifier for this hot fix is E9BD36 and the URL for downloading the Windows
version is http://ftp.sas.com/techsup/download/hotfix/e9_win_sbcs.html#E9BD36. For
other platforms, go to http://ftp.sas.com/techsup/download/hotfix/e9_sbcs_prod_list.html
and search on that page for E9BD36.
Steps
1
Verify that this hot fix has been installed following the standard SAS System hot
fix installation practices. Refer to the product documentation to identify which hot
fix is required. Additional information about hot fixes can be located at
http://ftp.sas.com/techsup/download/hotfix/hotfix.html
Sign-off
Test 1 – SAS Hot fix for ISO 8601 Informats has been installed
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 2 –SDTM 3.1.1 Validation
This test runs the sample program that ships as part of the SDTM 3.1.1 standard. If this
program runs successfully and produces the expected results, then the SDTM 3.1.1
standard is correctly installed and functioning properly.
Steps
1
Submit the SDTM 3.1.1 validation sample program
CST_SDTM_311/programs/validate_data.sas.
It outputs to the SAS log and generate two SAS data sets: Validation_results and
4
Test 2 –SDTM 3.1.1 Validation
Chapter 1
Validation_metrics. These data sets can be found in the results library within the
SAS Explorer window.
2
Review the log to see whether there are any errors or warnings. There should not
be any.
3
Review the data set named Validation_results for errors. It should be consistent
with the following table. It contains additional columns, but checking these is
sufficient.
Validation
Check
Identifier
Unique
Invocation
of resultid
Seq #
within
resultseq
Source Data
Row
Result
Identifier
1
CST0108
1
1
CST_SETPROPERTIES
2
CST0102
1
1
CST_CREATEDS
3
CST0200
1
1
CSTUTIL_PROCESSSETUP
4
CST0108
1
1
CST_SETPROPERTIES
5
CST0108
1
1
CST_SETPROPERTIES
6
CST0200
1
1
SDTM_VALIDATE
7
CST0200
1
2
SDTM_VALIDATE
8
CST0200
1
3
SDTM_VALIDATE
9
CST0200
1
4
SDTM_VALIDATE
10
CST0200
1
5
SDTM_VALIDATE
11
CST0200
1
6
SDTM_VALIDATE
12
CST0200
1
7
SDTM_VALIDATE
13
CST0200
1
8
SDTM_VALIDATE
14
CST0200
1
9
SDTM_VALIDATE
15
CST0025
SDTM0011 1
1
SRCDATA.SUPPAE
16
CST0025
SDTM0011 2
1
SRCDATA.SUPPAE
17
CST0025
SDTM0012 1
1
SRCDATA.SUPPAE
18
CST0025
SDTM0012 2
1
SRCDATA.SUPPAE
19132
Many additional similar rows are reported.
N = 132
The following are the additional columns for rows 1 – 18.
Row
Resolved message text from message file
Result Severity resultflag
_cst_rc
1
The properties were processed from the PATH
c:\cstGlobalLibrary/standards/cst-framework1.3/programs/initialize.properties
Info
0
0
2
work.sasreferences was created as requested
Info
0
0
3
Process setup is using this SASReferences:
C:\DOCUME~1\userid\LOCALS~1\Temp\2\SAS Temporary
Files\_TD2932/sasreferences
Info
0
0
4
The properties were processed from the PATH
c:\cstGlobalLibrary/standards/cdisc-sdtm-3.1.11.3/programs/initialize.properties
Info
0
0
Installation Qualification / /
Test 3 – SDTM 3.1.1 Report Process Results
Row
Resolved message text from message file
Result Severity resultflag
_cst_rc
5
The properties were processed from the PATH
Info
!sasroot/../../SASClinicalStandardsToolkitSDTM311/1.3/sample/c
disc-sdtm-3.1.1/sascstdemodata/programs/validation.properties
0
0
6
PROCESS STANDARD: CDISC-SDTM
Info
0
0
7
PROCESS STANDARDVERSION: 3.1.1
Info
0
0
8
PROCESS DRIVER: SDTM_VALIDATE
Info
0
0
9
PROCESS DATE: 2010-08-24T20:17:44
Info
0
0
10
PROCESS TYPE: VALIDATION
Info
0
0
11
PROCESS SASREFERENCES:
C:\DOCUME~1\userid\LOCALS~1\Temp\2\SAS Temporary
Files\_TD2932/sasreferences.sas7bdat
Info
0
0
12
PROCESS STUDYROOTPATH:
Info
!sasroot/../../SASClinicalStandardsToolkitSDTM311/1.3/sample/c
disc-sdtm-3.1.1/sascstdemodata
0
0
13
PROCESS GLOBALLIBRARY: c:\cstGlobalLibrary
Info
0
0
14
PROCESS CSTVERSION: 1.3
Info
0
0
15
Data set not found in reference standard - compliance not
assessed
Warning:
Check
incomplete
1
0
16
Data set not found in reference standard - compliance not
assessed
Warning:
Check
incomplete
1
0
17
Data set not found in reference standard - compliance not
assessed
Warning:
Check
incomplete
1
0
18
Data set not found in reference standard - compliance not
assessed
Warning:
Check
incomplete
1
0
19 132
Many additional similar rows are reported.
N = 132
4
Close the SAS session.
Sign-off
Test 2 –SDTM 3.1.1 Validation is installed and functioning properly.
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 3 – SDTM 3.1.1 Report Process Results
This test produces a sample report that is based on SDTM 3.1.1 process results.
5
6
Test 4 – SDTM 3.1.2 Validation
Chapter 1
Steps
1
Start a new SAS session. In the SAS Program Editor, select File->Open and select
CST_SDTM_311/
programs/cst_report.sas.
2
Select Run->Submit. This code outputs to the SAS log and generates a PDF file.
No result data set is created.
3
Review the log to see whether there are any errors or warnings. There should not
be any.
4
Review the PDF file. It is named cstreport.pdf and is located in the folder
CST_SDTM_311/results. As noted in the Notes and Assumptions section, this
PDF file should automatically be displayed in Windows. If you are on UNIX, then
refer back to this section for instructions for approaches for viewing the PDF.


5
All five of the following report panels should be generated.
 Report Summary
 Process Inputs/Outputs
 Process Metrics
 General Process Reporting
 Process Results
All titles, paths, dates, and so on, should appear correct.
Close the SAS session.
Sign-off
Test 4 – SDTM 3.1.1 Report Process Results
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 4 – SDTM 3.1.2 Validation
Now we will run some tests for SDTM 3.1.2, which are located in a different base
directory than those for SDTM 3.1.1. This test verifies that the files required to validate
a set of SDTM 3.1.2 domains are properly defined.
Steps
1
Start a new SAS session. In the SAS Program Editor, select File->Open and select
CST_SDTM_312/programs/validate_data.sas.
2
Select Run->Submit. This program outputs to the log and creates the data sets
named Validation_results and Validation_metrics. These data sets can be found in
the Results library within the SAS Explorer window.
3
Review the log to see whether there are any errors or warnings. There should not
be any.
Installation Qualification / /
4


For the records where the column labeled “validation check identifier” (named
checkid) is blank, examine the message column and check for correct paths
and process metadata.
The column labeled “process status” (named _cst_rc) should be 0 for all records
and there should not be any checks with result severity = ’Warning: Check not
run’.
The data set should contain 99 records.
Review the data set named Validation_metrics. It should contain the following in
the last few rows:
Metric Parameter
Count of Records
# of distinct check invocations
13
# check invocations not run
0
Errors (severity=High) reported
0
Warnings (severity=Medium) reported
10
Notes (severity=Low) reported
0
Structural errors, warnings, and notes
85
Content errors, warnings, and notes
0
6
7
Review the data set named Validation_results.

5
Test 5 – SDTM 3.1.2 Build Source Data
End the current SAS session.
Sign-off
Test 5 – SDTM 3.1.2 Validation
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 5 – SDTM 3.1.2 Build Source Data
This test references derived data from a CRT-DDS (define.xml) file to build a library of
SDTM 3.1.2 domains.
Steps
1
Start a new SAS session. In the SAS Program Editor, select File->Open and select
CST_SDTM_312/programs/create_sasdatafromxpt.sas.
2
Select Run->Submit. The code outputs to the SAS log and creates a data set
named xpt_results under CST_SDTM_312/results and 33 data sets under
CST_SDTM_312/derived/data. For this program, the library information was
cleaned up so these files are not immediately accessible under Libraries in the
SAS Explorer. In Windows, you can access these files through the SAS Explorer by
navigating from within the SAS Explorer starting at the node labeled “My
Computer.” On UNIX, it is necessary for you to copy these data sets into a folder
8
Test 6 – SDTM 3.1.2 Build Source Metadata
Chapter 1
that is viewable by the SAS Explorer (for example, your Home Directory listed
under Favorite Folders).
3
Review the log to see whether there are any errors or warnings. There should not
be any errors. You might sporadically see warnings in the SAS log such as
“WARNING: Libname <libref> is not assigned.” These warnings occur with
redundant requests to clear SAS librefs, filerefs, or both and do not indicate a
problem with the SAS Clinical Standards Toolkit installation.
4
Review the data set named xpt_results.



5
Review the folder CST_SDTM_312/derived/data.


6
For the records where the column labeled “validation check identifier” (named
checkid) is blank, examine the message column and check for correct paths
and process metadata.
The column labeled “process status” (named _cst_rc) should be 0 for all records
and there should not be any checks with resultseverity=’Warning: Check not
run’.
The data set should contain 14 records and the last record should report
“Process completed successfully.”
There should be 33 new SAS data sets.
The data set dm should have 70 records and 20 columns.
End the current SAS session.
Sign-off
Test 6 – SDTM 3.1.2 Build Source Data
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 6 – SDTM 3.1.2 Build Source Metadata
This test references derived data from a CRT-DDS (define.xml) file to build a set of
SDTM 3.1.2 metadata in a structure required by SAS Clinical Standards Toolkit.
Steps
1
Start a new SAS session. In the SAS Program Editor, select File->Open and select
CST_SDTM_312/programs/create_sourcemetadata.sas.
2
Select Run->Submit. This code outputs to the SAS log and creates data sets in
both the results and derived/metadata subfolders under CST_SDTM_312. As in
Test 5, the library information was cleaned up by the program, so these files are
not immediately accessible under Libraries in the SAS Explorer. In Windows, you
can access these files through the SAS Explorer by navigating from within the
SAS Explorer starting at the node labeled “My Computer.” On UNIX, it is
necessary for you to copy these data sets into a folder that is viewable by the SAS
Explorer.
Installation Qualification / /
Test 7 – SDTM 3.1.2 Build SAS Formats
3
Review the log to see whether there are any errors or warnings. There should not
be any.
4
Review the data set named srcmeta_results under CST_SDTM_312/results.



5
For the records where the column labeled “validation check identifier” (named
checkid) is blank, examine the message column and check for correct paths
and process metadata.
The column labeled “process status” (named _cst_rc) should be 0 for all
records.
The data set should contain 16 records. The last three records should report
that study reference data was created in folder
CST_SDTM_312/derived/metadata.
Review the folder CST_SDTM_312/derived/metadata.


6
9
There should be three new data sets: source_columns, source_study,
source_tables.
The data set named source_tables should have 33 records.
End the SAS session.
Sign-off
Test 3 – SDTM 3.1.1 Build Source Metadata
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 7 – SDTM 3.1.2 Build SAS Formats
This test referenced derived data from a CRT-DDS (define.xml) file to build a SAS
format catalog that represents the codelists in the CRT-DDS file.
Steps
1
Start a new SAS session. In the SAS Program Editor, select File->Open and select
CST_SDTM_312/programs/create_formatsfromcrtdds.sas.
2
Select Run->Submit. The code outputs to the SAS log and creates a data set
named codelist_results in CST_SDTM_312/results and creates a catalog named
cterms under CST_SDTM_312/derived/formats. As in Tests 5 and 6, the library
information was cleaned up by the program so these files are not immediately
accessible under Libraries in the SAS Explorer. In Windows, you can access these
files through the SAS Explorer by navigating from within the SAS Explorer
starting at the node labeled “My Computer.” On UNIX, it is necessary for you to
copy these data sets into a folder that is viewable by the SAS Explorer.
3
Review the log to see whether there are any errors or warnings. There should not
be any.
4
Review the data set named codelist_results under CST_SDTM_312/results.
10
Test 8 – SDTM 3.1.2 Report Check Metadata



Chapter 1
For the records where the column labeled “validation check identifier” (named
checkid) is blank, examine the message column and check for correct paths
and process metadata.
The column labeled “process status” (named _cst_rc) should be 0 for all records
and there should not be any checks with result severity=’Warning: Check not
run’.
The data set should contain 14 records. The last record should report “Process
completed successfully.”
5
Folder CST_SDTM_312/derived/formats should contain a catalog cterms (named
cterms.sas7bcat). Open cterms and verify that it has 48 formats.
6
End the current SAS session.
Sign-off
Test 7 – SDTM 3.1.2 Build SAS Formats
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 8 – SDTM 3.1.2 Report Check Metadata
This test verifies that all metadata about SDTM 3.1.2 validation checks has been
properly installed. A sample report itemizes this metadata.
Steps
1
Start a new SAS session. In the SAS Program Editor, select File->Open and select
CST_SDTM_312/programs/cst_metadatareport.sas.
2
Select Run->Submit. This code outputs to the SAS log and generates a PDF file
named cstcheckmetadatareport.pdf in the CST_SDTM_312/results directory. No
result data set is created.
3
Review the log to see whether there are any errors or warnings. There should not
be any.
4
Review the PDF file.



5
All four of the following report sections should be generated.
 The Report Procedure (Check Overview)
 Additional Check Details
 Validation Message Details
 Reference Information
All titles, footnotes, column headings, and cell contents should appear correct.
In the Reference Information section, look for at least one value of
“OpenCDISC” in the column named Source of Information (for example, the
row for validation check SDTM0231).
End the current SAS session.
Installation Qualification / /
Test 10 – CRT-DDS Create Define.xml
11
Sign-off
Test 8 – SDTM 3.1.2 Report Check Metadata
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 9 – CRT-DDS Create
If this program runs successfully and produces the expected results, then SAS Clinical
Standards Toolkit has derived CRT-DDS metadata from an SDTM study as a
prerequisite to building a define.xml file in Test 10.
Steps
1
Start a new SAS session and submit the CRT-DDS create sample program
CST_CRTDDS/programs/create_crtdds10_from_sdtm311.sas. The sample
program outputs to the SAS log and creates 39 data sets in the
CST_CRTDDS/data folder.
2
Review the log to see whether there are any errors or warnings. There should not
be any.
3
Review the folder CST_CRTDDS/data.


4
There should be 39 new SAS data sets.
The data set codelists should have 32 records and five columns.
Close the SAS session.
Sign-off
Test 9 – CRT-DDS Create is installed and functioning properly.
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 10 – CRT-DDS Create Define.xml
If this program runs successfully and produces the expected results, then SAS Clinical
Standards Toolkit Java and XML-related libraries have been installed correctly and can
be used to create a CRT-DDS (define.xml) file.
12
Test 10 – CRT-DDS Create Define.xml
Chapter 1
Steps
1
Start a new SAS session and submit the CRT-DDS create define.xml sample
program CST_CRTDDS/programs/create_crtdds_define.sas. It writes to the SAS
log and generates data sets in CST_CRTDDS/sourcexml.
2
Review the log to see whether there are any errors or warnings; there should not
be any. You might see one warning that states, “The JAVAOBJ is an experimental
feature in this release and is not intended for use in the development of production
applications.”
3
Two files should have been generated in CST_CRTDDS/sourcexml: define.xml
and define1-0-0.xsl.
4
You need to examine the define.xml file in a Web browser. In Windows, you can
open it by double-clicking on it in the SAS Program Editor. This renders the file in
your default Web browser. On UNIX, if you have not set up your browser
configuration in SAS, then you need to copy the two files to an environment where
you can bring up the define.xml in a Web browser. The style sheet information in
define1-0-0.xsl is not guaranteed to work for all browser types and versions to
produce the correct HTML, but it does work for Internet Explorer version 6.0 and
higher. In the browser, the define.xml contains a number of tables.
The first table should appear similar to the following table (only the first few rows
have been provided here). Minor variations in appearance are possible and are not
a problem. Reviewing these rows is sufficient to confirm that the product is
installed and functioning properly.
Datasets for Study study1
Dataset
Description
Structure
Purpose
Keys
AE
Adverse Events
Events - One record per
event per subject
Tabulation
STUDYID
USUBJID
AEDECOD
AESTDTC
CM
Concomitant
Medications
Interventions - One record
per medication intervention
episode per subject
Tabulation
STUDYID
USUBJID
CMTRT
CMSTDTC
CO
Comments
Special Purpose - One
record per comment per
subject
Tabulation
STUDYID
USUBJID
COSEQ
DM
Demographics
Special Purpose - One
record per subject
Tabulation
STUDYID
USUBJID
DS
Disposition
Events - One record per
disposition status or
protocol milestone per
subject
Tabulation
STUDYID
USUBJID
DSDECOD
DSSTDTC
DV
Protocol
Deviations
Events - One record per
protocol deviation per
subject
Tabulation
STUDYID
USUBJID
DVTERM
DSSTDTC
Location
Installation Qualification / /
Test 11 – ODM 1.3.0 Create SAS ODM from XML
EG
ECG Test Results
Findings - One record per
ECG observation per time
point per visit per subject
Tabulation
STUDYID
USUBJID
EGTESTCD
VISITNUM
EGTPTREF
EGTPTNUM
EX
Exposure
Interventions - One record
per constant dosing interval
per subject
Tabulation
STUDYID
USUBJID EXTRT
EXSTDTC
IE
Inclusion/Exclusio
n Exceptions
Findings - One record per
Inclusion/Exclusion criteria
exception per subject
Tabulation
STUDYID
USUBJID
IETESTCD
5
13
The define.xml also contains tables for the following:




For each domain, a table lists its variables.
Value Level Metadata
Computational Algorithms Section
Controlled Terminology
6
The last table in the define.xml file contains Controlled Terminology. The last few
items in the file should be values for VSTESTCD, including the values BMI and
WEIGHT.
7
End the SAS session.
Sign-off
Test 10 – CRT-DDS Create Define.xml is installed and functioning properly
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 11 – ODM 1.3.0 Create SAS ODM from XML
This test reads a CDISC ODM 1.3.0 XML file and builds a SAS representation of the
metadata that is defined in the XML.
Steps
1
Start a new SAS session. In the SAS Program Editor, select File->Open and select
CST_ODM/Programs/create_sasodm_fromxml.sas.
2
Select Run->Submit. This code outputs to the SAS log and creates data sets in the
results, metadata, and data subfolders under CST_ODM.
3
Review the log to see whether there are any errors or warnings. There should not
be any. You might see one warning that states, “The JAVAOBJ is an experimental
14
Test 12 – Controlled Terminology 200810
Chapter 1
feature in this release and is not intended for use in the development of production
applications.”
4
Review the data set read_results under CST_ODM/results. In the SAS Explorer,
you can also view it as Read_results in the Results library.




5
The folder CST_ODM/metadata should contain two data sets: source_tables and
source_columns. You can also view these data sets in the SAS Explorer in the
library named Srcmeta.


6
The data set source_tables should have 52 rows and 10 columns.
The data set source_columns should have 241 rows and 15 columns.
Review the folder CST_ODM/data.


7
Examine the message column to verify correct paths and process metadata.
The column labeled Process status (named _cst_rc) should be 0 for all records.
The data set should contain 15 records.
The last record should report that the ODM file was read successfully.
There should be 52 new SAS data sets.
The data set codelists should have six records and five columns.
End the current SAS session.
Sign-off
Test 11 – ODM1.3.0 Create SAS ODM From XML
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 12 – Controlled Terminology 200810
This test verifies that the controlled terminology package 200810 has been installed and
is available to SAS Clinical Standards Toolkit processes.
Steps
1
Start a new SAS session.
2
In the SAS Program, enter the following SAS code.
%cstutil_setcstgroot;
libname fmts "&_cstGRoot./standards/cdisc-terminology-2008101.3/formats";
options fmtsearch=(fmts.cterms);
* Does expected format exist? *;
data _null_;
result = put('Albumin/Creatinine Ratio',$LBTEST.);
run;
data _null_;
Installation Qualification / /
Test 13 – Controlled Terminology 201003
15
set fmts.cterms (where=(codelist='LBTEST')) end=last;
attrib result format=$200.;
retain found 0 result '';
if _n_=1 then
result='Albumin/Creatinine Ratio';
if cdisc_submission_value=result then
do;
found=1;
result=catx(' ','Formatted value',result,'found');
put result=;
end;
if last and found=0 then put result= 'not found';
run;
If the format cannot be found (SAS log reports “ERROR 48-59: The format
$LBTEST was not found or could not be loaded.”) or if the specific test value is not
found, then there are problems with the installation, availability of the Controlled
Terminology package to SAS Clinical Standards Toolkit processes, or both. You
should see the following line at the end of the SAS log:
result=Formatted value Albumin/Creatinine Ratio found
3
End the current SAS session.
Sign-off
Test 12 – Controlled Terminology 200810
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Test 13 – Controlled Terminology 201003
This test verifies that the controlled terminology package 201003 has been installed and
is available to SAS Clinical Standards Toolkit processes.
Steps
1
Start a new SAS session.
2
In the SAS Program, enter the following SAS code.
%cstutil_setcstgroot;
libname fmts "&_cstGRoot./standards/cdisc-terminology-2010031.3/formats";
options fmtsearch=(fmts.cterms);
* Does expected format exist? *;
data _null_;
result = put('BLM',$COUNTRY.);
run;
data _null_;
set fmts.cterms (where=(codelist='COUNTRY')) end=last;
attrib result format=$200.;
retain found 0 result '';
16
Final Sign-off
Chapter 1
if _n_=1 then
result='BLM';
if cdisc_submission_value=result then
do;
found=1;
result=catx(' ','Formatted value',result,'found');
put result=;
end;
if last and found=0 then put result='not found';
run;
If the format cannot be found (SAS log reports “ERROR 48-59: The format
$COUNTRY was not found or could not be loaded.”) or if the specific test value is
not found then there are problems with the installation, availability of the
Controlled Terminology package to SAS Clinical Standards Toolkit processes, or
both. You should see the following line at the end of the SAS log:
result=Formatted value BLM found
3
End the current SAS session.
Sign-off
Test 13 – Controlled Terminology 201003
Signature
Date Test Was Executed
Did the test pass? (Yes or No)
Comments
Final Sign-off
In the following table, indicate your final assessment about whether SAS Clinical
Standards Toolkit 1.3 is installed correctly and is functioning properly.
If any of the IQOQ tests listed above did not pass, then the final IQOQ assessment must
not be passed, unless you have provided sufficient documentation to explain otherwise.
Final assessment of all testing.
Signature
Date Test Was Executed
Did the IQOQ pass? (Yes or No)
Comments
Your Turn
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