SAS Clinical Standards Toolkit 1.6 Operational Qualification

SAS Clinical Standards Toolkit 1.6 Operational Qualification
SAS Clinical Standards
Toolkit 1.6
®
Operational Qualification
SAS® Documentation
The correct bibliographic citation for this manual is as follows: SAS Institute Inc. 2014. SAS® Clinical Standards Toolkit 1.6:
Operational Qualification. Cary, NC: SAS Institute Inc.
SAS® Clinical Standards Toolkit 1.6: Operational Qualification
Copyright © 2014, SAS Institute Inc., Cary, NC, USA
All rights reserved. Produced in the United States of America.
For a hard-copy book: No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any
form or by any means, electronic, mechanical, photocopying, or otherwise, without the prior written permission of the
publisher, SAS Institute Inc.
For a web download or e-book: Your use of this publication shall be governed by the terms established by the vendor at
the time you acquire this publication.
The scanning, uploading, and distribution of this book via the Internet or any other means without the permission of the
publisher is illegal and punishable by law. Please purchase only authorized electronic editions and do not participate in or
encourage electronic piracy of copyrighted materials. Your support of others' rights is appreciated.
U.S. Government License Rights; Restricted Rights: The Software and its documentation is commercial computer
software developed at private expense and is provided with RESTRICTED RIGHTS to the United States Government. Use,
duplication or disclosure of the Software by the United States Government is subject to the license terms of this Agreement
pursuant to, as applicable, FAR 12.212, DFAR 227.7202-1(a), DFAR 227.7202-3(a) and DFAR 227.7202-4 and, to the
extent required under U.S. federal law, the minimum restricted rights as set out in FAR 52.227-19 (DEC 2007). If FAR
52.227-19 is applicable, this provision serves as notice under clause (c) thereof and no other notice is required to be affixed
to the Software or documentation. The Government's rights in Software and documentation shall be only those set forth in
this Agreement.
SAS Institute Inc., SAS Campus Drive, Cary, North Carolina 27513-2414.
June 2014
SAS provides a complete selection of books and electronic products to help customers use SAS® software to its fullest
potential. For more information about our offerings, visit support.sas.com/bookstore or call 1-800-727-3228.
SAS® and all other SAS Institute Inc. product or service names are registered trademarks or trademarks of SAS Institute
Inc. in the USA and other countries. ® indicates USA registration.
Other brand and product names are trademarks of their respective companies.
Contents
PART 1
Before You Begin
1
Chapter 1 / Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Assumptions and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
The Standards in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
PART 2
Internal Validation
9
Chapter 2 / Installation Qualification and Operational Qualification . . . . . . . . . . . . . . . 11
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
PART 3
ODM 19
Chapter 3 / Test 1: Create SAS ODM from XML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Chapter 4 / Test 2: Validate SAS ODM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
vi Contents
Chapter 5 / Test 3: Create ODM XML from SAS ODM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Chapter 6 / Test 4: Find Unsupported Tags in ODM XML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
PART 4
CRT-DDS
37
Chapter 7 / Test 1: Validate CRT-DDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Chapter 8 / Test 2: Create SAS CRT-DDS from SDTM Metadata . . . . . . . . . . . . . . . . . . . . 43
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Chapter 9 / Test 3: Create SAS CRT-DDS from define.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Chapter 10 / Test 4: Create define.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Contents
PART 5
Define-XML
vii
55
Chapter 11 / Test 1: Create Define-XML 2.0 SAS Data Sets from
SDTM Source Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Chapter 12 / Test 2: Create Define-XML 2.0 File from SAS Data Sets . . . . . . . . . . . . . . 61
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Chapter 13 / Test 3: Create SAS Data Sets from Define-XML 2.0 File . . . . . . . . . . . . . . 65
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
PART 6
SDTM
69
Chapter 14 / Test 1: Validate SDTM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Chapter 15 / Test 2: Build Source Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Chapter 16 / Test 3: Build Source Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
viii Contents
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Chapter 17 / Test 4: Build SAS Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Chapter 18 / Test 5: Report Check Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
1
Part 1
Before You Begin
Chapter 1
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
2
3
1
Introduction
Purpose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Assumptions and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
General Assumptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
File Path Separator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
sample study library directory within This Document . . . . . . . . . . . . . . . 5
Variables Referred to by the Tests . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Generation of a PDF File . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
The Standards in This Document . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Purpose
Starting with SAS Clinical Standards Toolkit 1.5, an internal validation process is
provided. This process has been designed using tools and metadata already available
with the product. In other words, the SAS Clinical Standards Toolkit is set up as a
standard within the product and is validated against a set of reference metadata.
The SAS Clinical Standards Toolkit internal validation addresses two primary use
cases:
n
Perform installation qualification and operational qualification.
This is implemented with and illustrated by the use of the validate_iqoq sample
driver, located in the sample study library directory/cstframework-1.6/programs folder. This is a two-step process.
4 Chapter 1 / Introduction
1 Select the CST-FRAMEWORK standard, and run the checks that are defined in
the validation_control_glmeta view of the internal validation validation_master
data set. This is a set of 64 checks (checkid < CSTV100) that look only at the
global standards library metadata folder.
2 Select 1 to n specific standards, and run the checks that are defined in the
validation_control_stdiqoq view of the internal validation validation_master data
set. This is a set of 50 checks (checkid > CSTV100 that are relevant to
installation qualification and operational qualification issues) that look only at
metadata libraries other than the global standards library metadata folder.
n
Perform validation on standard-specific metadata.
This is implemented with and illustrated by the use of the validate_standard sample
driver. Select 1 to n specific standards, and run the checks that are defined in the
validation_control_std view of the internal validation validation_master data set.
This is a set of 66 checks (checkid > CSTV100) that look only at metadata libraries
other than the global standards library metadata folder.
For the purpose of operational qualification, this document implements the SAS Clinical
Standards Toolkit internal validation for installation qualification and operational
qualification.
For more information about internal validation, see Chapter 7, “Internal Validation,” in
the SAS Clinical Standards Toolkit: User’s Guide.
This document explains how to verify that the SAS Clinical Standards Toolkit 1.6 has
been installed correctly and is operating properly. The installation is tested by running a
series of SAS Clinical Standards Toolkit internal validation programs. These programs
must be run in the sequence that they are presented. In addition to the internal
validation process, a separate process enables you to manually run driver programs to
verify that the product is operating correctly.
Note: Driver programs for the standards (for example, ODM, CRT-DDS, and SDTM)
that are supplied with the SAS Clinical Standards Toolkit run off of the supplied sample
data. The sample data is not clean. Therefore, errors and warnings will be present in the
resulting data sets. This is normal.
Assumptions and Notes
5
Assumptions and Notes
General Assumptions
n
The second maintenance release for SAS 9.3 or SAS 9.4, has been installed and is
functioning correctly.
n
The SAS Clinical Standards Toolkit 1.6 has been installed, including the sample
study libraries.
n
The person running these tests is familiar with running SAS programs. This includes
being able to submit SAS programs via the Program Editor, review the SAS log, and
review the contents of SAS data sets.
n
The installation of the SAS Clinical Standards Toolkit has not been modified from the
default installation. If the sample studies have been modified before running these
tests, your results data sets can vary from what is described in this document.
Note: With a default installation, the results data sets must not contain errors or
warnings. With a modified installation, errors or warnings might be normal, but they
must be resolved by you.
File Path Separator
This document is used for both UNIX and Microsoft Windows environments. The
forward slash character ( / ) is used in file paths as the separator between path
components, which works in both operating system environments.
sample study library directory within This
Document
sample study library directory is used to denote the sample study libraries available with
SAS Clinical Standards Toolkit 1.6.
6 Chapter 1 / Introduction
The default value for SAS Clinical Standards Toolkit 1.6 on Microsoft Windows is C:/
cstSampleLibrary.
Variables Referred to by the Tests
The tests refer to the following variables, which are defined relative to sample study
library directory. When running the tests, substitute the variables with these associated
paths:
n
CST_FRAMEWORK
sample study library directory/cst-framework-1.6
n
CST_SDTM
sample study library directory/cdisc-sdtm-3.1.3–1.6/
sascstdemodata
n
CST_ODM
sample study library directory/cdisc-odm-1.3.1–1.6
n
CST_CRTDDS
sample study library directory/cdisc-crtdds-1.0–1.6
n
CST_DEFINEXML
sample study library directory/cdisc-definexml-2.0-1.6
Generation of a PDF File
The last manual test (see Chapter 18, “Test 5: Report Check Metadata,” on page 89)
generates a PDF file. On Microsoft Windows, when a PDF file is generated, the PDF
should automatically appear in a browser window. On UNIX, if you have not set up the
SAS configuration variable SAS.helpBrowser, you see this message:
The requested information could not be displayed because the
connection to the remote browser server failed.
Click OK to continue.
The Standards in This Document
7
Configure your UNIX SAS environment to support a browser that can display PDF files.
Or, copy the PDF file to an environment where you can display it.
The Standards in This Document
The parts in this document that describe the standards are samples of several
standards from the SAS Clinical Standards Toolkit. Each part describes how to access
the sample study data using the driver programs to verify that the data, the metadata,
and the SAS Clinical Standards Toolkit macros are functioning properly.
8 Chapter 1 / Introduction
9
Part 2
Internal Validation
Chapter 2
Installation Qualification and Operational Qualification . . . . . 11
10
11
2
Installation Qualification and
Operational Qualification
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
Introduction
Installation qualification and operational qualification is implemented with and illustrated
by the use of the validate_iqoq sample driver, located in the sample study library
directory/cst-framework-1.6/programs folder. This is a two-step process.
1 Select the CST-FRAMEWORK standard, and run the checks that are defined in the
validation_control_glmeta view of the internal validation validation_master data set.
This is a set of 64 checks (checkid < CSTV100) that look only at the global
standards library metadata folder.
2 Select 1 to n specific standards, and run the checks that are defined in the
validation_control_stdiqoq view of the internal validation validation_master data set.
This is a set of 50 checks (checkid > CSTV100 that are relevant to installation
qualification and operational qualification issues) that look only at the metadata
libraries other than the global standards library metadata folder.
12 Chapter 2 / Installation Qualification and Operational Qualification
Note: The validation Results data set that is generated by the internal validation
installation qualification and operational qualification contains many observations. Your
number of observations can differ from the numbers shown in this document due to
installation configurations that differ from a default installation of the SAS Clinical
Standards Toolkit. For example, CDISC SEND might not be installed.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_FRAMEWORK/programs/validate_iqoq.sas.
3 Select Run  Submit.
The program writes to the SAS log file and creates a cstrslt.validation_results data
set in the CST_FRAMEWORK/results directory.
Note: The SAS log might reach its limit depending on your system options. If it
does, print the contents to a file, and select APPEND in the pop-up menu. This can
happen several times during the run, so be sure to append each time it happens. To
maximize the log size, you can add the option –DMSLOGSIZE 999999 to the SAS
configuration file.
4 If the SAS log reaches it limit, perform these steps:
a In the pop-up window, select F to file.
Steps 13
b Enter a filename, and select APPEND or REPLACE.
Note: Select REPLACE for the first occurrence of the pop-up window only.
c Click END.
d Repeat steps a through c until finished.
Use the same filename each time, and select APPEND.
5 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
6 The column labeled Process status (named _cst_rc) is 0 for all records.
7 Review the cstrslt.validation_results data set using the SAS Explorer, especially for
the following conditions:
a The field resultflag is not 0.
When this value is not 0, a potential problem might exist. To more easily check
this value, subset the validation_results data set by entering where
resultflag ne 0 in the control box in the upper left:
14 Chapter 2 / Installation Qualification and Operational Qualification
b A number of observations can have result flag=1.
If the Result severity column is Note, these values are acceptable. To more
easily check these values, subset the validation_results data set by entering
where resultflag = "Note" (this is case sensitive) in the control box in the
upper left:
Here are examples of where resultseverity="Note" or "Info" and resultflag ne 0:
n
In this example of where resultseverity="Note", multiple records are detected
because there are multiple standard versions for ODM (1.3.0 and 1.3.1) and
SDTM (3.1.1, 3.1.2, 3.1.3, and 3.2). If multiple records were found for the
same standard version, this check would be in error.
n
In this example of where resultseverity="Info", a check was not run because
the check is not applicable to this standard. An informational check informs
you that check CSTV251 is not applicable to this standard.
Steps 15
n
In this example of where resultseverity="Info", a check was not run because
check CSTV262, included with the SAS Clinical Standards Toolkit, has not
yet been implemented in this release. Therefore, the check did not run.
n
In this example of where resultseverity="Note", these data sets are empty.
They are empty because they are templates and do not contain observations.
n
In this example of where resultseverity="Info", Result severity equals Info
because the controlled terminology does not have an sl_cntl folder associated
with it. There are no control type data sets associated with controlled
terminology.
No observations should appear when you enter where resultseverity =
"Error" in the control box in the upper left:
16 Chapter 2 / Installation Qualification and Operational Qualification
Any observation meeting the criterion where resultseverity =
"Warning" must be assessed individually. For example, in the validation of
the CDISC Define-XML 2.0.0 standard, the following result might be reported:
This message indicates that internal validation is correctly reporting that the
validation_master data set for CDISC Define-XML 2.0.0 is empty because
validation of the SAS representation of CDISC Define-XML 2.0.0 was not
implemented in SAS Clinical Standards Toolkit 1.6.
8 Close the SAS session.
Running the validate_iqoq internal validation program without error confirms that all
metadata is in place, all files are in place, and all access (whether Read or Write) to the
SAS Clinical Standards Toolkit is properly initialized. This process ensures that the
installation of the SAS Clinical Standards Toolkit was done properly and that the key
components are operational.
Sign-Off 17
Sign-Off
Internal Validation - Installation Qualification and Operational Qualification
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
18 Chapter 2 / Installation Qualification and Operational Qualification
19
Part 3
ODM
Chapter 3
Test 1: Create SAS ODM from XML . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Chapter 4
Test 2: Validate SAS ODM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Chapter 5
Test 3: Create ODM XML from SAS ODM . . . . . . . . . . . . . . . . . . . . . . . 29
Chapter 6
Test 4: Find Unsupported Tags in ODM XML . . . . . . . . . . . . . . . . . . 33
20
21
3
Test 1: Create SAS ODM from XML
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Introduction
This test reads a CDISC ODM 1.3.1 XML file and builds a SAS representation of the
metadata that is defined in the XML.
Note: To run against ODM 1.3.0, use the same information in this section, but
substitute 1.3.1 with 1.3.0. Running against ODM 1.3.0 creates fewer data sets and less
content (rows) within data sets.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/create_sasodm_fromxml.sas.
3 Select Run  Submit.
22 Chapter 3 / Test 1: Create SAS ODM from XML
This program writes to the SAS log file and creates data sets in the formats,
metadata, and data subdirectories in the CST_ODM/derived directory. It creates a
read_results data set in the CST_ODM/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the read_results data set in the CST_ODM/results directory to ensure that
the following conditions are met:
TIP In the SAS Explorer, you can view it as Read_results in the Results library.
n
The message column contains correct paths and process metadata.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
A record reports that the ODM file was read successfully.
6 Review the CST_ODM/derived/metadata directory to ensure that the following
conditions are met:
TIP In the SAS Explorer, you can view these data sets in the Srcmeta library.
n
The directory contains two data sets: source_tables and source_columns.
n
The source_tables data set contains 76 rows and 10 columns.
n
The source_columns data set contains 352 rows and 16 columns.
7 Review the CST_ODM/derived/data directory to ensure that the following
conditions are met:
n
There are 76 new SAS data sets. (Do not count any data sets that are not SAS,
such as .xpt files.)
n
The codelists data set contains 23 records and five columns.
8 Close the SAS session.
Sign-Off 23
Sign-Off
Test 1: Create SAS ODM from XML
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
24 Chapter 3 / Test 1: Create SAS ODM from XML
25
4
Test 2: Validate SAS ODM
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Introduction
This test validates a SAS representation of the metadata that is defined in the CDISC
ODM 1.3.1 XML file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/validate_odm_data.sas.
3 Select Run  Submit.
The program writes to the SAS log file and creates a validation_results data set and
a validation_metrics data set in the CST_ODM/results directory.
26 Chapter 4 / Test 2: Validate SAS ODM
Note: This program can fill up the log window if running interactively. If so, save the
output of the log to a file when prompted to do so.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the validation_results data set in the CST_ODM/results directory to ensure
that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are two failures of ODM0110.
n
The data set contains 385 records.
n
There are two records with resultflag=1 and resultseverity="Error". Both of
these records have checkid="ODM0110".
Note: The errors messages are expected and are included in the sample data to
cause a validation error for demonstration purposes.
6 Review the validation_metrics data set in the CST_ODM/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_metrics in the Results
library.
n
The data set contains 656 records.
n
The last record reports that there were two records with "Content errors,
warnings and notes".
7 Close the SAS session.
Sign-Off 27
Sign-Off
Test 2: Validate SAS ODM
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
28 Chapter 4 / Test 2: Validate SAS ODM
29
5
Test 3: Create ODM XML from SAS
ODM
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Introduction
This test creates a CDISC ODM 1.3.1 XML file from the SAS representation of the
metadata.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/create_odmxml.sas.
3 Select Run  Submit.
30 Chapter 5 / Test 3: Create ODM XML from SAS ODM
The program writes to the SAS log file and creates an XML file,
odm_sample_out.xml, in the CST_ODM/sourcexml directory. It creates a
write_results data set in the CST_ODM/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the write_results data set in the CST_ODM/results directory to ensure that
the following conditions are met:
TIP In the SAS Explorer, you can view it as Write_results in the Results library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
n
The data set contains 70 records.
n
There is a record where Source data is ODM_WRITE that reports that the ODM
file was created.
n
The last record where Source data contains ODM_XMLVALIDATE reports that
no errors were found in the ODM file.
6 Ensure that the CST_ODM/sourcexml directory contains a new XML file
odm_sample_out.xml that has the same size as the XML file odm_sample.xml in the
same directory.
7 Close the SAS session.
Sign-Off
Test 3: Create ODM XML from SAS ODM
Signature
Sign-Off 31
Test 3: Create ODM XML from SAS ODM
Date test was executed
Did the test pass? (Yes or No)
Comments
32 Chapter 5 / Test 3: Create ODM XML from SAS ODM
33
6
Test 4: Find Unsupported Tags in ODM
XML
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Introduction
This test parses a CDISC ODM 1.3.1 XML file and finds elements and attributes that the
SAS Clinical Standards Toolkit does not recognize by default. These elements and
attributes might be vendor extensions, customer extensions, or new tags implemented
in a later version of ODM.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_ODM/Programs/find_unsupported_tags.sas.
3 Select Run  Submit.
34 Chapter 6 / Test 4: Find Unsupported Tags in ODM XML
The program writes to the SAS log file and creates a readxmltags_results data set in
the CST_ODM/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the readxmltags_results data set in the CST_ODM/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as readxmltags_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for eight records, and 1 for all other records.
n
The data set contains 28 records.
n
There are four records that contain checkid="ODM0900" and 16 records that
contain checkid="ODM0901". For the ODM0900 check, the message indicates
"Element found in XML file that is not present in CDISC ODM Model". For
the ODM0901 check, the message indicates "Attribute found in XML file that
is not present in CDISC ODM Model".
6 Close the SAS session.
Sign-Off 35
Sign-Off
Test 4: Find Unsupported Tags in ODM XML
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
36 Chapter 6 / Test 4: Find Unsupported Tags in ODM XML
37
Part 4
CRT-DDS
Chapter 7
Test 1: Validate CRT-DDS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Chapter 8
Test 2: Create SAS CRT-DDS from SDTM Metadata . . . . . . . . . . 43
Chapter 9
Test 3: Create SAS CRT-DDS from define.xml . . . . . . . . . . . . . . . . . 47
Chapter 10
Test 4: Create define.xml . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
38
39
7
Test 1: Validate CRT-DDS
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Introduction
This test validates a SAS representation of the metadata and data that is defined in the
SAS representation of the CRT-DDS 1.0 model.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_CRTDDS/Programs/validate_crtdds_data.sas.
3 Select Run  Submit.
This program writes to the SAS log file and creates a validation_results data set and
a validation_metrics data set in the CST_CRTDDS/results directory.
40 Chapter 7 / Test 1: Validate CRT-DDS
Note: This program can fill up the log window if running interactively. If so, save the
output of the log to a file when prompted to do so.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the validation_results data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The data set contains 202 records.
n
There are 21 records that contain "Warning: Check not run". These records
contain checkid="CRT0100" and resultid="CST0022".
These warnings are the result of missing information, such as key variables.
Because these warnings apply to the metadata, a warning is issued, and the
check does not run.
6 Review the validation_metrics data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as validation_metrics in the Results
library.
n
The data set contains 326 records.
n
The last record reports that there were 21 records with "Content errors,
warnings and notes".
7 Close the SAS session.
Sign-Off 41
Sign-Off
Test 1: Validate CRT-DDS
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
42 Chapter 7 / Test 1: Validate CRT-DDS
43
8
Test 2: Create SAS CRT-DDS from
SDTM Metadata
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Introduction
If this program runs successfully and produces the expected results, the SAS Clinical
Standards Toolkit derived CRT-DDS 1.0 metadata from an SDTM study as a
prerequisite to building a define.xml file in Test 5.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_CRTDDS/programs/create_crtdds_from_sdtm.sas.
3 Select Run  Submit
44 Chapter 8 / Test 2: Create SAS CRT-DDS from SDTM Metadata
The program writes to the SAS log file and creates 39 data sets in the
CST_CRTDDS/data directory. It create a Results data set in the CST_CRTDDS/
results directory.
4 Review the log to see whether there are any errors or warnings.
5 Review the CST_CRTDDS/data directory to ensure that the following conditions are
met:
TIP In the SAS Explorer, you can view it in the srcdata library.
n
There are 39 new SAS data sets.
n
The codelists data set has 46 records and 5 columns.
6 Review the sdtmtodefine_results data set in the CST_CRTDDS/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as sdtmtodefine_results in the Results
library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The data set contains 40 records.
7 Close the SAS session.
Sign-Off 45
Sign-Off
Test 2: Create SAS CRT-DDS from SDTM Metadata
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
46 Chapter 8 / Test 2: Create SAS CRT-DDS from SDTM Metadata
47
9
Test 3: Create SAS CRT-DDS from
define.xml
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Introduction
This test creates a CRT-DDS 1.0 SAS representation file from a define.xml file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_CRTDDS/Programs/create_sascrtdds_fromxml.sas.
3 Select Run  Submit.
This program writes to the SAS log file and creates the SAS representation of the
CRT-DDS data sets in the CST_CRTDDS/deriveddata directory.
48 Chapter 9 / Test 3: Create SAS CRT-DDS from define.xml
TIP In the SAS Explorer, you can view it in the srcdata library.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the read_results data set in the CST_CRTDDS/results directory to ensure
that the following conditions are met:
TIP In the SAS Explorer, you can view it as read_results in the Results library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
n
There is a record where Source data is CRTDDS_READ that reports that the
define.xml file was read successfully.
n
There is a record where Source data is JAVA CHECK that reports No java
issues.
6 Ensure that the CST_CRTDDS/deriveddata directory contains 39 SAS data sets
that represent the SAS interpretation of the CRT-DDS format.
7 Open the clitemdecodetranslatedtext SAS data set.
It contains 4481 observations. The first 17 observations are shown in this figure.
Steps 49
8 Close the SAS session.
50 Chapter 9 / Test 3: Create SAS CRT-DDS from define.xml
Sign-Off
Test 3: Create SAS CRT-DDS from define.xml
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
51
10
Test 4: Create define.xml
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Introduction
If this program runs successfully and produces the expected results, the SAS Clinical
Standards Toolkit Java and XML-related libraries are installed correctly. The SAS
Clinical Standards Toolkit and libraries can create a CRT-DDS file (define.xml).
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_CRTDDS/Programs/create_crtdds_define.sas.
This program writes to the SAS log and generates two files in the CST_CRTDDS/
sourcexml directory. It creates a Results data set in the CST_CRTDDS/results
directory.
3 Select Run  Submit.
52 Chapter 10 / Test 4: Create define.xml
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Ensure that two files were generated in the CST_CRTDDS/sourcexml directory:
define.xml and define-v1-updated-html.xsl.
6 Open the define.xml file.
On Microsoft Windows, you can open it by double-clicking it in the SAS Program
Editor. This renders the file in your default web browser or any other application that
has been associated with XML files.
On UNIX, if you have not set up your browser configuration in SAS, you need to
copy define.xml and define-v1-updated-html.xsl to an environment where you can
display the define.xml file in a web browser.
Note: The style sheet information in define-v1-updated-html.xsl is not guaranteed to
work for all browser types and versions to produce the correct HTML, but it does
work for Internet Explorer 6.0 and higher.
7 Ensure that the first few rows of the first table appear similar to this image:
Note: 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.
8 Ensure that the define.xml file contains tables for the following:
Steps 53
n
For each domain, a table that lists the domain’s variables
n
Computational Algorithms Section
n
Controlled Terminology
9 In the Controlled Terminology section of the define.xml file, ensure that the last few
items in the file are values for VSTESTCD, including the values BMI and WEIGHT.
54 Chapter 10 / Test 4: Create define.xml
10 Close the SAS session.
Sign-Off
Test 5: Create define.xml
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
55
Part 5
Define-XML
Chapter 11
Test 1: Create Define-XML 2.0 SAS Data Sets
from SDTM Source Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Chapter 12
Test 2: Create Define-XML 2.0 File from SAS Data Sets . . . . . 61
Chapter 13
Test 3: Create SAS Data Sets from Define-XML 2.0 File . . . . . 65
56
57
11
Test 1: Create Define-XML 2.0 SAS
Data Sets from SDTM Source
Metadata
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
Introduction
If this program runs successfully and produces the expected results, the SAS Clinical
Standards Toolkit derived Define-XML 2.0 metadata from an SDTM study as a
prerequisite to building a define.xml file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_DEFINEXML/Programs/create_sasdefine_from_source.sas.
3 Select Run  Submit.
58 Chapter 11 / Test 1: Create Define-XML 2.0 SAS Data Sets from SDTM Source Metadata
This program writes to the SAS log file and creates 31 data sets in the
CST_DEFINEXML/data/cdisc-sdtm-3.1.2 directory. It creates a Results data
set in the CST_DEFINEXML/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the CST_DEFINEXML/data directory to ensure that the following conditions
are met:
TIP In the SAS Explorer, you can view it in the srcdata library.
n
There are 31 new SAS data sets.
n
The itemdefs data set contains 535 records and 13 columns.
6 Review the sourcetodefine_results data set in the CST_DEFINEXML/results
directory to ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as sourcetodefine_results in the
Results library.
n
The column labeled Process status (named _cst_rc) is 0 for all records
n
The data set contains 65 records.
7 Close the SAS session.
Sign-Off 59
Sign-Off
Test 1: Create Define-XML 2.0 SAS Data Sets from SDTM Source Metadata
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
60 Chapter 11 / Test 1: Create Define-XML 2.0 SAS Data Sets from SDTM Source Metadata
61
12
Test 2: Create Define-XML 2.0 File
from SAS Data Sets
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Introduction
If this program runs successfully and produces the expected results, the SAS Clinical
Standards Toolkit Java-related and XML-related libraries are installed correctly. The
SAS Clinical Standards Toolkit can create a Define-XML 2.0 file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_DEFINEXML/Programs/create_definexml.sas.
3 Select Run  Submit.
62 Chapter 12 / Test 2: Create Define-XML 2.0 File from SAS Data Sets
This program writes to the SAS log file and creates two files in the
CST_DEFINEXML/sourcexml directory. It creates a Results data set in the
CST_DEFINEXML/results directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Ensure that two files were created in the CST_DEFINEXML/sourcexml directory:
define-sdtm-3.1.2.xml and define2-0-0.xsl.
6 Open the define-sdtm-3.1.2.xml file.
On Microsoft Windows, you can open it by double-clicking it in the SAS Program
Editor. This renders the file in your default web browser or any other application that
has been associated with XML files.
On UNIX, if you have not set up your browser configuration in SAS, you need to
copy define-sdtm-3.1.2.xml and define2-0-0.xsl to an environment where you can
display the XML file in a web browser.
Note: The style sheet information in define2-0-0.xsl is not guaranteed to work for all
browser types and versions to produce the correct HTML, but it does work for
Internet Explorer 6.0 and higher. The Chrome browser, for example, does not allow
local XML and XSLT processing. Depending on your browser, you might see a
security warning because the style sheet uses Javascript.
7 Ensure that the display looks similar to this image:
Steps 63
Note: Minor variations in appearance are possible and are not a problem.
Reviewing the display is sufficient to confirm that the product is installed and
functioning properly.
8 Ensure that the last few rows (indicating that comments are being displayed) appear
similar to this image:
9 Review the write_results data set in the CST_DEFINEXML/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as write_results in the Results library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
n
The data set contains 78 records.
n
There is a record where Source data is DEFINE_WRITE that reports that the
XML file was created successfully.
64 Chapter 12 / Test 2: Create Define-XML 2.0 File from SAS Data Sets
n
There is a record where Source data is XML TRANSFORMER that reports The
document validated successfully.
10 Close the SAS session.
Sign-Off
Test 2: Create Define-XML 2.0 File from SAS Data Sets
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
65
13
Test 3: Create SAS Data Sets from
Define-XML 2.0 File
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Introduction
If this program runs successfully and produces the expected results, the SAS Clinical
Standards Toolkit derived a SAS representation of the metadata from a Define-XML 2.0
file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_DEFINEXML/Programs/create_sasdefine_fromxml.sas.
3 Select Run  Submit.
66 Chapter 13 / Test 3: Create SAS Data Sets from Define-XML 2.0 File
This program writes to the SAS log file, creates a Define-XML 2.0 SAS
representation in the CST_DEFINEXML/deriveddata/cdisc-sdtm-3.1.2
directory from the CST_DEFINEXML/sourcexml/define2-0-0-examplesdtm.xml file. It creates a Results data set in the CST_DEFINEXML/results
directory.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the CST_DEFINEXML/deriveddata/cdisc-sdtm-3.1.2 directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it in the srcdata library.
n
There are 46 new SAS data sets that represent the SAS interpretation of the
metadata in the define2-0-0-example-sdtm.xml file.
n
The itemdefs data set contains 423 records and 13 columns.
6 Review the read_results data set in the CST_DEFINEXML/results directory to
ensure that the following conditions are met:
TIP In the SAS Explorer, you can view it as read_results in the Results library.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
n
The column named resultflag is 0 for all records.
n
The data set contains 78 records.
n
There is a record where Source data is DEFINE_READ that reports that the
XML file was read successfully.
n
There is a record where Source data is XML TRANSFORMER that reports The
document validated successfully.
7 Close the SAS session.
Sign-Off 67
Sign-Off
Test 3: Create SAS Data Sets from Define-XML 2.0 File
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
68 Chapter 13 / Test 3: Create SAS Data Sets from Define-XML 2.0 File
69
Part 6
SDTM
Chapter 14
Test 1: Validate SDTM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Chapter 15
Test 2: Build Source Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Chapter 16
Test 3: Build Source Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Chapter 17
Test 4: Build SAS Formats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Chapter 18
Test 5: Report Check Metadata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
70
71
14
Test 1: Validate SDTM
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
Introduction
This test runs the sample program that is provided as part of the SDTM 3.1.3 standard.
If this program runs successfully and produces the expected results, the SDTM 3.1.3
standard is correctly installed and functioning properly.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/validate_data.sas.
3 Select Run  Submit.
The program writes to the SAS log file and generates a validation_results data set
and a validation_metrics data set in the CST_SDTM/data directory.
72 Chapter 14 / Test 1: Validate SDTM
TIP In the SAS Explorer, you can view these data sets in the Results library.
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the validation_results data set in the CST_SDTM/data directory to ensure
that the following conditions are met:
n
For the records where the column labeled Validation check identifier (named
checkid) is blank, examine the message column to ensure that paths and
process metadata are correct.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are not any checks with resultseverity='Warning: Check not run'.
n
The data set contains 312 records.
6 Review the validation_metrics data set in the CST_SDTM/data directory and ensure
that it contains these last few rows:
Metric Parameter
# of distinct check invocations
Count of Records
15
# check invocations not run
1
Errors (severity=High) reported
1
Warnings (severity=Medium) reported
Notes (severity=Low) reported
Structural errors, warnings and notes
Content errors, warnings and notes
7 Close the SAS session.
91
118
0
210
Sign-Off 73
Sign-Off
Test 1: Validate SDTM
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
74 Chapter 14 / Test 1: Validate SDTM
75
15
Test 2: Build Source Data
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
Introduction
This test references derived data from a CRT-DDS (define.xml) file to build a library of
SDTM 3.1.3 domains.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/create_sasdatafromxpt.
3 Select Run  Submit.
The program writes to the SAS log file and creates an xpt_results data set in the
CST_SDTM/results directory and 36 data sets in the CST_SDTM/derived/data
directory.
76 Chapter 15 / Test 2: Build Source Data
Note: For this program, the library information was cleaned up, so these files are
not immediately accessible under Libraries in the SAS Explorer. On Microsoft
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 directory that is viewable by the
SAS Explorer (for example, your Home Directory listed under Favorite Folders).
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
You might sporadically see warnings in the SAS log such as WARNING: Libname
<libref> is not assigned. These occur with redundant requests to clear
SAS librefs or filerefs and do not indicate a problem with the SAS Clinical Standards
Toolkit installation.
5 Review the xpt_results data set to ensure that the following conditions are met:
n
The Resolved message text from message file column (named message)
contains correct paths and process metadata.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are not any checks with resultseverity='Warning: Check not run'.
Steps 77
n
The data set contains 18 records. One of the last records reports Process
completed successfully.
Note: Values that refer to temporary directories, files, or PROCESS DATE: vary.
6 Review the CST_SDTM/derived/data directory to ensure that the following
conditions are met:
n
There are 36 new SAS data sets.
n
The dm data set has 70 records and 28 columns.
7 Close the SAS session.
78 Chapter 15 / Test 2: Build Source Data
Sign-Off
Test 2: Build Source Data
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
79
16
Test 3: Build Source Metadata
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Introduction
This test references derived data from a CRT-DDS (define.xml) file to build a set of
SDTM 3.1.3 metadata in a structure required by the SAS Clinical Standards Toolkit.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/create_sourcemetadata.sas.
3 Select Run  Submit.
This program writes to the SAS log file and creates data sets in the CST_SDTM/
results directory and the CST_SDTM/derived/metadata directory.
80 Chapter 16 / Test 3: Build Source Metadata
Note: For this program, the library information was cleaned up, so these files are
not immediately accessible under Libraries in the SAS Explorer. On Microsoft
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 directory that is viewable by the
SAS Explorer (for example, your Home Directory listed under Favorite Folders).
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the srcmeta_results data set in the CST_SDTM/results directory to ensure
that the following conditions are met:
n
The Resolved message text from message file column (named message)
contains correct paths and process metadata.
n
The column labeled Process status (named _cst_rc) is 0 for all records.
Steps 81
n
The data set contains 28 records.
Note: Values that refer to temporary directories, files, or PROCESS DATE: vary.
n
Where the Result identifier equals CST0074, the records report that study
reference data was created in folder CST_SDTM/derived/metadata.
82 Chapter 16 / Test 3: Build Source Metadata
6 Review the CST_SDTM/derived/metadata directory to ensure that the following
conditions are met:
n
There are five new data sets: source_columns, source_study,
source_documents, source_values, and source_tables.
n
The source_tables data set has 36 records and 15 columns.
7 Close the SAS session.
Sign-Off 83
Sign-Off
Test 3: Build Source Metadata
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
84 Chapter 16 / Test 3: Build Source Metadata
85
17
Test 4: Build SAS Formats
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Introduction
This test references derived data from a CRT-DDS (define.xml) file to build a SAS
format catalog representing the codelists in the CRT-DDS (define.xml) file.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/create_formatsfromcrtdds.sas.
3 Select Run  Submit.
The program writes to the SAS log file and creates a codelist_results data set in the
CST_SDTM/results directory and creates a catalog named cterms in the
CST_SDTM/derived/formats directory.
86 Chapter 17 / Test 4: Build SAS Formats
Note: For this program, the library information was cleaned up, so these files are
not immediately accessible under Libraries in the SAS Explorer. On Microsoft
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 directory that is viewable by the
SAS Explorer (for example, your Home Directory listed under Favorite Folders).
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the codelist_results data set in the CST_SDTM/results directory to ensure
that the following conditions are met:
n
The Resolved message text from message file column (named message)
contains correct paths and process metadata.
n
The column labeled Process status (named _cst_rc) is 0 for all records. There
are not any checks with resultseverity='Warning: Check not run'.
n
The data set contains 18 records. One of the last records reports Process
completed successfully.
Note: Values that refer to temporary directories, files, or PROCESS DATE: vary.
Sign-Off 87
6 Ensure that the CST_SDTM/derived/formats directory contains a cterms catalog
(cterms.sas7bcat).
7 Open the cterms catalog and verify that it has 53 formats.
Note: The data set can show a different number of formats if it previously existed. In
this case, the 53 formats are appended to the file.
8 Close the SAS session.
Sign-Off
Test 4: Build SAS Formats
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
88 Chapter 17 / Test 4: Build SAS Formats
89
18
Test 5: Report Check Metadata
Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Sign-Off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
Introduction
This test verifies that all metadata about SDTM 3.1.3 validation checks is properly
installed. A sample report itemizes this metadata.
Steps
1 Start a new SAS session.
2 In the SAS Program Editor, select File  Open Program, and then select
CST_SDTM/programs/cst_metadatareport.sas.
3 Select Run  Submit.
This program writes to the SAS log file and generates a PDF file named
cstcheckmetadatareport.pdf in the CST_SDTM/results directory.
Note: No result data set is created.
90 Chapter 18 / Test 5: Report Check Metadata
4 Review the log to see whether there are any errors or warnings.
There should be no errors or warnings.
5 Review the PDF file.
a Ensure that all four of these report sections were generated:
n
The Report Procedure (Check Overview)
n
Additional Check Details
n
Message Details
n
Reference Information
b Ensure that all titles, footnotes, column headings, and cell contents appear
correct.
c 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).
6 Close the SAS session.
Sign-Off 91
Sign-Off
Test 5: Report Check Metadata
Signature
Date test was executed
Did the test pass? (Yes or No)
Comments
92 Chapter 18 / Test 5: Report Check Metadata
Was this manual useful for you? yes no
Thank you for your participation!

* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project

Download PDF

advertisement