SUMMARY | DETAIL

Module ADaM V2.1 (Runtime)

This is the ADaM 2.1 runtime macro library.

%adam_createdisplay(_cstDisplaySrc=Metadata, _cstDisplayCode=, _cstUseAnalysisResults=, _cstUseTLFddt=, _cstDisplayID=, _cstDisplayPath=);

Creates an analysis result display from ADaM analysis data sets.

The path to the code to create the display is provided either directly in the
macro parameters or is derived from a metadata source. Examples of metadata
sources are analysis results metadata or Tables, Listings, and Figures data
definition metadata (TLFDDT) that you maintain and reference in the
SASReferences data set.

Two primary paths (parameter settings) are supported:
1. A code source is specified. A fully qualified path is required. The
expectation is that this macro is %included below to generate an
analysis result (display).
2. Metadata provides the information necessary to generate an analysis
result (display). This metadata is in the form of the CDISC ADaM
analysis results metadata, supplemental Tables, Listings, and Figures
data definition metadata (TLFDDT), or both.

Expected Macro Variables:

_CSTTLF_MASTERCODEPATH - Dynamically derived code segment path from
        TLF metadata.

_cstCTDescription - Description of controlled terminology packet

_cstDebug - Turns debugging on or off for the session

_cstGRoot - Root path of the global standards library

_cstResultSeq - Results: Unique invocation of check

_cstResultsDS - Results data set

_cstSASRefs - Run-time SASReferences data set derived in process setup

_cstSeqCnt - Results: Sequence number within _cstResultSeq

_cstSrcData - Results: Source entity being evaluated

_cstStandard - Name of a standard registered to the SAS Clinical
        Standards Toolkit

_cstStandardVersion - Version of the standard referenced in _cstStandard

_cstVersion - Version of the SAS Clinical Standards Toolkit

_cst_rc - Task error status

cstDefaultReportFormat - SAS ODS report destination

studyRootPath - Root path to the sample source study

workpath - Path to the SAS session work library

Parameters:

_cstDisplaySrc - - required - Where information comes from to generate
        the result.
        Values: Code | Metadata
        Default: Metadata

_cstDisplayCode - - conditional - Either a valid filename or the fully
        qualified path to code that produces an analysis result. If
        _cstDisplaySrc=Code, this parameter is used and is required. All of
        the remaining parameters are ignored.

_cstUseAnalysisResults - - conditional - The study-specific analysis
        results metadata are used to provide report metadata.
        If _cstDisplaySrc=Metadata, either this parameter or _cstUseTLFddt
        must be set to Y. If both _cstUseAnalysisResults and _cstUseTLFddt
        are set to Y, _cstUseAnalysisResults takes precedence.
        Values: N | Y
        Default: Y

_cstUseTLFddt - - conditional - The study-specific mock table shell
        metadata (known as Tables, Listings, and Figures data definition
        metadata (TLFDDT)) are used to provide report metadata.
        If _cstDisplaySrc=Metadata, either this parameter or
        _cstUseAnalysisResults must be set to Y. If both
        _cstUseAnalysisResults and _cstUseTLFddt are set to Y,
        _cstUseAnalysisResults takes precedence.
        Values: N | Y
        Default: Y

_cstDisplayID - - conditional - The ID of the display from the designated
        metadata source. If _cstDisplaySrc=Metadata, this parameter is
        required.

_cstDisplayPath - - optional - A valid filename or the fully qualified
        path to the generated display. If not provided, the code looks in
        SASReferences for type=report.

File: adam_createdisplay.sas

First available in version: 1.4

%adam_validate(_cstCallingPgm=Unspecified);

Validates CDISC ADAM model files.

This macro cycles through the validation checks to be run and writes
validation results to the process Results and Metrics data sets. These results
are persisted to any permanent location based on type=results records in
SASReferences. Process cleanup is based on the _cstDebug global macro
variable.

Expected Macro Variables:

_cstCTDescription - Description of controlled terminology packet

_cstCaseMgmt - Validation: Consider case sensitivity when comparing
        values

_cstCheckID - Check ID from the run-time check metadata

_cstCheckSortOrder - Order in which validation checks are to be run

_cstGRoot - Root path of the global standards library

_cstMetrics - Enables or disables metrics reporting

_cstMetricsCntNumBadChecks - Validation metrics: validation checks not
        run

_cstMetricsCntNumChecks - Validation metrics: distinct validation check
        invocations

_cstMetricsCntNumContent - Validation metrics: number of content
        problems detected

_cstMetricsCntNumErrors - Validation metrics: number of errors detected

_cstMetricsCntNumNotes - Validation metrics: number of notes detected

_cstMetricsCntNumStructural - Validation metrics: number of structural
        problems detected

_cstMetricsCntNumWarnings - Validation metrics: number of warnings
        detected

_cstMetricsDS - Data set used to accumulate metrics for a validation
        process

_cstMetricsNumBadChecks - Validation metrics: calculate validation
        checks not run

_cstMetricsNumChecks - Validation metrics: calculate distinct validation
        check invocations

_cstMetricsNumContent - Validation metrics: calculate number of content
        problems detected

_cstMetricsNumErrors - Validation metrics: calculate number of errors
        detected

_cstMetricsNumNotes - Validation metrics: calculate number of notes
        detected

_cstMetricsNumStructural - Validation metrics: calculate number of
        structural problems detected

_cstMetricsNumWarnings - Validation metrics: calculate number of
        warnings detected

_cstMetricsTimer - Validation metrics: estimate the elapsed time to
        perform each action

_cstResultSeq - Results: Unique invocation of check

_cstResultsDS - Results data set

_cstSASRefs - Run-time SASReferences data set derived in process setup

_cstSeqCnt - Results: Sequence number within _cstResultSeq

_cstSrcData - Results: Source entity being evaluated

_cstVersion - Version of the SAS Clinical Standards Toolkit

_cst_rc - Task error status

studyRootPath - Root path to the sample source study

Parameters:

_cstCallingPgm - - optional - The name of the driver module calling
        this macro.

File: adam_validate.sas

First available in version: 1.4

%adamutil_buildcheckclasslist(_cstCheckDS=, _cstWhereClause=, _cstOutputDS=);

Builds a data set that defines the classes to be validated by each check.

The validation_classbycheck data set identifies the classes to be validated
by each check based on the contents of the checks data set columns tableScope
and columnScope.

Expected Macro Variables:

_cstStandardVersion - Version of the standard referenced in _cstStandard

_cst_rc - Task error status

Parameters:

_cstCheckDS - - optional - The validation check data set that contains
        the checks for any standard and standardversion. Typically, this is
        the validation_master data set. If it is not specified, the code
        looks in the SASReferences data set for references to the
        validation_master or run-time validation_control data set.

_cstWhereClause - - optional - The WHERE clause to subset _cstCheckDS.
        The syntax must adhere to a SAS statement argument such as any of
        the following:
        VAR1=1
        upcase(var2)="Y" or checkstatus>0

_cstOutputDS - - required - The data set that is returned to the calling
        program. This data set contains a record for each class that is
        referenced by any given checkid, standardversion, and checksource.

File: adamutil_buildcheckclasslist.sas

First available in version: 1.4

%adamutil_createformatsfromcrtdds;

Derives codelists from a CRT-DDS data library.

This macro derives code lists from a CRT-DDS data library that is derived from
the define.xml file for a CDISC ADAM study.

These source metadata files are used by the SAS Clinical Standards Toolkit to
create codelists as provided in the CDISC CRT-DDS (define.xml) files:
codelists
codelistitems
clitemdecodetranslatedtext

This is the general strategy:
1. Combine CRT-DDS data to create the cntlin data set.
2. Read the cntlin data set using PROC FORMAT to create format catalog.


Assumptions:
1. The source data is read from a single SAS library. You can modify the
code to reference multiple libraries by using library concatenation.
2. You can specify only one study reference. Multiple study references
require modification of the code.
3. The following macro variables must be set either before invoking this
macro or be derived from the _cstSASRefs data set:
_cstCTCat (type=fmtsearch, format catalog name)
_cstCTLibrary (type=fmtsearch, target library for formats)
_cstSASrefLib (type=sourcedata, library of derived CRT-DDS data sets)
4. The following macro variables must be set before invoking this macro:
_cstStandard (for example, CDISC-ADAM)
_cstStandardVersion (for example, 2.1)

Expected Macro Variables:

_cstCTCat - Format catalog name

_cstCTLibrary - Target library for formats

_cstGRoot - Root path of the global standards library

_cstResultsDS - Results data set

_cstSASRefs - Run-time SASReferences data set derived in process setup

_cstSASrefLib - Library of derived CDT-DDS data sets

_cstSeqCnt - Results: Sequence number within _cstResultSeq

_cstSrcData - Results: Source entity being evaluated

_cstStandard - Name of a standard registered to the SAS Clinical
        Standards Toolkit

_cstStandardVersion - Version of the standard referenced in _cstStandard

_cstVersion - Version of the SAS Clinical Standards Toolkit

studyRootPath - Root path of the study library

File: adamutil_createformatsfromcrtdds.sas

First available in version: 1.3

%adamutil_createsrcmetafromcrtdds;

Derives source metadata files from a CRT-DDS data library.

This macro derives source metadata files from a CRT-DDS data library that is
derived from the define.xml file for a CDISC ADAM study.

These source metadata files are used by the SAS Clinical Standards Toolkit to
support CDISC ADAM validation and to derive CDISC CRT-DDS (define.xml) files:
source_study
source_tables
source_columns
source_values
source_documents

This is the general strategy:
1. Use PROC CONTENTS output as the primary source of the information.
2. Use reference_tables and reference_columns for matching the columns.

NOTE: This is ONLY an attempted approximation of source metadata. No
assumptions should be made that the result accurately represents the
study data.

Assumptions:
1. The source data is read from a single SAS library. You can modify the
code to reference multiple libraries by using library concatenation.
2. Only one study reference can be specified. Multiple study references
require modification of the code.

Expected Macro Variables:

_cstADAMDataLib - ADAM metadata library

_cstCRTDataLib - CRT-DDS source data library

_cstGRoot - Root path of the global standards library

_cstLRECL - Logical record length setting for filename statement

_cstRefColumnDS - ADAM reference column data set

_cstRefTableDS - ADAM reference table data set

_cstReflib - ADAM reference library

_cstResultsDS - Results data set

_cstSASRefs - Run-time SASReferences data set derived in process setup

_cstSeqCnt - Results: Sequence number within _cstResultSeq

_cstSrcData - Results: Source entity being evaluated

_cstStandard - Name of a standard registered to the SAS Clinical
        Standards Toolkit

_cstStandardVersion - Version of the standard referenced in _cstStandard

_cstTrgColumnDS - Target source column metadata data set

_cstTrgDocumentDS - Target source documents metadata data set

_cstTrgMetaLibrary - Target library for CRT-DDS source data

_cstTrgStudyDS - Target source study metadata data set

_cstTrgTableDS - Target source table metadata data set

_cstTrgValueDS - Target source value metadata data set

_cstVersion - Version of the SAS Clinical Standards Toolkit

studyRootPath - Root path of the study library

File: adamutil_createsrcmetafromcrtdds.sas

First available in version: 1.3

%adamutil_createsrcmetafromsaslib(_cstBuildAnalysisResults=Y);

Derives source metadata files from a SAS library for a CDISC ADaM study.

These source metadata files are used by the SAS Clinical Standards Toolkit to
support CDISC ADAM validation and derivation of CDISC CRT-DDS (define.xml):
source_study
source_tables
source_columns
source_documents
source_values

This is the general strategy:
1. Use PROC CONTENTS output as the primary source of the information.
2. Use reference_tables and reference_columns for matching the columns.

NOTE: This is ONLY an attempted APPROXIMATION of source metadata. No
assumptions should be made that the result completely represents the
study data.

Assumptions:
1. The source data is read from a single SAS library. The code can be
modified to reference multiple libraries using library concatenation.
2. The data set keys are estimated by the sort order of the source data
(if specified). If it is not specified, the data set keys are
estimated based on the columns that SAS uses to define keys in the
reference standard.
3. Most column values in source_study are hardcoded because there is no
metadata source. These values are used only to build the define.xml
file. These values are marked as <--- HARDCODE in code comments.

Limitations:
1. source_documents and source_values have no SAS library source metadata
and are initialized as 0-observation data sets

          

History:

   2013-11-11

Removed comment and role content because these are not
the intended source information for derivation of the define file.
Retained reference xmldatatype when known.
If *DTC, set xmldatatype=datetime.
Added initialization of source_values and source_documents.

Expected Macro Variables:

_cstADAMDataLib - Source data library

_cstCRTDataLib - Source data library

_cstCTDescription - Description of controlled terminology packet

_cstDebug - Turns debugging on or off for the session

_cstGRoot - Root path of the global standards library

_cstLRECL - Logical record length setting for filename statement

_cstRefColumnDS - Reference column metadata data set

_cstRefLib - Reference metadata library

_cstRefTableDS - Reference table metadata data set

_cstResultsDS - Results data set

_cstSASRefs - Run-time SASReferences data set derived in process setup

_cstSeqCnt - Results: Sequence number within _cstResultSeq

_cstSrcData - Results: Source entity being evaluated

_cstStandard - Name of a standard registered to the SAS Clinical
        Standards Toolkit

_cstStandardVersion - Version of the standard referenced in _cstStandard

_cstTLFmapfile - SAS XML map file that reads the TLF XML file

_cstTLFxmlfile - TLF metadata library (XML engine using map file)

_cstTrgAnalysesDS - Derived Analysis Results data set

_cstTrgColumnDS - Derived source_columns data set

_cstTrgMetaLibrary - Derived source metadata library

_cstTrgStudyDS - Derived source_study data set

_cstTrgTableDS - Derived source_tables data set

_cstVersion - Version of the SAS Clinical Standards Toolkit

studyRootPath - Root path to the sample source study

Parameters:

_cstBuildAnalysisResults - - optional - Build the analysis_results
        data set in the target metadata folder.
        Values: N | Y
        Default: Y

File: adamutil_createsrcmetafromsaslib.sas

First available in version: 1.4

%adamutil_gettlfmetadata(_cstOutLib=WORK, _cstMetaDataType=);

Creates SAS data sets with TLF metadata from an XML source.

The sources defined in SASReferences point to the TLF XML file and a SAS XML
map file to render that XML metadata in SAS.

Assumptions:
1. This macro references a specific XML representation of the mock table
shell metadata. Alternative representations of the metadata require
modifications to this macro to read that metadata content.
2. The implementation of the sample ADaM reports provided by the SAS
Clinical Standards Toolkit is intended to provide a sample workflow of
report generation within the context of the SAS Clinical Standards Toolkit
framework. You can use alternative means to capture and use metadata
to support the reports to be submitted.

Expected Macro Variables:

_cstDisplayID - ID of the display from the designated metadata source

_cstResultSeq - Results: Unique invocation of check

_cstResultsDS - Results data set

_cstSeqCnt - Results: Sequence number within _cstResultSeq

_cstSrcData - Results: Source entity being evaluated

_cstTLFxmlfile - TLF metadata library (XML engine using map file)

_cst_MsgID - Results: Result or validation check ID

_cst_MsgParm1 - Messages: Parameter 1

_cst_MsgParm2 - Messages: Parameter 2

_cst_rc - Task error status

Parameters:

_cstOutLib - - optional - The library for the SAS representation of TLF
        metadata.
        Default: WORK

_cstMetaDataType - - optional - The type of metadata. Example: tlf_master.
        If this parameter is not specified, all available metadata is
        created in _cstOutLib.

File: adamutil_gettlfmetadata.sas

First available in version: 1.4

%adamutil_settlfparmvalues(_cstTLFDS=, _cstTLFDSWhereClause=);

Translates TLF metadata values into macro variable values.

The macro variables created are in the form of _cst + <dataset> + <column>,
as in _CSTTLF_MASTERCODEPATH (where dataset=TLF_MASTER and column=CODEPATH).

Expected Macro Variables:

_cstDebug - Turns debugging on or off for the session

_cstTLFLibrary - SAS library containing TLF metadata, typically created
        via a call to %adamutil_gettlfmetadata(_cstOutLib=&_cstTLFLibrary)

Parameters:

_cstTLFDS - - required - The type of metadata. Example: tlf_master.

_cstTLFDSWhereClause - - optional - The WHERE clause to subset _cstTLFDS.
        Example: Linenum='1'

File: adamutil_settlfparmvalues.sas

First available in version: 1.4