Writing XML Files

The create_crtdds_from_sdtm.sas driver program sets up the required environment variables and library references to initiate the crtdds_sdtmtodefine macro. This macro extracts data from the SDTM 3.1.1 or 3.1.2 metadata files. (For more information about the source_tables and source_columns data sets, see Source Metadata.) Depending on the available source information, the macro attempts to convert the information into the 39 tables that represent the SAS interpretation of the CDISC CRT¬DDS 1.0 model. All 39 data sets are created, but only those data sets with the available data are populated. The other tables contain zero observations.

Here is an example of a call to the crtdds_sdtmtodefine macro:

%crtdds_sdtmtodefine(
_cstOutLib=srcdata,
_cstSourceTables=sampdata.source_tables,
_cstSourceColumns=sampdata.source_columns,
_cstSourceStudy=sampdata.source_study
);

In the example, the crtdds_sdtmtodefine macro sets _cstOutLib to srcdata. All of the CRT-DDS-defined tables are written to the SAS Srcdata library. The _cstSourceTables parameter accesses the source_tables data set that exists in the Sampdata library (sampdata.source_tables). The _cstSourceColumns parameter accesses the source_columns data set that exists in the Sampdata library (sampdata.source_columns). The _cstSourceStudy parameter accesses the source_study data set that exists in the sampdata library (sampdata.source_study).

The create_crtdds_from_sdtm.sas driver program is provided with SAS, and it is ready to run on any of the SDTM sample studies. The driver program can be run interactively or in batch. To run the program interactively, start a SAS session, and load the driver program into the SAS editor.

The driver program is located in:

As a part of each SAS Clinical Standards Toolkit process setup, a valid SASReferences data set is required. It references the input files that are needed, the librefs and filenames to use, and the names and locations of data sets to be created by the process. It can be modified to point to study-specific files. For an explanation of the SASReferences data set, see SASReferences File.

In the SASReferences data set, there are three input file references and one output reference that are key to successful completion of the create_crtdds_from_sdtm.sas driver program. Key Components of the SASReferences Data Set lists these files and data sets, and they are discussed in separate sections. In the sample create_crtdds_from_sdtm.sas driver program, these values are set for &studyRootPath and &studyOutputPath:

The sourcemetadata type refers to two data sets that contain the SDTM domain metadata, source_tables and source_columns. Both data sets are stored in the same library. Because the sample create_crtdds_from_sdtm.sas driver program provided with the SAS Clinical Standards Toolkit references a source CDISC SDTM 3.1.2 study, the source_tables data set contains SDTM 3.1.2 metadata about each standard domain defined in the CDISC-SDTM 3.1.2 Implementation Guide and includes any customizations that you have added. The source_columns type contains similar metadata, but it is at the column level. This source metadata is read from this location:

This location is represented in the driver program by the Srcmeta library name.

*All variables are required to be non-blank.

Multiple studies can be referenced in the source study data set, as well as source_columns and source_tables, by using different SASref values to link them across the tables.

The sourcedata type is the library where the metadata files are created. These metadata files are the data sets that constitute the SAS representation of the CDISC CRT-DDS 1.0 standard. The create_crtdds_from_sdtm.sas driver program creates 39 data sets. Most of these data sets have zero observations because there is no default SDTM metadata source. In the SAS Clinical Standards Toolkit sample study, these data sets are written to the !sasroot/../../SASClinicalStandardsToolkitCRTDDS10/1.4/sample/cdisc-crtdds-1.0/data directory. This location is represented in the driver program by the srcdata library name.

When the driver program finishes running, the sdtmtodefine_results data set is created. This data set contains informational, warning, and any error messages that were generated by the submitted driver program.

The create_crtdds_define.sas driver program sets up the required environment variables and library references to initiate the crtdds_write macro. This macro reads the 39 data sets that comprise the SAS representation of the CDISC CRT-DDS 1.0 model, and converts that information to the required define.xml structure. If source metadata or data are missing, then empty elements and attributes are not created in the define.xml file. The inputs and outputs are specified in the SASRferences data set.

Here is an example of a call to the crtdds_write.sas macro:

%crtdds_write(_cstCreateDisplayStyleSheet=1,
                    _cstOutputEncoding=UTF-16,
                    _cstResultsOverrideDS=&_cstResultsDS);

In this example, a default style sheet is generated in the same directory as the XML output based on the information in the SASReferences data set. XML encoding is set to UTF-16, and process results are written to the default &_cstResultsDS data set.

Here is the call to the macro from the sample create_crtdds_define.sas driver program:

%crtdds_write(_cstCreateDisplayStyleSheet=1);

The call creates a display style sheet and uses default values for the parameters.

The create_crtdds_define.sas driver program is ready to run on any of the CDISC SDTM sample studies. The driver program can be run interactively or in batch.

The driver program is located in:

Multiple tasks can be executed in any SAS Clinical Standards Toolkit driver program. The create_crtdds_define.sas driver program calls both the crtdds_write macro to create the define.xml file, and the crtdds_xmlvalidate macro to validate the syntax of the generated define.xml file. For more information about the crtdds_xmlvalidate macro, see Validation of XML-Based Standards.

As a part of each SAS Clinical Standards Toolkit process setup, a valid SASReferences data set is required. It references the input files that are needed, the librefs and filenames to use, and the names and locations of data sets to be created by the process. It can be modified to point to study-specific files. For an explanation of the SASReferences data set, see SASReferences File.

In the SASReferences data set, there are two input file references and three output references that are key to successful completion of the create_crtdds_define.sas driver program. Key Components of the SASReferences Data Set lists these files and data sets, and they are discussed in separate sections. In the sample create_crtdds_define.sas driver program, these values are set for &studyRootPath and &studyOutputPath:

Process Inputs Use of the control library name that points to the path in the &workpath macro variable illustrates a technique of documenting the derivation of the SASReferences data set in the SAS Work library. The driver program initiates the macro variable &workpath with this SAS code:

%let workPath=%sysfunc(pathname(work));

The sourcedata type is the library that contains the 39 data sets that might have been populated by the create_crtdds10_from_sdtm311.sas driver program. These metadata files are the data sets that constitute the SAS representation of the CDISC CRT-DDS 1.0 standard. In the SAS Clinical Standards Toolkit sample study, these data sets are read from the !sasroot/../../SASClinicalStandardsToolkitCRTDDS10/1.4/ sample/cdisc-crtdds-1.0/data directory. This location is represented in the driver program by the Srcdata library name.

The externalxml type refers to the define.xml file. This file is accessed in the driver program from the extxml filename statement, and is written to the !sasroot/../../SASClinicalStandardsToolkitCRTDDS10/1.4/ sample/cdisc-crtdds-1.0/sourcexml directory.

The referencexml type can serve as either an input or output file reference. Because the path and filename are not provided, the crtdds_write macro interprets the _cstCreateDisplayStyleSheet=1 parameter to use the default style sheet that is provided by the SAS Clinical Standards Toolkit in the Global Library. Had a path and filename been provided, the referencexml type would serve as an output file reference for the crtdds_write macro to copy the default style sheet from the Global Library to the path and filename that were specified. The results type refers to the write_results data set that documents the create define process results. In the SAS Clinical Standards Toolkit CDISC CRT-DDS folder hierarchy, this information is written to the !sasroot/../../SASClinicalStandardsToolkitCRTDDS10/1.4/sample/cdisc-crtdds-1.0/results directory.

Inclusion of the results record (row) in the SASReferences data set signals that the process results are to be copied to a write_results data set located in the specified SAS library.

The create_odmxml.sas driver program sets up the required environment variables and library references to initiate the odm_write macro. This macro reads the 66 data sets that comprise the default SAS representation of the CDISC ODM 1.3.0 model, and then converts that information to the required ODM XML structure. If source metadata or data are missing, then empty elements and attributes are not created in the ODM XML file. The inputs and outputs are specified in the SASRferences data set.

Here is an example of a call to the odm_write macro:

%odm_write(_cstOutputEncoding=UTF-16, _cstResultsOverrideDS=&_cstResultsDS);

In this example, no default style sheet is generated for the XML output, XML encoding is set to UTF-16, and process results are written to the default &_cstResultsDS data set.

This is the call to the macro from the sample create_odmxml.sas driver program, using default values for all parameters:

%odm_write();

The create_odmxml.sas driver program is ready to run on the sample CDISC ODM provided with the SAS Clinical Standards Toolkit.

The driver program is located in:

As a part of each SAS Clinical Standards Toolkit process setup, a valid SASReferences data set is required. It references the input files that are needed, the librefs and filenames to use, and the names and locations of data sets to be created by the process. It can be modified to point to study-specific files. For an explanation of the SASReferences data set, see SASReferences File.

In the SASReferences data set, one input file reference and two output references are key to successful completion of the create_odmxml.sas driver program. Key Components of the SASReferences Data Set lists these files and data sets, and they are discussed in separate sections. In the sample create_odmxml.sas driver program, these values are set for &studyRootPath and &studyOutputPath:

The sourcedata type is the library that contains the default 66 data sets that comprise the SAS representation of an ODM XML file. These data sets might have been populated by a previous odm_read task, or you might have processes in place that build these files from some set of source files. In the SAS Clinical Standards Toolkit sample data, these data sets are read from the !sasroot/../../SASClinicalStandardsToolkiODM130/1.4/sample/cdisc-odm-1.3.0/data directory. This location is represented in the driver program by the Srcdata library name.

The externalxml type refers to the ODM XML file that is to be derived by the process. This file is accessed in the driver program using the extxml filename statement and is written to the !sasroot/../../SASClinicalStandardsToolkiODM130/1.4/sample/cdisc-odm-1.3.0/sourcexml directory.

The results type refers to the write_results data set that documents the create define process results. In the SAS Clinical Standards Toolkit CDISC CRT-DDS folder hierarchy, this information is written to this location:

Inclusion of the results record (row) in the SASReferences data set signals that the process results are to be copied to a write_results data set located in the specified SAS library.