This repository contains the NCICT2ODM java source code for converting the NCI EVS curated CIDSC Controlled Terminology tab delimited text files into ODM-based CT-XML files. It implements version 1.1.1 of the CT-XML extension to ODM v1.3.2. NCICT2ODM is a java command-line application.
The NCI EVS provides the CDISC Controlled Terminology (CT) text files on their CDISC CT FTP site.
Usage for NCICT2ODM: java -jar ncict2odm.jar txt=<text CT file> odm=<ODM CT file> std=<standard> date=<package date> ver=<schema version>
The command-line arguments include:
- txt (required): the NCI EVS delimited text input CT path and file name for a specific standard and quarter
- odm (required): the CT-XML output path and file name generated based on the input file
- std (required): the standard being processed (e.g. SDTM) used in generating certain descriptive text strings in the output XML
- date (required): the date of the quarterly text-based load file in YYYY-MM-DD format (e.g. 2015-12-18)
- ver (optional): the version of CT-XML to generate - defaults to 1.1.1
Example:
java -jar ncict2odm.jar odm=c:/temp/sdtm-odm-2015-12-18.xml txt=c:/temp/sdtm-2015-12-18.txt date=2015-12-18 std=SDTM ver=1.1.1
Note: this application should convert any of the tab delimited text CT files, but a few of the older ones have may have some invalid binary characters that will need to be scrubbed prior to running the conversion. For example, the 2013-12-20 SDTM text file contains several extra line-feed characters that break the row mid-line. In this case ncict2odm will display an error and cease processing the conversion.
The ncict2odm application was built using java 8 and uses the JDOM2 XML library.
Use the JDOM2 downloads to retrieve the jar files.
JDOM2 Lib files inlcuded:
- jdom-2.0.6.jar
- jdom-2.0.6-contrib.jar
- jdom-2.0.6-javadoc.jar