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Performing Batch MRCXT Builder Runs
This document is a guide to running the MetamorphoSys MRCXT Builder
in a programmatic
way rather than through the standard GUI interface.
Getting Started
To perform an scripted run of the MetamorphoSys MRCXT Builder
you will need three things:
The easiest way to obtain all five pieces is to start with a UMLS
distribution: either the DVD or downloaded files from the Knowledge
Sources Server. Run MetamorphoSys to generate an RRF subset
of the data for which a MRCXT is to be built.
This process generates a MRCXT.RRF file from the existing
MRCONSO.RRF and MRHIER.RRF files. There are a number of
configuration options you can use to change the result:
Configuring and Running a Script
In
the sections below, you can follow a sample series of steps for putting
together the pieces above into a script and actually generating a
subset.
Windows
Consider the following script:
@echo off
REM
REM Specify RRF Directory
REM
set source_dir=C:\UMLS\METASUBSET
REM
REM Set Parameter properties
REM
set build_sibs=true
set build_children=true
set compute_xc=true
set versioned_sabs=true
set add_unicode_bom=true
set write_mrcxt_file_statistics=true
set max_contexts=true
set max_contexts_count=10
REM
REM Specify source list restriction (if desired) - in this case do not
REM
REM set
source_list_prop="-Dselected.source.list=%source_list%"
REM
REM Specify MetamorphoSys
directory
REM
set MMSYS_HOME=C:\UMLS\MMSYS
REM
REM Specify CLASSPATH
REM
set
CLASSPATH=%MMSYS_HOME%;%MMSYS_HOME%/lib/mms.jar;%MMSYS_HOME%/lib/objects.jar
REM
REM Specify JAVA_HOME
REM
set
JAVA_HOME="C:\Program Files\Java\jre1.5.0_11"
REM
REM Run from MMSYS_HOME to avoid release.dat errors
REM
cd %MMSYS_HOME%
%JAVA_HOME%\bin\javaw -Djava.awt.headless=true -Xms200M -Xmx800M
-Dbuild.sibs=%build_sibs% -Dbuild.children=%build_children%
-Dcompute.xc=%compute_xc% -Dversioned.sabs=%versioned_sabs%
-Dadd.unicode.bom=%add_unicode_bom%
-Dwrite.mrcxt.file.statistics=%write_mrcxt_file_statistics% \
-Dmax.contexts=%max_contexts%
-Dmax.contexts.count=%max_contexts_count% -Dsource.dir=%source_dir%
%source_list_prop% gov.nih.nlm.mms.cxt.BatchMRCXTBuilder
The script sets the various configuration options, paths, and environment variables. It then invokes a Java call from the MMSYS_HOME directory. This will produce a MRCXT.RRF file in the specified directory. A log of the progress will also be generated as it runs.
Linux, Macintosh, or Solaris
#!/bin/sh -f
#
# Set Parameter properties
#
build_sibs=true
build_children=true
compute_xc=true
versioned_sabs=true
add_unicode_bom=true
write_mrcxt_file_statistics=true
max_contexts=true
max_contexts_count=10
source_dir=/d1/UMLS/METASUBSET
#
# Set source list restriction (if desired) - do not in this case
#
# set
source_list_prop=-Dselected.source.list=
#
# Specify MetamorphoSys directory
#
MMSYS_HOME=/d1/UMLS/MMSYS
#
# Specify CLASSPATH
#
CLASSPATH="${MMSYS_HOME}:$MMSYS_HOME/lib/mms.jar:$MMSYS_HOME/lib/objects.jar"
#
# Specify JAVA_HOME
#
JAVA_HOME=$MMSYS_HOME/jre/linux
#
# Run from MMSYS_HOME to avoid release.dat errors
#
export MMSYS_HOME
export CLASSPATH
export JAVA_HOME
cd $MMSYS_HOME
$JAVA_HOME/bin/java
-Djava.awt.headless=true -Xms200M -Xmx800M \
-Dbuild.sibs=$build_sibs \
-Dbuild.children=$build_children \
-Dcompute.xc=$compute_xc \
-Dversioned.sabs=$versioned_sabs \
-Dadd.unicode.bom=$add_unicode_bom \
-Dwrite.mrcxt.file.statistics=$write_mrcxt_file_statistics \
-Dmax.contexts=$max_contexts \
-Dmax.contexts.count=$max_contexts_count \
-Dsource.dir=$source_dir \
$source_list_prop gov.nih.nlm.mms.cxt.BatchMRCXTBuilder
The script sets the various configuration options, paths, and
environment variables. It then invokes a java call from the
MMSYS_HOME
directory. This will produce a MRCXT.RRF file in the specified
directory. A log of the progress will also be generated as it
runs.
Last reviewed: 17 December 2007
Last updated: 17 December 2007
First published: 17 December 2007
Metadata| Permanence level: Permanence Not Guaranteed