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<div class="h1">MetamorphoSys MRCXT Builder batch/shell scripts</div>
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<p><span style="font-weight: bold;">Performing Batch MRCXT Builder Runs<br /></span></p>
<p>This document is a guide to running the MetamorphoSys MRCXT Builder in a programmatic way rather than through the standard GUI interface.<br /><span style="font-weight: bold;"><br /></span></p>
<p><span style="font-weight: bold;">Getting Started<br /><br /></span>To perform an scripted run of the MetamorphoSys MRCXT Builder you will need three things:</p>
<ol>
<li>An installed RRF Metathesaurus subset.</li>
<li>MetamorphoSys installation (like an unpacked mmsys.zip file).</li>
<li>JRE matching the version of the MetamorphoSys distribution.&nbsp; An unpacked mmsys.zip file will contain a JRE directory you can use.</li>
</ol>
<p>The easiest way to obtain all five pieces is to start with a UMLS distribution:&nbsp;downloaded files from the Knowledge Sources Server.&nbsp;&nbsp; Run MetamorphoSys to generate an RRF subset of the data for which a MRCXT is to be built.</p>
<p>This process generates a MRCXT.RRF file from the existing MRCONSO.RRF and MRHIER.RRF files.&nbsp; There are a number of configuration options you can use to change the result:</p>
<ul>
<li><span style="font-family: monospace;">add_unicode_bom</span>: Use <span style="font-family: monospace;">true</span> to prepend MRCXT.RRF with a Unicode byte order mark (BOM), <span style="font-family: monospace;">false</span> otherwise.</li>
<li><span style="font-family: monospace;">build_sibs</span>: Use <span style="font-family: monospace;">true</span> to build SIB entries, <span style="font-family: monospace;">false</span> otherwise.</li>
<li><span style="font-family: monospace;">build_children</span>: Use <span style="font-family: monospace;">true</span> to build CHD entries, <span style="font-family: monospace;">false</span> otherwise.</li>
<li><span style="font-family: monospace;">compute_xc</span>: Use <span style="font-family: monospace;">true</span> to compute the MRCXT.XC flag, <span style="font-family: monospace;">false</span> otherwise.</li>
<li><span style="font-family: monospace;">max_contexts</span>: Use <span style="font-family: monospace;">true</span> to restrict the number of tree positions per atom, <span style="font-family: monospace;">false</span> otherwise.</li>
<li><span style="font-family: monospace;">max_contexts_count</span>: If max_contexts is <span style="font-family: monospace;">true</span>, the maximum number of tree positions per atom.&nbsp; After this number is encountered, all others in MRHIER.RRF are ignored.</li>
<li><span style="font-family: monospace;">source_list</span>: Use a semi-colon separated list of RSAB or VSAB values to indicate which sources to build contexts for.</li>
<li><span style="font-family: monospace;">versioned_sabs</span>: Use <span style="font-family: monospace;">true</span> to used versioned SAB values for MRCXT.SAB, <span style="font-family: monospace;">false</span> otherwise.</li>
<li><span style="font-family: monospace;">write_mrcxt_file_statistics</span>: Use <span style="font-family: monospace;">true</span> to update MRCOLS.RRF and MRFILES.RRF to accurately reflect the compute d MRCXT.RRF file, <span style="font-family: monospace;">false</span> otherwise.</li>
</ul>
<p>&nbsp;</p>
<p><span style="font-weight: bold;">Configuring and Running a Script<br /></span></p>
<p>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.<span style="font-style: italic;"><br /></span></p>
<p><span style="font-style: italic;">Windows<br /></span><br />Consider the following script:<span style="font-style: italic;"><br /></span></p>
<p><span style="font-family: monospace;">@echo off<br /></span></p>
<p><span style="font-family: monospace;">REM<br />REM Specify RRF Directory<br />REM<br />set source_dir=C:\UMLS\METASUBSET<br /></span></p>
<p><span style="font-family: monospace;">REM<br />REM Set Parameter properties<br />REM<br />set build_sibs=true<br />set build_children=true<br />set compute_xc=true<br />set versioned_sabs=true<br />set add_unicode_bom=true<br />set write_mrcxt_file_statistics=true<br />set max_contexts=true<br />set max_contexts_count=10</span><span style="font-family: monospace;"><br /><br />REM<br />REM Specify source list restriction (if desired) - in this case do not<br />REM<br />REM set source_list_prop="-Dselected.source.list=%source_list%"<br /></span><span style="font-family: monospace;"><br />REM <br /></span><span style="font-family: monospace;">REM Specify MetamorphoSys directory<br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">set MMSYS_HOME=C:\UMLS\MMSYS<br /><br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">REM Specify CLASSPATH<br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">set CLASSPATH=%MMSYS_HOME%;%MMSYS_HOME%\lib\jpf-boot.jar<br /><br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">REM Specify JAVA_HOME<br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">set JAVA_HOME="%MMSYS_HOME%\jre\windows"</span><span style="font-family: monospace;"><br /><br />REM<br />REM Run from MMSYS_HOME to avoid release.dat errors<br />REM<br />cd %MMSYS_HOME%<br />%JAVA_HOME%\bin\javaw -Djava.awt.headless=true -Xms300M -Xmx1000M -Djpf.boot.config=%MMSYS_HOME%/etc/cxt.boot.properties -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% org.java.plugin.boot.Boot </span></p>
<p>The script sets the various configuration options, paths, and environment variables.&nbsp; It then invokes a Java call from the MMSYS_HOME directory.&nbsp; This will produce a MRCXT.RRF file in the specified directory.&nbsp; A log of the progress will also be generated as it runs.</p>
<p>&nbsp;</p>
<p><span style="font-style: italic;"><br />Linux, Macintosh, or Solaris</span></p>
<p>Consider the following script:</p>
<p><span style="font-family: monospace;">#!/bin/sh -f<br />#<br /># Set Parameter properties<br />#<br />build_sibs=true<br />build_children=true<br />compute_xc=true<br />versioned_sabs=true<br />add_unicode_bom=true<br />write_mrcxt_file_statistics=true<br />max_contexts=true<br />max_contexts_count=10<br />source_dir=/d1/UMLS/METASUBSET<br /></span></p>
<p><span style="font-family: monospace;">#<br /># Set source list restriction (if desired) - do not in this case<br />#<br /># set source_list_prop=-Dselected.source.list=</span></p>
<p><span style="font-family: monospace;">#<br /># Specify MetamorphoSys directory<br />#<br /></span><span style="font-family: monospace;">MMSYS_HOME=/d1/UMLS/MMSYS<br /><br /></span><span style="font-family: monospace;">#<br /># Specify CLASSPATH<br />#<br /></span><span style="font-family: monospace;">CLASSPATH="${MMSYS_HOME}:$MMSYS_HOME/lib/mms.jar:$MMSYS_HOME/lib/objects.jar"<br /><br /></span><span style="font-family: monospace;">#<br /># Specify JAVA_HOME<br />#<br /></span><span style="font-family: monospace;">JAVA_HOME=$MMSYS_HOME/jre/linux</span><span style="font-family: monospace;"><br /><br />#<br /># Run from MMSYS_HOME to avoid release.dat errors<br />#<br /></span><span style="font-family: monospace;">export MMSYS_HOME<br />export CLASSPATH<br />export JAVA_HOME<br />cd $MMSYS_HOME</span><br /><span style="font-family: monospace;">$JAVA_HOME/bin/java -Djava.awt.headless=true -Xms300M -Xmx1000M \<br />-Djpf.boot.config=$MMSYS_HOME/etc/cxt.boot.properties -Dbuild.sibs=$build_sibs \<br />-Dbuild.children=$build_children -Dcompute.xc=$compute_xc \<br />-Dversioned.sabs=$versioned_sabs -Dadd.unicode.bom=$add_unicode_bom \<br />-Dwrite.mrcxt.file.statistics=$write_mrcxt_file_statistics -Dmax.contexts=$max_contexts \<br />-Dmax.contexts.count=$max_contexts_count -Dsource.dir=$source_dir \<br />$source_list_prop org.java.plugin.boot.Boot<br /><br /></span>The script sets the various configuration options, paths, and environment variables.&nbsp; It then invokes a java call from the MMSYS_HOME directory.&nbsp;This will produce a MRCXT.RRF file in the specified directory.&nbsp; A log of the progress will also be generated as it runs.</p>
<p class=”margin-top-5”><small>Last Reviewed: July 29, 2016</small></p>
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