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<div class="h1">MetaMorphoSys Batch Run documentation</div>
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<p><strong>Performing Batch MetamorphoSys Runs</strong></p>
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<p>This document is a guide to running MetamorphoSys in a programmatic way rather than through the standard GUI interface. This can be very useful if you need to make a variety of runs to produce multiple subsets and want to reuse standard configuration files.</p>
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<p><strong>Getting Started</strong><br /><br />To perform an scripted run of MetamorphoSys you will need five things.</p>
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<ol>
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<li>Input data files in a directory. The data files can either be an installed RRF or ORF subset, or could be the raw .nlm files that come with a UMLS distribution.</li>
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<li>Destination directory where the scripted subset is to be created</li>
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<li>MetamorphoSys installation (like an unpacked mmsys.zip file).</li>
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<li>JRE matching the version of the MetamorphoSys distribution.
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<ul>
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<li>An unpacked mmsys.zip file will contain a JRE directory you can use for Linux, Solaris, or Windows.</li>
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</ul>
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</li>
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<li>MetamorphoSys configuration file.</li>
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</ol>
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<p>The easiest way to obtain all five pieces is to start with a UMLS distribution: downloaded files from the Knowledge Sources Server. Either the Metathesaurus .nlm files or an installed .RRF subset can serve as the input data. You can choose any directory to hold output data. Unpacking the mmsys.zip file to a known location on your machine can serve as both the MetamorphoSys installation <span style="font-style: italic;">and</span> as the JRE.</p>
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<p>For the final piece, the easiest way to obtain a configuration file that you want to use is to run the MetamorphoSys application and work your way to the configuration screens in the GUI. After having selected your source list and other configuration options, save your configuration to a file in a known place. The resulting configuration file may contain path information that is overridden by properties specified in the script. This is not a problem. The switches to the Java call above will override any path information int the file.</p>
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<p><strong>Configuring and Running a Script</strong></p>
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<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.</p>
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<p><em>Windows</em></p>
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<p><span style="font-family: monospace;">@echo off<br /><br />REM <br /></span><span style="font-family: monospace;">REM Specify directory containing .RRF or .nlm files<br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">set METADIR=C:\UMLS<br /><br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">REM Specify output directory<br /></span><span style="font-family: monospace;">REM</span> <br /><span style="font-family: monospace;">set DESTDIR=C:\UMLS\METASUBSET<br /></span></p>
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<p><span style="font-family: monospace;">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 /></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"<br /><br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">REM Specify configuration file<br /></span><span style="font-family: monospace;">REM <br /></span><span style="font-family: monospace;">set CONFIG_FILE=C:\config.properties<br /><br /></span><span style="font-family: monospace;"><span style="font-family: monospace;">REM<br />REM Call Batch MetamorphoSys<br />REM<br />cd %MMSYS_HOME%<br />%JAVA_HOME%\bin\java -Djava.awt.headless=true -Djpf.boot.config=%MMSYS_HOME%\etc\subset.boot.properties -Dlog4j.configuration=%MMSYS_HOME%\etc\subset.log4j.properties -Dinput.uri=%METADIR% -Doutput.uri=%DESTDIR% -Dmmsys.config.uri=%CONFIG_FILE% -Xms300M -Xmx1000M org.java.plugin.boot.Boot <br /></span></span></p>
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<p>The script defines the five needed pieces: input directory, output directory, MetamorphoSys installation, JRE, and configuration file. JAVA_HOME and the CLASSPATH are configured. The script makes the required java call from the MMSYS_HOME directory.</p>
|
||
<p>This will produce an output subset based on the input data specified. The subset will contain either ORF or RRF files (depending upon which you indicated in the configuration file). The style of input data must be correctly specified in the configuration file(choose from .nlm files, RRF, or ORF files). A log of the progress will also be generated as it runs.</p>
|
||
<p><em><br />Linux, Macintosh, or Solaris</em></p>
|
||
<p>Consider the following script:</p>
|
||
<p><span style="font-family: monospace;">#!/bin/sh -f<br /><br />#<br /># Specify directory containing .RRF or .nlm files<br />#<br /><br />METADIR=/d1/UMLS<br /><br /></span><span style="font-family: monospace;">#<br /># Specify output directory<br />#<br /></span><span style="font-family: monospace;">DESTDIR=/d1/UMLS/METASUBSET<br /><br /></span><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/jpf-boot.jar<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<br /><br /></span><span style="font-family: monospace;">#<br /># Specify configuration file<br />#<br /></span><span style="font-family: monospace;">CONFIG_FILE=/d1/umls/config.properties<br /><br /></span><span style="font-family: monospace;">#<br /># Run Batch MetamorphoSys<br />#<br /></span><span style="font-family: monospace;">export METADIR<br />export DESTDIR<br />export MMSYS_HOME<br />export CLASSPATH<br />export JAVA_HOME<br />cd $MMSYS_HOME<br />$JAVA_HOME/bin/java -Djava.awt.headless=true -Djpf.boot.config=$MMSYS_HOME/etc/subset.boot.properties \<br />-Dlog4j.configuration=$MMSYS_HOME/etc/subset.log4j.properties -Dinput.uri=$METADIR \<br />-Doutput.uri=$DESTDIR -Dmmsys.config.uri=$CONFIG_FILE -Xms300M -Xmx1000M org.java.plugin.boot.Boot<br /></span></p>
|
||
<p>The script defines the five needed pieces: input directory, output directory, MetamorphoSys installation, JRE, and configuration file. JAVA_HOME and the CLASSPATH are configured. The script makes the required java call from the MMSYS_HOME directory.</p>
|
||
<p>This will produce an output subset based on the input data specified. The subset will contain either ORF or RRF files (depending upon which you indicated in the configuration file). The style of input data must be correctly specified in the configuration file(choose from .nlm files, RRF, or ORF files). A log of the progress will also be generated as it runs.</p>
|
||
<p><br /><strong>Configuration File Notes</strong><br /><br />As indicated above, the configuration file you use is best generated using the MMSYS GUI. There are a couple of things you may want to consider when reusing a configuration file.</p>
|
||
<ul>
|
||
<li>Input data to a batch MetamorphoSys process can take the form of an installed RRF subset. If you create your configuration file using the GUI, this will be managed for you. If you want to change your mind after the fact, you can edit a few properties file settings to fix this.<br />
|
||
<ul>
|
||
<li>First, choose one of the following two settings:
|
||
<ul>
|
||
<li style="font-family: monospace;">mmsys_input_stream=gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysInputStream</li>
|
||
<li><span style="font-family: monospace;">mmsys_input_stream=gov.nih.nlm.umls.mmsys.io.NLMFileMetamorphoSysInputStream</span></li>
|
||
</ul>
|
||
</li>
|
||
<li>Now, if you chose, say <span style="font-family: monospace;">RRFMetamorphoSysInputStream</span>, make sure you express the relevant properties for this input stream. For example (in this case we assume the path /d1/UMLS contains RRF files):
|
||
<ul>
|
||
<li><span style="font-family: monospace;">gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysInputStream.meta_source_uri=/d1/UMLS/<br /></span></li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
||
</li>
|
||
<li>Output data can take either the form of RRF or ORF data. If you create your configuration file using the GUI, this will be managed for you. If you want to change your mind after the fact, you can edit a property file settings to fix this. Choose one of the following two settings:<br />
|
||
<ul>
|
||
<li style="font-family: monospace;">mmsys_output_stream=gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream</li>
|
||
</ul>
|
||
<ul>
|
||
<li><span style="font-family: monospace;">mmsys_output_stream=gov.nih.nlm.umls.mmsys.io.ORFMetamorphoSysOutputStream<br /><br /></span></li>
|
||
</ul>
|
||
</li>
|
||
<li>Each time the UMLS Metathesaurus is updated, some of the various "default" data sets may change. For example, the source list, default SAB,TTY list, and list of suppressible (CUI,AUI). If your configurations rely on these properties (e.g. <span style="font-family: monospace;">sources</span> or <span style="font-family: monospace;">termgroups</span> properties), make sure you compare the previous version value list to the current version value list. To avoid this kind of problem, it is often better to express your configurations in terms of things to <span style="font-style: italic;">include</span> instead of things to <span style="font-style: italic;">exclude</span>. Furthermore, you can always re-open your configuration file in the GUI for the latest release of MetamorphoSys and see a report of changes that may affect your configuration. Then you can make desired changes, save it again, and reuse it in your batch environment.</li>
|
||
</ul>
|
||
<p><br />Instead of using the MetamorphoSys GUI to create your configuration file, you may want to consider a programmatic approach to editing the default user.a.prop (in config/ directory of the distribution) config file that comes with a MetamorphoSys distribution. Consider this code snippet:<br /><br /><span style="font-family: monospace;">% grep ^sources $MMSYS_HOME/config/2009AB/user.a.prop | /usr/local/bin/perl -pe 's/sources=//; s/;/\n/g' | \</span><br /><span style="font-family: monospace;"> awk -F\| '{print $1"|"$1}' | /usr/local/bin/perl -pe 's/\n/;/g' >! /tmp/sab_list.txt</span><br /><span style="font-family: monospace;">% /usr/local/bin/perl -pe 'open(SOURCES,"/tmp/sab_list.txt"); \</span><br /><span style="font-family: monospace;"> $sources = <SOURCES>; \</span><br /><span style="font-family: monospace;"> chop($sources); \</span><br /><span style="font-family: monospace;"> s/(gov.nih.nlm.umls.mmsys.filter.SourceListFilter.selected_sources).*/$1=$sources/; \</span><br /><span style="font-family: monospace;"> s/^(mmsys_input_stream)=.*/$1=gov.nih.nlm.umls.mmsys.io.NLMFileMetamorphoSysInputStream/; \</span><br /><span style="font-family: monospace;"> s/^(mmsys_output_stream)=.*/$1=gov.nih.nlm.umls.mmsys.io.RRFMetamorphoSysOutputStream/; \</span><br /><span style="font-family: monospace;"> s/^(.*)\.remove_selected_sources=true/$1.remove_selected_sources=false/; ' \</span><br /><span style="font-family: monospace;"> $INIT_CONFIG_FILE >! my_config.prop</span><br /><br />In this example, we are starting by looking up the complete list of sources in the "sources" property in the default configuration file and compiling a SAB list. The second command makes four modifications to the default configuration file and writes a new configuration file (<span style="font-family: monospace;">my_config.prop</span>).</p>
|
||
<ol>
|
||
<li>The <span style="font-family: monospace;">selected_sources</span> property of the source list filter is set to the complete source list (taken from the prior command).</li>
|
||
<li>The <span style="font-family: monospace;">mmsys_input_stream</span> property is set to <span style="font-family: monospace;">NLMFileMetamorphoSysInputStream</span> (.nlm Files).</li>
|
||
<li>The <span style="font-family: monospace;">mmsys_output_stream</span> property is set to <span style="font-family: monospace;">RRFMetamorphoSysOutputStream</span> (RRF Files).</li>
|
||
<li>The <span style="font-family: monospace;">remove_selected_sources</span> property (of the source list filter) is set to <span style="font-family: monospace;">false</span> (causing the source list filter to operate in <em>include</em> mode).</li>
|
||
</ol>
|
||
<p>The effect of this is the output <span style="font-family: monospace;">my_config.prop</span> file which is now configured (correctly for this version of the data) to be a "keep everything" subset of the NLM data files. Now, this config file can be passed along with other parameters to the scripted MetamorphoSys call to make the desired subset.</p>
|
||
|
||
|
||
|
||
|
||
<p class=”margin-top-5”><small>Last Reviewed: July 29, 2016</small></p>
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