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<title>Alignment API: Command line interface</title>
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<center><h1>Alignment API: Command line interface</h1></center>
<p>
The implementation offers various command line tools available in
the <tt>fr.inrialpes.exmo.align.cli</tt> package:
<dl>
<dt>Procalign</dt><dd>Runs a matcher on a pair of ontologies</dd>
<dt>ParserPrinter</dt><dd>Parses and alignment and displays it in
various formats.</dd>
<!--dt>DiffAlign</dt><dd>TODO</dd-->
<dt>EvalAlign</dt><dd>Evaluates and alignment with respect to a
reference alignment.</dd>
<dt>TestGen</dt><dd>Generates tests for evaluating matchers.</dd>
<dt>GroupAlign</dt><dd>Runs a matcher against several different test cases.</dd>
<dt>GroupEval</dt><dd>Evaluates several matcher results in several different test cases.</dd>
<dt>ExtGroupEval</dt><dd>Same as above with extended evaluators</dd>
<dt>WGroupEval</dt><dd>Same as above with weighted evaluators.</dd>
<dt>GenPlot</dt><dd>Generates various pliots from matcher resulst
(ROC curves or precision/recall graphs).</dd>
<dt>GroupOutput</dt><dd>Generates other representations of matcher results.</dd>
</dl>
</p>
<p>
These command line operations usually share switch conventions:
<ul>
<li>displaying help (-h);</li>
<li>displaying debug information (-d);</li>
<li>directing the output to a file (-o);</li>
</ul></p>
<h2>Displaying alignments</h2>
<p>
Another such utility (<tt>ParserPrinter</tt>) allows to read an
alignment, to manipulate it and to output it without processing
the <tt>align</tt> method.
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</p>
<h2>Matching</h2>
<p>
The implementation offers a stand-alone program (<tt>fr.inrialpes.exmo.align.util.Procalign</tt>) which:
<ul>
<li>Reads two OWL/RDF ontologies;</li>
<li>Creates an alignment object;</li>
<li>Computes the alignment between these ontologies;</li>
<li>Eventually cut the alignment under a threhold:</li>
<li>Displays the result.</li>
</ul>
Additional options are available:
<ul>
<li>controlling the way of rendering the output (-r);</li>
<li>deciding the implementation of the matching method (-i);</li>
<li>providing an input alignment (-a).</li>
</ul>
</p>
<p>Running the program is achieved through:
<div class="terminal">
$ java -jar lib/procalign.jar
Two URIs required
usage: Procalign [options] URI1 URI2
options are:
--impl=className -i classname Use the given alignment implementation.
--renderer=className -r className Specifies the alignment renderer
--output=filename -o filename Output the alignment in filename
--params=filename -p filename Reads parameters from filename
--alignment=filename -a filename Start from an XML alignment file
--threshold=double -t double Filters the similarities under threshold
--cutmethod=hard|perc|prop|best|span -T hard|perc|prop|best|span method for computing the threshold
--debug[=n] -d [n] Report debug info at level n
-Dparam=value Set parameter
--help -h Print this message
$Id$
</div>
</p>
<p>
Parameters can be passed to all the command line interfaces through the "-Dname=value" scheme. These parameters are either used by the command line utility or transmitted to the called programs, e.g., <tt>align()</tt>. Parameters can also be passed through an XML file through the "-P filename" option.
</p>
<h2>Batch matching</h2>
<p>There is a small utility (<tt>GroupAlign</tt>) which allows to implement batch matching. It starts with a directory containing a set of subdirectories. Each subdirectory contains an ontology to align (usually called <tt>onto.rdf</tt>) and there exist an ontology to be aligned againts these (-n argument, e.g., named <tt>./onto.rdf</tt>).</p>
<p>Invoking <tt>GroupAlign</tt> with some implementation (-i argument), some set of parameters (-p argument), the name of the output file (-o argument) and optionally a renderer (-r argument) will output the resulting alignment in each of these directories:
<div class="terminal">
$ java -cp $CWD/../lib/procalign.jar fr.inrialpes.exmo.align.util.GroupAlign
-o edna -n file://$CWD/101/onto.rdf
-i fr.inrialpes.exmo.align.impl.method.EditDistNameAlignment
</div>
</p>
<p>
This will compare each onto.rdf file in each of the subdirectory to the <tt>file://$CWD/101/onto.rdf</tt> with the <tt>EditDistNameAlignment</tt> method and output the result in a <tt>edna.rdf</tt> file in each directory.
</p>
<p>
The output is ready to be evaluated by <tt>GroupEval</tt>.
</p>
<h3>Generating tests</h3>
<p>
Tools for generating matching tests (<tt>TestGen</tt>) are described
in the <a href="testgen.html">test generation page</a>.
</p>
<h3>Evaluating alignments</h3>
<p>
Tools for evaluating (<tt>EvalAlign</tt>) and batch evaluating
alignments (<tt>GroupEval</tt>, <tt>ExtGroupEval</tt>, <tt>WGroupEval</tt>) and displaying
results (<tt>GenPlot</tt>, <tt>GroupOutput</tt>) are described in the <a href="eval.html">evaluation page</a>.