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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>taking parameerst (-Dv=n) and parameter files (-P);</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.
</p>
<h2>Matching</h2>
<p>
The implementation offers a stand-alone program (<tt>fr.inrialpes.exmo.align.cli.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
usage: java fr.inrialpes.exmo.align.cli.Procalign [options] ontoURI ontoURI
Matches the two ontologies identified by <ontoURI>
Options:
-a,--alignment <FILE> Use initial alignment FILE
-D <NAME=VALUE> Use value for given property
-d,--debug <LEVEL> debug argument is deprecated, use logging instead
See http://alignapi.gforge.inria.fr/logging.html
-h,--help Print this page
-i,--impl <CLASS> Use the given CLASS for matcher
-o,--output <FILENAME> Send output to FILENAME
-P,--params <FILE> Read parameters from FILE
-r,--renderer <CLASS> Use the given CLASS for output
-T,--cutmethod <METHOD> Method to use for triming (hard|perc|prop|best|span)
-t,--threshold <DOUBLE> Trim the alignment with regard to threshold
Alignment API implementation 4.5 (1864M)
</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>
<div class="terminal">
$ java -cp lib/procalign.jar fr.inrialpes.exmo.align.cli.GroupAlign --help
usage: java fr.inrialpes.exmo.align.cli.GroupAlign [options]
Matches pairs of ontologies in subdirectories
Options:
-a,--alignment <FILE> Use an initial alignment FILE
-D <NAME=VALUE> Use value for given property
-d,--debug <LEVEL> debug argument is deprecated, use logging instead
See http://alignapi.gforge.inria.fr/logging.html
-h,--help Print this page
-i,--impl <CLASS> Use the given Alignment implementation
-n,--name <URI> Use the given URI as common source ontology
-o,--output <FILENAME> Send output to FILENAME
-P,--params <FILE> Read parameters from FILE
-r,--renderer <CLASS> Use the given CLASS for rendering
-s,--source <FILE> Source ontology FILEname (default onto1.rdf)
-t,--target <FILE> Target ontology FILEname (default onto.rdf)
-u,--uriprefix <URI> URI prefix of the target
-w,--directory <DIR> The DIRectory containing the data to match
Alignment API implementation 4.5 (1864M)
</div>
<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 $CWD/../lib/procalign.jar fr.inrialpes.exmo.align.cli@.GroupAlign
-o edna -n file://$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>.
</p>
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