view OPPL/README @ 10:3f31c0eb7539

Interface improved

			===========
			OPPL-GALAXY
			===========



INSTALLATION
============

1.- Stop Galaxy.

2.- Copy oppl_galaxy_tool.jar, FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ 
and oppl_galaxy_tool_lib/ to /galaxy-dist/tool-data/shared/jars/

3.- Create directory /galaxy-dist/tools/OPPL/

4.- Copy oppl.xml to /galaxy-dist/tools/OPPL/

5.- Add the following lines to /galaxy-dist/tool_conf.xml:

  <section name="Ontology Pre Processor Language" id="oppl">
    <tool file="OPPL/oppl.xml"/>
  </section>

6.- Start Galaxy.



USAGE
=====

An ontology and an OPPL file are needed (test.owl and test.oppl can be 
used as samples). Load both:

Get Data 
	>> Upload File from your computer 

Then execute the OPPL file against the OWL file: 

Ontology Pre Processor Language
	>> Execute an OPPL file against an OWL file 

An ontology produced by another galaxy tool can also be used.

Test.oppl and test.owl can be used as examples. More OPPL-Galaxy 
examples can be obtained at http://miuras.inf.um.es/OPPL-Galaxy/, and 
general OPPL script that may be useful to use with OPPL-Galaxy can be 
obtained at http://oppl2.sourceforge.net/taggedexamples/.

A public instance of Galaxy with pre-installed OPPL-Galaxy can be used 
at http://sele.inf.um.es:8080/.



FORESEEN FEATURES
=================

Choose which inferred axioms to add to the output ontology (Right now 
only subsumption between named classes is available).

Rendering definition (URI fragment, label, etc).

XML catalog support for imported URIs.

OWLLink and Racer support.



KNOWN BUGS AND ISSUES
=====================

Currently Galaxy interprets any information thrown to stderr as a tool
error, which is bad since OPPL (And many other tools) throw info to 
sdterr even if working properly. In OPPL Galaxy, stderr is redirected to 
/dev/null to avoid the problem, but that means that OPPL Galaxy does not 
fail gracefully (It simply stops). A wrapper will be implemented.

http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr



TESTS
=====

To run the functional test, first complete installation and then:

1.- Copy test.owl and test.oppl to /galaxy-dist/test-data/

2.- Add the following lines to /galaxy-dist/tool_conf.xml.sample

  <section name="Ontology Pre Processor Language" id="oppl">
    <tool file="OPPL/oppl.xml"/>
  </section>

3.- Execute /galaxy-dist/run_functional_tests.sh -id oppl



CONTACT
=======

Please send any request or comment to [e-mail].



ACKNOWLEDGEMENTS
================

This work is funded by the Marie Curie Cofund program of the EU, FP7.



COPYRIGHT AND LICENSE
=====================

Copyright (c) 2011 Mikel Egaña Aranguren. 

OPPL-Galaxy is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses.