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First commit (1.0.0)
author mikel-egana-aranguren
date Tue, 06 Sep 2011 14:53:59 -0400
parents
children 036c6ec459b9
files OPPL/README OPPL/oppl.sh OPPL/oppl.xml OPPL/oppl_galaxy_tool.jar OPPL/oppl_galaxy_tool_lib/antlr-runtime-3.2.jar OPPL/oppl_galaxy_tool_lib/aterm-java-1.6.jar OPPL/oppl_galaxy_tool_lib/jgrapht-jdk1.5.jar OPPL/oppl_galaxy_tool_lib/org.coode.oppl-API.jar OPPL/oppl_galaxy_tool_lib/owlapi-bin.jar OPPL/oppl_galaxy_tool_lib/parsers.jar OPPL/oppl_galaxy_tool_lib/pellet-core.jar OPPL/oppl_galaxy_tool_lib/pellet-datatypes.jar OPPL/oppl_galaxy_tool_lib/pellet-el.jar OPPL/oppl_galaxy_tool_lib/pellet-owlapiv3.jar OPPL/oppl_galaxy_tool_lib/pellet-query.jar OPPL/oppl_galaxy_tool_lib/pellet-rules.jar OPPL/test.oppl OPPL/test.owl OPPL/test_new.owl
diffstat 19 files changed, 337 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/README	Tue Sep 06 14:53:59 2011 -0400
@@ -0,0 +1,113 @@
+
+
+
+			===========
+			OPPL-GALAXY
+			===========
+
+
+
+INSTALLATION
+============
+
+1.- Stop galaxy.
+
+2.- Copy oppl_galaxy_tool.jar 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.
+
+Note that if you want you can use any java parameter by editing oppl.xml
+, eg: <command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 
+-jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL 
+> $output </command>
+
+
+
+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 
+
+
+
+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 mikel.egana.aranguren@gmail.com.
+
+
+
+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, OWL API and Pellet have their own licenses.
+
+Galaxy is distributed as open source under the conditions of the 
+Academic Free License (http://www.opensource.org/licenses/academic.php).
+
+
+
+
+
+
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/oppl.sh	Tue Sep 06 14:53:59 2011 -0400
@@ -0,0 +1,5 @@
+#!/bin/sh
+
+java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar oppl_galaxy_tool.jar test.owl test.oppl > test_new.owl
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/oppl.xml	Tue Sep 06 14:53:59 2011 -0400
@@ -0,0 +1,70 @@
+<tool id="oppl" name="Execute an OPPL file against an OWL file" version="1.0.0">
+  <description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
+  <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL > $output </command>
+  <inputs>
+    <param format="text" name="input" type="data" label="Source OWL file"/>
+    <param format="text" name="OPPL" type="data" label="OPPL file"/>
+  </inputs>
+  <outputs>
+    <data format="text" name="output" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="test.owl"/>
+      <param name="OPPL" value="test.oppl"/>
+      <output name="out_file" file="test_new.owl"/>	
+    </test>
+  </tests>
+
+  <help>
+
+**About OPPL-Galaxy**
+
+  OPPL-Galaxy can be used to execute an OPPL script against an (OWL) ontology, generating a new ontology. OPPL (Ontology Pre Processor Language) is a high level scripting language, based in the Manchester OWL Syntax, to automate the manipulation of an ontology (Adding or removing axioms). An OPPL script (See bellow or test.oppl) defines a query to be performed against the ontology, and some actions that affect the entities that will be retrieved. Those entities can be named or defined by a variable. OPPL is a powerful method for defining and executing modelling patterns that are repeated in a given ontology, saving time and effort.  
+
+**Formats**
+
+  OPPL-Galaxy uses the OWL API, and therefore can work with any ontology format that such API is able to load. That includes: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS.
+
+**Usage**
+
+  An ontology and an OPPL file are needed (test.owl and test.oppl can be used as samples). Load both with Get Data >> Upload File from your computer. 
+
+  Then execute the OPPL file against the OWL file with Ontology Pre Processor Language >> Execute an OPPL file against an OWL file.
+
+  This is the OPPL script provided in the bundle, test.oppl. Variables start with ?: 
+
+  ?whole:CLASS,
+  ?part:CLASS
+  SELECT
+  ?part SubClassOf part_of some ?whole WHERE ?part != Nothing
+  BEGIN
+  ADD ?part SubClassOf part_of only ?whole
+  END;
+
+**More information**
+
+  http://oppl2.sourceforge.net/
+
+  http://owlapi.sourceforge.net/
+
+  http://www.w3.org/TR/owl2-manchester-syntax/
+
+  http://clarkparsia.com/pellet
+
+**Features that will be implemented soon**
+
+  OWL import closure
+
+  Choose output format (Right now only OWL RDF/XML is available)
+
+  Choose reasoner (Right now only Pellet is available)
+
+**Contact**
+
+  Please send any request or comment to mikel.egana.aranguren@gmail.com.
+
+  </help>
+
+</tool>
Binary file OPPL/oppl_galaxy_tool.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/antlr-runtime-3.2.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/aterm-java-1.6.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/jgrapht-jdk1.5.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/org.coode.oppl-API.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/owlapi-bin.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/parsers.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/pellet-core.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/pellet-datatypes.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/pellet-el.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/pellet-owlapiv3.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/pellet-query.jar has changed
Binary file OPPL/oppl_galaxy_tool_lib/pellet-rules.jar has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test.oppl	Tue Sep 06 14:53:59 2011 -0400
@@ -0,0 +1,8 @@
+?whole:CLASS,
+?part:CLASS
+SELECT
+?part SubClassOf part_of some ?whole WHERE ?part != Nothing
+BEGIN
+ADD ?part SubClassOf part_of only ?whole
+END;
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test.owl	Tue Sep 06 14:53:59 2011 -0400
@@ -0,0 +1,73 @@
+<?xml version="1.0"?>
+
+
+<!DOCTYPE rdf:RDF [
+    <!ENTITY owl "http://www.w3.org/2002/07/owl#" >
+    <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#" >
+    <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#" >
+    <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#" >
+    <!ENTITY Ontology1314715036188 "http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/" >
+]>
+
+
+<rdf:RDF xmlns="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#"
+     xml:base="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:Ontology1314715036188="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+    <owl:Ontology rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of -->
+
+    <owl:ObjectProperty rdf:about="&Ontology1314715036188;part_of"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part -->
+
+    <owl:Class rdf:about="&Ontology1314715036188;part">
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="&Ontology1314715036188;part_of"/>
+                <owl:someValuesFrom rdf:resource="&Ontology1314715036188;whole"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole -->
+
+    <owl:Class rdf:about="&Ontology1314715036188;whole"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 3.2.2.1782) http://owlapi.sourceforge.net -->
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OPPL/test_new.owl	Tue Sep 06 14:53:59 2011 -0400
@@ -0,0 +1,68 @@
+<?xml version="1.0"?>
+<rdf:RDF xmlns="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#"
+     xml:base="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl"
+     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
+     xmlns:Ontology1314715036188="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/"
+     xmlns:owl="http://www.w3.org/2002/07/owl#"
+     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
+    <owl:Ontology rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Object Properties
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of -->
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part">
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of"/>
+                <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part_of"/>
+                <owl:allValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole"/>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 3.2.4.1806) http://owlapi.sourceforge.net -->
+