# HG changeset patch
# User Mikel Egana Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1350228111 -7200
# Node ID 8d4bbaa99b4a20f4b53de86f71cb36a6d76d76ab
# Parent  ffde1fafa0665320deb976e44c40d6b2c2792a7f
Minor changes for JBS paper

diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query.jar
Binary file OPPL/oppl_query.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar
Binary file OPPL/oppl_query_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/HermiT.jar
Binary file OPPL/oppl_query_lib/HermiT.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/antlr-runtime-3.2.jar
Binary file OPPL/oppl_query_lib/antlr-runtime-3.2.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/aterm-java-1.6.jar
Binary file OPPL/oppl_query_lib/aterm-java-1.6.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/elk-owlapi.jar
Binary file OPPL/oppl_query_lib/elk-owlapi.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/jgrapht-jdk1.5.jar
Binary file OPPL/oppl_query_lib/jgrapht-jdk1.5.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/log4j-sources.jar
Binary file OPPL/oppl_query_lib/log4j-sources.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/log4j.jar
Binary file OPPL/oppl_query_lib/log4j.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/org.coode.oppl-API.jar
Binary file OPPL/oppl_query_lib/org.coode.oppl-API.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/owlapi-bin.jar
Binary file OPPL/oppl_query_lib/owlapi-bin.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/parsers.jar
Binary file OPPL/oppl_query_lib/parsers.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/pellet-core.jar
Binary file OPPL/oppl_query_lib/pellet-core.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/pellet-datatypes.jar
Binary file OPPL/oppl_query_lib/pellet-datatypes.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/pellet-el.jar
Binary file OPPL/oppl_query_lib/pellet-el.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/pellet-owlapiv3.jar
Binary file OPPL/oppl_query_lib/pellet-owlapiv3.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/pellet-query.jar
Binary file OPPL/oppl_query_lib/pellet-query.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a OPPL/oppl_query_lib/pellet-rules.jar
Binary file OPPL/oppl_query_lib/pellet-rules.jar has changed
diff -r ffde1fafa066 -r 8d4bbaa99b4a README
--- a/README	Mon Oct 08 13:10:44 2012 +0200
+++ b/README	Sun Oct 14 17:21:51 2012 +0200
@@ -32,7 +32,7 @@
 
 2.- Move to galaxy-dist/tools/oppl/
 
-3.- Pull changes adn update working copy: 
+3.- Pull changes and update working copy with mercurial: 
 
 hg pull
 hg update
@@ -41,7 +41,7 @@
 
 ./install.sh
 
-5.- Only edit /galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
+5.- Only edit galaxy-dist/tool_conf.xml in case a tool (an XML file) has been added/removed.
 
 6.- Start Galaxy.
 
@@ -55,7 +55,7 @@
 1.- Stop Galaxy.
 
 2.- Copy the following files and directories to
-/galaxy-dist/tool-data/shared/jars/:
+galaxy-dist/tool-data/shared/jars/:
 
 oppl_galaxy_tool.jar
 inference.jar
@@ -70,12 +70,12 @@
 FaCT++-linux-v1.5.2/ 
 FaCT++-OSX-v1.5.2/
  
-3.- Create directory /galaxy-dist/tools/oppl/
+3.- Create directory galaxy-dist/tools/oppl/
 
 4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and 
-merge.xml to /galaxy-dist/tools/oppl/
+merge.xml to galaxy-dist/tools/oppl/
 
-5.- Add the following lines to /galaxy-dist/tool_conf.xml:
+5.- Add the following lines to galaxy-dist/tool_conf.xml:
 
   <section name="Ontology Pre Processor Language" id="oppl">
     <tool file="oppl/oppl.xml"/>
@@ -107,6 +107,8 @@
 - Support for DataPropertyAssertion, DataPropertyHierarchy,
 DifferentIndividuals, ...
 
+- A new tool for wrapping the ontology modularisation function of the OWL API.
+
 
 
 KNOWN BUGS AND ISSUES
diff -r ffde1fafa066 -r 8d4bbaa99b4a oppl.xml
--- a/oppl.xml	Mon Oct 08 13:10:44 2012 +0200
+++ b/oppl.xml	Sun Oct 14 17:21:51 2012 +0200
@@ -80,15 +80,13 @@
 
 **More information**
 
-  Galaxy public instances with OPPL-Galaxy pre-installed:
+  Galaxy public instance with OPPL-Galaxy pre-installed:
   
-  http://sele.inf.um.es:9080/
-  
-  http://linkeddata2.dia.fi.upm.es:8080
+  http://biordf.org:8080/
   
   OPPL-Galaxy Examples: 
   
-  http://miuras.inf.um.es/OPPL-Galaxy/
+  http://biordf.org/OPPL-Galaxy/
   
   OPPL examples:
   
diff -r ffde1fafa066 -r 8d4bbaa99b4a test-data/ontology/single/test.owl
--- a/test-data/ontology/single/test.owl	Mon Oct 08 13:10:44 2012 +0200
+++ b/test-data/ontology/single/test.owl	Sun Oct 14 17:21:51 2012 +0200
@@ -32,6 +32,12 @@
     
 
 
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#participates_in -->
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#participates_in"/>
+    
+
+
     <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#transitive_prop -->
 
     <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#transitive_prop">
@@ -69,6 +75,28 @@
     
 
 
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#agent -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#agent">
+        <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#participates_in"/>
+                <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#process"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#process -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#process">
+        <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/>
+    </owl:Class>
+    
+
+
     <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test -->
 
     <owl:Class rdf:about="&Ontology1314715036188;OPPL_test"/>
diff -r ffde1fafa066 -r 8d4bbaa99b4a test-data/ontology/single/test_outcome.owl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ontology/single/test_outcome.owl	Sun Oct 14 17:21:51 2012 +0200
@@ -0,0 +1,202 @@
+<?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:Ontology13147150361882="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#"
+     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#participates_in -->
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#participates_in"/>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#transitive_prop -->
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#transitive_prop">
+        <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>
+    </owl:ObjectProperty>
+    
+
+
+    <!-- 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"/>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/prop -->
+
+    <owl:ObjectProperty rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/prop"/>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Classes
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#Ind_test_OPPL_query -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#Ind_test_OPPL_query"/>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#agent -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#agent">
+        <rdfs:subClassOf rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#participates_in"/>
+                <owl:allValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#process"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#participates_in"/>
+                <owl:allValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#participates_in"/>
+                <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#process"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#process -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#process">
+        <rdfs:subClassOf rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test"/>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test"/>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test"/>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/child_class -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/child_class">
+        <rdfs:subClassOf rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/prop"/>
+                <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/filler"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/filler -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/filler">
+        <rdfs:subClassOf rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test"/>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/parent_class -->
+
+    <owl:Class rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/parent_class">
+        <owl:equivalentClass>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/prop"/>
+                <owl:someValuesFrom rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/filler"/>
+            </owl:Restriction>
+        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test"/>
+    </owl:Class>
+    
+
+
+    <!-- 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 rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test"/>
+        <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>
+    </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">
+        <rdfs:subClassOf rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test"/>
+    </owl:Class>
+    
+
+
+    <!-- 
+    ///////////////////////////////////////////////////////////////////////////////////////
+    //
+    // Individuals
+    //
+    ///////////////////////////////////////////////////////////////////////////////////////
+     -->
+
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#A -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#A">
+        <rdf:type rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#Ind_test_OPPL_query"/>
+        <Ontology1314715036188:prop rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#B"/>
+    </owl:NamedIndividual>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#B -->
+
+    <owl:NamedIndividual rdf:about="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#B">
+        <rdf:type rdf:resource="http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl#Ind_test_OPPL_query"/>
+    </owl:NamedIndividual>
+</rdf:RDF>
+
+
+
+<!-- Generated by the OWL API (version 3.2.4.1806) http://owlapi.sourceforge.net -->
+
diff -r ffde1fafa066 -r 8d4bbaa99b4a test-data/oppl_script/test.oppl
--- a/test-data/oppl_script/test.oppl	Mon Oct 08 13:10:44 2012 +0200
+++ b/test-data/oppl_script/test.oppl	Sun Oct 14 17:21:51 2012 +0200
@@ -1,7 +1,7 @@
-?whole:CLASS,
-?part:CLASS
-SELECT
-?part SubClassOf part_of some ?whole WHERE ?part != Nothing
+?agent:CLASS,
+?process:CLASS
+SELECT ?agent SubClassOf participates_in some ?process 
+WHERE ?agent != Nothing
 BEGIN
-ADD ?part SubClassOf part_of only ?whole
+ADD ?agent SubClassOf participates_in only ?process
 END;
\ No newline at end of file