# HG changeset patch
# User Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1316022726 -7200
# Node ID 4f60202c58d9448f58ebd038ef5443ca06d37ff3
# Parent  5255f1333cc4a1d77837179c56c21401e61facf7
Added option to push inferred subsumption axioms into output ontology

diff -r 5255f1333cc4 -r 4f60202c58d9 OPPL/README
--- a/OPPL/README	Wed Sep 07 10:46:29 2011 +0200
+++ b/OPPL/README	Wed Sep 14 19:52:06 2011 +0200
@@ -49,6 +49,17 @@
 	>> Execute an OPPL file against an OWL file 
 
 
+FORESEEN FEATURES
+=================
+
+OWL import closure.
+
+Choose which inferred axioms to add to the output ontology (Right now 
+only subsumption is available).
+
+Choose reasoner (Right now only Pellet is available).
+
+
 
 TESTS
 =====
diff -r 5255f1333cc4 -r 4f60202c58d9 OPPL/Tool.java
--- a/OPPL/Tool.java	Wed Sep 07 10:46:29 2011 +0200
+++ b/OPPL/Tool.java	Wed Sep 14 19:52:06 2011 +0200
@@ -25,6 +25,7 @@
 import java.io.OutputStream;
 import java.io.PipedOutputStream;
 import java.io.PrintStream;
+import java.util.ArrayList;
 import java.util.List;
 import java.util.Scanner;
 import java.util.logging.Level;
@@ -44,13 +45,18 @@
 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
 import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLAxiom;
 import org.semanticweb.owlapi.model.OWLAxiomChange;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
+import org.semanticweb.owlapi.reasoner.InferenceType;
 import org.semanticweb.owlapi.reasoner.OWLReasoner;
 import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
+import org.semanticweb.owlapi.util.InferredAxiomGenerator;
+import org.semanticweb.owlapi.util.InferredOntologyGenerator;
+import org.semanticweb.owlapi.util.InferredSubClassAxiomGenerator;
 
 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
 
@@ -74,6 +80,7 @@
 		String OWLFilePath = args [0]; 
 		String OPPL_script_file = args [1];
 		String Output_format = args [2];
+		String Add_inferred = args [3];
 		String OPPL_script_source = "";
 		
 		// Load the flat file with script in memory
@@ -107,15 +114,22 @@
 		List<OWLAxiomChange> changes = extractor.visit(OPPLscript);
 		manager.applyChanges(changes);
 		
+		// Add the inferred axioms as asserted axioms to the original ontology
+		if(Add_inferred.equals("Add_inferred")){
+			reasoner.precomputeInferences(InferenceType.CLASS_HIERARCHY);
+			List<InferredAxiomGenerator<? extends OWLAxiom>> gens = new ArrayList<InferredAxiomGenerator<? extends OWLAxiom>>();
+			gens.add(new InferredSubClassAxiomGenerator());
+			InferredOntologyGenerator iog = new InferredOntologyGenerator(reasoner, gens);
+			iog.fillOntology(manager, OWL_ontology);
+		}
+
 		// Print the ontology to the standard output so other galaxy tools can operate on the output
-		OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();
-		
+		OWLOntologyDocumentTarget documentTarget = new SystemOutDocumentTarget();	
 		if(Output_format.equals("OBO")){
 			manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
 		}
 		else{
 			manager.saveOntology(OWL_ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget());
 		}
-
 	}
 }
diff -r 5255f1333cc4 -r 4f60202c58d9 OPPL/oppl.xml
--- a/OPPL/oppl.xml	Wed Sep 07 10:46:29 2011 +0200
+++ b/OPPL/oppl.xml	Wed Sep 14 19:52:06 2011 +0200
@@ -1,6 +1,7 @@
-<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.1">
+<tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.2">
   <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 $format > $output </command>
+  <command>java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred > $output </command>
+  <!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output </command>-->
   <inputs>
     <param format="text" name="input" type="data" label="Input ontology file"/>
     <param format="text" name="OPPL" type="data" label="OPPL file"/>
@@ -8,6 +9,7 @@
         <option value="OWL" selected="true">OWL</option>
 	<option value="OBO">OBO</option>
     </param>
+    <param name="inferred" type="boolean" value="False" truevalue="Add_inferred" falsevalue="Gora_ni" label="Add inferred subsumption axioms to output ontology"/>
   </inputs>
   <outputs>
     <data format="text" name="output" />
@@ -18,6 +20,7 @@
       <param name="input" value="test.owl"/>
       <param name="OPPL" value="test.oppl"/>
       <param name="format" value="OWL"/>
+      <param name="inferred" value="False"/>
       <output name="out_file" file="test_new.owl"/>	
     </test>
   </tests>
@@ -50,7 +53,7 @@
 
 **More information**
 
-  http://oppl2.sourceforge.net/
+  http://oppl.sf.net/
 
   http://owlapi.sourceforge.net/
 
@@ -58,12 +61,6 @@
 
   http://clarkparsia.com/pellet
 
-**Features that will be implemented soon**
-
-  OWL import closure.
-
-  Choose reasoner (Right now only Pellet is available).
-
 **Contact**
 
   Please send any request or comment to mikel.egana.aranguren@gmail.com.
diff -r 5255f1333cc4 -r 4f60202c58d9 OPPL/oppl_galaxy_tool.jar
Binary file OPPL/oppl_galaxy_tool.jar has changed
diff -r 5255f1333cc4 -r 4f60202c58d9 OPPL/test.owl
--- a/OPPL/test.owl	Wed Sep 07 10:46:29 2011 +0200
+++ b/OPPL/test.owl	Wed Sep 14 19:52:06 2011 +0200
@@ -38,6 +38,12 @@
     
 
 
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/prop -->
+
+    <owl:ObjectProperty rdf:about="&Ontology1314715036188;prop"/>
+    
+
+
     <!-- 
     ///////////////////////////////////////////////////////////////////////////////////////
     //
@@ -49,9 +55,58 @@
     
 
 
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/OPPL_test -->
+
+    <owl:Class rdf:about="&Ontology1314715036188;OPPL_test"/>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/Taxonomy_test -->
+
+    <owl:Class rdf:about="&Ontology1314715036188;Taxonomy_test"/>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/child_class -->
+
+    <owl:Class rdf:about="&Ontology1314715036188;child_class">
+        <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/>
+        <rdfs:subClassOf>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="&Ontology1314715036188;prop"/>
+                <owl:someValuesFrom rdf:resource="&Ontology1314715036188;filler"/>
+            </owl:Restriction>
+        </rdfs:subClassOf>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/filler -->
+
+    <owl:Class rdf:about="&Ontology1314715036188;filler">
+        <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/>
+    </owl:Class>
+    
+
+
+    <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/parent_class -->
+
+    <owl:Class rdf:about="&Ontology1314715036188;parent_class">
+        <owl:equivalentClass>
+            <owl:Restriction>
+                <owl:onProperty rdf:resource="&Ontology1314715036188;prop"/>
+                <owl:someValuesFrom rdf:resource="&Ontology1314715036188;filler"/>
+            </owl:Restriction>
+        </owl:equivalentClass>
+        <rdfs:subClassOf rdf:resource="&Ontology1314715036188;Taxonomy_test"/>
+    </owl:Class>
+    
+
+
     <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/part -->
 
     <owl:Class rdf:about="&Ontology1314715036188;part">
+        <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/>
         <rdfs:subClassOf>
             <owl:Restriction>
                 <owl:onProperty rdf:resource="&Ontology1314715036188;part_of"/>
@@ -64,7 +119,9 @@
 
     <!-- http://www.semanticweb.org/ontologies/2011/7/Ontology1314715036188.owl/whole -->
 
-    <owl:Class rdf:about="&Ontology1314715036188;whole"/>
+    <owl:Class rdf:about="&Ontology1314715036188;whole">
+        <rdfs:subClassOf rdf:resource="&Ontology1314715036188;OPPL_test"/>
+    </owl:Class>
 </rdf:RDF>