# HG changeset patch
# User Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu>
# Date 1316342118 -7200
# Node ID 3740505b579cc41df170ab489b4221f1e99defef
# Parent  68935f90c2db8f6abde923f4abfbae9a640bb1ed
Added reasoner option: Pellet or HermiT

diff -r 68935f90c2db -r 3740505b579c OPPL/README
--- a/OPPL/README	Sat Sep 17 13:41:28 2011 +0200
+++ b/OPPL/README	Sun Sep 18 12:35:18 2011 +0200
@@ -27,11 +27,6 @@
 
 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 $OPPL 
-$format > $output </command>
-
 
 
 USAGE
@@ -56,7 +51,7 @@
 Choose which inferred axioms to add to the output ontology (Right now 
 only subsumption is available).
 
-Choose reasoner (Right now only Pellet is available).
+FaCT++ and OWLLink support.
 
 
 
diff -r 68935f90c2db -r 3740505b579c OPPL/Tool.java
--- a/OPPL/Tool.java	Sat Sep 17 13:41:28 2011 +0200
+++ b/OPPL/Tool.java	Sun Sep 18 12:35:18 2011 +0200
@@ -17,14 +17,8 @@
 
 package es.upm.fi.dia.oeg.oppl.galaxy;
 
-import java.io.BufferedOutputStream;
-import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileNotFoundException;
-import java.io.FilterOutputStream;
-import java.io.OutputStream;
-import java.io.PipedOutputStream;
-import java.io.PrintStream;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Scanner;
@@ -41,7 +35,6 @@
 import org.coode.parsers.ErrorListener;
 import org.coode.parsers.LoggerErrorListener;
 import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.io.OWLOntologyDocumentTarget;
 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
 import org.semanticweb.owlapi.io.SystemOutDocumentTarget;
 import org.semanticweb.owlapi.model.IRI;
@@ -63,6 +56,8 @@
 
 import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory;
 
+import org.semanticweb.HermiT.Reasoner;
+
 /**
  * @author Mikel Egaña Aranguren
  */
@@ -80,6 +75,7 @@
 		String Output_format = args [2]; // OWL|OBO
 		String Add_inferred = args [3]; // Add_inferred|Whatever
 		String imports_file_path = args [4]; // Flat tab delimited file: URI	Document URI
+		String reasoner_type = args [5]; // Pellet|HermiT
 		
 		// Load the main ontology		
 		File owl_file = new File(OWLFilePath);
@@ -92,11 +88,7 @@
 			while(imports_input.hasNext()){
 			    String nextLine = imports_input.nextLine();
 			    if(!nextLine.startsWith("#")){
-				    String [] URI_documentURI = nextLine.split("\t");
-		//		    System.out.println(URI_documentURI[0]);
-		//		    System.out.println(URI_documentURI[1]);
-		//			IRI ontology_IRI = IRI.create("http://purl.obolibrary.org/obo/CHEBI_ONTOLOGY_chebi_ontology");
-		//			IRI document_IRI = IRI.create("file://" + "/home/pik/UPM/OPPL_galaxy/SWAT4LS_2011/GONG/chebi.owl");		
+				    String [] URI_documentURI = nextLine.split("\t");	
 				    IRI ontology_IRI = IRI.create(URI_documentURI[0]);
 					IRI document_IRI = IRI.create("file://" + URI_documentURI[1]);	
 					OWLOntologyIRIMapper iriMapper = new SimpleIRIMapper(ontology_IRI,document_IRI);
@@ -109,9 +101,16 @@
 		OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file);
 		
 		// Reasoner
-		OWLReasonerFactory reasonerFactory = new PelletReasonerFactory(); 
-		OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology);
-		reasoner.isConsistent();
+		OWLReasonerFactory reasonerFactory = null;
+		OWLReasoner reasoner = null;
+		if(reasoner_type.equals("Pellet")){
+			reasonerFactory = new PelletReasonerFactory(); 
+			reasoner = reasonerFactory.createReasoner(OWL_ontology);
+		}
+		else{
+			reasonerFactory = new Reasoner.ReasonerFactory();
+			reasoner = reasonerFactory.createReasoner(OWL_ontology);
+		}
 		
 		// Load the flat file with script in memory
 		String OPPL_script_source = "";
@@ -126,7 +125,7 @@
 		// Parse the OPPL script
 		ParserFactory parserFactory = new ParserFactory(manager, OWL_ontology, reasoner); 
 		Logger logger = Logger.getLogger(Tool.class.getName());
-		Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy
+		Logging.getQueryLogger().setLevel(Level.OFF); // The normal messages are errors for galaxy (Fixed in Galaxy by 2 > /dev/null)
 		ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger);
 		OPPLParser opplparser = parserFactory.build(errorListener);
 		OPPLScript OPPLscript = opplparser.parse(OPPL_script_source);
@@ -142,11 +141,10 @@
 			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);
+			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();	
+		// Print the ontology to the standard output so other galaxy tools can operate on the output	
 		if(Output_format.equals("OBO")){
 			manager.saveOntology(OWL_ontology, new OBOOntologyFormat(), new SystemOutDocumentTarget());
 		}
diff -r 68935f90c2db -r 3740505b579c OPPL/oppl.xml
--- a/OPPL/oppl.xml	Sat Sep 17 13:41:28 2011 +0200
+++ b/OPPL/oppl.xml	Sun Sep 18 12:35:18 2011 +0200
@@ -1,15 +1,17 @@
 <tool id="oppl" name="Execute an OPPL file against an ontology" version="1.0.3">
 	<description>It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script</description>
 
-	<!-- The conditional is tacky, I think, but it works! -->
+	<!-- The command execution of the conditional is tacky, I think, but it works! -->
+	<!-- Galaxy is not happy with OPPL throwing info into stderr, and I have redirected stderr to /dev/null, which is a bad solution since OPPL galaxy does not inform properly when it fails -->
+	<!-- More info on the stderr issue: http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr -->
 
 	<command>
-		#if $import_opts.imports_select==False #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports > $output 2>/dev/null
-		#else #java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null
+		#if $import_opts.imports_select==False #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred NoImports $reasoner > $output 2>/dev/null
+		#else #java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports $reasoner > $output 2>/dev/null
 		#end if
 	</command>
 		
-	<!--<command>java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format $inferred $imports > $output 2>/dev/null</command>-->
+	<!-- For big ontologies use something like java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar-->
 
 	<inputs>
 		<param format="text" name="input" type="data" label="Input ontology file"/>
@@ -29,6 +31,10 @@
 			<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"/>
+		<param name="reasoner" type="select" label="Choose reasoner">
+			<option value="Pellet" selected="true">Pellet</option>
+			<option value="HermiT">HermiT</option>
+		</param>
 
 	</inputs>
 	<outputs>
@@ -38,9 +44,10 @@
 		<test>
 			<param name="input" value="test.owl"/>
 			<param name="OPPL" value="test.oppl"/>
+			<param name="imports" value="NoImports"/>
 			<param name="format" value="OWL"/>
 			<param name="inferred" value="False"/>
-			<param name="imports" value="NoImports"/>
+			<param name="reasoner" value="Pellet"/>
 			<output name="out_file" file="test_new.owl"/>	
 		</test>
 	</tests>
@@ -48,7 +55,7 @@
 
 **About OPPL-Galaxy**
 
-  OPPL-Galaxy can be used to execute an OPPL script against an 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.  
+  OPPL-Galaxy can be used to execute an OPPL script against an 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. An OPPL script (See test.oppl) defines a query to be performed against the ontology, and some actions (Adding or removing axioms) 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 an ontology, saving time and effort.  
 
 **Formats**
 
@@ -70,6 +77,8 @@
  
   The inferred subsumption axioms can be added to the output ontology as asserted axioms. 
 
+  The reasoner can be Pellet or HermiT. Sometimes, if an execution fails it can be fixed by using a different reasoner. 
+
 **More information**
 
   http://oppl.sf.net/
@@ -80,6 +89,8 @@
 
   http://clarkparsia.com/pellet
 
+  http://hermit-reasoner.com/
+
 **Contact**
 
   Please send any request or comment to mikel.egana.aranguren@gmail.com.
diff -r 68935f90c2db -r 3740505b579c OPPL/oppl_galaxy_tool.jar
Binary file OPPL/oppl_galaxy_tool.jar has changed