# HG changeset patch # User Mikel Egaña Aranguren # Date 1315385189 -7200 # Node ID 5255f1333cc4a1d77837179c56c21401e61facf7 # Parent 0a374d0b77590cd6a9210a85d5fdcb66da10b623 Version 1.0.1 Added output choice: OBO or OWL(RDF/XML) diff -r 0a374d0b7759 -r 5255f1333cc4 OPPL/README --- a/OPPL/README Tue Sep 06 14:55:49 2011 -0400 +++ b/OPPL/README Wed Sep 07 10:46:29 2011 +0200 @@ -30,7 +30,7 @@ Note that if you want you can use any java parameter by editing oppl.xml , eg: java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL -> $output +$format > $output diff -r 0a374d0b7759 -r 5255f1333cc4 OPPL/Tool.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/Tool.java Wed Sep 07 10:46:29 2011 +0200 @@ -0,0 +1,121 @@ +/** + * Copyright (C) 2011, Mikel Egaña Aranguren + * + * This program 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 . + */ + +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.List; +import java.util.Scanner; +import java.util.logging.Level; +import java.util.logging.Logger; + +import org.coode.oppl.ChangeExtractor; +import org.coode.oppl.OPPLParser; +import org.coode.oppl.OPPLScript; +import org.coode.oppl.ParserFactory; +import org.coode.oppl.exceptions.QuickFailRuntimeExceptionHandler; +import org.coode.oppl.log.Logging; +import org.coode.owlapi.obo.parser.OBOOntologyFormat; +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; +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.OWLReasoner; +import org.semanticweb.owlapi.reasoner.OWLReasonerFactory; + +import com.clarkparsia.pellet.owlapiv3.PelletReasonerFactory; + + +/** + * @author Mikel Egaña Aranguren + * + */ +public class Tool { + + /** + * @param OWL file + * @param OPPL script + * @throws FileNotFoundException + * @throws OWLOntologyCreationException + * @throws OWLOntologyStorageException + */ + public static void main(String[] args) throws FileNotFoundException, OWLOntologyCreationException, OWLOntologyStorageException { + + // Get the arguments from command-line + String OWLFilePath = args [0]; + String OPPL_script_file = args [1]; + String Output_format = args [2]; + String OPPL_script_source = ""; + + // Load the flat file with script in memory + File file = new File(OPPL_script_file); + Scanner input = new Scanner(file); + while(input.hasNext()) { + String nextToken = input.next(); + OPPL_script_source = OPPL_script_source + " " + nextToken; + } + input.close(); + + // Load the OWL ontology + File owl_file = new File(OWLFilePath); + OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); + OWLOntology OWL_ontology = manager.loadOntologyFromOntologyDocument(owl_file); + + // Sync reasoner and check consistency + OWLReasonerFactory reasonerFactory = new PelletReasonerFactory(); + OWLReasoner reasoner = reasonerFactory.createReasoner(OWL_ontology); + + // 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 + ErrorListener errorListener = (ErrorListener)new LoggerErrorListener(logger); + OPPLParser opplparser = parserFactory.build(errorListener); + OPPLScript OPPLscript = opplparser.parse(OPPL_script_source); + + // Execute the script + ChangeExtractor extractor = new ChangeExtractor(new QuickFailRuntimeExceptionHandler(), true); + List changes = extractor.visit(OPPLscript); + manager.applyChanges(changes); + + // Print the ontology to the standard output so other galaxy tools can operate on the output + 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 0a374d0b7759 -r 5255f1333cc4 OPPL/oppl.sh --- a/OPPL/oppl.sh Tue Sep 06 14:55:49 2011 -0400 +++ b/OPPL/oppl.sh Wed Sep 07 10:46:29 2011 +0200 @@ -3,3 +3,4 @@ java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar oppl_galaxy_tool.jar test.owl test.oppl > test_new.owl + diff -r 0a374d0b7759 -r 5255f1333cc4 OPPL/oppl.xml --- a/OPPL/oppl.xml Tue Sep 06 14:55:49 2011 -0400 +++ b/OPPL/oppl.xml Wed Sep 07 10:46:29 2011 +0200 @@ -1,9 +1,13 @@ - + It executes an OPPL script against the input ontology and generates a new ontology with the changes described in the OPPL script - java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL > $output + java -jar ${__tool_data_path__}/shared/jars/oppl_galaxy_tool.jar $input $OPPL $format > $output - + + + + + @@ -13,6 +17,7 @@ + @@ -21,11 +26,11 @@ **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. + 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. **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. + OPPL-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The available output formats are OBO flat file and OWL (RDF/XML). **Usage** @@ -33,7 +38,7 @@ 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 ?: + This is the OPPL script provided in the bundle, test.oppl (Variables start with ?): ?whole:CLASS, ?part:CLASS @@ -55,11 +60,9 @@ **Features that will be implemented soon** - OWL import closure + OWL import closure. - Choose output format (Right now only OWL RDF/XML is available) - - Choose reasoner (Right now only Pellet is available) + Choose reasoner (Right now only Pellet is available). **Contact** diff -r 0a374d0b7759 -r 5255f1333cc4 OPPL/oppl_galaxy_tool.jar Binary file OPPL/oppl_galaxy_tool.jar has changed