Previous changeset 16:6c25e717c896 (2012-08-02) Next changeset 18:d3616fac4ca5 (2012-09-20) |
Commit message:
New tool added for merging imported ontologies (GalaxyOWLAPI and README changed and test ontologies added accordingly). Memory settings changed in all the tools XML files |
modified:
OPPL/README OPPL/inference.xml OPPL/oppl.xml OPPL/oppl_query.xml OPPL/query.xml OPPL/src/GalaxyOWLAPI.java |
added:
OPPL/merge.jar OPPL/merge.xml OPPL/merge_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar OPPL/merge_lib/HermiT.jar OPPL/merge_lib/antlr-runtime-3.2.jar OPPL/merge_lib/aterm-java-1.6.jar OPPL/merge_lib/jgrapht-jdk1.5.jar OPPL/merge_lib/org.coode.oppl-API.jar OPPL/merge_lib/owlapi-bin.jar OPPL/merge_lib/parsers.jar OPPL/merge_lib/pellet-core.jar OPPL/merge_lib/pellet-datatypes.jar OPPL/merge_lib/pellet-el.jar OPPL/merge_lib/pellet-owlapiv3.jar OPPL/merge_lib/pellet-query.jar OPPL/merge_lib/pellet-rules.jar OPPL/src/MergeImportedOntologies.java OPPL/test-data/ontology/imports/merge.owl OPPL/test-data/ontology/imports/merge_test.owl |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/README --- a/OPPL/README Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/README Mon Aug 20 11:39:56 2012 +0200 |
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@@ -6,24 +6,26 @@ 1.- Stop Galaxy. -2.- Copy the following files and dirs to +2.- Copy the following files and directories to /galaxy-dist/tool-data/shared/jars/: oppl_galaxy_tool.jar inference.jar query.jar oppl_query.jar +merge.jar oppl_galaxy_lib/ inference_lib/ query_lib/ oppl_query_lib/ +merge_lib/ FaCT++-linux-v1.5.2/ FaCT++-OSX-v1.5.2/ 3.- Create directory /galaxy-dist/tools/OPPL/ -4.- Copy oppl.xml, inference.xml and query.xml to -/galaxy-dist/tools/OPPL/ +4.- Copy oppl.xml, inference.xml, query.xml, oppl_query.xml and +merge.xml to /galaxy-dist/tools/OPPL/ 5.- Add the following lines to /galaxy-dist/tool_conf.xml: @@ -31,7 +33,8 @@ <tool file="OPPL/oppl.xml"/> <tool file="OPPL/inference.xml"/> <tool file="OPPL/query.xml"/> - <tool file="OPPL/oppl_query.xml"/> + <tool file="OPPL/oppl_query.xml"/> + <tool file="OPPL/merge.xml"/> </section> 6.- Start Galaxy. @@ -41,31 +44,21 @@ FORESEEN FEATURES ================= -General (OPPL, Inference, Query, OPPL query): - - Support for processing ontologies that import other ontologies loaded -in galaxy. +in galaxy (i.e. to resolve imports within galaxy). - Entities rendering definition (URI fragment, rdfs:label, QName, etc). -- OWLLink and Racer support. - - -OPPL: +- OWLLink, Racer and ELK support. - Standalone OPPL assertions parsing (e.g. ADD phagocyte subClassOf cell). - Other output formats apart from RDF/XML. - -Inference: - - Support for DataPropertyAssertion, DataPropertyHierarchy, DifferentIndividuals, ... -OPPL query: - KNOWN BUGS AND ISSUES @@ -100,7 +93,7 @@ Copyright (c) 2011 Mikel Egaña Aranguren. -(OPPL|Inference|Query)-Galaxy +(OPPL|Inference|Query|OPPL-Query|Merge)-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 @@ -117,9 +110,3 @@ OPPL API, OWL API, Pellet, HermiT, and FaCT++ have their own licenses. - - - - - - |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/inference.xml --- a/OPPL/inference.xml Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/inference.xml Mon Aug 20 11:39:56 2012 +0200 |
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@@ -1,10 +1,10 @@ <tool id="inference" name="Perform inference in an OWL ontology" version="1.0.1"> <description>It performs inference in an OWL ontology and it generates a new ontology with the inferred axioms as asserted axioms</description> - <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> + <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> <command> - java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/inference.jar $input $reasoner $axioms > $output </command> <inputs> @@ -25,14 +25,14 @@ <outputs> <data format="text" name="output" /> </outputs> - <tests> + <!--<tests> <test> <param name="input" value="test.owl"/> <param name="reasoner" value="Pellet"/> <param name="axioms" value="CLASS_ASSERTIONS,CLASS_HIERARCHY,OBJECT_PROPERTY_HIERARCHY"/> <output name="out_file" file="test_new.owl"/> </test> - </tests> + </tests>--> <help> **About Inference-Galaxy** |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge.jar |
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Binary file OPPL/merge.jar has changed |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/merge.xml Mon Aug 20 11:39:56 2012 +0200 |
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@@ -0,0 +1,42 @@ +<tool id="merge" name="Merge the imported ontologies" version="1.0.1"> + <description>If an ontology with import axioms is provided, it will merge the imported ontologies into the main ontology</description> + + <!-- DEFAULT SETTINGS --> + + <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> + + <command> + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/merge.jar $ontology "$uri" > $output + </command> + + <inputs> + <param name="ontology" type="data" label="Input ontology file"/> + <param name="uri" type="text" size="100" value="" label="IRI for the new ontology" /> + </inputs> + <outputs> + <data type="data" format="text" name="output" /> + </outputs> + <!--<tests> + <test> + <param name="ontology" value="merge_test.owl"/> + <param name="uri" value="http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"/> + <output name="out_file" file="merge.owl"/> + </test> + </tests>--> + <help> + +**About Merge-Galaxy** + + Merge-Galaxy can be used to merge any imported ontologies into the main ontology, creating a new ontology. + +**Formats** + + Merge-Galaxy uses the OWL API, and therefore it can load any ontology format that such API is able to load, provided that imports are correctly represented: OBO flat file, OWL (RDF/XML, OWL/XML, Functional, Manchester), turtle, and KRSS. The output is an OWL ontology in RDF/XML format. + +**Contact** + + Please send any request or comment to mikel.egana.aranguren@gmail.com. + + </help> + +</tool> |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar |
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Binary file OPPL/merge_lib/FaCTpp-OWLAPI-3.2-v1.5.2.jar has changed |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/HermiT.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/antlr-runtime-3.2.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/aterm-java-1.6.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/jgrapht-jdk1.5.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/org.coode.oppl-API.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/owlapi-bin.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/parsers.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/pellet-core.jar |
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Binary file OPPL/merge_lib/pellet-core.jar has changed |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/pellet-datatypes.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/pellet-el.jar |
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Binary file OPPL/merge_lib/pellet-el.jar has changed |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/pellet-owlapiv3.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/pellet-query.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/merge_lib/pellet-rules.jar |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/oppl.xml --- a/OPPL/oppl.xml Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/oppl.xml Mon Aug 20 11:39:56 2012 +0200 |
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@@ -9,10 +9,10 @@ <!-- DEFAULT SETTINGS --> - <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> + <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> <command> - java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null </command> @@ -23,7 +23,7 @@ <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> <!--<command> - java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null + java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output 2>/dev/null </commadn>--> @@ -34,7 +34,7 @@ <!-- For debugging simply remove 2>/dev/null Or uncomment bellow (And comment the default settings above). It will fail always (Due to OPPL messages) but at least it will be informative --> <!--<command> - java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_galaxy.jar $input $reasoner $OPPL $format > $output </command>--> @@ -56,7 +56,7 @@ <outputs> <data format="text" name="output" /> </outputs> - <tests> + <!--<tests> <test> <param name="input" value="test.owl"/> <param name="OPPL" value="test.oppl"/> @@ -64,7 +64,7 @@ <param name="reasoner" value="Pellet"/> <output name="out_file" file="test_new.owl"/> </test> - </tests> + </tests>--> <help> **About OPPL-Galaxy** |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/oppl_query.xml --- a/OPPL/oppl_query.xml Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/oppl_query.xml Mon Aug 20 11:39:56 2012 +0200 |
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@@ -7,10 +7,10 @@ <!-- DEFAULT SETTINGS --> - <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> + <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> <command> - java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null </command> <!-- FACT++ --> @@ -19,7 +19,7 @@ <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> <!--<command> - java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null + java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/oppl_query.jar $ontology $reasoner $answer_format "$query" > $output 2>/dev/null </commadn>--> @@ -40,7 +40,7 @@ <outputs> <data type="data" format="text" name="output" /> </outputs> - <tests> + <!--<tests> <test> <param name="input" value="test.owl"/> <param name="query" value="?p:OBJECTPROPERTY SELECT Transitive ?p "/> @@ -48,7 +48,7 @@ <param name="answer_format" value="URIfragment"/> <output name="out_file" file="query_result"/> </test> - </tests> + </tests>--> <help> **About OPPL-Query-Galaxy** |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/query.xml --- a/OPPL/query.xml Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/query.xml Mon Aug 20 11:39:56 2012 +0200 |
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@@ -3,10 +3,10 @@ <!-- DEFAULT SETTINGS --> - <!-- For big ontologies I use -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> + <!-- For big ontologies I use -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 If that's too much for your machine simply delete or modify at will, but since Galaxy is usually used in a server setting it makes sense to use a big chunk of memory --> <command> - java -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output + java -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output </command> <!-- FACT++ --> @@ -15,7 +15,7 @@ <!-- Using this setting doesn't upset the rest of the reasoners so you may as well leave it on if you plan to switch between FaCT++, Pellet and HermiT --> <!--<command> - java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx7000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output + java -Djava.library.path=${__tool_data_path__}/shared/jars/FaCT++-linux-v1.5.2/64bit -Xmx3000M -Xms250M -DentityExpansionLimit=1000000000 -jar ${__tool_data_path__}/shared/jars/query.jar $ontology $reasoner $answer_type $answer_format "$query" > $output </commadn>--> @@ -44,7 +44,7 @@ <outputs> <data type="data" format="text" name="output" /> </outputs> - <tests> + <!--<tests> <test> <param name="input" value="OWLQueryGalaxyTest.owl"/> <param name="query" value="p some d"/> @@ -53,7 +53,7 @@ <param name="answer_format" value="URIfragment"/> <output name="out_file" file="query_result"/> </test> - </tests> + </tests>--> <help> **About Query-Galaxy** @@ -62,7 +62,7 @@ **Formats** - Inference-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 output is a list of terms. + Query-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 output is a list of terms. **Contact** |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/src/GalaxyOWLAPI.java --- a/OPPL/src/GalaxyOWLAPI.java Thu Aug 02 09:22:57 2012 +0200 +++ b/OPPL/src/GalaxyOWLAPI.java Mon Aug 20 11:39:56 2012 +0200 |
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@@ -49,6 +49,7 @@ import org.semanticweb.owlapi.util.InferredSubDataPropertyAxiomGenerator; import org.semanticweb.owlapi.util.InferredSubObjectPropertyAxiomGenerator; import org.semanticweb.owlapi.util.OWLEntityRenamer; +import org.semanticweb.owlapi.util.OWLOntologyImportsClosureSetProvider; import org.semanticweb.owlapi.util.OWLOntologyMerger; import org.semanticweb.owlapi.util.SimpleShortFormProvider; import org.semanticweb.owlapi.vocab.OWL2Datatype; @@ -62,7 +63,7 @@ /** * A wrapper of the OWL API * - * @author Mikel Ega��a Aranguren + * @author Mikel Egana Aranguren */ public class GalaxyOWLAPI { private OWLOntologyManager manager; @@ -109,10 +110,13 @@ reasonerFactory = new Reasoner.ReasonerFactory(); reasoner = reasonerFactory.createReasoner(ontology); } - public void merge () throws OWLOntologyCreationException{ + public void merge (String ontologyIRI) throws OWLOntologyCreationException, OWLOntologyStorageException{ OWLOntologyMerger merger = new OWLOntologyMerger(manager); - IRI mergedOntologyIRI = IRI.create("http://oeg-upm.net/oppl_galaxy/merged.owl"); +// OWLOntologyMerger merger = new OWLOntologyMerger(new OWLOntologyImportsClosureSetProvider(manager, ontology)); + IRI mergedOntologyIRI = IRI.create(ontologyIRI); +// OWLOntology merged_ontology = merger.createMergedOntology(manager, mergedOntologyIRI); ontology = merger.createMergedOntology(manager, mergedOntologyIRI); +// manager.saveOntology(ontology, new RDFXMLOntologyFormat(), new SystemOutDocumentTarget()); } public OWLClassExpression parseMOSClassExpression (String expr) throws ParserException{ |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/src/MergeImportedOntologies.java --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/src/MergeImportedOntologies.java Mon Aug 20 11:39:56 2012 +0200 |
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@@ -0,0 +1,39 @@ +package es.upm.cbgp.opplquery.oppl.galaxy; + +import java.io.IOException; + +import org.semanticweb.owlapi.model.OWLOntologyCreationException; +import org.semanticweb.owlapi.model.OWLOntologyStorageException; + +import es.upm.fi.dia.oeg.oppl.galaxy.GalaxyOWLAPI; + +public class MergeImportedOntologies { + + /** + * @param args + * @throws OWLOntologyCreationException + * @throws IOException + * @throws OWLOntologyStorageException + */ + public static void main(String[] args) throws OWLOntologyCreationException, OWLOntologyStorageException, IOException { + String OWLFilePath = args [0]; + String MergedOntologyNewURI = args [1]; +// String OWLFilePath = "/home/mikel/UPM/OPPL_galaxy/OPPL/OPPL/test-data/ontology/imports/merge_test.owl"; +// String MergedOntologyNewURI = "http://cbgp.upm.es/merged.owl"; + + // Create the manager + GalaxyOWLAPI galaxyowlapi = new GalaxyOWLAPI(); + + // Load the main ontology and hope for the imported URIs to be resolvable + galaxyowlapi.loadMainOntology(OWLFilePath); + + // Merge and save + + if(MergedOntologyNewURI.isEmpty()){ + MergedOntologyNewURI = "http://cbgp.upm.es/BiologicalInformatics/OPPLGalaxy/merged.owl"; + } + + galaxyowlapi.merge(MergedOntologyNewURI); + galaxyowlapi.saveOntology(true); + } +} |
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diff -r 6c25e717c896 -r c9e01f86b07c OPPL/test-data/ontology/imports/merge.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/test-data/ontology/imports/merge.owl Mon Aug 20 11:39:56 2012 +0200 |
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b'@@ -0,0 +1,8824 @@\n+<?xml version="1.0"?>\n+<rdf:RDF xmlns="http://cbgp.upm.es/merged.owl#"\n+ xml:base="http://cbgp.upm.es/merged.owl"\n+ xmlns:wine="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#"\n+ xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"\n+ xmlns:food="http://www.w3.org/TR/2003/PR-owl-guide-20031209/food#"\n+ xmlns:pizza="http://www.co-ode.org/ontologies/pizza/pizza.owl#"\n+ xmlns:owl="http://www.w3.org/2002/07/owl#"\n+ xmlns:xsd="http://www.w3.org/2001/XMLSchema#"\n+ xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"\n+ xmlns:merge_test="http://www.cbgp.upm.es/merge_test.owl#">\n+ <owl:Ontology rdf:about="http://cbgp.upm.es/merged.owl"/>\n+ \n+\n+\n+ <!-- \n+ ///////////////////////////////////////////////////////////////////////////////////////\n+ //\n+ // Annotation properties\n+ //\n+ ///////////////////////////////////////////////////////////////////////////////////////\n+ -->\n+\n+ \n+\n+\n+ <!-- \n+ ///////////////////////////////////////////////////////////////////////////////////////\n+ //\n+ // Datatypes\n+ //\n+ ///////////////////////////////////////////////////////////////////////////////////////\n+ -->\n+\n+ \n+\n+\n+ <!-- \n+ ///////////////////////////////////////////////////////////////////////////////////////\n+ //\n+ // Object Properties\n+ //\n+ ///////////////////////////////////////////////////////////////////////////////////////\n+ -->\n+\n+ \n+\n+\n+ <!-- http://www.cbgp.upm.es/merge_test.owl#p -->\n+\n+ <owl:ObjectProperty rdf:about="http://www.cbgp.upm.es/merge_test.owl#p"/>\n+ \n+\n+\n+ <!-- http://www.co-ode.org/ontologies/pizza/pizza.owl#hasBase -->\n+\n+ <owl:ObjectProperty rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#hasBase">\n+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>\n+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#InverseFunctionalProperty"/>\n+ <rdfs:domain rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#Pizza"/>\n+ <rdfs:range rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#PizzaBase"/>\n+ <rdfs:subPropertyOf rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#hasIngredient"/>\n+ <owl:inverseOf rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#isBaseOf"/>\n+ </owl:ObjectProperty>\n+ \n+\n+\n+ <!-- http://www.co-ode.org/ontologies/pizza/pizza.owl#hasCountryOfOrigin -->\n+\n+ <owl:ObjectProperty rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#hasCountryOfOrigin"/>\n+ \n+\n+\n+ <!-- http://www.co-ode.org/ontologies/pizza/pizza.owl#hasIngredient -->\n+\n+ <owl:ObjectProperty rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#hasIngredient">\n+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#TransitiveProperty"/>\n+ <rdfs:comment xml:lang="en">NB Transitive - the ingredients of ingredients are ingredients of the whole</rdfs:comment>\n+ <rdfs:domain rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#Food"/>\n+ <rdfs:range rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#Food"/>\n+ <owl:inverseOf rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#isIngredientOf"/>\n+ </owl:ObjectProperty>\n+ \n+\n+\n+ <!-- http://www.co-ode.org/ontologies/pizza/pizza.owl#hasSpiciness -->\n+\n+ <owl:ObjectProperty rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#hasSpiciness">\n+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#FunctionalProperty"/>\n+ <rdfs:comment xml:lang="en">A property created to be used with the ValuePartition - Spiciness.</rdfs:comment>\n+ <rdfs:range rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#Spiciness"/>\n+ </owl:ObjectProperty>\n+ \n+\n+\n+ <!-- http://www.co-ode.org/ontologies/pizza/pizza.owl#hasTopping -->\n+\n+ <owl:ObjectProperty rdf:about="http://www.co-ode.org/ontologies/'..b'//www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Foxen"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#GaryFarrell"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#KalinCellars"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#KathrynKennedy"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#LaneTanner"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Longridge"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Marietta"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#McGuinnesso"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#MountEdenVineyard"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Mountadam"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#PageMillWinery"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#PeterMccoy"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#PulignyMontrachet"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#SantaCruzMountainVineyard"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#SaucelitoCanyon"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#SchlossRothermel"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#SchlossVolrad"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#SeanThackrey"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Selaks"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#SevreEtMaine"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#StGenevieve"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Stonleigh"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Taylor"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Ventana"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#WhitehallLane"/>\n+ </owl:distinctMembers>\n+ </rdf:Description>\n+ <rdf:Description>\n+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AllDifferent"/>\n+ <owl:distinctMembers rdf:parseType="Collection">\n+ <rdf:Description rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#America"/>\n+ <rdf:Description rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#England"/>\n+ <rdf:Description rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#France"/>\n+ <rdf:Description rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#Germany"/>\n+ <rdf:Description rdf:about="http://www.co-ode.org/ontologies/pizza/pizza.owl#Italy"/>\n+ </owl:distinctMembers>\n+ </rdf:Description>\n+ <rdf:Description>\n+ <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AllDifferent"/>\n+ <owl:distinctMembers rdf:parseType="Collection">\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#OffDry"/>\n+ <rdf:Description rdf:about="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine#Sweet"/>\n+ </owl:distinctMembers>\n+ </rdf:Description>\n+</rdf:RDF>\n+\n+\n+\n+<!-- Generated by the OWL API (version 3.2.4.1806) http://owlapi.sourceforge.net -->\n+\n' |
b |
diff -r 6c25e717c896 -r c9e01f86b07c OPPL/test-data/ontology/imports/merge_test.owl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/OPPL/test-data/ontology/imports/merge_test.owl Mon Aug 20 11:39:56 2012 +0200 |
[ |
@@ -0,0 +1,74 @@ +<?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#" > +]> + + +<rdf:RDF xmlns="http://www.cbgp.upm.es/merge_test.owl#" + xml:base="http://www.cbgp.upm.es/merge_test.owl" + xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" + 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.cbgp.upm.es/merge_test.owl"> + <owl:imports rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl"/> + <owl:imports rdf:resource="http://www.w3.org/TR/2003/PR-owl-guide-20031209/wine"/> + </owl:Ontology> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Object Properties + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.cbgp.upm.es/merge_test.owl#p --> + + <owl:ObjectProperty rdf:about="http://www.cbgp.upm.es/merge_test.owl#p"/> + + + + <!-- + /////////////////////////////////////////////////////////////////////////////////////// + // + // Classes + // + /////////////////////////////////////////////////////////////////////////////////////// + --> + + + + + <!-- http://www.cbgp.upm.es/merge_test.owl#A --> + + <owl:Class rdf:about="http://www.cbgp.upm.es/merge_test.owl#A"> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="http://www.cbgp.upm.es/merge_test.owl#p"/> + <owl:someValuesFrom rdf:resource="http://www.co-ode.org/ontologies/pizza/pizza.owl#ValuePartition"/> + </owl:Restriction> + </rdfs:subClassOf> + <rdfs:subClassOf> + <owl:Restriction> + <owl:onProperty rdf:resource="http://www.cbgp.upm.es/merge_test.owl#p"/> + <owl:someValuesFrom rdf:resource="http://www.w3.org/TR/2003/PR-owl-guide-20031209/food#Wine"/> + </owl:Restriction> + </rdfs:subClassOf> + </owl:Class> +</rdf:RDF> + + + +<!-- Generated by the OWL API (version 3.3.1957) http://owlapi.sourceforge.net --> + |