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  1. Apache Taverna
  2. TAVERNA-1008

Ontology links broken in robundle

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Details

    • Bug
    • Status: To Do
    • Minor
    • Resolution: Unresolved
    • language 0.15.1
    • None
    • Taverna Language
    • None

    Description

      When running
      src/test/java/org/apache/taverna/robundle/TestExample.java
      in taverna.robundle
      some of the ontologies cannot be resolved resulting in the following warnings and errors.
      It seems that the ontology URLs moved and must be updated accordingly.

      ```
      WARN (OntDocumentManager.java:1076) - An error occurred while attempting to read from http://purl.org/ao/core/. Msg was '404 - Not Found'.
      org.apache.jena.atlas.web.HttpException: 404 - Not Found
      at org.apache.jena.riot.web.HttpOp.exec(HttpOp.java:1107)
      at org.apache.jena.riot.web.HttpOp.execHttpGet(HttpOp.java:378)
      at org.apache.jena.riot.web.HttpOp.execHttpGet(HttpOp.java:413)
      at org.apache.jena.riot.system.stream.LocatorHTTP.performOpen(LocatorHTTP.java:42)
      at org.apache.jena.riot.system.stream.LocatorURL.open(LocatorURL.java:44)
      at org.apache.jena.riot.system.stream.StreamManager.openNoMapOrNull(StreamManager.java:139)
      at org.apache.jena.riot.system.stream.StreamManager.open(StreamManager.java:100)
      at org.apache.jena.riot.RDFDataMgr.open(RDFDataMgr.java:862)
      at org.apache.jena.riot.RDFDataMgr.open(RDFDataMgr.java:851)
      at org.apache.jena.riot.RDFDataMgr.parse(RDFDataMgr.java:683)
      at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:209)
      at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:142)
      at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:131)
      at org.apache.jena.riot.adapters.AdapterFileManager.readModelWorker(AdapterFileManager.java:282)
      at org.apache.jena.util.FileManager.readModel(FileManager.java:341)
      at org.apache.jena.util.FileManager.readModel(FileManager.java:325)
      at org.apache.jena.ontology.OntDocumentManager.read(OntDocumentManager.java:1062)
      at org.apache.jena.ontology.OntDocumentManager$1.readModel(OntDocumentManager.java:1032)
      at org.apache.jena.rdf.model.impl.ModelMakerImpl.getModel(ModelMakerImpl.java:104)
      at org.apache.jena.ontology.OntDocumentManager.fetchLoadedImportModel(OntDocumentManager.java:1029)
      at org.apache.jena.ontology.OntDocumentManager.fetchPossiblyCachedImportModel(OntDocumentManager.java:1001)
      at org.apache.jena.ontology.OntDocumentManager.loadImport(OntDocumentManager.java:974)
      at org.apache.jena.ontology.OntDocumentManager.loadImports(OntDocumentManager.java:768)
      at org.apache.jena.ontology.OntDocumentManager.loadImports(OntDocumentManager.java:706)
      at org.apache.jena.ontology.impl.OntModelImpl.loadImports(OntModelImpl.java:1964)
      at org.apache.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:2134)
      at org.apache.taverna.robundle.manifest.RDFToManifest.loadOntologyFromClasspath(RDFToManifest.java:322)
      at org.apache.taverna.robundle.manifest.RDFToManifest.loadBundle(RDFToManifest.java:250)
      at org.apache.taverna.robundle.manifest.RDFToManifest.loadOntologies(RDFToManifest.java:311)
      at org.apache.taverna.robundle.manifest.RDFToManifest.<init>(RDFToManifest.java:182)
      at org.apache.taverna.robundle.Bundle.readOrPopulateManifest(Bundle.java:114)
      at org.apache.taverna.robundle.Bundle.getManifest(Bundle.java:87)
      at org.apache.taverna.robundle.Bundle.close(Bundle.java:61)
      at org.apache.taverna.robundle.Bundle.close(Bundle.java:52)
      at org.cy3sbml.oven.ROBundle.roBundleTest(ROBundle.java:84)
      at org.cy3sbml.oven.ROBundle.main(ROBundle.java:108)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at com.intellij.rt.execution.application.AppMain.main(AppMain.java:147)
      ERROR (ErrorHandlerFactory.java:84) - [line: 1, col: 1 ] Content is not allowed in prolog.
      WARN (OntDocumentManager.java:1076) - An error occurred while attempting to read from http://purl.org/NET/dc_owl2dl/terms_od. Msg was '[line: 1, col: 1 ] Content is not allowed in prolog.'.
      org.apache.jena.riot.RiotException: [line: 1, col: 1 ] Content is not allowed in prolog.
      at org.apache.jena.riot.system.ErrorHandlerFactory$ErrorHandlerStd.fatal(ErrorHandlerFactory.java:136)
      at org.apache.jena.riot.lang.LangRDFXML$ErrorHandlerBridge.fatalError(LangRDFXML.java:252)
      at org.apache.jena.rdfxml.xmlinput.impl.ARPSaxErrorHandler.fatalError(ARPSaxErrorHandler.java:47)
      at org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.warning(XMLHandler.java:199)
      at org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.fatalError(XMLHandler.java:229)
      at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown Source)
      at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
      at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
      at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
      at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentScannerImpl$PrologDispatcher.dispatch(Unknown Source)
      at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
      at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
      at org.apache.xerces.parsers.DTDConfiguration.parse(Unknown Source)
      at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
      at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
      at org.apache.jena.rdfxml.xmlinput.impl.RDFXMLParser.parse(RDFXMLParser.java:150)
      at org.apache.jena.rdfxml.xmlinput.ARP.load(ARP.java:118)
      at org.apache.jena.riot.lang.LangRDFXML.parse(LangRDFXML.java:142)
      at org.apache.jena.riot.RDFParserRegistry$ReaderRIOTLang.read(RDFParserRegistry.java:175)
      at org.apache.jena.riot.RDFDataMgr.process(RDFDataMgr.java:905)
      at org.apache.jena.riot.RDFDataMgr.parse(RDFDataMgr.java:686)
      at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:209)
      at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:142)
      at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:131)
      at org.apache.jena.riot.adapters.AdapterFileManager.readModelWorker(AdapterFileManager.java:282)
      at org.apache.jena.util.FileManager.readModel(FileManager.java:341)
      at org.apache.jena.util.FileManager.readModel(FileManager.java:325)
      at org.apache.jena.ontology.OntDocumentManager.read(OntDocumentManager.java:1062)
      at org.apache.jena.ontology.OntDocumentManager$1.readModel(OntDocumentManager.java:1032)
      at org.apache.jena.rdf.model.impl.ModelMakerImpl.getModel(ModelMakerImpl.java:104)
      at org.apache.jena.ontology.OntDocumentManager.fetchLoadedImportModel(OntDocumentManager.java:1029)
      at org.apache.jena.ontology.OntDocumentManager.fetchPossiblyCachedImportModel(OntDocumentManager.java:1001)
      at org.apache.jena.ontology.OntDocumentManager.loadImport(OntDocumentManager.java:974)
      at org.apache.jena.ontology.OntDocumentManager.loadImports(OntDocumentManager.java:768)
      at org.apache.jena.ontology.OntDocumentManager.loadImports(OntDocumentManager.java:706)
      at org.apache.jena.ontology.impl.OntModelImpl.loadImports(OntModelImpl.java:1964)
      at org.apache.jena.ontology.impl.OntModelImpl.read(OntModelImpl.java:2134)
      at org.apache.taverna.robundle.manifest.RDFToManifest.loadOntologyFromClasspath(RDFToManifest.java:322)
      at org.apache.taverna.robundle.manifest.RDFToManifest.loadBundle(RDFToManifest.java:250)
      at org.apache.taverna.robundle.manifest.RDFToManifest.loadOntologies(RDFToManifest.java:311)
      at org.apache.taverna.robundle.manifest.RDFToManifest.<init>(RDFToManifest.java:182)
      at org.apache.taverna.robundle.Bundle.readOrPopulateManifest(Bundle.java:114)
      at org.apache.taverna.robundle.Bundle.getManifest(Bundle.java:87)
      at org.apache.taverna.robundle.Bundle.close(Bundle.java:61)
      at org.apache.taverna.robundle.Bundle.close(Bundle.java:52)
      at org.cy3sbml.oven.ROBundle.roBundleTest(ROBundle.java:84)
      at org.cy3sbml.oven.ROBundle.main(ROBundle.java:108)
      at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
      at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
      at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
      at java.lang.reflect.Method.invoke(Method.java:498)
      at com.intellij.rt.execution.application.AppMain.main(AppMain.java:147)
      ```

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            Unassigned Unassigned
            konigmatt Matthias Koenig
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            Dates

              Created:
              Updated: