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Posted to dev@taverna.apache.org by "Matthias Koenig (JIRA)" <ji...@apache.org> on 2016/08/16 16:09:21 UTC
[jira] [Created] (TAVERNA-1008) Ontology links broken in robundle
Matthias Koenig created TAVERNA-1008:
----------------------------------------
Summary: Ontology links broken in robundle
Key: TAVERNA-1008
URL: https://issues.apache.org/jira/browse/TAVERNA-1008
Project: Apache Taverna
Issue Type: Bug
Components: Taverna Language
Affects Versions: language 0.15.1
Reporter: Matthias Koenig
Priority: Minor
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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