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https://issues.apache.org/jira/browse/TAVERNA-1027?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=16316289#comment-16316289
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Stian Soiland-Reyes commented on TAVERNA-1027:
----------------------------------------------
My mistake in Jira :) Are you sure "::" would be legal anyway?
That's what I would have thought.
But rules seems stricter when parsing RDF/XML as it uses a differently
configured IRIFactory and deliberately bails out on the IANA violation.
I'll try to make a separate test and report on dev@jena
to see if this is intentional or not.
Hmm.. perhaps the classpath didn't fully update? In Eclipse it seemed
like it only had the new Jena version, but of course Maven might think
otherwise. Will triple-check with mvn help
--
Stian Soiland-Reyes
The University of Manchester
http://www.esciencelab.org.uk/
http://orcid.org/0000-0001-9842-9718
> COMBINE parsing fails with updated Jena - app URI scheme not supported
> ----------------------------------------------------------------------
>
> Key: TAVERNA-1027
> URL: https://issues.apache.org/jira/browse/TAVERNA-1027
> Project: Apache Taverna
> Issue Type: Bug
> Components: Taverna Language
> Affects Versions: language 0.16.0
> Reporter: Stian Soiland-Reyes
> Assignee: Stian Soiland-Reyes
>
> I'm trying to update taverna-language to use Jena 3.6.0 (already updated in
> taverna-maven-parent 3-incubating-SNAPSHOT), but then taverna-robundle fails
> a test:
> "Resolving against bad URI
> <app:://4a8a0ff8-eab0-3930-8257-017dec3a8356/manifest0.xml>"
> This seems to be because Jena's IRI support now fails for non-IANA URI
> schemes like "app" when parsing RDF/XML - as within the COMBINE archive's
> metadata.
> In RO Bundle we use UUID-based [app: URL
> scheme|https://www.w3.org/TR/app-uri/] as specified by W3C to represent files
> within a Research Object zip archive.
> That means naturally when parsing RDF files within that archive that we'll
> use URIs like app://4a8a0ff8-eab0-3930-8257-017dec3a8356/manifest0.xml as a
> base URI, so that a reference "fred.doc" becomes
> "app://4a8a0ff8-eab0-3930-8257-017dec3a8356/fred.xml"
> A workaround would be to replace "app" with "file", pretending the UUID is a
> hostname, but somehow this also fails with Jena as it mangles
> "file://4a8a0ff8-eab0-3930-8257-017dec3a8356/fred.xml" into
> file:///4a8a0ff8-eab0-3930-8257-017dec3a8356/fred.xml after parsing - so it
> becomes tricky tyo ask the RDF model about fred.xml afterwards.
> A workaround to the workaround would be to use host-less file:/// URIs --
> another to drop the UUID and pretend file:/// is the root of the local file
> system rather than the root of the zip archive. (This would also then
> correctly support relative URIs like /fred.xml although those don't occur in
> COMBINE archive)
> Stack trace:
> {code}
> Jan 05, 2018 3:45:58 PM
> org.apache.taverna.robundle.manifest.combine.CombineManifest findAnnotations
> WARNING: Can't parse /manifest0.xml
> org.apache.jena.riot.RiotException: [line: 3, col: 48] {E214} Resolving
> against bad URI <app://4a8a0ff8-eab0-3930-8257-017dec3a8356/manifest0.xml>:
> <./BorisEJB.xml>
> at
> org.apache.jena.riot.system.ErrorHandlerFactory$ErrorHandlerStd.error(ErrorHandlerFactory.java:140)
> at
> org.apache.jena.riot.lang.ReaderRIOTRDFXML$ErrorHandlerBridge.error(ReaderRIOTRDFXML.java:254)
> at
> org.apache.jena.rdfxml.xmlinput.impl.ARPSaxErrorHandler.error(ARPSaxErrorHandler.java:37)
> at
> org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.warning(XMLHandler.java:196)
> at
> org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.warning(XMLHandler.java:173)
> at
> org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.warning(XMLHandler.java:168)
> at
> org.apache.jena.rdfxml.xmlinput.impl.XMLBaselessContext.checkBaseUse(XMLBaselessContext.java:108)
> at
> org.apache.jena.rdfxml.xmlinput.impl.AbsXMLContext.resolveAsURI(AbsXMLContext.java:131)
> at
> org.apache.jena.rdfxml.xmlinput.impl.AbsXMLContext.resolveAsURI(AbsXMLContext.java:123)
> at
> org.apache.jena.rdfxml.xmlinput.impl.URIReference.resolve(URIReference.java:166)
> at
> org.apache.jena.rdfxml.xmlinput.states.WantDescription.startElement(WantDescription.java:63)
> at
> org.apache.jena.rdfxml.xmlinput.impl.XMLHandler.startElement(XMLHandler.java:111)
> at org.apache.xerces.parsers.AbstractSAXParser.startElement(Unknown
> Source)
> at org.apache.xerces.impl.XMLNamespaceBinder.handleStartElement(Unknown
> Source)
> at org.apache.xerces.impl.XMLNamespaceBinder.startElement(Unknown
> Source)
> at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown
> Source)
> at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.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.ReaderRIOTRDFXML.parse(ReaderRIOTRDFXML.java:135)
> at
> org.apache.jena.riot.lang.ReaderRIOTRDFXML.read(ReaderRIOTRDFXML.java:79)
> at org.apache.jena.riot.RDFParser.read(RDFParser.java:334)
> at org.apache.jena.riot.RDFParser.parseNotUri(RDFParser.java:324)
> at org.apache.jena.riot.RDFParser.parse(RDFParser.java:273)
> at
> org.apache.jena.riot.RDFParserBuilder.parse(RDFParserBuilder.java:498)
> at
> org.apache.jena.riot.RDFDataMgr.parseFromInputStream(RDFDataMgr.java:870)
> at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:268)
> at org.apache.jena.riot.RDFDataMgr.read(RDFDataMgr.java:254)
> at
> org.apache.taverna.robundle.manifest.combine.CombineManifest.parseRDF(CombineManifest.java:240)
> at
> org.apache.taverna.robundle.manifest.combine.CombineManifest.findAnnotations(CombineManifest.java:332)
> at
> org.apache.taverna.robundle.manifest.combine.CombineManifest.readCombineArchive(CombineManifest.java:465)
> at
> org.apache.taverna.robundle.Bundle.readOrPopulateManifest(Bundle.java:121)
> 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.apache.taverna.robundle.manifest.combine.TestCombineManifest.convertDirectoryMadnessZipped(TestCombineManifest.java:152)
> 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
> org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:47)
> at
> org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
> at
> org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:44)
> at
> org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
> at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:271)
> at
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:70)
> at
> org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:50)
> at org.junit.runners.ParentRunner$3.run(ParentRunner.java:238)
> at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:63)
> at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:236)
> at org.junit.runners.ParentRunner.access$000(ParentRunner.java:53)
> at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:229)
> at org.junit.runners.ParentRunner.run(ParentRunner.java:309)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.execute(JUnit4Provider.java:367)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.executeWithRerun(JUnit4Provider.java:274)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.executeTestSet(JUnit4Provider.java:238)
> at
> org.apache.maven.surefire.junit4.JUnit4Provider.invoke(JUnit4Provider.java:161)
> at
> org.apache.maven.surefire.booter.ForkedBooter.invokeProviderInSameClassLoader(ForkedBooter.java:290)
> at
> org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:242)
> at
> org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:121)
> {code}
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