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From Lewis John Mcgibbney <lewis.mcgibb...@gmail.com>
Subject Re: org.openrdf.rio.RDFHandlerException when attempting to parse CSV
Date Thu, 08 Jan 2015 19:45:03 GMT
Ah OK, I think that this is our problem.

This only happens under the following conditions

OUTPUT FORMAT: RDFXML
VALIDATION: Validate + Fix
REPORT: Yes
ANNOTATE: Yes

I am going to experiment a bit more with where this goes wrong.


On Thu, Jan 8, 2015 at 11:38 AM, Lewis John Mcgibbney <
lewis.mcgibbney@gmail.com> wrote:

> Hi Folks,
> With the Any23 webservice [0] when I try to extract triples from the
> following CSV [1], I get the following stack trace
>
> <?xml version="1.0" encoding="UTF-8" ?>
> <report>
> <message>Internal error.</message>
> <error>
> <![CDATA[
> java.lang.RuntimeException: Error while receiving triple http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvrow/0
http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvKeywordVersion:8.0
"Category"^^<http://www.w3.org/2001/XMLSchema#string>
> 	at org.apache.any23.extractor.ExtractionResultImpl.writeTriple(ExtractionResultImpl.java:163)
> 	at org.apache.any23.extractor.ExtractionResultImpl.writeTriple(ExtractionResultImpl.java:171)
> 	at org.apache.any23.extractor.csv.CSVExtractor.produceRowStatements(CSVExtractor.java:238)
> 	at org.apache.any23.extractor.csv.CSVExtractor.run(CSVExtractor.java:96)
> 	at org.apache.any23.extractor.csv.CSVExtractor.run(CSVExtractor.java:51)
> 	at org.apache.any23.extractor.SingleDocumentExtraction.runExtractor(SingleDocumentExtraction.java:462)
> 	at org.apache.any23.extractor.SingleDocumentExtraction.run(SingleDocumentExtraction.java:254)
> 	at org.apache.any23.Any23.extract(Any23.java:298)
> 	at org.apache.any23.Any23.extract(Any23.java:450)
> 	at org.apache.any23.servlet.WebResponder.runExtraction(WebResponder.java:114)
> 	at org.apache.any23.servlet.Servlet.doGet(Servlet.java:79)
> 	at javax.servlet.http.HttpServlet.service(HttpServlet.java:618)
> 	at javax.servlet.http.HttpServlet.service(HttpServlet.java:725)
> 	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:301)
> 	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
> 	at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
> 	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239)
> 	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
> 	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
> 	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:106)
> 	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:503)
> 	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:136)
> 	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:74)
> 	at org.apache.catalina.valves.AbstractAccessLogValve.invoke(AbstractAccessLogValve.java:610)
> 	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:88)
> 	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:526)
> 	at org.apache.coyote.ajp.AbstractAjpProcessor.process(AbstractAjpProcessor.java:794)
> 	at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:652)
> 	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1575)
> 	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1533)
> 	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
> 	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
> 	at java.lang.Thread.run(Thread.java:745)
> Caused by: org.apache.any23.writer.TripleHandlerException: Error while receiving triple
http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvrow/0 http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvKeywordVersion:8.0
"Category"^^<http://www.w3.org/2001/XMLSchema#string>
> 	at org.apache.any23.filter.ExtractionContextBlocker.receiveTriple(ExtractionContextBlocker.java:106)
> 	at org.apache.any23.filter.IgnoreAccidentalRDFa.receiveTriple(IgnoreAccidentalRDFa.java:82)
> 	at org.apache.any23.writer.CompositeTripleHandler.receiveTriple(CompositeTripleHandler.java:89)
> 	at org.apache.any23.extractor.ExtractionResultImpl.writeTriple(ExtractionResultImpl.java:161)
> 	... 32 more
> Caused by: org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipeException:
Error while opening the triple handler
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.sendTriple(ExtractionContextBlocker.java:248)
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.receiveTriple(ExtractionContextBlocker.java:197)
> 	at org.apache.any23.filter.ExtractionContextBlocker.receiveTriple(ExtractionContextBlocker.java:104)
> 	... 35 more
> Caused by: org.apache.any23.writer.TripleHandlerException: Error while receiving triple
http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvrow/0 http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvKeywordVersion:8.0
"Category"^^<http://www.w3.org/2001/XMLSchema#string>
> 	at org.apache.any23.filter.ExtractionContextBlocker.receiveTriple(ExtractionContextBlocker.java:106)
> 	at org.apache.any23.filter.IgnoreTitlesOfEmptyDocuments.receiveTriple(IgnoreTitlesOfEmptyDocuments.java:62)
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.sendTriple(ExtractionContextBlocker.java:246)
> 	... 37 more
> Caused by: org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipeException:
Error while opening the triple handler
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.sendTriple(ExtractionContextBlocker.java:248)
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.receiveTriple(ExtractionContextBlocker.java:197)
> 	at org.apache.any23.filter.ExtractionContextBlocker.receiveTriple(ExtractionContextBlocker.java:104)
> 	... 39 more
> Caused by: org.apache.any23.writer.TripleHandlerException: Error while receiving triple
http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvrow/0 http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvKeywordVersion:8.0
"Category"^^<http://www.w3.org/2001/XMLSchema#string>
> 	at org.apache.any23.filter.ExtractionContextBlocker.receiveTriple(ExtractionContextBlocker.java:106)
> 	at org.apache.any23.filter.IgnoreAccidentalRDFa.receiveTriple(IgnoreAccidentalRDFa.java:82)
> 	at org.apache.any23.writer.CompositeTripleHandler.receiveTriple(CompositeTripleHandler.java:89)
> 	at org.apache.any23.writer.ReportingTripleHandler.receiveTriple(ReportingTripleHandler.java:96)
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.sendTriple(ExtractionContextBlocker.java:246)
> 	... 41 more
> Caused by: org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipeException:
Error while opening the triple handler
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.sendTriple(ExtractionContextBlocker.java:248)
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.receiveTriple(ExtractionContextBlocker.java:197)
> 	at org.apache.any23.filter.ExtractionContextBlocker.receiveTriple(ExtractionContextBlocker.java:104)
> 	... 45 more
> Caused by: org.apache.any23.writer.TripleHandlerException: Error while receiving triple:
http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvrow/0 http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvKeywordVersion:8.0
"Category"^^<http://www.w3.org/2001/XMLSchema#string> http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csv
> 	at org.apache.any23.writer.RDFWriterTripleHandler.receiveTriple(RDFWriterTripleHandler.java:96)
> 	at org.apache.any23.filter.ExtractionContextBlocker$ValvedTriplePipe.sendTriple(ExtractionContextBlocker.java:246)
> 	... 47 more
> Caused by: org.openrdf.rio.RDFHandlerException: Unable to create XML namespace-qualified
name for predicate: http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csvKeywordVersion:8.0
> 	at org.openrdf.rio.rdfxml.RDFXMLWriter.handleStatement(RDFXMLWriter.java:237)
> 	at org.apache.any23.writer.RDFWriterTripleHandler.receiveTriple(RDFWriterTripleHandler.java:93)
> 	... 48 more
> ]]>
> </error>
> <issueReport>
>
> The Any23 service is effectively running of of trunk. Therefore I am going
> to head over to the openrdf.rio lists and check this out out. I just wanted
> to post it here first though.
> Thanks
> Lewis
>
> [0] http://any23-vm.apache.org
> [1]
> http://gcmdservices.gsfc.nasa.gov/static/kms/sciencekeywords/sciencekeywords.csv
>
> --
> *Lewis*
>



-- 
*Lewis*

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