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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 19:50:45 GMT
I can extract triples from this CSV and serialize to turtle, ntriples, trix
and json.
The barrier here is serializing this as rdfxml.
Specifically:

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



On Thu, Jan 8, 2015 at 11:45 AM, Lewis John Mcgibbney <
lewis.mcgibbney@gmail.com> wrote:

> 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*
>



-- 
*Lewis*

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