VIVO-1024: RiotParseException loading instance data

[chenejac]

Justin Littman (Migrated from VIVO-1024) said:

Steps to reproduce:

1. Goto Add or Remove RDF Data admin page.
2. Select Add instance data, Turtle serialization, and provide the attached file.
3. Click submit.

Expected result: RDF upload successful.

Actual result: Could not load from file: edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException: org.apache.jena.riot.RiotParseException: [line: 1, col: 1 ] Bad character encoding and in the logs: 2015-04-21 17:02:26,011 ERROR [IndexingChangeListener] Failed to parse triple http://vivo.gwu.edu/individual/per-9281502e56ea7b05196e47c556c9ba08 http://vivoweb.org/ontology/core#overview "Ernest Forman is a Professor of Decision Sciences at The George Washington University's School of Business. He has extensive experience with executive decision-making methodologies, resource allocation, project portfolio management, risk analysis and risk management, operations management and statistics. He received one of the first United States patents issued for computer software and designed Expert Choice, a computerized implementation of the Analytic Hierarchy Process, which is now used extensively throughout the United States as well as in Canada, South and Central America, Europe, the Middle East, and the Far East. Applications include a wide range of government and business decisions involving tradeoffs among conflicting objectives, some quantitative, some qualitative. Examples of such problems include government policy, allocation of R&D funds, cost/benefit analysis, employee evaluation, setting corporate priorities, group decision-making, conflict resolution and strategic planning. Dr. Forman's expertise is widely recognized and he is frequently consulted by organizations such as IBM, MERCK, John Deere, Ford, AOL, NIST, Boeing, GAO, IRS, NASA, CIA, DoD, state, and local governments.\nDr. Forman holds six U.S. Patents related to decision-making and is co-founder of Expert Choice Inc. In addition to developing Expert Choice, Dr. Forman is the creator of other commercial software products including, Expert Choice Comparion, Riskion, The Accountant, The Business Accountant, and Stratatree. He has conducted national and international seminars on decision support, group decision-making, resource allocation, data base management, distributed processing, and forecasting. \nDr. Forman has authored Decision by Objectives, and has co-authored An Analytic Framework for Marketing Decisions, The Hierarchon - A Dictionary of Hierarchies, and Advances in Telematics. He is engaged in research, development and writing about the theory of measurement, evaluation and choice; corporate and public sector applications of decision analysis; strategic planning; resource allocation; conflict resolution and project portfolio management. \nPrior to joining the faculty of George Washington University, Dr. Forman was a member of the technical staff of the MITRE Corporation, where he conducted seminal research and development of a distributed data base system and evaluated remote utilization of a variety of unique computer resources on the experimental ARPA computer network (forerunner of the INTERNET).  Other research areas at MITRE included computer performance evaluation, computer security, source data automation, and data base management systems. Dr. Forman was a Lieutenant in the United States Navy and was selected by Admiral Rickover to serve at the U.S. Naval Nuclear Power School, where he taught mathematics and electrical engineering. Education\nBachelor of Science degree in electrical engineering from the University of Rochester, \nMaster of Science in Management Science from Johns Hopkins University, Doctor of Science in Operations Research from The George Washington University.\n" . org.apache.jena.riot.RiotParseException: [line: 1, col: 1 ] Bad character encoding at org.apache.jena.riot.tokens.TokenizerText.hasNext(TokenizerText.java:105) at org.apache.jena.atlas.iterator.PeekIterator.fill(PeekIterator.java:50) at org.apache.jena.atlas.iterator.PeekIterator.(PeekIterator.java:44) at org.apache.jena.riot.lang.LangEngine.(LangEngine.java:45) at org.apache.jena.riot.lang.LangBase.(LangBase.java:32) at org.apache.jena.riot.lang.LangNTuple.(LangNTuple.java:61) at org.apache.jena.riot.lang.LangNTriples.(LangNTriples.java:42) at org.apache.jena.riot.RiotReader.createParserNTriples(RiotReader.java:360) at org.apache.jena.riot.RiotReader.createParserNTriples(RiotReader.java:354) at org.apache.jena.riot.RiotReader.createIteratorTriples(RiotReader.java:244) at edu.cornell.mannlib.vitro.webapp.searchindex.IndexingChangeListener.parseTriple(IndexingChangeListener.java:147) at edu.cornell.mannlib.vitro.webapp.searchindex.IndexingChangeListener.addedStatement(IndexingChangeListener.java:116) at edu.cornell.mannlib.vitro.webapp.utils.developer.listeners.DeveloperDisabledChangeListener.addedStatement(DeveloperDisabledChangeListener.java:35) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl.notifyListeners(RDFServiceImpl.java:119) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.ListeningGraph.performAdd(ListeningGraph.java:60) at com.hp.hpl.jena.graph.GraphUtil.addIteratorWorker(GraphUtil.java:194) at com.hp.hpl.jena.graph.GraphUtil.addInto(GraphUtil.java:183) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:208) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:202) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.operateOnModel(RDFServiceJena.java:117) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.notifyListenersOfChanges(RDFServiceJena.java:99) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.sdb.RDFServiceSDB.changeSetUpdate(RDFServiceSDB.java:90) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:35) at edu.cornell.mannlib.vitro.webapp.controller.jena.RDFUploadController.addUsingRDFService(RDFUploadController.java:239) at edu.cornell.mannlib.vitro.webapp.controller.jena.RDFUploadController.doPost(RDFUploadController.java:147) at javax.servlet.http.HttpServlet.service(HttpServlet.java:648) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) 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 edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:108) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:99) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:31) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:56) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:60) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.produceBasicResponse(CachingResponseFilter.java:321) at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.doFilter(CachingResponseFilter.java:115) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:62) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:34) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:64) 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:502) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) 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:518) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1091) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:668) at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:223) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1517) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1474) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) 2015-04-21 17:02:26,033 ERROR [RDFServiceSDB] org.apache.jena.riot.RiotParseException: [line: 1, col: 1 ] Bad character encoding org.apache.jena.riot.RiotParseException: [line: 1, col: 1 ] Bad character encoding at org.apache.jena.riot.tokens.TokenizerText.hasNext(TokenizerText.java:105) at org.apache.jena.atlas.iterator.PeekIterator.fill(PeekIterator.java:50) at org.apache.jena.atlas.iterator.PeekIterator.(PeekIterator.java:44) at org.apache.jena.riot.lang.LangEngine.(LangEngine.java:45) at org.apache.jena.riot.lang.LangBase.(LangBase.java:32) at org.apache.jena.riot.lang.LangNTuple.(LangNTuple.java:61) at org.apache.jena.riot.lang.LangNTriples.(LangNTriples.java:42) at org.apache.jena.riot.RiotReader.createParserNTriples(RiotReader.java:360) at org.apache.jena.riot.RiotReader.createParserNTriples(RiotReader.java:354) at org.apache.jena.riot.RiotReader.createIteratorTriples(RiotReader.java:244) at edu.cornell.mannlib.vitro.webapp.searchindex.IndexingChangeListener.parseTriple(IndexingChangeListener.java:147) at edu.cornell.mannlib.vitro.webapp.searchindex.IndexingChangeListener.addedStatement(IndexingChangeListener.java:116) at edu.cornell.mannlib.vitro.webapp.utils.developer.listeners.DeveloperDisabledChangeListener.addedStatement(DeveloperDisabledChangeListener.java:35) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.RDFServiceImpl.notifyListeners(RDFServiceImpl.java:119) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.ListeningGraph.performAdd(ListeningGraph.java:60) at com.hp.hpl.jena.graph.GraphUtil.addIteratorWorker(GraphUtil.java:194) at com.hp.hpl.jena.graph.GraphUtil.addInto(GraphUtil.java:183) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:208) at com.hp.hpl.jena.rdf.model.impl.ModelCom.add(ModelCom.java:202) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.operateOnModel(RDFServiceJena.java:117) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.RDFServiceJena.notifyListenersOfChanges(RDFServiceJena.java:99) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.jena.sdb.RDFServiceSDB.changeSetUpdate(RDFServiceSDB.java:90) at edu.cornell.mannlib.vitro.webapp.rdfservice.impl.logging.LoggingRDFService.changeSetUpdate(LoggingRDFService.java:35) at edu.cornell.mannlib.vitro.webapp.controller.jena.RDFUploadController.addUsingRDFService(RDFUploadController.java:239) at edu.cornell.mannlib.vitro.webapp.controller.jena.RDFUploadController.doPost(RDFUploadController.java:147) at javax.servlet.http.HttpServlet.service(HttpServlet.java:648) at javax.servlet.http.HttpServlet.service(HttpServlet.java:729) at edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet.service(VitroHttpServlet.java:71) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:291) 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 edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doNonDisplayPage(PageRoutingFilter.java:108) at edu.cornell.mannlib.vitro.webapp.filters.PageRoutingFilter.doFilter(PageRoutingFilter.java:99) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.ClickjackFilter.doFilter(ClickjackFilter.java:31) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.RequestModelsPrep.doFilter(RequestModelsPrep.java:56) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.URLRewriterFilter.doFilter(URLRewriterFilter.java:38) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.JSessionStripFilter.doFilter(JSessionStripFilter.java:60) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.produceBasicResponse(CachingResponseFilter.java:321) at edu.cornell.mannlib.vitro.webapp.filters.CachingResponseFilter.doFilter(CachingResponseFilter.java:115) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.i18n.selection.LocaleSelectionFilter.doFilter(LocaleSelectionFilter.java:62) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.CharsetEncodingFilter.doFilter(CharsetEncodingFilter.java:34) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.SessionTimeoutLimitingFilter.doFilter(SessionTimeoutLimitingFilter.java:39) at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:239) at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206) at edu.cornell.mannlib.vitro.webapp.filters.StartupStatusDisplayFilter.doFilter(StartupStatusDisplayFilter.java:64) 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:502) at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:142) at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:79) 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:518) at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1091) at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:668) at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:223) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1517) at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:1474) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615) at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) at java.lang.Thread.run(Thread.java:745) 2015-04-21 17:02:26,040 WARN [TransactionHandlerSDB] abort: Not in a transaction

Additional notes:

1. This defect can also be reproduced loading via the SPARQL Update interface.
2. This defect cannot be reproduced in version 1.7.

[chenejac]

Jim Blake said:

Checking to see whether this duplicates VIVO-1018.

[chenejac]

Jim Blake said:

Justin -- the symptoms are the same as VIVO-1018, right down to the stack trace. I'll try ingesting your file, but I think we're good.

[chenejac]

Jim Blake said:

I was able to reproduce this problem on 1.8 rc1, but it was corrected in rc3.

[chenejac]

Justin Littman said:

Thanks Jim!