Problem retrieving protein throug uk.ac.ebi.intact.uniprot.service
Leonardo Briganti
we have a problem when inserting new protein,like Q96EU7, on MINT
it gaves us this error
java.lang.IllegalArgumentException: Cannot get id from cross
reference: neXtProtImpl [ NX_Q96EU7:-; ]
uk.ac.ebi.intact.uniprot.service.crossRefAdapter.ReflectionCrossReferenceBuilder.build(ReflectionCrossReferenceBuilder.java:184)
uk.ac.ebi.intact.uniprot.service.UniprotRemoteService.convert(UniprotRemoteService.java:381)
uk.ac.ebi.intact.uniprot.service.UniprotRemoteService.processCrossReference(UniprotRemoteService.java:388)
uk.ac.ebi.intact.uniprot.service.UniprotRemoteService.buildUniprotProtein(UniprotRemoteService.java:248)
uk.ac.ebi.intact.uniprot.service.UniprotRemoteService.retrieve(UniprotRemoteService.java:80)
uk.ac.ebi.intact.uniprot.service.UniprotRemoteService.retrieve(UniprotRemoteService.java:56)
uk.ac.ebi.intact.util.protein.ProteinServiceImpl.retrieveFromUniprot(ProteinServiceImpl.java:1397)
uk.ac.ebi.intact.util.protein.ProteinServiceImpl.retrieve(ProteinServiceImpl.java:148)
it.uniroma2.bio.mint.mint.helpers.MintProteinHelper.safeRetrieveProtein(MintProteinHelper.java:214)
it.uniroma2.bio.mint.mint.helpers.MintProteinHelper.getProteinsFromUniprot(MintProteinHelper.java:183)
probably like here it cannot find method for neXtProt access or something else
011-04-04 14:31:34,994 DEBUG
[uk.ac.ebi.intact.uniprot.service.crossRefAdapter.ReflectionCrossReferenceBuilder]
getMimAccessionNumber returned a class
uk.ac.ebi.kraken.model.uniprot.dbx.mim.MimAccessionNumberImpl
2011-04-04 14:31:34,994 DEBUG
[uk.ac.ebi.intact.uniprot.service.crossRefAdapter.ReflectionCrossReferenceBuilder]
Converting uk.ac.ebi.kraken.model.uniprot.dbx.nextprot.neXtProtImpl
into a UniprotCrossReference.
2011-04-04 14:31:34,994 DEBUG
[uk.ac.ebi.intact.uniprot.service.crossRefAdapter.ReflectionCrossReferenceBuilder]
Trying to find the method giving access to neXtProt's ID via
reflection.
2011-04-04 14:31:34,998 WARN
[org.apache.struts.chain.commands.AbstractExceptionHandler] Unhandled
exception
com.sun.tools.ws.processor.ProcessorException: [failed to localize]
Problem trying to update proteins using Uniprot AC:
Q96EU7(java.lang.IllegalArgumentException: Cannot get id from cross
reference: neXtProtImpl [ NX_Q96EU7:-; ])
at it.uniroma2.bio.mint.mint.helpers.MintProteinHelper.safeRetrieveProtein(MintProteinHelper.java:232)
at it.uniroma2.bio.mint.mint.helpers.MintProteinHelper.getProteinsFromUniprot(MintProteinHelper.java:183)
at it.uniroma2.bio.mint.mint.helpers.MintProteinHelper.getProteins(MintProteinHelper.java:119)
at it.uniroma2.bio.mint.mint.web.curation.action.SubmitAction.execute(SubmitAction.java:51)
at org.apache.struts.chain.commands.servlet.ExecuteAction.execute(ExecuteAction.java:58)
at org.apache.struts.chain.commands.AbstractExecuteAction.execute(AbstractExecuteAction.java:67)
at org.apache.struts.chain.commands.ActionCommandBase.execute(ActionCommandBase.java:51)
at org.apache.commons.chain.impl.ChainBase.execute(ChainBase.java:191)
at org.apache.commons.chain.generic.LookupCommand.execute(LookupCommand.java:305)
at org.apache.commons.chain.impl.ChainBase.execute(ChainBase.java:191)
at org.apache.struts.chain.ComposableRequestProcessor.process(ComposableRequestProcessor.java:283)
at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:462)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:710)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:803)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at it.uniroma2.bio.mint.mint.web.filters.CatchExceptionRequestFilter.doFilter(CatchExceptionRequestFilter.java:68)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at it.uniroma2.bio.mint.mint.web.filters.MintTransactionFilter.doFilter(MintTransactionFilter.java:119)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.jboss.web.tomcat.filters.ReplyHeaderFilter.doFilter(ReplyHeaderFilter.java:96)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:230)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:175)
at org.jboss.web.tomcat.security.SecurityAssociationValve.invoke(SecurityAssociationValve.java:182)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:524)
at org.jboss.web.tomcat.security.JaccContextValve.invoke(JaccContextValve.java:84)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.jboss.web.tomcat.service.jca.CachedConnectionValve.invoke(CachedConnectionValve.java:157)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:262)
at org.apache.coyote.http11.Http11AprProcessor.process(Http11AprProcessor.java:856)
at org.apache.coyote.http11.Http11AprProtocol$Http11ConnectionHandler.process(Http11AprProtocol.java:566)
at org.apache.tomcat.util.net.AprEndpoint$Worker.run(AprEndpoint.java:1508)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.IllegalArgumentException: Cannot get id from
cross reference: neXtProtImpl [ NX_Q96EU7:-; ]
at uk.ac.ebi.intact.uniprot.service.crossRefAdapter.ReflectionCrossReferenceBuilder.build(ReflectionCrossReferenceBuilder.java:184)
at uk.ac.ebi.intact.uniprot.service.UniprotRemoteService.convert(UniprotRemoteService.java:381)
Thanks to all
Leonardo
MINT GROUP