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NPE for processPatentTXT #325

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lfoppiano opened this issue Jun 14, 2018 · 1 comment
Closed

NPE for processPatentTXT #325

lfoppiano opened this issue Jun 14, 2018 · 1 comment
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bug From Hemiptera and especially its suborder Heteroptera

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@lfoppiano
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I've been pointed out to this request: https://grobid.readthedocs.io/en/latest/Grobid-service/#citation-extraction-and-normalization-from-patents

which is failing with 500:

ERROR [2018-06-14 18:18:24,432] org.grobid.service.process.GrobidRestProcessString: An unexpected exception occurs. 
! java.lang.NullPointerException: null
! at org.grobid.service.process.GrobidRestProcessString.processCitationPatentTXT(GrobidRestProcessString.java:363)
! at org.grobid.service.GrobidRestService.processCitationPatentTXT_post(GrobidRestService.java:335)
! 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.glassfish.jersey.server.model.internal.ResourceMethodInvocationHandlerFactory$1.invoke(ResourceMethodInvocationHandlerFactory.java:81)
! at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher$1.run(AbstractJavaResourceMethodDispatcher.java:144)
! at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.invoke(AbstractJavaResourceMethodDispatcher.java:161)
! at org.glassfish.jersey.server.model.internal.JavaResourceMethodDispatcherProvider$ResponseOutInvoker.doDispatch(JavaResourceMethodDispatcherProvider.java:160)
! at org.glassfish.jersey.server.model.internal.AbstractJavaResourceMethodDispatcher.dispatch(AbstractJavaResourceMethodDispatcher.java:99)
! at org.glassfish.jersey.server.model.ResourceMethodInvoker.invoke(ResourceMethodInvoker.java:389)
! at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:347)
! at org.glassfish.jersey.server.model.ResourceMethodInvoker.apply(ResourceMethodInvoker.java:102)
! at org.glassfish.jersey.server.ServerRuntime$2.run(ServerRuntime.java:326)
! at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
! at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
! at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
! at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
! at org.glassfish.jersey.internal.Errors.process(Errors.java:267)
! at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:317)
! at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:305)
! at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1154)
! at org.glassfish.jersey.servlet.WebComponent.serviceImpl(WebComponent.java:473)
! at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:427)
! at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:388)
! at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:341)
! at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:228)
! at io.dropwizard.jetty.NonblockingServletHolder.handle(NonblockingServletHolder.java:49)
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1689)
! at io.dropwizard.servlets.ThreadNameFilter.doFilter(ThreadNameFilter.java:34)
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676)
! at io.dropwizard.jersey.filter.AllowedMethodsFilter.handle(AllowedMethodsFilter.java:50)
! at io.dropwizard.jersey.filter.AllowedMethodsFilter.doFilter(AllowedMethodsFilter.java:44)
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676)
! at com.google.inject.servlet.FilterChainInvocation.doFilter(FilterChainInvocation.java:89)
! at com.google.inject.servlet.ManagedFilterPipeline.dispatch(ManagedFilterPipeline.java:119)
! at com.google.inject.servlet.GuiceFilter$1.call(GuiceFilter.java:133)
! at com.google.inject.servlet.GuiceFilter$1.call(GuiceFilter.java:130)
! at com.google.inject.servlet.GuiceFilter$Context.call(GuiceFilter.java:203)
! at com.google.inject.servlet.GuiceFilter.doFilter(GuiceFilter.java:130)
! at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1676)
! at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:581)
! at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1174)
! at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:511)
! at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1106)
! at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141)
! at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
! at com.codahale.metrics.jetty9.InstrumentedHandler.handle(InstrumentedHandler.java:240)
! at io.dropwizard.jetty.RoutingHandler.handle(RoutingHandler.java:51)
! at org.eclipse.jetty.server.handler.gzip.GzipHandler.handle(GzipHandler.java:396)
! at io.dropwizard.jetty.BiDiGzipHandler.handle(BiDiGzipHandler.java:68)
! at org.eclipse.jetty.server.handler.RequestLogHandler.handle(RequestLogHandler.java:56)
! at org.eclipse.jetty.server.handler.StatisticsHandler.handle(StatisticsHandler.java:169)
! at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:134)
! at org.eclipse.jetty.server.Server.handle(Server.java:524)
! at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:319)
! at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:253)
! at org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded(AbstractConnection.java:273)
! at org.eclipse.jetty.io.FillInterest.fillable(FillInterest.java:95)
! at org.eclipse.jetty.io.SelectChannelEndPoint$2.run(SelectChannelEndPoint.java:93)
! at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.executeProduceConsume(ExecuteProduceConsume.java:303)
! at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.produceConsume(ExecuteProduceConsume.java:148)
! at org.eclipse.jetty.util.thread.strategy.ExecuteProduceConsume.run(ExecuteProduceConsume.java:136)
! at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:671)
! at org.eclipse.jetty.util.thread.QueuedThreadPool$2.run(QueuedThreadPool.java:589)
! at java.lang.Thread.run(Thread.java:748)

It's probably something we forgot to test after the migration to dropwizard, I'm opening the ticket not to forget ;-)

@lfoppiano lfoppiano added the bug From Hemiptera and especially its suborder Heteroptera label Jun 14, 2018
@lfoppiano
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The issue was the parameter name (text instead of input), I've uniformed to input as any other there to avoid confusion.

@lfoppiano lfoppiano self-assigned this Sep 11, 2018
de-code pushed a commit to elifesciences/grobid that referenced this issue Nov 29, 2019
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