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moltimate / moltimate-backend

A protein active site alignment tool
GNU General Public License v2.0
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Null Error in search #65

Closed jmiller656 closed 5 years ago

jmiller656 commented 5 years ago 
java.lang.NullPointerException: null
    at org.hibernate.engine.internal.StatefulPersistenceContext.getLoadedCollectionOwnerOrNull(StatefulPersistenceContext.java:788) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.event.spi.AbstractCollectionEvent.getLoadedOwnerOrNull(AbstractCollectionEvent.java:58) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.event.spi.InitializeCollectionEvent.<init>(InitializeCollectionEvent.java:22) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.internal.SessionImpl.initializeCollection(SessionImpl.java:2183) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.collection.internal.AbstractPersistentCollection$4.doWork(AbstractPersistentCollection.java:565) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.collection.internal.AbstractPersistentCollection.withTemporarySessionIfNeeded(AbstractPersistentCollection.java:247) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.collection.internal.AbstractPersistentCollection.initialize(AbstractPersistentCollection.java:561) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.collection.internal.AbstractPersistentCollection.read(AbstractPersistentCollection.java:132) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.hibernate.collection.internal.PersistentMap.keySet(PersistentMap.java:223) ~[hibernate-core-5.2.12.Final.jar:5.2.12.Final]
    at org.moltimate.moltimatebackend.model.Motif.runQueries(Motif.java:61) ~[classes/:na]
    at org.moltimate.moltimatebackend.service.AlignmentService.alignActiveSites(AlignmentService.java:66) ~[classes/:na]
    at org.moltimate.moltimatebackend.service.AlignmentService.lambda$null$0(AlignmentService.java:56) ~[classes/:na]
    at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) ~[na:1.8.0_181]
    at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382) ~[na:1.8.0_181]
    at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) ~[na:1.8.0_181]
    at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) ~[na:1.8.0_181]
    at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:747) ~[na:1.8.0_181]
    at java.util.stream.ReduceOps$ReduceTask.doLeaf(ReduceOps.java:721) ~[na:1.8.0_181]
    at java.util.stream.AbstractTask.compute(AbstractTask.java:316) ~[na:1.8.0_181]
    at java.util.concurrent.CountedCompleter.exec(CountedCompleter.java:731) ~[na:1.8.0_181]
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289) ~[na:1.8.0_181]
    at java.util.concurrent.ForkJoinPool.helpComplete(ForkJoinPool.java:1870) ~[na:1.8.0_181]
    at java.util.concurrent.ForkJoinPool.externalHelpComplete(ForkJoinPool.java:2467) ~[na:1.8.0_181]
    at java.util.concurrent.ForkJoinTask.externalAwaitDone(ForkJoinTask.java:324) ~[na:1.8.0_181]
    at java.util.concurrent.ForkJoinTask.doInvoke(ForkJoinTask.java:405) ~[na:1.8.0_181]
    at java.util.concurrent.ForkJoinTask.invoke(ForkJoinTask.java:734) ~[na:1.8.0_181]
    at java.util.stream.ReduceOps$ReduceOp.evaluateParallel(ReduceOps.java:714) ~[na:1.8.0_181]
    at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:233) ~[na:1.8.0_181]
    at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499) ~[na:1.8.0_181]
    at org.moltimate.moltimatebackend.service.AlignmentService.lambda$alignActiveSites$1(AlignmentService.java:61) ~[classes/:na]
    at java.util.ArrayList.forEach(ArrayList.java:1257) ~[na:1.8.0_181]
    at org.moltimate.moltimatebackend.service.AlignmentService.alignActiveSites(AlignmentService.java:53) ~[classes/:na]
    at org.moltimate.moltimatebackend.service.AlignmentService.alignActiveSites(AlignmentService.java:45) ~[classes/:na]
    at org.moltimate.moltimatebackend.controller.AlignmentController.activeSiteAlignment(AlignmentController.java:31) ~[classes/:na]
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) ~[na:1.8.0_181]
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) ~[na:1.8.0_181]
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_181]
    at java.lang.reflect.Method.invoke(Method.java:498) ~[na:1.8.0_181]
    at org.springframework.web.method.support.InvocableHandlerMethod.doInvoke(InvocableHandlerMethod.java:209) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.method.support.InvocableHandlerMethod.invokeForRequest(InvocableHandlerMethod.java:136) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.mvc.method.annotation.ServletInvocableHandlerMethod.invokeAndHandle(ServletInvocableHandlerMethod.java:102) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.invokeHandlerMethod(RequestMappingHandlerAdapter.java:891) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.mvc.method.annotation.RequestMappingHandlerAdapter.handleInternal(RequestMappingHandlerAdapter.java:797) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.mvc.method.AbstractHandlerMethodAdapter.handle(AbstractHandlerMethodAdapter.java:87) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:991) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:925) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:974) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:877) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:661) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.springframework.web.servlet.FrameworkServlet.service(FrameworkServlet.java:851) ~[spring-webmvc-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:742) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:231) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) ~[tomcat-embed-websocket-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.springframework.web.filter.RequestContextFilter.doFilterInternal(RequestContextFilter.java:99) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.springframework.web.filter.HttpPutFormContentFilter.doFilterInternal(HttpPutFormContentFilter.java:109) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.springframework.web.filter.HiddenHttpMethodFilter.doFilterInternal(HiddenHttpMethodFilter.java:93) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:200) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) ~[spring-web-5.0.9.RELEASE.jar:5.0.9.RELEASE]
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:193) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:166) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:198) ~[tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:96) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:493) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:140) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:81) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:87) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:342) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.coyote.http11.Http11Processor.service(Http11Processor.java:800) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.coyote.AbstractProcessorLight.process(AbstractProcessorLight.java:66) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.coyote.AbstractProtocol$ConnectionHandler.process(AbstractProtocol.java:806) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.doRun(NioEndpoint.java:1498) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at org.apache.tomcat.util.net.SocketProcessorBase.run(SocketProcessorBase.java:49) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) [na:1.8.0_181]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) [na:1.8.0_181]
    at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-embed-core-8.5.34.jar:8.5.34]
    at java.lang.Thread.run(Thread.java:748) [na:1.8.0_181]

2019-01-30 14:56:14.600  WARN 13848 --- [onPool-worker-0] o.h.engine.jdbc.spi.SqlExceptionHelper   : SQL Error: 90008, SQLState: 90008
2019-01-30 14:56:14.603 ERROR 13848 --- [onPool-worker-0] o.h.engine.jdbc.spi.SqlExceptionHelper   : Invalid value "2" for parameter "columnIndex" [90008-197]