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bug #8132
closedphycobank cdm-server instance problems with db connections
Start date:
Due date:
% Done:
0%
Estimated time:
Severity:
critical
Found in Version:
Description
the phycobank cdm-server instance which is running in a docker container got problems with the db connections
Problem accessing /phycobank/registrationDTO/identifier/http%3A%2F%2Fphycobank.org%2F100530.json. Reason:
com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: The last packet successfully received from the server was 89,950,095 milliseconds ago. The last packet sent successfully to the server was 89,950,096 milliseconds ago. is longer than the server configured value of 'wait_timeout'. You should consider either expiring and/or testing connection validity before use in your application, increasing the server configured values for client timeouts, or using the Connector/J connection property 'autoReconnect=true' to avoid this problem. at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) at java.lang.reflect.Constructor.newInstance(Constructor.java:423) at com.mysql.jdbc.Util.handleNewInstance(Util.java:404) at com.mysql.jdbc.SQLError.createCommunicationsException(SQLError.java:981) at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3652) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2460) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2625) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2551) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1861) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1962) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:353) at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:70) at org.hibernate.loader.Loader.getResultSet(Loader.java:2116) at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1899) at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1875) at org.hibernate.loader.Loader.doQuery(Loader.java:919) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:336) at org.hibernate.loader.Loader.doList(Loader.java:2611) at org.hibernate.loader.Loader.doList(Loader.java:2594) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2423) at org.hibernate.loader.Loader.list(Loader.java:2418) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:109) at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1774) at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:363) at org.hibernate.internal.CriteriaImpl.uniqueResult(CriteriaImpl.java:385) at eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmEntityDaoBase.countByParamWithRestrictions(CdmEntityDaoBase.java:1197) at eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase.countByTitleWithRestrictions(IdentifiableDaoBase.java:344) at eu.etaxonomy.cdm.api.service.IdentifiableServiceBase.findByTitleWithRestrictions(IdentifiableServiceBase.java:147) at sun.reflect.GeneratedMethodAccessor189.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208) at com.sun.proxy.$Proxy187.findByTitleWithRestrictions(Unknown Source) at eu.etaxonomy.cdm.service.CdmFilterablePagingProvider.size(CdmFilterablePagingProvider.java:182) at org.vaadin.viritin.fields.LazyComboBox$7.size(LazyComboBox.java:261) at org.vaadin.viritin.LazyList.size(LazyList.java:229) at org.vaadin.viritin.ListContainer.size(ListContainer.java:368) at com.vaadin.ui.ComboBox.getOptionsWithFilter(ComboBox.java:461) at com.vaadin.ui.ComboBox.paintContent(ComboBox.java:261) at com.vaadin.server.LegacyPaint.paint(LegacyPaint.java:65) at com.vaadin.server.communication.LegacyUidlWriter.write(LegacyUidlWriter.java:82) at com.vaadin.server.communication.UidlWriter.write(UidlWriter.java:143) at com.vaadin.server.communication.UidlRequestHandler.writeUidl(UidlRequestHandler.java:124) at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:92) at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:41) at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1435) at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:380) at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1669) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:316) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:122) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:169) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:48) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:158) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.oauth2.provider.authentication.OAuth2AuthenticationProcessingFilter.doFilter(OAuth2AuthenticationProcessingFilter.java:176) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:120) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:64) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:91) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:53) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:213) at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:176) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:262) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:121) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) at org.eclipse.jetty.server.Server.handle(Server.java:497) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257) at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555) at java.lang.Thread.run(Thread.java:748) Caused by: java.net.SocketException: Broken pipe (Write failed) at java.net.SocketOutputStream.socketWrite0(Native Method) at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:111) at java.net.SocketOutputStream.write(SocketOutputStream.java:155) at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3634) ... 107 more Caused by: java.net.SocketException: Broken pipe (Write failed) at java.net.SocketOutputStream.socketWrite0(Native Method) at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:111) at java.net.SocketOutputStream.write(SocketOutputStream.java:155) at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) at com.mysql.jdbc.MysqlIO.send(MysqlIO.java:3634) at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:2460) at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:2625) at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2551) at com.mysql.jdbc.PreparedStatement.executeInternal(PreparedStatement.java:1861) at com.mysql.jdbc.PreparedStatement.executeQuery(PreparedStatement.java:1962) at com.mchange.v2.c3p0.impl.NewProxyPreparedStatement.executeQuery(NewProxyPreparedStatement.java:353) at org.hibernate.engine.jdbc.internal.ResultSetReturnImpl.extract(ResultSetReturnImpl.java:70) at org.hibernate.loader.Loader.getResultSet(Loader.java:2116) at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1899) at org.hibernate.loader.Loader.executeQueryStatement(Loader.java:1875) at org.hibernate.loader.Loader.doQuery(Loader.java:919) at org.hibernate.loader.Loader.doQueryAndInitializeNonLazyCollections(Loader.java:336) at org.hibernate.loader.Loader.doList(Loader.java:2611) at org.hibernate.loader.Loader.doList(Loader.java:2594) at org.hibernate.loader.Loader.listIgnoreQueryCache(Loader.java:2423) at org.hibernate.loader.Loader.list(Loader.java:2418) at org.hibernate.loader.criteria.CriteriaLoader.list(CriteriaLoader.java:109) at org.hibernate.internal.SessionImpl.list(SessionImpl.java:1774) at org.hibernate.internal.CriteriaImpl.list(CriteriaImpl.java:363) at org.hibernate.internal.CriteriaImpl.uniqueResult(CriteriaImpl.java:385) at eu.etaxonomy.cdm.persistence.dao.hibernate.common.CdmEntityDaoBase.countByParamWithRestrictions(CdmEntityDaoBase.java:1197) at eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase.countByTitleWithRestrictions(IdentifiableDaoBase.java:344) at eu.etaxonomy.cdm.api.service.IdentifiableServiceBase.findByTitleWithRestrictions(IdentifiableServiceBase.java:147) at sun.reflect.GeneratedMethodAccessor189.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:302) at org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157) at org.springframework.transaction.interceptor.TransactionInterceptor$1.proceedWithInvocation(TransactionInterceptor.java:99) at org.springframework.transaction.interceptor.TransactionAspectSupport.invokeWithinTransaction(TransactionAspectSupport.java:281) at org.springframework.transaction.interceptor.TransactionInterceptor.invoke(TransactionInterceptor.java:96) at org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179) at org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:208) at com.sun.proxy.$Proxy187.findByTitleWithRestrictions(Unknown Source) at eu.etaxonomy.cdm.service.CdmFilterablePagingProvider.size(CdmFilterablePagingProvider.java:182) at org.vaadin.viritin.fields.LazyComboBox$7.size(LazyComboBox.java:261) at org.vaadin.viritin.LazyList.size(LazyList.java:229) at org.vaadin.viritin.ListContainer.size(ListContainer.java:368) at com.vaadin.ui.ComboBox.getOptionsWithFilter(ComboBox.java:461) at com.vaadin.ui.ComboBox.paintContent(ComboBox.java:261) at com.vaadin.server.LegacyPaint.paint(LegacyPaint.java:65) at com.vaadin.server.communication.LegacyUidlWriter.write(LegacyUidlWriter.java:82) at com.vaadin.server.communication.UidlWriter.write(UidlWriter.java:143) at com.vaadin.server.communication.UidlRequestHandler.writeUidl(UidlRequestHandler.java:124) at com.vaadin.server.communication.UidlRequestHandler.synchronizedHandleRequest(UidlRequestHandler.java:92) at com.vaadin.server.SynchronizedRequestHandler.handleRequest(SynchronizedRequestHandler.java:41) at com.vaadin.server.VaadinService.handleRequest(VaadinService.java:1435) at com.vaadin.server.VaadinServlet.service(VaadinServlet.java:380) at javax.servlet.http.HttpServlet.service(HttpServlet.java:790) at org.eclipse.jetty.servlet.ServletHolder.handle(ServletHolder.java:808) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1669) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:316) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:126) at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:90) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:114) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:122) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:111) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:169) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:48) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilterInternal(BasicAuthenticationFilter.java:158) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.oauth2.provider.authentication.OAuth2AuthenticationProcessingFilter.doFilter(OAuth2AuthenticationProcessingFilter.java:176) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:120) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.header.HeaderWriterFilter.doFilterInternal(HeaderWriterFilter.java:64) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:91) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:53) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:330) at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:213) at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:176) at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:346) at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:262) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) at org.springframework.web.filter.CharacterEncodingFilter.doFilterInternal(CharacterEncodingFilter.java:121) at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:107) at org.eclipse.jetty.servlet.ServletHandler$CachedChain.doFilter(ServletHandler.java:1652) at org.eclipse.jetty.servlet.ServletHandler.doHandle(ServletHandler.java:585) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:143) at org.eclipse.jetty.security.SecurityHandler.handle(SecurityHandler.java:577) at org.eclipse.jetty.server.session.SessionHandler.doHandle(SessionHandler.java:223) at org.eclipse.jetty.server.handler.ContextHandler.doHandle(ContextHandler.java:1127) at org.eclipse.jetty.servlet.ServletHandler.doScope(ServletHandler.java:515) at org.eclipse.jetty.server.session.SessionHandler.doScope(SessionHandler.java:185) at org.eclipse.jetty.server.handler.ContextHandler.doScope(ContextHandler.java:1061) at org.eclipse.jetty.server.handler.ScopedHandler.handle(ScopedHandler.java:141) at org.eclipse.jetty.server.handler.ContextHandlerCollection.handle(ContextHandlerCollection.java:215) at org.eclipse.jetty.server.handler.HandlerWrapper.handle(HandlerWrapper.java:97) at org.eclipse.jetty.server.Server.handle(Server.java:497) at org.eclipse.jetty.server.HttpChannel.handle(HttpChannel.java:310) at org.eclipse.jetty.server.HttpConnection.onFillable(HttpConnection.java:257) at org.eclipse.jetty.io.AbstractConnection$2.run(AbstractConnection.java:540) at org.eclipse.jetty.util.thread.QueuedThreadPool.runJob(QueuedThreadPool.java:635) at org.eclipse.jetty.util.thread.QueuedThreadPool$3.run(QueuedThreadPool.java:555) at java.lang.Thread.run(Thread.java:748) Powered by Jetty://
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