org.fcrepo.server.errors.StreamWriteException: Error writing temp stream

Sakai JIRA | Adam Vessey | 9 months ago
  1. 0

    PHP stat cache becomes inconsistent, leading to Tuque failures. This long-standing bug appears to have been uncovered with the Drupal 7.42 release, in which [static caching was added to {{module_load_include()}}|https://github.com/drupal/drupal/commit/f0d59102f528a9c66b1c3355bb6b2ee48f8b0282]. The general flow of code necessary to make this happen, is: # {{fopen()}} a file # Perform an operation which performs a "stat" on the file ({{filesize()}}, among others). # Change the content of the file, which will change the previously stat'd value (deleting from the file, reducing its length). # Stat the file again; the value will match that from before. A small test script, to see the error happen: https://gist.github.com/adam-vessey/386494830670a19e0f97 It so happens this flow would occur when generating HOCR, when we strip out the HTML DOCTYPE declarations; however, it appears that the {{is_file()}} check which would always be performed prior to the static caching in {{module_load_include()}} would result in a general wipe of the stat cache, masking the issue. With HOCR in particular: # {{fopen()}} a file: https://github.com/Islandora/islandora_ocr/blob/8c1248bdc29324cee7863d835b22832085763d1d/includes/hocr.inc#L584-L585 # Perform an operation which performs a "stat" on the file: https://github.com/Islandora/islandora_ocr/blob/8c1248bdc29324cee7863d835b22832085763d1d/includes/hocr.inc#L587 (the {{filesize()}} call) # Change the content of the file, which will change the previously stat'd value: https://github.com/Islandora/islandora_ocr/blob/8c1248bdc29324cee7863d835b22832085763d1d/includes/hocr.inc#L588-L591 # Stat the file again; the value will match that from before: https://github.com/Islandora/tuque/blob/5c6bb1c831f52d9bc014729e325a7f731d772d0f/HttpConnection.php#L657 This caused Tuque to tell Fedora that it would be sending more bytes then Tuque had to send, so it would end up with errors as Fedora waits for the rest of the bytes to come in: {noformat} WARN 2016-03-08 08:49:48.807 [http-bio-8080-exec-29] (DatastreamResource) Error writing temp stream org.fcrepo.server.errors.StreamWriteException: Error writing temp stream at org.fcrepo.server.management.DefaultManagement.putTempStream(DefaultManagement.java:1344) ~[fcrepo-server-3.8.1.jar:na] at sun.reflect.GeneratedMethodAccessor206.invoke(Unknown Source) ~[na:na] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_60] at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_60] at org.fcrepo.server.messaging.NotificationInvocationHandler.invoke(NotificationInvocationHandler.java:71) ~[fcrepo-server-3.8.1.jar:na] at com.sun.proxy.$Proxy11.putTempStream(Unknown Source) ~[na:na] at org.fcrepo.server.management.ManagementModule.putTempStream(ManagementModule.java:536) ~[fcrepo-server-3.8.1.jar:na] at org.fcrepo.server.rest.DatastreamResource.addOrUpdateDatastream(DatastreamResource.java:572) [fcrepo-server-3.8.1.jar:na] at org.fcrepo.server.rest.DatastreamResource.modifyDatastream(DatastreamResource.java:351) [fcrepo-server-3.8.1.jar:na] at sun.reflect.GeneratedMethodAccessor205.invoke(Unknown Source) ~[na:na] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_60] at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_60] at org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:180) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:192) [cxf-rt-frontend-jaxrs-2.7.7.jar:2.7.7] at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:100) [cxf-rt-frontend-jaxrs-2.7.7.jar:2.7.7] at org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:57) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:93) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:272) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:239) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:248) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:222) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:153) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:167) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:286) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPut(AbstractHTTPServlet.java:223) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at javax.servlet.http.HttpServlet.service(HttpServlet.java:653) [tomcat-servlet-3.0-api.jar:na] at org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:262) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.65] at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.65] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:369) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.fcrepo.server.security.jaas.AuthFilterJAAS.doFilter(AuthFilterJAAS.java:329) [fcrepo-security-jaas-3.8.1.jar:na] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:109) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:168) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237) [spring-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167) [spring-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.65] at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170) [catalina.jar:7.0.65] at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.65] at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.65] at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423) [catalina.jar:7.0.65] at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079) [tomcat-coyote.jar:7.0.65] at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625) [tomcat-coyote.jar:7.0.65] at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318) [tomcat-coyote.jar:7.0.65] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_60] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_60] at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.65] at java.lang.Thread.run(Thread.java:745) [na:1.8.0_60] Caused by: java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) ~[na:1.8.0_60] at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) ~[na:1.8.0_60] at java.net.SocketInputStream.read(SocketInputStream.java:170) ~[na:1.8.0_60] at java.net.SocketInputStream.read(SocketInputStream.java:141) ~[na:1.8.0_60] at org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:535) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:504) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.InternalInputBuffer$InputStreamInputBuffer.doRead(InternalInputBuffer.java:566) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.filters.IdentityInputFilter.doRead(IdentityInputFilter.java:137) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.AbstractInputBuffer.doRead(AbstractInputBuffer.java:341) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.Request.doRead(Request.java:431) ~[tomcat-coyote.jar:7.0.65] at org.apache.catalina.connector.InputBuffer.realReadBytes(InputBuffer.java:290) ~[catalina.jar:7.0.65] at org.apache.tomcat.util.buf.ByteChunk.substract(ByteChunk.java:449) ~[tomcat-coyote.jar:7.0.65] at org.apache.catalina.connector.InputBuffer.read(InputBuffer.java:315) ~[catalina.jar:7.0.65] at org.apache.catalina.connector.CoyoteInputStream.read(CoyoteInputStream.java:167) ~[catalina.jar:7.0.65] at org.fcrepo.server.utilities.StreamUtility.pipeStream(StreamUtility.java:255) ~[fcrepo-server-3.8.1.jar:na] at org.fcrepo.server.management.DefaultManagement.putTempStream(DefaultManagement.java:1335) ~[fcrepo-server-3.8.1.jar:na] ... 58 common frames omitted {noformat} h2. Steps to Reproduce Attempt to regenerate HOCR on an object, running Drupal 7.42 (or a newer 7). h2. Test Case HOCR is regenerated successfully. ---- Adam Vessey Developer discoverygarden inc. | Managing Digital Content

    Sakai JIRA | 9 months ago | Adam Vessey
    org.fcrepo.server.errors.StreamWriteException: Error writing temp stream
  2. 0

    PHP stat cache becomes inconsistent, leading to Tuque failures. This long-standing bug appears to have been uncovered with the Drupal 7.42 release, in which [static caching was added to {{module_load_include()}}|https://github.com/drupal/drupal/commit/f0d59102f528a9c66b1c3355bb6b2ee48f8b0282]. The general flow of code necessary to make this happen, is: # {{fopen()}} a file # Perform an operation which performs a "stat" on the file ({{filesize()}}, among others). # Change the content of the file, which will change the previously stat'd value (deleting from the file, reducing its length). # Stat the file again; the value will match that from before. A small test script, to see the error happen: https://gist.github.com/adam-vessey/386494830670a19e0f97 It so happens this flow would occur when generating HOCR, when we strip out the HTML DOCTYPE declarations; however, it appears that the {{is_file()}} check which would always be performed prior to the static caching in {{module_load_include()}} would result in a general wipe of the stat cache, masking the issue. With HOCR in particular: # {{fopen()}} a file: https://github.com/Islandora/islandora_ocr/blob/8c1248bdc29324cee7863d835b22832085763d1d/includes/hocr.inc#L584-L585 # Perform an operation which performs a "stat" on the file: https://github.com/Islandora/islandora_ocr/blob/8c1248bdc29324cee7863d835b22832085763d1d/includes/hocr.inc#L587 (the {{filesize()}} call) # Change the content of the file, which will change the previously stat'd value: https://github.com/Islandora/islandora_ocr/blob/8c1248bdc29324cee7863d835b22832085763d1d/includes/hocr.inc#L588-L591 # Stat the file again; the value will match that from before: https://github.com/Islandora/tuque/blob/5c6bb1c831f52d9bc014729e325a7f731d772d0f/HttpConnection.php#L657 This caused Tuque to tell Fedora that it would be sending more bytes then Tuque had to send, so it would end up with errors as Fedora waits for the rest of the bytes to come in: {noformat} WARN 2016-03-08 08:49:48.807 [http-bio-8080-exec-29] (DatastreamResource) Error writing temp stream org.fcrepo.server.errors.StreamWriteException: Error writing temp stream at org.fcrepo.server.management.DefaultManagement.putTempStream(DefaultManagement.java:1344) ~[fcrepo-server-3.8.1.jar:na] at sun.reflect.GeneratedMethodAccessor206.invoke(Unknown Source) ~[na:na] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_60] at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_60] at org.fcrepo.server.messaging.NotificationInvocationHandler.invoke(NotificationInvocationHandler.java:71) ~[fcrepo-server-3.8.1.jar:na] at com.sun.proxy.$Proxy11.putTempStream(Unknown Source) ~[na:na] at org.fcrepo.server.management.ManagementModule.putTempStream(ManagementModule.java:536) ~[fcrepo-server-3.8.1.jar:na] at org.fcrepo.server.rest.DatastreamResource.addOrUpdateDatastream(DatastreamResource.java:572) [fcrepo-server-3.8.1.jar:na] at org.fcrepo.server.rest.DatastreamResource.modifyDatastream(DatastreamResource.java:351) [fcrepo-server-3.8.1.jar:na] at sun.reflect.GeneratedMethodAccessor205.invoke(Unknown Source) ~[na:na] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) ~[na:1.8.0_60] at java.lang.reflect.Method.invoke(Method.java:497) ~[na:1.8.0_60] at org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:180) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:192) [cxf-rt-frontend-jaxrs-2.7.7.jar:2.7.7] at org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:100) [cxf-rt-frontend-jaxrs-2.7.7.jar:2.7.7] at org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:57) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:93) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:272) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121) [cxf-api-2.7.7.jar:2.7.7] at org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:239) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:248) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:222) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:153) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:167) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:286) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPut(AbstractHTTPServlet.java:223) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at javax.servlet.http.HttpServlet.service(HttpServlet.java:653) [tomcat-servlet-3.0-api.jar:na] at org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:262) [cxf-rt-transports-http-2.7.7.jar:2.7.7] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303) [catalina.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.65] at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52) [tomcat7-websocket.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.65] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:369) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.fcrepo.server.security.jaas.AuthFilterJAAS.doFilter(AuthFilterJAAS.java:329) [fcrepo-security-jaas-3.8.1.jar:na] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:109) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:168) [spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237) [spring-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167) [spring-web-3.0.7.RELEASE.jar:3.0.7.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241) [catalina.jar:7.0.65] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122) [catalina.jar:7.0.65] at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170) [catalina.jar:7.0.65] at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103) [catalina.jar:7.0.65] at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956) [catalina.jar:7.0.65] at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116) [catalina.jar:7.0.65] at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423) [catalina.jar:7.0.65] at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079) [tomcat-coyote.jar:7.0.65] at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625) [tomcat-coyote.jar:7.0.65] at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318) [tomcat-coyote.jar:7.0.65] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_60] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_60] at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61) [tomcat-coyote.jar:7.0.65] at java.lang.Thread.run(Thread.java:745) [na:1.8.0_60] Caused by: java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) ~[na:1.8.0_60] at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) ~[na:1.8.0_60] at java.net.SocketInputStream.read(SocketInputStream.java:170) ~[na:1.8.0_60] at java.net.SocketInputStream.read(SocketInputStream.java:141) ~[na:1.8.0_60] at org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:535) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:504) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.InternalInputBuffer$InputStreamInputBuffer.doRead(InternalInputBuffer.java:566) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.filters.IdentityInputFilter.doRead(IdentityInputFilter.java:137) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.http11.AbstractInputBuffer.doRead(AbstractInputBuffer.java:341) ~[tomcat-coyote.jar:7.0.65] at org.apache.coyote.Request.doRead(Request.java:431) ~[tomcat-coyote.jar:7.0.65] at org.apache.catalina.connector.InputBuffer.realReadBytes(InputBuffer.java:290) ~[catalina.jar:7.0.65] at org.apache.tomcat.util.buf.ByteChunk.substract(ByteChunk.java:449) ~[tomcat-coyote.jar:7.0.65] at org.apache.catalina.connector.InputBuffer.read(InputBuffer.java:315) ~[catalina.jar:7.0.65] at org.apache.catalina.connector.CoyoteInputStream.read(CoyoteInputStream.java:167) ~[catalina.jar:7.0.65] at org.fcrepo.server.utilities.StreamUtility.pipeStream(StreamUtility.java:255) ~[fcrepo-server-3.8.1.jar:na] at org.fcrepo.server.management.DefaultManagement.putTempStream(DefaultManagement.java:1335) ~[fcrepo-server-3.8.1.jar:na] ... 58 common frames omitted {noformat} h2. Steps to Reproduce Attempt to regenerate HOCR on an object, running Drupal 7.42 (or a newer 7). h2. Test Case HOCR is regenerated successfully. ---- Adam Vessey Developer discoverygarden inc. | Managing Digital Content

    Sakai JIRA | 9 months ago | Adam Vessey
    org.fcrepo.server.errors.StreamWriteException: Error writing temp stream
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Root Cause Analysis

  1. java.net.SocketTimeoutException

    Read timed out

    at java.net.SocketInputStream.socketRead0()
  2. Java RT
    SocketInputStream.read
    1. java.net.SocketInputStream.socketRead0(Native Method)[na:1.8.0_60]
    2. java.net.SocketInputStream.socketRead(SocketInputStream.java:116)[na:1.8.0_60]
    3. java.net.SocketInputStream.read(SocketInputStream.java:170)[na:1.8.0_60]
    4. java.net.SocketInputStream.read(SocketInputStream.java:141)[na:1.8.0_60]
    4 frames
  3. Grizzly HTTP
    Request.doRead
    1. org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:535)[tomcat-coyote.jar:7.0.65]
    2. org.apache.coyote.http11.InternalInputBuffer.fill(InternalInputBuffer.java:504)[tomcat-coyote.jar:7.0.65]
    3. org.apache.coyote.http11.InternalInputBuffer$InputStreamInputBuffer.doRead(InternalInputBuffer.java:566)[tomcat-coyote.jar:7.0.65]
    4. org.apache.coyote.http11.filters.IdentityInputFilter.doRead(IdentityInputFilter.java:137)[tomcat-coyote.jar:7.0.65]
    5. org.apache.coyote.http11.AbstractInputBuffer.doRead(AbstractInputBuffer.java:341)[tomcat-coyote.jar:7.0.65]
    6. org.apache.coyote.Request.doRead(Request.java:431)[tomcat-coyote.jar:7.0.65]
    6 frames
  4. Glassfish Core
    InputBuffer.realReadBytes
    1. org.apache.catalina.connector.InputBuffer.realReadBytes(InputBuffer.java:290)[catalina.jar:7.0.65]
    1 frame
  5. Tomcat Util
    ByteChunk.substract
    1. org.apache.tomcat.util.buf.ByteChunk.substract(ByteChunk.java:449)[tomcat-coyote.jar:7.0.65]
    1 frame
  6. Glassfish Core
    CoyoteInputStream.read
    1. org.apache.catalina.connector.InputBuffer.read(InputBuffer.java:315)[catalina.jar:7.0.65]
    2. org.apache.catalina.connector.CoyoteInputStream.read(CoyoteInputStream.java:167)[catalina.jar:7.0.65]
    2 frames
  7. org.fcrepo.server
    DefaultManagement.putTempStream
    1. org.fcrepo.server.utilities.StreamUtility.pipeStream(StreamUtility.java:255)[fcrepo-server-3.8.1.jar:na]
    2. org.fcrepo.server.management.DefaultManagement.putTempStream(DefaultManagement.java:1335)[fcrepo-server-3.8.1.jar:na]
    2 frames
  8. Java RT
    Method.invoke
    1. sun.reflect.GeneratedMethodAccessor206.invoke(Unknown Source)[na:na]
    2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)[na:1.8.0_60]
    3. java.lang.reflect.Method.invoke(Method.java:497)[na:1.8.0_60]
    3 frames
  9. org.fcrepo.server
    NotificationInvocationHandler.invoke
    1. org.fcrepo.server.messaging.NotificationInvocationHandler.invoke(NotificationInvocationHandler.java:71)[fcrepo-server-3.8.1.jar:na]
    1 frame
  10. com.sun.proxy
    $Proxy11.putTempStream
    1. com.sun.proxy.$Proxy11.putTempStream(Unknown Source)[na:na]
    1 frame
  11. org.fcrepo.server
    DatastreamResource.modifyDatastream
    1. org.fcrepo.server.management.ManagementModule.putTempStream(ManagementModule.java:536)[fcrepo-server-3.8.1.jar:na]
    2. org.fcrepo.server.rest.DatastreamResource.addOrUpdateDatastream(DatastreamResource.java:572)[fcrepo-server-3.8.1.jar:na]
    3. org.fcrepo.server.rest.DatastreamResource.modifyDatastream(DatastreamResource.java:351)[fcrepo-server-3.8.1.jar:na]
    3 frames
  12. Java RT
    Method.invoke
    1. sun.reflect.GeneratedMethodAccessor205.invoke(Unknown Source)[na:na]
    2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)[na:1.8.0_60]
    3. java.lang.reflect.Method.invoke(Method.java:497)[na:1.8.0_60]
    3 frames
  13. Apache CXF Core
    AbstractInvoker.invoke
    1. org.apache.cxf.service.invoker.AbstractInvoker.performInvocation(AbstractInvoker.java:180)[cxf-api-2.7.7.jar:2.7.7]
    2. org.apache.cxf.service.invoker.AbstractInvoker.invoke(AbstractInvoker.java:96)[cxf-api-2.7.7.jar:2.7.7]
    2 frames
  14. Apache CXF Runtime JAX-RS Frontend
    JAXRSInvoker.invoke
    1. org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:192)[cxf-rt-frontend-jaxrs-2.7.7.jar:2.7.7]
    2. org.apache.cxf.jaxrs.JAXRSInvoker.invoke(JAXRSInvoker.java:100)[cxf-rt-frontend-jaxrs-2.7.7.jar:2.7.7]
    2 frames
  15. Apache CXF Core
    ChainInitiationObserver.onMessage
    1. org.apache.cxf.interceptor.ServiceInvokerInterceptor$1.run(ServiceInvokerInterceptor.java:57)[cxf-api-2.7.7.jar:2.7.7]
    2. org.apache.cxf.interceptor.ServiceInvokerInterceptor.handleMessage(ServiceInvokerInterceptor.java:93)[cxf-api-2.7.7.jar:2.7.7]
    3. org.apache.cxf.phase.PhaseInterceptorChain.doIntercept(PhaseInterceptorChain.java:272)[cxf-api-2.7.7.jar:2.7.7]
    4. org.apache.cxf.transport.ChainInitiationObserver.onMessage(ChainInitiationObserver.java:121)[cxf-api-2.7.7.jar:2.7.7]
    4 frames
  16. Apache CXF Runtime HTTP Transport
    AbstractHTTPServlet.doPut
    1. org.apache.cxf.transport.http.AbstractHTTPDestination.invoke(AbstractHTTPDestination.java:239)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    2. org.apache.cxf.transport.servlet.ServletController.invokeDestination(ServletController.java:248)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    3. org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:222)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    4. org.apache.cxf.transport.servlet.ServletController.invoke(ServletController.java:153)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    5. org.apache.cxf.transport.servlet.CXFNonSpringServlet.invoke(CXFNonSpringServlet.java:167)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    6. org.apache.cxf.transport.servlet.AbstractHTTPServlet.handleRequest(AbstractHTTPServlet.java:286)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    7. org.apache.cxf.transport.servlet.AbstractHTTPServlet.doPut(AbstractHTTPServlet.java:223)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    7 frames
  17. JavaServlet
    HttpServlet.service
    1. javax.servlet.http.HttpServlet.service(HttpServlet.java:653)[tomcat-servlet-3.0-api.jar:na]
    1 frame
  18. Apache CXF Runtime HTTP Transport
    AbstractHTTPServlet.service
    1. org.apache.cxf.transport.servlet.AbstractHTTPServlet.service(AbstractHTTPServlet.java:262)[cxf-rt-transports-http-2.7.7.jar:2.7.7]
    1 frame
  19. Glassfish Core
    ApplicationFilterChain.doFilter
    1. org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)[catalina.jar:7.0.65]
    2. org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)[catalina.jar:7.0.65]
    2 frames
  20. Tomcat WS
    WsFilter.doFilter
    1. org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)[tomcat7-websocket.jar:7.0.65]
    1 frame
  21. Glassfish Core
    ApplicationFilterChain.doFilter
    1. org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)[catalina.jar:7.0.65]
    2. org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)[catalina.jar:7.0.65]
    2 frames
  22. Spring Security
    FilterChainProxy$VirtualFilterChain.doFilter
    1. org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:369)[spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    1 frame
  23. org.fcrepo.server
    AuthFilterJAAS.doFilter
    1. org.fcrepo.server.security.jaas.AuthFilterJAAS.doFilter(AuthFilterJAAS.java:329)[fcrepo-security-jaas-3.8.1.jar:na]
    1 frame
  24. Spring Security
    FilterChainProxy.doFilter
    1. org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)[spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    2. org.springframework.security.web.access.channel.ChannelProcessingFilter.doFilter(ChannelProcessingFilter.java:109)[spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    3. org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:381)[spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    4. org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:168)[spring-security-web-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    4 frames
  25. Spring
    DelegatingFilterProxy.doFilter
    1. org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:237)[spring-web-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    2. org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:167)[spring-web-3.0.7.RELEASE.jar:3.0.7.RELEASE]
    2 frames
  26. Glassfish Core
    CoyoteAdapter.service
    1. org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)[catalina.jar:7.0.65]
    2. org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)[catalina.jar:7.0.65]
    3. org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)[catalina.jar:7.0.65]
    4. org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)[catalina.jar:7.0.65]
    5. org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)[catalina.jar:7.0.65]
    6. org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)[catalina.jar:7.0.65]
    7. org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)[catalina.jar:7.0.65]
    8. org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:956)[catalina.jar:7.0.65]
    9. org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)[catalina.jar:7.0.65]
    10. org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)[catalina.jar:7.0.65]
    10 frames
  27. Grizzly HTTP
    JIoEndpoint$SocketProcessor.run
    1. org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)[tomcat-coyote.jar:7.0.65]
    2. org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:625)[tomcat-coyote.jar:7.0.65]
    3. org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:318)[tomcat-coyote.jar:7.0.65]
    3 frames
  28. Java RT
    ThreadPoolExecutor$Worker.run
    1. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)[na:1.8.0_60]
    2. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)[na:1.8.0_60]
    2 frames
  29. Tomcat Util
    TaskThread$WrappingRunnable.run
    1. org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)[tomcat-coyote.jar:7.0.65]
    1 frame
  30. Java RT
    Thread.run
    1. java.lang.Thread.run(Thread.java:745)[na:1.8.0_60]
    1 frame