D4Science Infrastructure

here's the server log

Hi Jesus,
please find the server log related oto a VME update report 

2018-09-26 08:29:51,578 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extract:84][PORTAL] 750491568 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting section #5
2018-09-26 08:29:51,578 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extract:86][PORTAL] 750491568 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Section has 2 components:
2018-09-26 08:29:51,579 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInternal:110][PORTAL] 750491569 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting component SEQUENCE_LIST [ ID: -1 ]
2018-09-26 08:29:51,579 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInternal:110][PORTAL] 750491569 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting component HIDDEN [ ID: ]
2018-09-26 08:29:51,579 INFO o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:162][PORTAL] 750491569 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Attempting to find #.mediaReferenceList[0] in CompiledReport : null #
2018-09-26 08:29:51,579 WARN o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:177][PORTAL] 750491569 [http-bio-9090-exec-100] WARN org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Unable to find #.mediaReferenceList[0] in CompiledReport : null #
2018-09-26 08:29:51,580 INFO o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:162][PORTAL] 750491570 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Attempting to find #.mediaReferenceList in CompiledReport : null #
2018-09-26 08:29:51,581 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractHidden:243][PORTAL] 750491571 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Component HIDDEN [ ID: - Binding: #.mediaReferenceList[0].id ] updating parent sequence entry ID to -1
2018-09-26 08:29:51,581 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInternal:110][PORTAL] 750491571 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting component TEXT_INPUT [ ID: -1 ]
2018-09-26 08:29:51,581 INFO o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:162][PORTAL] 750491571 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Attempting to find #.mediaReferenceList[0].title in CompiledReport : null #
2018-09-26 08:29:51,582 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInput:217][PORTAL] 750491572 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Component TEXT_INPUT [ ID: -1 - Binding: #.mediaReferenceList[0].title ] value is
2018-09-26 08:29:51,582 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInternal:110][PORTAL] 750491572 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting component TEXT_INPUT [ ID: -1 ]
2018-09-26 08:29:51,582 INFO o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:162][PORTAL] 750491572 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Attempting to find #.mediaReferenceList[0].description in CompiledReport : null #
2018-09-26 08:29:51,583 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInput:217][PORTAL] 750491573 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Component TEXT_INPUT [ ID: -1 - Binding: #.mediaReferenceList[0].description ] value is
2018-09-26 08:29:51,583 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInternal:110][PORTAL] 750491573 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting component TEXT_INPUT [ ID: -1 ]
2018-09-26 08:29:51,583 INFO o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:162][PORTAL] 750491573 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Attempting to find #.mediaReferenceList[0].credits in CompiledReport : null #
2018-09-26 08:29:51,583 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInput:217][PORTAL] 750491573 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Component TEXT_INPUT [ ID: -1 - Binding: #.mediaReferenceList[0].credits ] value is
2018-09-26 08:29:51,583 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInternal:110][PORTAL] 750491573 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting component TEXT_INPUT [ ID: -1 ]
2018-09-26 08:29:51,584 INFO o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:162][PORTAL] 750491574 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Attempting to find #.mediaReferenceList[0].url in CompiledReport : null #
2018-09-26 08:29:51,584 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInput:217][PORTAL] 750491574 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Component TEXT_INPUT [ ID: -1 - Binding: #.mediaReferenceList[0].url ] value is
2018-09-26 08:29:51,584 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractInternal:110][PORTAL] 750491574 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Inspecting component BOXAREA [ ID: ]
2018-09-26 08:29:51,585 INFO o.g.a.r.s.m.u.CompiledReportUtils [http-bio-9090-exec-100,find:162][PORTAL] 750491575 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.model.utils.CompiledReportUtils - Attempting to find #.mediaReferenceList[0].type in CompiledReport : null #
2018-09-26 08:29:51,585 INFO o.g.a.r.s.b.i.ReportManagerReportBuilder [http-bio-9090-exec-100,extractChoice:284][PORTAL] 750491575 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.support.builder.impl.ReportManagerReportBuilder - Component BOXAREA [ ID: - Binding: #.mediaReferenceList[0].type ] value is [null]
2018-09-26 08:29:51,585 INFO o.g.p.u.r.s.s.ReportServiceImpl [http-bio-9090-exec-100,exportReportToRSG:1586][PORTAL] 750491575 [http-bio-9090-exec-100] INFO org.gcube.portlets.user.reportgenerator.server.servlet.ReportServiceImpl - Exporting VME Report
2018-09-26 08:29:51,585 INFO o.g.a.r.c.RsgWriteClient [http-bio-9090-exec-100,endpointFor:100][PORTAL] 750491575 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.client.RsgWriteClient - Endpoint for update/report is http://www.fao.org/figis/secure-reports-store-gateway/rest/write/update/report
[PORTAL] 750491596 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.javax.filters.TokenSecuredRequestDecorator - Requesting token from remote token provider...
[PORTAL] 750491597 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Requesting and extracting token from http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request
[PORTAL] 750491597 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Requesting token from http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request
[PORTAL] 750491597 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Building token request to http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request
[PORTAL] 750491597 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Token request to http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request has been built in 0 mSec.
[PORTAL] 750491841 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Token has been received from http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request in 244 mSec.
[PORTAL] 750491841 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Extracting token from response received by http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request
[PORTAL] 750491841 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Reading response entity...
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Response entity has been read in 1 mSec. (32 bytes in total)
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Processing token before consumption via org.fao.fi.security.common.support.token.impl.IdentityTokenProcessor@6ecf18b9...
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Processing token before consumption via org.fao.fi.security.common.support.token.impl.IdentityTokenProcessor@6ecf18b9 took 0 mSec.
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Token has been extracted and processed from response received by http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request in 1 mSec.
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.providers.token.impl.BasicTokenProviderServiceClient - Token has been requested and extracted from http://www.fao.org/figis/secure-reports-store-gateway/security/token/plain/request in 245 mSec.
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.javax.filters.TokenSecuredRequestDecorator - Remote token has been received, extracted and processed in 246 mSec.
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.javax.filters.TokenSecuredRequestDecorator - Client-side processing received token...
[PORTAL] 750491842 [http-bio-9090-exec-100] INFO org.fao.fi.security.client.javax.filters.TokenSecuredRequestDecorator - Received token has been processed on the client-side in 0 mSec.
2018-09-26 08:29:51,853 INFO o.g.a.r.w.s.JAXBContextProvider [http-bio-9090-exec-100,:34][PORTAL] 750491843 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.webservice.support.JAXBContextProvider - Initializing org.gcube.application.rsg.webservice.support.JAXBContextProvider
2018-09-26 08:29:51,854 INFO o.g.a.r.c.s.JAXBClientContextProvider [http-bio-9090-exec-100,:36][PORTAL] 750491844 [http-bio-9090-exec-100] INFO org.gcube.application.rsg.client.support.JAXBClientContextProvider - Initializing org.gcube.application.rsg.client.support.JAXBClientContextProvider

javax.ws.rs.ProcessingException: java.net.SocketTimeoutException: Read timed out
at org.glassfish.jersey.client.HttpUrlConnector.apply(HttpUrlConnector.java:229)
at org.glassfish.jersey.client.ClientRuntime.invoke(ClientRuntime.java:224)
at org.glassfish.jersey.client.JerseyInvocation$1.call(JerseyInvocation.java:655)
at org.glassfish.jersey.client.JerseyInvocation$1.call(JerseyInvocation.java:652)
at org.glassfish.jersey.internal.Errors.process(Errors.java:315)
at org.glassfish.jersey.internal.Errors.process(Errors.java:297)
at org.glassfish.jersey.internal.Errors.process(Errors.java:228)
at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:424)
at org.glassfish.jersey.client.JerseyInvocation.invoke(JerseyInvocation.java:652)
at org.glassfish.jersey.client.JerseyInvocation$Builder.method(JerseyInvocation.java:412)
at org.glassfish.jersey.client.JerseyInvocation$Builder.post(JerseyInvocation.java:321)
at org.gcube.application.rsg.client.RsgWriteClient.update(RsgWriteClient.java:59)
at org.gcube.portlets.user.reportgenerator.server.servlet.ReportServiceImpl.exportReportToRSG(ReportServiceImpl.java:1587)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:561)
at com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:208)
at com.google.gwt.user.server.rpc.RemoteServiceServlet.processPost(RemoteServiceServlet.java:248)
at com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet.doPost(AbstractRemoteServiceServlet.java:62)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:116)
at sun.reflect.GeneratedMethodAccessor1916.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at com.liferay.portal.kernel.bean.ClassLoaderBeanHandler.invoke(ClassLoaderBeanHandler.java:67)
at com.sun.proxy.$Proxy952.doFilter(Unknown Source)
at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:116)
at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDirectCallFilter(InvokerFilterChain.java:165)
at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:96)
at com.liferay.portal.kernel.servlet.PortalClassLoaderFilter.doFilter(PortalClassLoaderFilter.java:74)
at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.processDoFilter(InvokerFilterChain.java:204)
at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilterChain.doFilter(InvokerFilterChain.java:109)
at com.liferay.portal.kernel.servlet.filters.invoker.InvokerFilter.doFilter(InvokerFilter.java:119)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:505)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:957)
at org.gcube.portal.threadlocalexec.SmartGearsPortalValve.invoke(SmartGearsPortalValve.java:69)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.ha.tcp.ReplicationValve.invoke(ReplicationValve.java:333)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:423)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1079)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:620)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:316)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
at java.net.SocketInputStream.read(SocketInputStream.java:171)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
at sun.net.
at sun.net.
at sun.net.
at sun.net.
at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)
at org.glassfish.jersey.client.HttpUrlConnector._apply(HttpUrlConnector.java:321)
at org.glassfish.jersey.client.HttpUrlConnector.apply(HttpUrlConnector.java:227)
... 59 more

The log is showing a timeout error due to the time that takes the service to respond.
Due to the current performance the service takes up to 10 seconds to answer, also in this case an error message appears to the user indicating that the report exporting has failed when the report has been in fact updated.

Could the timeout of the org.gcube.application.rsg.client be updated to 15 seconds?

Jesus Santamaria Fernandez wrote:

The log is showing a timeout error due to the time that takes the service to respond.
Due to the current performance the service takes up to 10 seconds to answer, also in this case an error message appears to the user indicating that the report exporting has failed when the report has been in fact updated.

Could the timeout of the org.gcube.application.rsg.client be updated to 15 seconds?

As per you knowledge is the timeout indicated in the code somewhere? I mean org.gcube.application.rsg.client component was written by FAO former employee (Fabio Fiorellato), although the code is committed on d4science svn.

I am checking the reports-store-gateway-client version 1.0.2 where the timeout is set in the AbstractRSGClient abstract class within the org.gcube.application.rsg.client package, but I use a decompiled version to see the real code.

Jesus Santamaria Fernandez wrote:

I am checking the reports-store-gateway-client version 1.0.2 where the timeout is set in the AbstractRSGClient abstract class within the org.gcube.application.rsg.client package, but I use a decompiled version to see the real code.

oh... I didn't know you had no info about this, this will be really helpful then:

The current version used by the Reports Manager app is 1.0.3 (http://eticsbuild2.research-infrastructures.eu/BuildReport/home/AllBuilds/org.gcube.4-12-1/BUILD_21)

and the source code can be found here on SVN anonymous access: http://svn.research-infrastructures.eu/public/d4science/gcube/branches/application/reports-store-gateway/1.0.3/

The read timeout is set in the AbstractRSGClient class (line 93):
http://svn.research-infrastructures.eu/public/d4science/gcube/branches/application/reports-store-gateway/1.0.3/reports-store-gateway-client/src/main/java/org/gcube/application/rsg/client/AbstractRSGClient.java

By default is infinity (0), in this case is set to 5000ms (5 seconds) but we would need to increase it to 15000 (15 seconds)

Is this library maintained by FAO or by d4science?

Regards.

D4Science only hosts the source code and build it to provide the Reports Manager webapp. The library was developed by one FAO former colleague (Fabio Fiorellato) so I'm guessing FAO is maintaining it (no maintenance was requires in the last few years though).

We can give you write access to the SVN project so that you can modify the code, or as I understand the required change code is a sole matter of replacing 5000 with 15000, we can make it for this time and release the fixed version of the library.

Please tell me what you prefer

The change is just replacing 5000 in the read timeout by 15000 so if possible please go ahead with the modification.

Dear Massimiliano, would be still possible to give write access to the SVN project using the email address jesus.santamariafernandez@fao.org ?
Best regards,
Jesus.

No sorry, it is not possible. You need to be a member of the gCube VRE to get access to SVN in write mode.

Dear Massimiliano,

We have tried again but still a warning message appears after updating a report even if the report is modified in the remote server. If the application has already been deployed in production, would it be possible to check the logs again?

Thank you in advance.

Jesus, Production has not been updated yet. The fix is in integration now. Will let you know when we put the Reports Manager containing the fix on production (likely tomorrow evening)