I'm deploying the graphdb standard edition. I used the startup.sh in a ubuntu machine. But it gives me the error "Couldn't find openrdf-sesame in the same container", I can still use the graphdb workbench, but the problem is that I cannot connect to the sesame server. I'm using tomcat6. I'm really new to this, could you tell me where should I put my openrdf-sesame.war file? I tried to put it in /var/lib/tomcat6/webapps, but it does not work. Also, I have to stop the tomcat6 service for the startup.sh script to run correctly.

Thank you very much.

The error message: 17:24:06.317 [http-bio-8080-exec-7] INFO c.o.f.c.s.SemanticDataManagement - Couldn't find openrdf-sesame in the same container java.net.SocketTimeoutException: Read timed out at java.net.SocketInputStream.socketRead0(Native Method) ~[na:1.8.0_40] at java.net.SocketInputStream.socketRead(SocketInputStream.java:116) ~[na:1.8.0_40] at java.net.SocketInputStream.read(SocketInputStream.java:170) ~[na:1.8.0_40] at java.net.SocketInputStream.read(SocketInputStream.java:141) ~[na:1.8.0_40] at java.io.BufferedInputStream.fill(BufferedInputStream.java:246) ~[na:1.8.0_40] at java.io.BufferedInputStream.read1(BufferedInputStream.java:286) ~[na:1.8.0_40] at java.io.BufferedInputStream.read(BufferedInputStream.java:345) ~[na:1.8.0_40] at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:704) ~[na:1.8.0_40] at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:647) ~[na:1.8.0_40] at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1535) ~[na:1.8.0_40] at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440) ~[na:1.8.0_40] at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480) ~[na:1.8.0_40] at com.ontotext.forest.core.semantic.SemanticDataManagement.tryToConnectToSesame(SemanticDataManagement.java:262) [graphdb-framework-core-2.3.7.jar:na] at com.ontotext.forest.core.semantic.SemanticDataManagement.getSesameLocation(SemanticDataManagement.java:220) [graphdb-framework-core-2.3.7.jar:na] at com.ontotext.forest.core.semantic.SemanticDataManagement.getCurrentLocation(SemanticDataManagement.java:190) [graphdb-framework-core-2.3.7.jar:na] at com.ontotext.forest.security.RepositoryAccessVoter.vote(RepositoryAccessVoter.java:56) [graphdb-framework-security-2.3.7.jar:na] at com.ontotext.forest.security.RepositoryAccessVoter.vote(RepositoryAccessVoter.java:24) [graphdb-framework-security-2.3.7.jar:na] at org.springframework.security.access.vote.UnanimousBased.decide(UnanimousBased.java:77) [spring-security-core-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.access.intercept.AbstractSecurityInterceptor.beforeInvocation(AbstractSecurityInterceptor.java:206) [spring-security-core-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:115) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.access.intercept.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:84) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.access.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:113) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.session.SessionManagementFilter.doFilter(SessionManagementFilter.java:103) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.authentication.AnonymousAuthenticationFilter.doFilter(AnonymousAuthenticationFilter.java:113) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.servletapi.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:154) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.savedrequest.RequestCacheAwareFilter.doFilter(RequestCacheAwareFilter.java:45) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.authentication.www.BasicAuthenticationFilter.doFilter(BasicAuthenticationFilter.java:150) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.authentication.ui.DefaultLoginPageGeneratingFilter.doFilter(DefaultLoginPageGeneratingFilter.java:155) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.authentication.AbstractAuthenticationProcessingFilter.doFilter(AbstractAuthenticationProcessingFilter.java:199) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.authentication.logout.LogoutFilter.doFilter(LogoutFilter.java:110) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.context.request.async.WebAsyncManagerIntegrationFilter.doFilterInternal(WebAsyncManagerIntegrationFilter.java:50) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:106) [spring-web-3.2.10.RELEASE.jar:3.2.10.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.context.SecurityContextPersistenceFilter.doFilter(SecurityContextPersistenceFilter.java:87) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:342) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy.doFilterInternal(FilterChainProxy.java:192) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at org.springframework.security.web.FilterChainProxy.doFilter(FilterChainProxy.java:160) [spring-security-web-3.2.5.RELEASE.jar:3.2.5.RELEASE] at com.ontotext.forest.security.AdminDelegatingFilterProxy.doFilter(AdminDelegatingFilterProxy.java:26) [graphdb-framework-security-2.3.7.jar:na] at org.springframework.web.filter.DelegatingFilterProxy.invokeDelegate(DelegatingFilterProxy.java:343) [spring-web-3.2.10.RELEASE.jar:3.2.10.RELEASE] at org.springframework.web.filter.DelegatingFilterProxy.doFilter(DelegatingFilterProxy.java:260) [spring-web-3.2.10.RELEASE.jar:3.2.10.RELEASE] at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243) [graphdb-tomcat.jar:na] at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210) [graphdb-tomcat.jar:na] at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222) [graphdb-tomcat.jar:na] at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123) [graphdb-tomcat.jar:na] at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:472) [graphdb-tomcat.jar:na] at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171) [graphdb-tomcat.jar:na] at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:99) [graphdb-tomcat.jar:na] at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118) [graphdb-tomcat.jar:na] at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:407) [graphdb-tomcat.jar:na] at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1004) [graphdb-tomcat.jar:na] at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:589) [graphdb-tomcat.jar:na] at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312) [graphdb-tomcat.jar:na] at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_40] at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_40] at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]

asked 15 Apr '15, 20:34

al3xtouch's gravatar image

al3xtouch
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accept rate: 0%


Hi al3xtouch

This is an INFO message(although it has a stacktrace) and shouldn't be something to worry about. It just indicates that we couldn't detect the openrdf-sesame application in same container(in your case tomcat).

The startup script is something for just starting up with the application - it just deploys the war files found in the graphdb_sesame directory.

If you already have tomcat installed you don't need to use the startup script - just put both of the war files in /var/lib/tomcat6/webapps and restart tomcat. If you now access the graphdb-workbench context in tomcat, you should be already connected to the openrdf-sesame server and the INFO message will obviously be gone :)

Hope this helps :)

link

answered 16 Apr '15, 05:22

nikolavp's gravatar image

nikolavp ♦
26
accept rate: 33%

Thanks for your reply. Should I use the openrdf-sesame.war file in the sesame_graphdb directory or the openrdf-sesame.war file I got from the rdf4j website? I tried to put both war files in the sesame_graphdb directory in my /var/lib/tomcat6/webapps, and access the graphdb-workbench, but it gives me the error "HTTP Status 404 - /graphdb-workbench-se/

type Status report

message /graphdb-workbench-se/

description The requested resource is not available.

Apache Tomcat/6.0.39"

I can access open-sesame in this way though, do you know what is wrong? Thanks.

(16 Apr '15, 12:41) al3xtouch

I fixed the problem, it turns out I have to use tomcat7 to deploy it. Thanks.

link

answered 16 Apr '15, 14:24

al3xtouch's gravatar image

al3xtouch
469813
accept rate: 0%

Glad that you was able to fix the problem. We will double check why it didn't work on tomcat6 though. Although we recommend a recent version of tomcat, we should state in the docs that we don't work with tomcat6 if that's the case.

Thank again al3xtouch ;)

link

answered 17 Apr '15, 06:31

nikolavp's gravatar image

nikolavp ♦
26
accept rate: 33%

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Asked: 15 Apr '15, 20:34

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Last updated: 17 Apr '15, 06:31

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