Connection error with Rserve and TwoRavens

28 views
Skip to first unread message

ip.crai....@gmail.com

unread,
Apr 12, 2019, 4:48:36 PM4/12/19
to Dataverse Users Community
I have installed the tworavens explorer tool on our Dataverse, the button is displaying on the data but when I click the explore button the tworavens screen has no data and the logs display an error with rserve. I have checked the user and password of rserver and they are well configured in glassfish, the glassfish directory belongs glassfish and the tworavens directory belongs to apache. We are storing our files with Amazon S3, could this be the issue?


[2019-04-12T15:30:28.638-0500] [glassfish 4.1] [SEVERE] [] [] [tid: _ThreadID=31 _ThreadName=Thread-9] [timeMillis: 1555101028638] [levelValue: 1000] [[
org.rosuda.REngine.Rserve.RserveException: Cannot connect: Connection refused (Connection refused)
    at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:88)
    at org.rosuda.REngine.Rserve.RConnection.<init>(RConnection.java:60)
    at edu.harvard.iq.dataverse.rserve.RemoteDataFrameService.runDataPreprocessing(RemoteDataFrameService.java:548)
    at edu.harvard.iq.dataverse.dataaccess.DataConverter.runFormatConversion(DataConverter.java:277)
    at edu.harvard.iq.dataverse.dataaccess.DataConverter.performFormatConversion(DataConverter.java:112)
    at edu.harvard.iq.dataverse.api.DownloadInstanceWriter.writeTo(DownloadInstanceWriter.java:136)
    at edu.harvard.iq.dataverse.api.DownloadInstanceWriter.writeTo(DownloadInstanceWriter.java:44)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.invokeWriteTo(WriterInterceptorExecutor.java:263)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor$TerminalWriterInterceptor.aroundWriteTo(WriterInterceptorExecutor.java:250)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.server.internal.JsonWithPaddingInterceptor.aroundWriteTo(JsonWithPaddingInterceptor.java:106)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.server.internal.MappableExceptionWrapperInterceptor.aroundWriteTo(MappableExceptionWrapperInterceptor.java:89)
    at org.glassfish.jersey.message.internal.WriterInterceptorExecutor.proceed(WriterInterceptorExecutor.java:162)
    at org.glassfish.jersey.message.internal.MessageBodyFactory.writeTo(MessageBodyFactory.java:1154)
    at org.glassfish.jersey.server.ServerRuntime$Responder.writeResponse(ServerRuntime.java:621)
    at org.glassfish.jersey.server.ServerRuntime$Responder.processResponse(ServerRuntime.java:377)
    at org.glassfish.jersey.server.ServerRuntime$Responder.process(ServerRuntime.java:367)
    at org.glassfish.jersey.server.ServerRuntime$1.run(ServerRuntime.java:274)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:271)
    at org.glassfish.jersey.internal.Errors$1.call(Errors.java:267)
    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:267)
    at org.glassfish.jersey.process.internal.RequestScope.runInScope(RequestScope.java:297)
    at org.glassfish.jersey.server.ServerRuntime.process(ServerRuntime.java:254)
    at org.glassfish.jersey.server.ApplicationHandler.handle(ApplicationHandler.java:1028)
    at org.glassfish.jersey.servlet.WebComponent.service(WebComponent.java:372)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:381)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:344)
    at org.glassfish.jersey.servlet.ServletContainer.service(ServletContainer.java:221)
    at org.apache.catalina.core.StandardWrapper.service(StandardWrapper.java:1682)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:344)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
    at org.ocpsoft.rewrite.servlet.RewriteFilter.doFilter(RewriteFilter.java:226)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
    at edu.harvard.iq.dataverse.api.ApiBlockingFilter.doFilter(ApiBlockingFilter.java:162)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
    at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:30)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
    at org.apache.catalina.core.ApplicationDispatcher.doInvoke(ApplicationDispatcher.java:873)
    at org.apache.catalina.core.ApplicationDispatcher.invoke(ApplicationDispatcher.java:739)
    at org.apache.catalina.core.ApplicationDispatcher.processRequest(ApplicationDispatcher.java:575)
    at org.apache.catalina.core.ApplicationDispatcher.doDispatch(ApplicationDispatcher.java:546)
    at org.apache.catalina.core.ApplicationDispatcher.dispatch(ApplicationDispatcher.java:428)
    at org.apache.catalina.core.ApplicationDispatcher.forward(ApplicationDispatcher.java:378)
    at edu.harvard.iq.dataverse.api.ApiRouter.doFilter(ApiRouter.java:34)
    at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:256)
    at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:214)
    at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:316)
    at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:160)
    at org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:734)
    at org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:673)
    at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:99)
    at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:174)
    at org.apache.catalina.connector.CoyoteAdapter.doService(CoyoteAdapter.java:415)
    at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:282)
    at com.sun.enterprise.v3.services.impl.ContainerMapper$HttpHandlerCallable.call(ContainerMapper.java:459)
    at com.sun.enterprise.v3.services.impl.ContainerMapper.service(ContainerMapper.java:167)
    at org.glassfish.grizzly.http.server.HttpHandler.runService(HttpHandler.java:201)
    at org.glassfish.grizzly.http.server.HttpHandler.doHandle(HttpHandler.java:175)
    at org.glassfish.grizzly.http.server.HttpServerFilter.handleRead(HttpServerFilter.java:235)
    at org.glassfish.grizzly.filterchain.ExecutorResolver$9.execute(ExecutorResolver.java:119)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeFilter(DefaultFilterChain.java:284)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.executeChainPart(DefaultFilterChain.java:201)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.execute(DefaultFilterChain.java:133)
    at org.glassfish.grizzly.filterchain.DefaultFilterChain.process(DefaultFilterChain.java:112)
    at org.glassfish.grizzly.ProcessorExecutor.execute(ProcessorExecutor.java:77)
    at org.glassfish.grizzly.nio.transport.TCPNIOTransport.fireIOEvent(TCPNIOTransport.java:561)
    at org.glassfish.grizzly.strategies.AbstractIOStrategy.fireIOEvent(AbstractIOStrategy.java:112)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.run0(WorkerThreadIOStrategy.java:117)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy.access$100(WorkerThreadIOStrategy.java:56)
    at org.glassfish.grizzly.strategies.WorkerThreadIOStrategy$WorkerThreadRunnable.run(WorkerThreadIOStrategy.java:137)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.doWork(AbstractThreadPool.java:565)
    at org.glassfish.grizzly.threadpool.AbstractThreadPool$Worker.run(AbstractThreadPool.java:545)
    at java.lang.Thread.run(Thread.java:748)]]

[2019-04-12T15:30:28.639-0500] [glassfish 4.1] [WARNING] [] [edu.harvard.iq.dataverse.dataaccess] [tid: _ThreadID=31 _ThreadName=http-listener-1(5)] [timeMillis: 1555101028639] [levelValue: 900] [[
Format-converted file was not properly created.]]

danny...@g.harvard.edu

unread,
Apr 15, 2019, 11:04:15 AM4/15/19
to Dataverse Users Community
Hi, 

You may get an answer here, but the TwoRavens support is provided by a different group. I'd suggest reaching out to the group here: http://2ra.vn/community/index.html

Thanks,

Danny

Michel Bamouni

unread,
Apr 17, 2019, 4:40:04 AM4/17/19
to Dataverse Users Community
Hi,

When I install tworavens, I also get this error. It's mean that your rserve is not started.
So check if rserve is running and if not, start it.

If after starting rserve, you continue to get an empty view in tworavens, follow the steps describing in the "Troubleshooting" part of this documentation : http://guides.dataverse.org/en/latest/installation/r-rapache-tworavens.html

Hope that helps you.

regards,

Michel

Le lundi 15 avril 2019 17:04:15 UTC+2, danny...@g.harvard.edu a écrit :
Hi, 

You may get an answer here, but the TwoRavens support is provided by a different group. I'd suggest reaching out to the group here: http://2ra.vn/community/index.html

Thanks,

Danny
Reply all
Reply to author
Forward
0 new messages