Exactly Syed, it was exactly that. I had errors in the proxy configuration file. Now it works and I can add the sources from biomart.org.
Thank you for your help. Joan De: [email protected] [mailto:[email protected]] En nombre de Syed Haider Enviado el: lunes, 10 de septiembre de 2012 13:54 Para: PROTASIO, JOAN (IDIBAPS) CC: [email protected] Asunto: Re: [BioMart Users] Adding new source java error Hi Joan, please check whether you need to set proxy to access sites outside your intranet ? also, whats the exact series of steps you do to reproduce this error ? Syed On 6 September 2012 11:44, <[email protected]<mailto:[email protected]>> wrote: > Hi all, > > > > > > I'm working with Biomart 0.8 rc7 and I am having some problems when I try to > add new sources by the martconfigurator. I don't understand what's the > problem because I could do it some months ago. > > > > I'm setting the parameters: Type url, host: http://www.biomart.org , port 80 > and Path: /biomart/martservice > > > > But I see in the terminal the error: > > > > /dades/Biomart_Development/biomart_COPD > > bioinfo-new:/dades/Biomart_Development/biomart_COPD # > ./scripts/martconfigurator.sh > > Starting MartConfigurator please wait .... > > [AWT-EventQueue-0] INFO martconfigurator - ...martconfigurator started. > > [AWT-EventQueue-0] INFO martconfigurator - Loading resources from > org/biomart/configurator/resources/messages > > [AWT-EventQueue-0] INFO martconfigurator - Done loading resources > > [AWT-EventQueue-0] INFO martconfigurator - Done loading settings > > 2012-09-06T12:32:55.171+0200 unknown: Java 1.6.0_26 (VM 20.1-b02, runtime > 1.6.0_26-b03) > > 2012-09-06T12:32:55.172+0200 unknown: Linux 2.6.16.21-0.8-smp/i386 x8 > > 2012-09-06T12:32:55.172+0200 unknown: (hang #1) event dispatch thread stuck > processing event for 1.08s so far: > > java.net.PlainSocketImpl.socketConnect(Native Method) > > java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:351) > > java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:213) > > java.net.PlainSocketImpl.connect(PlainSocketImpl.java:200) > > java.net.Socket.connect(Socket.java:529) > > java.net.Socket.connect(Socket.java:478) > > sun.net.NetworkClient.doConnect(NetworkClient.java:163) > > sun.net.www.http.HttpClient.openServer(HttpClient.java:394) > > . > > . > > . > > > > > > It seems to be a problem of Java but I haven't changed the version... > > > > > > Thanks, > > > > Joan > > > > > > > > > > > > > > Joan Protasio, Bioinformatician & Software Engineer > Bioinformatics Unit http://bioinformatics.fcrb.es/ > August Pi i Sunyer Biomedical Research Institute (IDIBAPS) > Phone: 93.227.54.00 (Ext. 4522) > C/ Rosselló 153 > 08036 Barcelona > > > > > _______________________________________________ > Users mailing list > [email protected]<mailto:[email protected]> > https://lists.biomart.org/mailman/listinfo/users >
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
