I just tried both- with the command line, starts and stops without the connection exceptions; using deploy button in MConf (using X forwarding from a remote box) I get the connection exceptions, on both a first-run and a redeploy after starting/stopping from the CLI.
tj _____ T.J. Esposito La Jolla Research Business Technology - Bioinformatics & Innovation Please consider the environment before printing email. -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Syed Haider Sent: Thursday, January 13, 2011 4:05 AM To: Phil Jones @ EBI Cc: [email protected] Subject: Re: [Users] Bug Report: BioMart 0.8 release candidate 3 Hi Phil, Have you tried deploying it through command line ? Just wondering whether its just the deploy button or a general problem. Also, are you running MartConfigurator over X client ? Best, Syed PS: please note the new mailing list :) On 13/01/2011 11:52, Phil Jones @ EBI wrote: > Hi BioMart developers, > > Thank you for the announcement of release candidate 3. I have just attempted > to follow the instructions in the documentation. At the point of clicking > the "Deploy" button for the MSD Protein Structure data set (page 7 of the > docs), repeated stack traces are being displayed in the console (no error > message from the interface however) as follows: > > java.net.ConnectException: Connection refused at > java.net.PlainSocketImpl.socketConnect(Native Method) at > java.net.PlainSocketImpl.doConnect(PlainSocketImpl.java:333) > at java.net.PlainSocketImpl.connectToAddress(PlainSocketImpl.java:195) > at java.net.PlainSocketImpl.connect(PlainSocketImpl.java:182) > at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:366) > at java.net.Socket.connect(Socket.java:529) > at java.net.Socket.connect(Socket.java:478) > at sun.net.NetworkClient.doConnect(NetworkClient.java:163) > at sun.net.www.http.HttpClient.openServer(HttpClient.java:394) > at sun.net.www.http.HttpClient.openServer(HttpClient.java:529) > at sun.net.www.http.HttpClient.<init>(HttpClient.java:233) > at sun.net.www.http.HttpClient.New(HttpClient.java:306) > at sun.net.www.http.HttpClient.New(HttpClient.java:323) > at > sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLCo > nnection.java:975) at > sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnec > tion.java:916) at > sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection. > java:841) at > org.biomart.configurator.utils.McUtils.isHttpServerAvailable(McUtils.j > ava:851) at > org.biomart.configurator.view.menu.McMenus.deploy(McMenus.java:654) > at > org.biomart.configurator.view.menu.McMenus.access$200(McMenus.java:76) > at > org.biomart.configurator.view.menu.McMenus$3.construct(McMenus.java:53 > 8) at > org.biomart.common.view.gui.SwingWorker$2.run(SwingWorker.java:128) > at java.lang.Thread.run(Thread.java:662) > > My platform is: > Ubuntu 10.04 > Java 1.6.0_22 > ant 1.7.1 (not that there were any problems with the build reported, so this > is probably irrelevant. > > best regards, > > Phil. > > On 18 December 2010 18:29, Syed > Haider<[email protected]<mailto:[email protected]>> wrote: > Hello everyone, > > The BioMart 0.8 rc3 is now available for deployer testing. The new version is > a Java based, out-of-the-box single integrated application to facilitate mart > building, configuration and web server deployment. > > For installation and a user instructions, please see a deployer's guide > available here: > > http://www.biomart.org/rc3_documentation.pdf > > This release is tested on Mac OS X (Leopard and Snow Leapord), Linux (Debian > 4.1.1-21), Java 6. See docs for details. > > The following features are now available for your testing: > > 1- Support for 5 database platforms (MySQL, Oracle, PgSQL, MS SQL, > DB2) > > 2- Virtual Marts (non-materialised querying against source database) > > 4- A range of different web interfaces from Basic Form to Advanced > Querying interfaces (MartAnalysis, MartForm, MartWizard, MartExplorer) > and a Report page (MartReport) > > 5- Backwards compatibility for BioMart 0.7 sources > > 6- Secure access > > 7- Multi-dataset linking with Link-Indices for faster and scalable > joins > > 8- Processor framework for specialised data visualisations (e.g > charts) > > FEATURES NOT AVAILABLE YET: > - Full Mbuilder component including source schema modifications > - Updates > - Processors (Genomic Sequence, GFF, DAS, WSDL, Gzip, Excel) > > Please send your feedback and bug reports to > [email protected]<mailto:[email protected]> > > Best Wishes, > Syed Haider on behalf of the BioMart Team. > > > > -- > Phil Jones > Software Development Coordinator > InterPro Team > PANDA Group, EMBL-EBI > Wellcome Trust Genome Campus > Hinxton, Cambridge, CB10 1SD > UK. > > Work phone: +44 1223 492685 > Mobile: +44 7789 900964 > Skype: philip-jones > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
