Hi Yue I just tried exactly the same procedure from Tokyo where i an now and got all the marts ok, deployed with MSD and queried OK. It seems like it must be something on your side
a. On 2011-02-22, at 2:55, "Yue W Webster"ke <[email protected]<mailto:[email protected]>> wrote: Hello Arek, Jian and I are trying to install biomart on one of our Linux server. We followed instructions in “BioMart 0.8 User Manual, release candidate 4, 1st February 2010”. We were able to complete step 1-4(START MARTCONFIGURATOR). On step 5, we were able to open “Add Data Source” window, but when we clicked the Get… button, none of the available marts appear in the left panel (see following picture). Could you help? <ATT00002..gif> After a while, we got a Java time out error on the Linux command line window: java.net.ConnectException: Connection timed out at java.net.PlainSocketImpl.socketConnect(Native Method) at java.net.PlainSocketImpl.doConnect(Unknown Source) at java.net.PlainSocketImpl.connectToAddress(Unknown Source) at java.net.PlainSocketImpl.connect(Unknown Source) at java.net.Socket.connect(Unknown Source) at java.net.Socket.connect(Unknown Source) at sun.net.NetworkClient.doConnect(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.openServer(Unknown Source) at sun.net.www.http.HttpClient.<init>(Unknown Source) at sun.net.www.http.HttpClient.New(Unknown Source) at sun.net.www.http.HttpClient.New(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source) at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source) at org.apache.xerces.impl.XMLEntityManager.setupCurrentEntity(Unknown Source) at org.apache.xerces.impl.XMLVersionDetector.determineDocVersion(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source) at org.apache.xerces.parsers.XMLParser.parse(Unknown Source) at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source) at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) at org.jdom.input.SAXBuilder.build(SAXBuilder.java:453) at org.jdom.input.SAXBuilder.build(SAXBuilder.java:810) at org.biomart.configurator.utils.McGuiUtils.getMartsFromURL(McGuiUtils.java:563) at org.biomart.configurator.view.gui.dialogs.DataLinkDialog.setUrlMetaTree(DataLinkDialog.java:425) at org.biomart.configurator.view.gui.dialogs.DataLinkDialog.access$1100(DataLinkDialog.java:61) at org.biomart.configurator.view.gui.dialogs.DataLinkDialog$4.actionPerformed(DataLinkDialog.java:377) at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source) at javax.swing.DefaultButtonModel.setPressed(Unknown Source) at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.Dialog$1.run(Unknown Source) at java.awt.Dialog$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.awt.Dialog.show(Unknown Source) at java.awt.Component.show(Unknown Source) at java.awt.Component.setVisible(Unknown Source) at java.awt.Window.setVisible(Unknown Source) at java.awt.Dialog.setVisible(Unknown Source) at org.biomart.configurator.view.gui.dialogs.DataLinkDialog.showDialog(DataLinkDialog.java:75) at org.biomart.configurator.controller.ObjectController.addMarts(ObjectController.java:79) at org.biomart.configurator.view.idwViews.McViewSourceTree.mousePressed(McViewSourceTree.java:248) at java.awt.AWTEventMulticaster.mousePressed(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) our server is running Linux X86_64 Thank you for your help
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