Hi Yue,
Can you connect (ping/wget) to www.biomart.org from the machine you are
running MartConfigurator ?
Also, what happens when you try 'Relational Mart' option instead of 'URL
Mart'?
Syed
On 21/02/2011 17:54, Yue W Webster 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?
[cid:_1_0B293AB40B2936F8006267E48525783E]
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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