[BioMart Users] problem installing biomart

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[BioMart Users] problem installing biomart

Yue W Webster

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?


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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Re: [BioMart Users] problem installing biomart

Syed Haider
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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Re: [BioMart Users] problem installing biomart

Arek Kasprzyk-2
In reply to this post by Yue W Webster
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  <[hidden email]> 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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Re: [BioMart Users] problem installing biomart

Yue W Webster
In reply to this post by Syed Haider

Hi Syed,

I can ping to www.biomart.org.  I got the same connection time out error when trying "Relational Mart" or "Database Schema".

Thank you in advance for your help
Yue


Syed Haider <[hidden email]>

02/21/2011 01:42 PM

To
Yue W Webster <[hidden email]>
cc
Arek Kasprzyk <[hidden email]>, "[hidden email]" <[hidden email]>, Jian WJ Wang <[hidden email]>
Subject
Re: [BioMart Users] problem installing biomart





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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Re: [BioMart Users] problem installing biomart

Syed Haider
Yue,

when using the web browser from the same machine, do you set any http
proxy ?

are you aware of any firewall setting that you might have on your system ?

Syed

On 21/02/2011 19:27, Yue W Webster wrote:
> java.net.ConnectException: Connection timed out
>>            at java.net.PlainSocketImpl.socketConnect(Native Method)
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Re: [BioMart Users] problem installing biomart

Yue W Webster

Hi Syed,

Yes, you are right. Our Linux server sits inside a firewall. I have to set the HTTP proxy when using web browser. Is there any way to set proxy for biomart?

Thanks
Yue


Syed Haider <[hidden email]>

02/21/2011 03:29 PM

To
Yue W Webster <[hidden email]>
cc
Arek Kasprzyk <[hidden email]>, "[hidden email]" <[hidden email]>, Jian WJ Wang <[hidden email]>
Subject
Re: [BioMart Users] problem installing biomart





Yue,

when using the web browser from the same machine, do you set any http
proxy ?

are you aware of any firewall setting that you might have on your system ?

Syed

On 21/02/2011 19:27, Yue W Webster wrote:
> java.net.ConnectException: Connection timed out
>>            at java.net.PlainSocketImpl.socketConnect(Native Method)


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Re: [BioMart Users] problem installing biomart

Syed Haider
Hmm, let me see, we should be able to add the proxy string in
configuration and offer a patch subsequently.

apologies for the inconvenience.

Syed

On 21/02/2011 20:35, Yue W Webster wrote:

>
> Hi Syed,
>
> Yes, you are right. Our Linux server sits inside a firewall. I have to set the HTTP proxy when using web browser. Is there any way to set proxy for biomart?
>
> Thanks
> Yue
>
>
> Syed Haider<[hidden email]>
>
> 02/21/2011 03:29 PM
> To
> Yue W Webster<[hidden email]>
> cc
> Arek Kasprzyk<[hidden email]>, "[hidden email]"<[hidden email]>, Jian WJ Wang<[hidden email]>
> Subject
> Re: [BioMart Users] problem installing biomart
>
>
>
>
>
> Yue,
>
> when using the web browser from the same machine, do you set any http
> proxy ?
>
> are you aware of any firewall setting that you might have on your system ?
>
> Syed
>
> On 21/02/2011 19:27, Yue W Webster wrote:
>> java.net.ConnectException: Connection timed out
>>>             at java.net.PlainSocketImpl.socketConnect(Native Method)
>
>
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[BioMart Users] two more problems during installation

Yue W Webster
In reply to this post by Arek Kasprzyk-2

Hello Arek,

I am trying to install biomart on a server outside of Lilly firewall and seems to get a bit future in the process. However, I am still having difficulties and have to bother you again.

Issue #1: After opening “Add Data Source” window. I couldn’t see icgc3.xml after I scrolled through n the [Marts] list.

Issue #2: Not able to find icgi, I tried to add MSD as mentioned in the installation document (BioMart 0.8 User Manual, release candidate 4, 1st February 2010). But after I clicked on msd proteinstructures and clicked OK, I was never prompted to choose a name. Nor was a new config created and shown in the right-hand panel. Here is the message from the terminal

Starting MartConfigurator please wait ....
[Thread-3] ERROR martconfigurator - Trying to connect to: msd http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default
ERROR [Thread-3] (Log.java:197) - Trying to connect to: msd http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default
[Thread-3] ERROR martconfigurator - Checking exportable
ERROR [Thread-3] (Log.java:197) - Checking exportable
[Thread-3] ERROR martconfigurator - Done
ERROR [Thread-3] (Log.java:197) - Done



Thanks
Yue


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Re: [BioMart Users] two more problems during installation

Arek Kasprzyk-2
Hi Yue
#1. The icgc3 config is not part of the central registry yet that is available over webservice from biomart.org. For now you need to load it directly from a file called icgc3.XML available in the registry directory in  biomart-java. Jonathan will be adding a dedicated section on the icgc deployment in the next rc5 release docs so hopefully this should be clear then

#2 I did not experience any issues with msd when testing recently. Perhaps someone else could comment on that?

a




On 2011-02-23, at 23:59, "Yue W Webster" <[hidden email]> wrote:


Hello Arek,

I am trying to install biomart on a server outside of Lilly firewall and seems to get a bit future in the process. However, I am still having difficulties and have to bother you again.

Issue #1: After opening “Add Data Source” window. I couldn’t see icgc3.xml after I scrolled through n the [Marts] list.

<ATT00003..gif>

Issue #2: Not able to find icgi, I tried to add MSD as mentioned in the installation document (BioMart 0.8 User Manual, release candidate 4, 1st February 2010). But after I clicked on msd proteinstructures and clicked OK, I was never prompted to choose a name. Nor was a new config created and shown in the right-hand panel. Here is the message from the terminal

Starting MartConfigurator please wait ....
[Thread-3] ERROR martconfigurator - Trying to connect to: msd http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default
ERROR [Thread-3] (Log.java:197) - Trying to connect to: msd http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default
[Thread-3] ERROR martconfigurator - Checking exportable
ERROR [Thread-3] (Log.java:197) - Checking exportable
[Thread-3] ERROR martconfigurator - Done
ERROR [Thread-3] (Log.java:197) - Done

<ATT00004..gif>



Thanks
Yue


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Re: [BioMart Users] two more problems during installation

Syed Haider
Hi Yue,

what exactly are you doing in terms of steps, when you add MSD ?

thanks
Syed

On 23/02/2011 18:52, Arek Kasprzyk wrote:

> Hi Yue
> #1. The icgc3 config is not part of the central registry yet that is available over webservice from biomart.org<http://biomart.org>. For now you need to load it directly from a file called icgc3.XML available in the registry directory in  biomart-java. Jonathan will be adding a dedicated section on the icgc deployment in the next rc5 release docs so hopefully this should be clear then
>
> #2 I did not experience any issues with msd when testing recently. Perhaps someone else could comment on that?
>
> a
>
>
>
>
> On 2011-02-23, at 23:59, "Yue W Webster"<[hidden email]<mailto:[hidden email]>>  wrote:
>
>
> Hello Arek,
>
> I am trying to install biomart on a server outside of Lilly firewall and seems to get a bit future in the process. However, I am still having difficulties and have to bother you again.
>
> Issue #1: After opening “Add Data Source” window. I couldn’t see icgc3.xml after I scrolled through n the [Marts] list.
>
> <ATT00003..gif>
>
> Issue #2: Not able to find icgi, I tried to add MSD as mentioned in the installation document (BioMart 0.8 User Manual, release candidate 4, 1st February 2010). But after I clicked on msd proteinstructures and clicked OK, I was never prompted to choose a name. Nor was a new config created and shown in the right-hand panel. Here is the message from the terminal
>
> Starting MartConfigurator please wait ....
> [Thread-3] ERROR martconfigurator - Trying to connect to: msd<http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default>  http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default
> ERROR [Thread-3] (Log.java:197) - Trying to connect to: msd<http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default>  http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&virtualschema=default
> [Thread-3] ERROR martconfigurator - Checking exportable
> ERROR [Thread-3] (Log.java:197) - Checking exportable
> [Thread-3] ERROR martconfigurator - Done
> ERROR [Thread-3] (Log.java:197) - Done
>
> <ATT00004..gif>
>
>
> Thanks
> Yue
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Re: [BioMart Users] two more problems during installation

Yong Liang
Hi Yue,

You need to clicked on 'msd protein structures' and clicked 'OK'. Sorry for
the inconvenience. We will improve the GUI later that the 'OK' button
enabled only when some sources are selected.


On 11-02-23 1:57 PM, "Syed Haider" <[hidden email]> wrote:

> Hi Yue,
>
> what exactly are you doing in terms of steps, when you add MSD ?
>
> thanks
> Syed
>
> On 23/02/2011 18:52, Arek Kasprzyk wrote:
>> Hi Yue
>> #1. The icgc3 config is not part of the central registry yet that is
>> available over webservice from biomart.org<http://biomart.org>. For now you
>> need to load it directly from a file called icgc3.XML available in the
>> registry directory in  biomart-java. Jonathan will be adding a dedicated
>> section on the icgc deployment in the next rc5 release docs so hopefully this
>> should be clear then
>>
>> #2 I did not experience any issues with msd when testing recently. Perhaps
>> someone else could comment on that?
>>
>> a
>>
>>
>>
>>
>> On 2011-02-23, at 23:59, "Yue W
>> Webster"<[hidden email]<mailto:[hidden email]>>  wrote:
>>
>>
>> Hello Arek,
>>
>> I am trying to install biomart on a server outside of Lilly firewall and
>> seems to get a bit future in the process. However, I am still having
>> difficulties and have to bother you again.
>>
>> Issue #1: After opening ³Add Data Source² window. I couldn¹t see icgc3.xml
>> after I scrolled through n the [Marts] list.
>>
>> <ATT00003..gif>
>>
>> Issue #2: Not able to find icgi, I tried to add MSD as mentioned in the
>> installation document (BioMart 0.8 User Manual, release candidate 4, 1st
>> February 2010). But after I clicked on msd proteinstructures and clicked OK,
>> I was never prompted to choose a name. Nor was a new config created and shown
>> in the right-hand panel. Here is the message from the terminal
>>
>> Starting MartConfigurator please wait ....
>> [Thread-3] ERROR martconfigurator - Trying to connect to:
>> msd<http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=
>> msd&virtualschema=default>
>> http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&
>> virtualschema=default
>> ERROR [Thread-3] (Log.java:197) - Trying to connect to:
>> msd<http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=
>> msd&virtualschema=default>
>> http://www.biomart.org:80/biomart/martservice?type=configuration&dataset=msd&
>> virtualschema=default
>> [Thread-3] ERROR martconfigurator - Checking exportable
>> ERROR [Thread-3] (Log.java:197) - Checking exportable
>> [Thread-3] ERROR martconfigurator - Done
>> ERROR [Thread-3] (Log.java:197) - Done
>>
>> <ATT00004..gif>
>>
>>
>> Thanks
>> Yue
> _______________________________________________
> Users mailing list
> [hidden email]
> https://lists.biomart.org/mailman/listinfo/users


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