Web Service Connection Problem

Jalview Discussion
1

Hello,

I have used Jalview for over a year now without problem (v2.6-2.7). Recently upgraded to v2.8, and now cannot use the JABAWS. Error message alerts me when opening program. This happens whether my firewall is up or not. I use Win7 64-bit. Here is my console output after refreshing the services:

Jalview Desktop 2.8
Build Date: 12 November 2012
Java version: 1.6.0_01
x86 Windows Vista 6.1
WARN - Exception when discovering One Way services:
WARN - Exception when discovering One Way services:
WARN - Exception when discovering Jws2 services.
INFO - Not enabling Google Tracking.
INFO - Constructing news reader.
INFO - Completed construction of reader.
INFO - Saved last read date as Nov 12, 2012 6:00:00 AM
INFO - Saved last read date as Nov 12, 2012 6:00:00 AM
INFO - Saved last read date as Nov 12, 2012 6:00:00 AM
WARN - GET request for “http://www.dasregistry.org/das1/sources//sources” resulted in 404 (Not Found); invoking error handler
Failed to contact DAS1 registry at http://www.dasregistry.org/das1/sources/
org.biodas.jdas.exceptions.
DASClientException: 404 Not Found
at org.biodas.jdas.client.SourcesClient.fetchData(SourcesClient.java:77)
at org.biodas.jdas.client.SourcesClient.fetchDataRegistry(SourcesClient.java:126)
at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:117)
at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getDASSources(DasSourceRegistry.java:100)
at jalview.ws.dbsources.das.datamodel.DasSourceRegistry.getSources(DasSourceRegistry.java:166)
at jalview.gui.DasSourceBrowser.(DasSourceBrowser.java:103)
at jalview.gui.DasSourceBrowser.(DasSourceBrowser.java:115)
at jalview.gui.Preferences.(Preferences.java:110)
at jalview.gui.Desktop.preferences_actionPerformed(Desktop.java:1356)
at jalview.jbgui.GDesktop$7.actionPerformed(GDesktop.java:198)
at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)
at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at javax.swing.DefaultButtonModel.setPressed(Unknown Source)
at javax.swing.AbstractButton.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)
at javax.swing.plaf.basic.BasicMenuItemUI$Handler.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.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
WARN - Exception when discovering One Way services:
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service JronnWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service DisemblWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/DisemblWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service GlobPlotWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/GlobPlotWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service IUPredWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/IUPredWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
Connecting to JABAWS version 2 service
Jws2 Discoverer: Problem on http://www.compbio.dundee.ac.uk/jabaws with service AAConWS:
Could not connect to http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl the server is down?
java.net.ConnectException: Could not connect to http://www.compbio.dundee.ac.uk/jabaws/AAConWS?wsdl the server is down?
at compbio.ws.client.Jws2Client.connect(Unknown Source)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:150)
at java.lang.Thread.run(Unknown Source)
WARN - Exception when discovering Jws2 services.
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@187d27e
java.lang.NullPointerException
at jalview.ws.jws2.Jws2Discoverer.addService(Jws2Discoverer.java:253)
at jalview.ws.jws2.JabaWsServerQuery.run(JabaWsServerQuery.java:181)
at java.lang.Thread.run(Unknown Source)

Thanks,

Charles

2

Hi Charles.

I have used Jalview for over a year now without problem (v2.6-2.7).
Recently upgraded to v2.8, and now cannot use the JABAWS. Error
message alerts me when opening program. This happens whether my
firewall is up or not. I use Win7 64-bit.

Sorry to hear you're having problems. There are a couple of things that might have gone wrong here, but we were also having some server issues over the weekend which might have caused some instabilities, so I'm just going to ask you to check a couple of things.

Can you double check that the proxy settings in the connections tab are correct - and that when you browse to the following URL you see an XML document: http://www.compbio.dundee.ac.uk/jabaws/JronnWS?wsdl

Also, if you are using webstart to launch Jalview (clicking on the 'launch jalview desktop' from www.jalview.org), then its possible you have an out of date version of java on your system, and you'll probably want to update it (the version reported in the log is v 1.6.0_01). Since you are using 64 bit windows, you will want to check that you get the 64 bit version of java, and that its actually being used to launch jalview (you can see which versions of java are used to run applications from the java dialogs in the control panel .. javaws -viewer also gets you to the same display).

I've also noticed that there is a bug which generates one of the errors in your log. I've lodged that here (http://issues.jalview.org/browse/JAL-1217), and will get a patch into the next build, though I don't think that's the problem, so if you can check the above and get back to me, that would be great.

Jim.

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On Mon Dec 10 01:12:13 2012, Charles Bridges wrote: