Sorry here is the error in the console when i tried to import biomart
ERROR 2011-03-26 14:52:31,129
(net.sf.taverna.t2.workbench.ui.servicepanel.actions.ExportServiceDescriptionsAction:94)
- Service descriptions import: failed to import services from
http://www.biomart.org/biomart/martservice
net.sf.taverna.t2.workflowmodel.serialization.DeserializationException:
Could not deserialize stream containing service descriptions from
http://www.biomart.org/biomart/martservice
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionDeserializer.xmlToServiceRegistry(ServiceDescriptionDeserializer.java:83)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl.loadServiceProviders(ServiceDescriptionRegistryImpl.java:448)
at
net.sf.taverna.t2.workbench.ui.servicepanel.actions.ImportServiceDescriptionsFromURLAction.addServices(ImportServiceDescriptionsFromURLAction.java:138)
at
net.sf.taverna.t2.workbench.ui.servicepanel.actions.ImportServiceDescriptionsFromURLAction.actionPerformed(ImportServiceDescriptionsFromURLAction.java:89)
at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2012)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2335)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:404)
at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
at javax.swing.AbstractButton.doClick(AbstractButton.java:374)
at
javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:829)
at
javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:873)
at java.awt.Component.processMouseEvent(Component.java:6203)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:5968)
at java.awt.Container.processEvent(Container.java:2105)
at java.awt.Component.dispatchEventImpl(Component.java:4564)
at java.awt.Container.dispatchEventImpl(Container.java:2163)
at java.awt.Component.dispatchEvent(Component.java:4390)
at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4461)
at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4125)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4055)
at java.awt.Container.dispatchEventImpl(Container.java:2149)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4390)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:649)
at java.awt.EventQueue.access$000(EventQueue.java:96)
at java.awt.EventQueue$1.run(EventQueue.java:608)
at java.awt.EventQueue$1.run(EventQueue.java:606)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:116)
at java.awt.EventQueue$2.run(EventQueue.java:622)
at java.awt.EventQueue$2.run(EventQueue.java:620)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:619)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
Caused by: org.jdom.input.JDOMParseException: Error on line 36: The
element type "meta" must be terminated by the matching end-tag "</meta>".
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:468)
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:770)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionDeserializer.xmlToServiceRegistry(ServiceDescriptionDeserializer.java:35)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionDeserializer.xmlToServiceRegistry(ServiceDescriptionDeserializer.java:80)
... 41 more
Caused by: org.xml.sax.SAXParseException; lineNumber: 36; columnNumber:
3; The element type "meta" must be terminated by the matching end-tag
"</meta>".
at
org.apache.xerces.util.ErrorHandlerWrapper.createSAXParseException(Unknown
Source)
at org.apache.xerces.util.ErrorHandlerWrapper.fatalError(Unknown
Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLErrorReporter.reportError(Unknown Source)
at org.apache.xerces.impl.XMLScanner.reportFatalError(Unknown Source)
at
org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(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$JAXPSAXParser.parse(Unknown
Source)
at org.jdom.input.SAXBuilder.build(SAXBuilder.java:453)
... 44 more
WARN 2011-03-26 14:52:43,640
(net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl:579)
- Provider Biomart service http://somehost/biomart: Failed to load
Biomart from http://somehost/biomart
org.biomart.martservice.MartServiceException: Error posting to
http://somehost/biomart/martservice
type=registry&requestid=taverna
at
org.biomart.martservice.MartServiceUtils.constructException(MartServiceUtils.java:722)
at
org.biomart.martservice.MartServiceUtils.executeMethod(MartServiceUtils.java:642)
at
org.biomart.martservice.MartServiceUtils.getRegistry(MartServiceUtils.java:131)
at
org.biomart.martservice.MartService.getRegistry(MartService.java:201)
at
net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProvider.findServiceDescriptionsAsync(BiomartServiceProvider.java:51)
at
net.sf.taverna.t2.servicedescriptions.impl.ServiceDescriptionRegistryImpl$FindServiceDescriptionsThread.run(ServiceDescriptionRegistryImpl.java:670)
Caused by: java.net.UnknownHostException: somehost
at
java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:175)
at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:384)
at java.net.Socket.connect(Socket.java:546)
at java.net.Socket.connect(Socket.java:495)
at java.net.Socket.<init>(Socket.java:392)
at java.net.Socket.<init>(Socket.java:266)
at
org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:80)
at
org.apache.commons.httpclient.protocol.DefaultProtocolSocketFactory.createSocket(DefaultProtocolSocketFactory.java:122)
at
org.apache.commons.httpclient.HttpConnection.open(HttpConnection.java:707)
at
org.apache.commons.httpclient.HttpMethodDirector.executeWithRetry(HttpMethodDirector.java:387)
at
org.apache.commons.httpclient.HttpMethodDirector.executeMethod(HttpMethodDirector.java:171)
at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:397)
at
org.apache.commons.httpclient.HttpClient.executeMethod(HttpClient.java:323)
at
org.biomart.martservice.MartServiceUtils.executeMethod(MartServiceUtils.java:636)
... 4 more
On 26/03/11 14:51, Andrea Edwards wrote:
HI
I have just tried to install taverna 2.2 (downloaded yesterday) on
Ubuntu 10.10. When i load the application there is an ontology-related
error. Please find a screenshot attached. I also tried to capture the
error messages displayed in the console. They are also attached.
After the application had loaded I noticed the biomart plugin was not
available so i tried 'import new serverice' -> biomart service and
then entered this url (which is what i had to do on my windows
installation of taverna) http://www.biomart.org/biomart/martservice
but nothing happened. No error message and biomart did nor appear in
the service panel
thanks a lot
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------------------------------------------------------------------------------
Enable your software for Intel(R) Active Management Technology to meet the
growing manageability and security demands of your customers. Businesses
are taking advantage of Intel(R) vPro (TM) technology - will your software
be a part of the solution? Download the Intel(R) Manageability Checker
today! http://p.sf.net/sfu/intel-dev2devmar
_______________________________________________
taverna-users mailing list
[email protected]
[email protected]
Web site: http://www.taverna.org.uk
Mailing lists: http://www.taverna.org.uk/about/contact-us/
