Hello,
I am trying to set-up a local Jabaws server. We are running on
GNU/Linux. So far this is what I've done:
1) downloaded the jaba.war file and dropped it in my Tomcat webapps dir,
2) compiled the binaries and set permissions to execute (via
compilebin.sh and setexecflag.sh)
3) added new service to Jalview: http://zome-dev.jgi-psf.org:8089/jaba
The service validation step fails and I get the error pasted at the
bottom of this message. Any tips?
Thanks,
Joni Fazo
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net
···
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Connecting to service ClustalWS on http://zome-dev.jgi-psf.org:8089/jaba ... OK
Testing alignment with default
parameters:javax.xml.ws.soap.SOAPFaultException: Executable is not
provided for any runtime environments
at com.sun.xml.internal.ws.fault.SOAP11Fault.getProtocolException(SOAP11Fault.java:178)
at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:119)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:108)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:78)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:107)
at $Proxy22.align(Unknown Source)
at compbio.ws.client.WSTester.testDefaultAlignment(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:645)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:279)
at jalview.gui.WsPreferences.newWsUrl_actionPerformed(WsPreferences.java:309)
at jalview.jbgui.GWsPreferences$9.actionPerformed(GWsPreferences.java:200)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6288)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6053)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4651)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4481)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4481)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:643)
at java.awt.EventQueue.access$000(EventQueue.java:84)
at java.awt.EventQueue$1.run(EventQueue.java:602)
at java.awt.EventQueue$1.run(EventQueue.java:600)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:616)
at java.awt.EventQueue$2.run(EventQueue.java:614)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:613)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.security.InvalidParameterException: Executable is not
provided for any runtime environments
at compbio.engine.client.Util.getSupportedRuntimes(Unknown Source)
at compbio.engine.client.ConfExecutable.getSupportedRuntimes(Unknown Source)
at compbio.engine.Configurator.getExecProvider(Unknown Source)
at compbio.engine.Configurator.configureExecutable(Unknown Source)
at compbio.ws.server.ClustalWS.init(Unknown Source)
at compbio.ws.server.ClustalWS.align(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.sun.xml.ws.api.server.InstanceResolver$1.invoke(InstanceResolver.java:246)
at com.sun.xml.ws.server.InvokerTube$2.invoke(InvokerTube.java:146)
at com.sun.xml.ws.server.sei.EndpointMethodHandler.invoke(EndpointMethodHandler.java:257)
at com.sun.xml.ws.server.sei.SEIInvokerTube.processRequest(SEIInvokerTube.java:95)
at com.sun.xml.ws.api.pipe.Fiber.__doRun(Fiber.java:629)
at com.sun.xml.ws.api.pipe.Fiber._doRun(Fiber.java:588)
at com.sun.xml.ws.api.pipe.Fiber.doRun(Fiber.java:573)
at com.sun.xml.ws.api.pipe.Fiber.runSync(Fiber.java:470)
at com.sun.xml.ws.server.WSEndpointImpl$2.process(WSEndpointImpl.java:295)
at com.sun.xml.ws.transport.http.HttpAdapter$HttpToolkit.handle(HttpAdapter.java:519)
at com.sun.xml.ws.transport.http.HttpAdapter.handle(HttpAdapter.java:288)
at com.sun.xml.ws.transport.http.servlet.ServletAdapter.handle(ServletAdapter.java:143)
at com.sun.xml.ws.transport.http.servlet.WSServletDelegate.doGet(WSServletDelegate.java:155)
at com.sun.xml.ws.transport.http.servlet.WSServletDelegate.doPost(WSServletDelegate.java:189)
at com.sun.xml.ws.transport.http.servlet.WSServlet.doPost(WSServlet.java:76)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:879)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:662)
Hi Joni,
It is good to hear from someone with local installation of JABAWS!
This looks like something is not quite right with the JABAWS configuration.
Please check that you have at least one of the execution engines enabled.
Look at the conf/Engine.local.properties and conf/Engine.cluster.properties.
If you want to enable local execution than the first file should have
engine.local.enable=true
local.tmp.directory=jobsout (check that there is a directory called jobsout in your jaba web application folder)
If you want to enable cluster execution than conf/Engine.cluster.properties file should look
something like this
engine.cluster.enable=true
cluster.tmp.directory=<absolute path to the temporary directory on the
Please make sure that either engine.local.enable or engine.cluster.enable properties are set to true otherwise JABAWS is not going to work.
If that was not the problem, then look at the conf/Executable.properties and check that you have valid paths to the binaries,
## This is the path used by the local engine
local.clustalw.bin=relative or absolute path to the clustalw binary e.g. binaries/src/clustalw/src/clustalw2
## This is the path used by the cluster engine
cluster.clustalw.bin=absolute path to the clustalw binary /binaries/src/clustalw/src/clustalw2
Please check the same paths for other programmes.
Hopefully this should solve the problem.
Which version of Tomcat and Java are you using? Is your Java version from Sun/Oracle?
Regards,
Peter
P.S. I'd recommend you to sing up to the jabaws-discuss mailing list (http://www.jalview.org/mailman/listinfo/jabaws-discuss) to keep up to date with the JABAWS development.
···
On 11/08/2011 22:37, Joni Fazo wrote:
Hello,
I am trying to set-up a local Jabaws server. We are running on
GNU/Linux. So far this is what I've done:
1) downloaded the jaba.war file and dropped it in my Tomcat webapps dir,
2) compiled the binaries and set permissions to execute (via
compilebin.sh and setexecflag.sh)
3) added new service to Jalview: http://zome-dev.jgi-psf.org:8089/jaba
The service validation step fails and I get the error pasted at the
bottom of this message. Any tips?
Thanks,
Joni Fazo
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Connecting to service ClustalWS on http://zome-dev.jgi-psf.org:8089/jaba ... OK
Testing alignment with default
parameters:javax.xml.ws.soap.SOAPFaultException: Executable is not
provided for any runtime environments
at com.sun.xml.internal.ws.fault.SOAP11Fault.getProtocolException(SOAP11Fault.java:178)
at com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:119)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:108)
at com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:78)
at com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:107)
at $Proxy22.align(Unknown Source)
at compbio.ws.client.WSTester.testDefaultAlignment(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:645)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:279)
at jalview.gui.WsPreferences.newWsUrl_actionPerformed(WsPreferences.java:309)
at jalview.jbgui.GWsPreferences$9.actionPerformed(GWsPreferences.java:200)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6288)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6053)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4651)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4481)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4481)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:643)
at java.awt.EventQueue.access$000(EventQueue.java:84)
at java.awt.EventQueue$1.run(EventQueue.java:602)
at java.awt.EventQueue$1.run(EventQueue.java:600)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:616)
at java.awt.EventQueue$2.run(EventQueue.java:614)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:613)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.security.InvalidParameterException: Executable is not
provided for any runtime environments
at compbio.engine.client.Util.getSupportedRuntimes(Unknown Source)
at compbio.engine.client.ConfExecutable.getSupportedRuntimes(Unknown Source)
at compbio.engine.Configurator.getExecProvider(Unknown Source)
at compbio.engine.Configurator.configureExecutable(Unknown Source)
at compbio.ws.server.ClustalWS.init(Unknown Source)
at compbio.ws.server.ClustalWS.align(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at com.sun.xml.ws.api.server.InstanceResolver$1.invoke(InstanceResolver.java:246)
at com.sun.xml.ws.server.InvokerTube$2.invoke(InvokerTube.java:146)
at com.sun.xml.ws.server.sei.EndpointMethodHandler.invoke(EndpointMethodHandler.java:257)
at com.sun.xml.ws.server.sei.SEIInvokerTube.processRequest(SEIInvokerTube.java:95)
at com.sun.xml.ws.api.pipe.Fiber.__doRun(Fiber.java:629)
at com.sun.xml.ws.api.pipe.Fiber._doRun(Fiber.java:588)
at com.sun.xml.ws.api.pipe.Fiber.doRun(Fiber.java:573)
at com.sun.xml.ws.api.pipe.Fiber.runSync(Fiber.java:470)
at com.sun.xml.ws.server.WSEndpointImpl$2.process(WSEndpointImpl.java:295)
at com.sun.xml.ws.transport.http.HttpAdapter$HttpToolkit.handle(HttpAdapter.java:519)
at com.sun.xml.ws.transport.http.HttpAdapter.handle(HttpAdapter.java:288)
at com.sun.xml.ws.transport.http.servlet.ServletAdapter.handle(ServletAdapter.java:143)
at com.sun.xml.ws.transport.http.servlet.WSServletDelegate.doGet(WSServletDelegate.java:155)
at com.sun.xml.ws.transport.http.servlet.WSServletDelegate.doPost(WSServletDelegate.java:189)
at com.sun.xml.ws.transport.http.servlet.WSServlet.doPost(WSServlet.java:76)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:879)
at org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:662)
_______________________________________________
Jalview-discuss mailing list
Jalview-discuss@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
Hi Peter,
Thanks for your help. I verified all the config settings and
everything was set as you described as a default in the jaba.war file.
I was able to solve my problem by just renaming the war from file from
jaba.war to jabaws.war.
Thanks,
Joni
···
On Fri, Aug 12, 2011 at 2:35 AM, Peter Troshin <p.v.troshin@dundee.ac.uk> wrote:
Hi Joni,
It is good to hear from someone with local installation of JABAWS!
This looks like something is not quite right with the JABAWS configuration.
Please check that you have at least one of the execution engines enabled.
Look at the conf/Engine.local.properties and conf/Engine.cluster.properties.
If you want to enable local execution than the first file should have
engine.local.enable=true
local.tmp.directory=jobsout (check that there is a directory called jobsout
in your jaba web application folder)
If you want to enable cluster execution than conf/Engine.cluster.properties
file should look
something like this
engine.cluster.enable=true
cluster.tmp.directory=<absolute path to the temporary directory on the
>
Please make sure that either engine.local.enable or engine.cluster.enable
properties are set to true otherwise JABAWS is not going to work.
If that was not the problem, then look at the conf/Executable.properties and
check that you have valid paths to the binaries,
## This is the path used by the local engine
local.clustalw.bin=relative or absolute path to the clustalw binary e.g.
binaries/src/clustalw/src/clustalw2
## This is the path used by the cluster engine
cluster.clustalw.bin=absolute path to the clustalw binary
/binaries/src/clustalw/src/clustalw2
Please check the same paths for other programmes.
Hopefully this should solve the problem.
Which version of Tomcat and Java are you using? Is your Java version from
Sun/Oracle?
Regards,
Peter
P.S. I'd recommend you to sing up to the jabaws-discuss mailing list
(http://www.jalview.org/mailman/listinfo/jabaws-discuss) to keep up to date
with the JABAWS development.
On 11/08/2011 22:37, Joni Fazo wrote:
Hello,
I am trying to set-up a local Jabaws server. We are running on
GNU/Linux. So far this is what I've done:
1) downloaded the jaba.war file and dropped it in my Tomcat webapps dir,
2) compiled the binaries and set permissions to execute (via
compilebin.sh and setexecflag.sh)
3) added new service to Jalview: http://zome-dev.jgi-psf.org:8089/jaba
The service validation step fails and I get the error pasted at the
bottom of this message. Any tips?
Thanks,
Joni Fazo
Plant and Computational Genomics Group
Joint Genome Institute - U.S. Dept. of Energy
http://www.phytozome.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~
Connecting to service ClustalWS on http://zome-dev.jgi-psf.org:8089/jaba
... OK
Testing alignment with default
parameters:javax.xml.ws.soap.SOAPFaultException: Executable is not
provided for any runtime environments
at
com.sun.xml.internal.ws.fault.SOAP11Fault.getProtocolException(SOAP11Fault.java:178)
at
com.sun.xml.internal.ws.fault.SOAPFaultBuilder.createException(SOAPFaultBuilder.java:119)
at
com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:108)
at
com.sun.xml.internal.ws.client.sei.SyncMethodHandler.invoke(SyncMethodHandler.java:78)
at
com.sun.xml.internal.ws.client.sei.SEIStub.invoke(SEIStub.java:107)
at $Proxy22.align(Unknown Source)
at compbio.ws.client.WSTester.testDefaultAlignment(Unknown Source)
at compbio.ws.client.WSTester.checkService(Unknown Source)
at compbio.ws.client.WSTester.main(Unknown Source)
at
jalview.ws.jws2.Jws2Discoverer.testServiceUrl(Jws2Discoverer.java:645)
at jalview.gui.WsPreferences.editUrl(WsPreferences.java:279)
at
jalview.gui.WsPreferences.newWsUrl_actionPerformed(WsPreferences.java:309)
at
jalview.jbgui.GWsPreferences$9.actionPerformed(GWsPreferences.java:200)
at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
at java.awt.Component.processMouseEvent(Component.java:6288)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
at java.awt.Component.processEvent(Component.java:6053)
at java.awt.Container.processEvent(Container.java:2041)
at java.awt.Component.dispatchEventImpl(Component.java:4651)
at java.awt.Container.dispatchEventImpl(Container.java:2099)
at java.awt.Component.dispatchEvent(Component.java:4481)
at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4577)
at
java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)
at
java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)
at java.awt.Container.dispatchEventImpl(Container.java:2085)
at java.awt.Window.dispatchEventImpl(Window.java:2478)
at java.awt.Component.dispatchEvent(Component.java:4481)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:643)
at java.awt.EventQueue.access$000(EventQueue.java:84)
at java.awt.EventQueue$1.run(EventQueue.java:602)
at java.awt.EventQueue$1.run(EventQueue.java:600)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
at java.awt.EventQueue$2.run(EventQueue.java:616)
at java.awt.EventQueue$2.run(EventQueue.java:614)
at java.security.AccessController.doPrivileged(Native Method)
at
java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:613)
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.security.InvalidParameterException: Executable is not
provided for any runtime environments
at compbio.engine.client.Util.getSupportedRuntimes(Unknown Source)
at
compbio.engine.client.ConfExecutable.getSupportedRuntimes(Unknown Source)
at compbio.engine.Configurator.getExecProvider(Unknown Source)
at compbio.engine.Configurator.configureExecutable(Unknown Source)
at compbio.ws.server.ClustalWS.init(Unknown Source)
at compbio.ws.server.ClustalWS.align(Unknown Source)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
at
com.sun.xml.ws.api.server.InstanceResolver$1.invoke(InstanceResolver.java:246)
at com.sun.xml.ws.server.InvokerTube$2.invoke(InvokerTube.java:146)
at
com.sun.xml.ws.server.sei.EndpointMethodHandler.invoke(EndpointMethodHandler.java:257)
at
com.sun.xml.ws.server.sei.SEIInvokerTube.processRequest(SEIInvokerTube.java:95)
at com.sun.xml.ws.api.pipe.Fiber.__doRun(Fiber.java:629)
at com.sun.xml.ws.api.pipe.Fiber._doRun(Fiber.java:588)
at com.sun.xml.ws.api.pipe.Fiber.doRun(Fiber.java:573)
at com.sun.xml.ws.api.pipe.Fiber.runSync(Fiber.java:470)
at
com.sun.xml.ws.server.WSEndpointImpl$2.process(WSEndpointImpl.java:295)
at
com.sun.xml.ws.transport.http.HttpAdapter$HttpToolkit.handle(HttpAdapter.java:519)
at
com.sun.xml.ws.transport.http.HttpAdapter.handle(HttpAdapter.java:288)
at
com.sun.xml.ws.transport.http.servlet.ServletAdapter.handle(ServletAdapter.java:143)
at
com.sun.xml.ws.transport.http.servlet.WSServletDelegate.doGet(WSServletDelegate.java:155)
at
com.sun.xml.ws.transport.http.servlet.WSServletDelegate.doPost(WSServletDelegate.java:189)
at
com.sun.xml.ws.transport.http.servlet.WSServlet.doPost(WSServlet.java:76)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:647)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:729)
at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:269)
at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:188)
at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:213)
at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:172)
at
org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)
at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:117)
at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:108)
at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:174)
at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:879)
at
org.apache.coyote.http11.Http11BaseProtocol$Http11ConnectionHandler.processConnection(Http11BaseProtocol.java:665)
at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint.java:528)
at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollowerWorkerThread.java:81)
at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool.java:689)
at java.lang.Thread.run(Thread.java:662)
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Hi Joni,
I am glad you have found the solution.
As for the creating a new web service within JABAWS framework I can only add a few things to Jim’s answer.
You can download the most recent pre-release quality JABAWS code base, from here:
http://www.compbio.dundee.ac.uk/jabaws/jaba-project.zip
There is a web page - website/man_server_dev.html, that explains JABAWS structure and describes how to add a new web service. I cannot say that this web page is particularly detailed, but it should point you in the right direction.
Please let me know if you have any questions about JABAWS I will be happy to assist.
Regards,
Peter