[Jalview-discuss] trouble setting up jabaws server
Peter Troshin
p.v.troshin at dundee.ac.uk
Tue Aug 16 12:49:34 BST 2011
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
On 12/08/2011 20:33, Joni Fazo wrote:
> 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 at 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
>> cluster>
>>
>> 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 at jalview.org
>>> http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss
>>
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