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[protege-discussion] WebProtege not connecting to external server

Shahim Essaid sielists at gmail.com
Thu Oct 1 10:35:38 PDT 2009


Hello,

I reverted Protégé server to the default ports and WebProtege was able to
connect.  Another minor problem after the connection was established was
that
WebProtege doesn’t like projects that do not have a description in the meta
project.  There were exceptions logged and the project was not listed in
WebProtege. The projects showed up once I added a description. See from
Protege and from Glassfish/WebProtege are below.

Back to the original problem, how do I get WebProtege to connect to a
Protege
server running on something other than localhost with or without a default
port?

Thank you,
Shahim


=================== From Protégé server: ===================

essaid at skynet:~$ WARNING: Errors at retrieving project instance from
metaproject. Project na
meMSTProject -- edu.stanford.smi.protege.exception.OntologyException: The
description slot should take on string values
        at
edu.stanford.smi.protege.server.metaproject.impl.PolicyControlledObjectImpl.getDescription(Unknown
Source)
        at
edu.stanford.smi.protege.server.Server.getAvailableProjectInfo(Unknown
Source)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        at
sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322)
        at sun.rmi.transport.Transport$1.run(Transport.java:177)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
        at
sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
        at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
        at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
        at java.lang.Thread.run(Thread.java:636)

WARNING: Errors at retrieving project instance from metaproject. Project
nameMSTProject -- edu.stanford.smi.protege.exception.OntologyException: The
description slot should take on string values
        at
edu.stanford.smi.protege.server.metaproject.impl.PolicyControlledObjectImpl.getDescription(Unknown
Source)
        at
edu.stanford.smi.protege.server.Server.getAvailableProjectInfo(Unknown
Source)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
        at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:616)
        at
sun.rmi.server.UnicastServerRef.dispatch(UnicastServerRef.java:322)
        at sun.rmi.transport.Transport$1.run(Transport.java:177)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.rmi.transport.Transport.serviceCall(Transport.java:173)
        at
sun.rmi.transport.tcp.TCPTransport.handleMessages(TCPTransport.java:553)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run0(TCPTransport.java:808)
        at
sun.rmi.transport.tcp.TCPTransport$ConnectionHandler.run(TCPTransport.java:667)
        at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
        at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
        at java.lang.Thread.run(Thread.java:636)

essaid at skynet:~$ ./protege/server/Protege_3.4.1/shutdown_protege_server.sh

================ From Glassfish:
==============================================

[#|2009-10-01T10:12:00.762-0700|SEVERE|sun-appserver2.1|javax.enterprise.system.container.web|_ThreadID=17;_ThreadName=httpSSLWorkerThread-38080-0;_RequestID=32c041e1-6cf0-4ff6-a07d-c52986c60964;|WebModule[/webprotege]Exception
while dispatching incoming RPC call
com.google.gwt.user.server.rpc.UnexpectedException: Service method 'public
abstract void
edu.stanford.bmir.protege.web.client.rpc.AdminService.refreshMetaproject()'
threw an unexpected exception: java.lang.NullPointerException
    at
com.google.gwt.user.server.rpc.RPC.encodeResponseForFailure(RPC.java:360)
    at
com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:546)
    at
com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:166)
    at
com.google.gwt.user.server.rpc.RemoteServiceServlet.doPost(RemoteServiceServlet.java:86)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:754)
    at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
    at
org.apache.catalina.core.ApplicationFilterChain.servletService(ApplicationFilterChain.java:427)
    at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:315)
    at
org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:287)
    at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:218)
    at
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:648)
    at
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:593)
    at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:94)
    at
com.sun.enterprise.web.PESessionLockingStandardPipeline.invoke(PESessionLockingStandardPipeline.java:98)
    at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:222)
    at
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:648)
    at
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:593)
    at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:587)
    at
org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1096)
    at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:166)
    at
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:648)
    at
org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:593)
    at
org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:587)
    at
org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1096)
    at
org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:288)
    at
com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.invokeAdapter(DefaultProcessorTask.java:647)
    at
com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.doProcess(DefaultProcessorTask.java:579)
    at
com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.process(DefaultProcessorTask.java:831)
    at
com.sun.enterprise.web.connector.grizzly.DefaultReadTask.executeProcessorTask(DefaultReadTask.java:341)
    at
com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:263)
    at
com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:214)
    at
com.sun.enterprise.web.connector.grizzly.TaskBase.run(TaskBase.java:265)
    at
com.sun.enterprise.web.connector.grizzly.ssl.SSLWorkerThread.run(SSLWorkerThread.java:106)
Caused by: java.lang.NullPointerException
    at
edu.stanford.bmir.protege.web.server.RemoteMetaProjectManager.reloadMetaProject(Unknown
Source)
    at
edu.stanford.bmir.protege.web.server.AdminServiceImpl.refreshMetaproject(Unknown
Source)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
    at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:616)
    at
com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:527)
    ... 31 more
|#]


On Thu, Oct 1, 2009 at 1:12 AM, Shahim Essaid <sielists at gmail.com> wrote:

> Hi all,
>
> I installed Protege 3.4.1 as a server-client setup and the Protege client
> works fine.  I setup the server's RMI registry to port 35100 and the server
> to 35200.
>
> I then installed WebProtege build 200 but it can not connect to the
> server.  Here is the properties file for WebProtege:
>
> #Protege Properties
> #Thu Oct 01 00:29:35 PDT 2009
> load.ontologies.from.protege.server=true
> webprotege.password=webprotege
> webprotege.user=webprotege
> server.hostname=thehostname\:35100
> server.save.interval.sec=120
>
> I also tried the other port because I wasn't sure if it should be the RMI
> or the server port.  I also tried my Protege client login information but it
> also didn't work.
>
> The war is deployed and I do see WebProtege but there are no ontologies
> listed.  Bellow are the log entries I get when I load WebProtege in a
> browser.  WebProtege is unable to connect to the server.
>
> I noticed that there is a line that keeps saying localhost even when I
> change the host name and the port number in the properties file.  (I need to
> use a non default hostname and port number)
>
> Protege server is listening on this:
> tcp6       0      0 :::35200                :::*
> LISTEN      15787/java
> tcp6       0      0 :::35100                :::*
> LISTEN      8110/rmiregistry
>
> The log entries are from Glassfish. Thanks in advance.
>
> Shahim
>
>
>
> [#|2009-10-01T00:41:35.086-0700|INFO|sun-appserver2.1|javax.enterprise.system.core|_ThreadID=10;_ThreadName=main;|Application
> server startup complete.|#]
>
> [#|2009-10-01T00:41:50.814-0700|WARNING|sun-appserver2.1|javax.enterprise.system.stream.err|_ThreadID=15;_ThreadName=httpSSLWorkerThread-38080-1;_RequestID=d8eafcdd-e6c6-48bc-94f3-98589e7d9f42;|WebProtege
> running in:
> /home/essaid/as/glassfish/domains/domain1/applications/j2ee-modules/webprotege/
> |#]
>
> [#|2009-10-01T00:41:50.848-0700|WARNING|sun-appserver2.1|javax.enterprise.system.stream.err|_ThreadID=15;_ThreadName=httpSSLWorkerThread-38080-1;_RequestID=d8eafcdd-e6c6-48bc-94f3-98589e7d9f42;|SEVERE:
> Could not connect to server: localhost -- ProjectManager.getServer()
> |#]
>
> [#|2009-10-01T00:41:50.849-0700|WARNING|sun-appserver2.1|javax.enterprise.system.stream.err|_ThreadID=15;_ThreadName=httpSSLWorkerThread-38080-1;_RequestID=d8eafcdd-e6c6-48bc-94f3-98589e7d9f42;|WebProtege
> server running with remote projects loaded from the Protege server:
> localhost
> |#]
>
> [#|2009-10-01T00:41:50.915-0700|WARNING|sun-appserver2.1|javax.enterprise.system.stream.err|_ThreadID=15;_ThreadName=httpSSLWorkerThread-38080-1;_RequestID=d8eafcdd-e6c6-48bc-94f3-98589e7d9f42;|SEVERE:
> Could not connect to server: localhost -- ProjectManager.getServer()
> |#]
>
> [#|2009-10-01T00:41:50.915-0700|WARNING|sun-appserver2.1|javax.enterprise.system.stream.err|_ThreadID=15;_ThreadName=httpSSLWorkerThread-38080-1;_RequestID=d8eafcdd-e6c6-48bc-94f3-98589e7d9f42;|WARNING:
> Could not get remote projects. Reason: Cannot connect to remote server. --
> RemoteMetaProjectManager.getProjectsData()
> |#]
>
> [#|2009-10-01T00:41:50.917-0700|SEVERE|sun-appserver2.1|javax.enterprise.system.container.web|_ThreadID=15;_ThreadName=httpSSLWorkerThread-38080-1;_RequestID=d8eafcdd-e6c6-48bc-94f3-98589e7d9f42;|WebModule[/webprotege]Exception
> while dispatching incoming RPC call
> com.google.gwt.user.server.rpc.UnexpectedException: Service method 'public
> abstract java.util.ArrayList
> edu.stanford.bmir.protege.web.client.rpc.AdminService.getProjects(java.lang.String)'
> threw an unexpected exception: java.lang.RuntimeException: Could not
> retrieve the remote projects from the Protege server. Reason: Cannot connect
> to remote Protege server.
>     at
> com.google.gwt.user.server.rpc.RPC.encodeResponseForFailure(RPC.java:360)
>     at
> com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:546)
>     at
> com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:166)
>     at
> com.google.gwt.user.server.rpc.RemoteServiceServlet.doPost(RemoteServiceServlet.java:86)
>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:754)
>     at javax.servlet.http.HttpServlet.service(HttpServlet.java:847)
>     at
> org.apache.catalina.core.ApplicationFilterChain.servletService(ApplicationFilterChain.java:427)
>     at
> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:315)
>     at
> org.apache.catalina.core.StandardContextValve.invokeInternal(StandardContextValve.java:287)
>     at
> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:218)
>     at
> org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:648)
>     at
> org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:593)
>     at com.sun.enterprise.web.WebPipeline.invoke(WebPipeline.java:94)
>     at
> com.sun.enterprise.web.PESessionLockingStandardPipeline.invoke(PESessionLockingStandardPipeline.java:98)
>     at
> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:222)
>     at
> org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:648)
>     at
> org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:593)
>     at
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:587)
>     at
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1096)
>     at
> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:166)
>     at
> org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:648)
>     at
> org.apache.catalina.core.StandardPipeline.doInvoke(StandardPipeline.java:593)
>     at
> org.apache.catalina.core.StandardPipeline.invoke(StandardPipeline.java:587)
>     at
> org.apache.catalina.core.ContainerBase.invoke(ContainerBase.java:1096)
>     at
> org.apache.coyote.tomcat5.CoyoteAdapter.service(CoyoteAdapter.java:288)
>     at
> com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.invokeAdapter(DefaultProcessorTask.java:647)
>     at
> com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.doProcess(DefaultProcessorTask.java:579)
>     at
> com.sun.enterprise.web.connector.grizzly.DefaultProcessorTask.process(DefaultProcessorTask.java:831)
>     at
> com.sun.enterprise.web.connector.grizzly.DefaultReadTask.executeProcessorTask(DefaultReadTask.java:341)
>     at
> com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:263)
>     at
> com.sun.enterprise.web.connector.grizzly.DefaultReadTask.doTask(DefaultReadTask.java:214)
>     at
> com.sun.enterprise.web.connector.grizzly.TaskBase.run(TaskBase.java:265)
>     at
> com.sun.enterprise.web.connector.grizzly.ssl.SSLWorkerThread.run(SSLWorkerThread.java:106)
> Caused by: java.lang.RuntimeException: Could not retrieve the remote
> projects from the Protege server. Reason: Cannot connect to remote Protege
> server.
>     at
> edu.stanford.bmir.protege.web.server.RemoteMetaProjectManager.getProjectsData(Unknown
> Source)
>     at
> edu.stanford.bmir.protege.web.server.AdminServiceImpl.getProjects(Unknown
> Source)
>     at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
>     at
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57)
>     at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>     at java.lang.reflect.Method.invoke(Method.java:616)
>     at
> com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:527)
>     ... 31 more
> |#]
>
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