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[protege-dev] Bug report WebProtégé OWL Entity Description Editor

Karl Hammar karl at karlhammar.com
Tue May 19 04:32:10 PDT 2015


Hi,

I've found what I believe to be two bugs in WebProtégé, using the latest
development branch. I attach two reports below. One of these (the latter)
is rather critical as it makes it impossible for users to construct value
or cardinality restrictions, which are used rather frequently in many
modeling scenarios. Could someone else confirm whether I'm alone in seeing
this or whether there actually are real bugs here that need be looked into?

I attach the exception thrown on the server when the second bug is
triggered. However, on quick inspection, it looks as if this exception may
be related to the fact that the server in question does not have a working
email configuration, so I don't know whether it is helpful? If you want
more information, please let me know and I'd be happy to provide it.

/Karl


### BUG 1

Issue: OWL Entity Description Editor now added correctly
Environment: Mac OS X 10.10.3, Safari 8.0.6. WebProtégé running on Tomcat
7, behind an Apache proxy.

Steps to reproduce:
1) Open an existing project.
2) Use "Add content to this tab > OWL Entity Description Editor"
Result: nothing happens.
Expected result: a new portlet should be spawned containing the OWL Entity
Description Editor.

Workaround: switch to another tab, and back to the initial tab again, and
the portlet will be found to have spawned in the rightmost column.

### BUG 2

Issue: OWL Entity Description Editor not working correctly
Environment: Mac OS X 10.10.3, Safari 8.0.6. WebProtégé running on Tomcat
7, behind an Apache proxy.

Steps to reproduce:
1) Open an existing project
2) Open the OWL Entity Description Editor (using workaround described
above) and place in main column.
3) Select a class.
4) Type something in the OWL Entity Description Editor

Result: WebProtégé shows a Internal Server Error dialog box, referring to
an error 500 on the server. The server throws an uncaught exception (see
attachment).
Expected result: User should be able to enter Manchester OWL axioms and
once done, persist those to the ontology.
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[WebProtege] ***** SEVERE *****                                                                                                                                                      [Tue May 19 13:18:35 CEST 2015]
             An unexpected exception was thrown on the server
             
             Date and time: Tue May 19 13:18:35 CEST 2015
             
             User: karl
             email: karl at karlhammar.com
             groups:
             48580583-3597-47d8-a69b-bc87894e231b_Writers
             World
             Request URI: /webprotege/dispatchservice
             Remote address: 0:0:0:0:0:0:0:1
             Remote host: 0:0:0:0:0:0:0:1
             
             Headers:
             host: wp.ostag.se
             accept: */*
             x-gwt-module-base: http://wp.ostag.se/webprotege/
             accept-encoding: gzip, deflate
             accept-language: sv-se
             x-gwt-permutation: FE3D55930B8ACF9156862D151841C53B
             content-type: text/x-gwt-rpc; charset=UTF-8
             origin: http://wp.ostag.se
             user-agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_10_3) AppleWebKit/600.6.3 (KHTML, like Gecko) Version/8.0.6 Safari/600.6.3
             referer: http://wp.ostag.se/
             dnt: 1
             cookie: JSESSIONID=F3AEA0DB4FB2F3D7913257A00F10D418
             x-forwarded-for: 193.11.5.202
             x-forwarded-host: wp.ostag.se
             x-forwarded-server: wp.ostag.se
             connection: Keep-Alive
             content-length: 862
             
             
             Message: Type 'com.google.inject.CreationException' was not included in the set of types which can be serialized by this SerializationPolicy or its Class
             object could not be loaded. For security purposes, this type will not be serialized.: instance = com.google.inject.CreationException: Guice creation errors:
             
             1) No implementation for edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLClass> was bound.
             while locating edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLClass>
             for parameter 1 at edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder.<init>(IndirectlyWatchedEntitiesFinder.java:35)
             while locating edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             2) No implementation for edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLDataProperty> was bound.
             while locating edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLDataProperty>
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder.<init>(IndirectlyWatchedEntitiesFinder.java:35)
             while locating edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             3) No implementation for edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLObjectProperty> was bound.
             while locating edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLObjectProperty>
             for parameter 2 at edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder.<init>(IndirectlyWatchedEntitiesFinder.java:35)
             while locating edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             4) No implementation for edu.stanford.bmir.protege.web.server.logging.WebProtegeLogger was bound.
             while locating edu.stanford.bmir.protege.web.server.logging.WebProtegeLogger
             for parameter 2 at edu.stanford.bmir.protege.web.server.watches.WatchStoreImpl.<init>(WatchStoreImpl.java:46)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:64)
             
             5) No implementation for edu.stanford.bmir.protege.web.server.mail.SendMail was bound.
             while locating edu.stanford.bmir.protege.web.server.mail.SendMail
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchTriggeredHandlerImpl.<init>(WatchTriggeredHandlerImpl.java:42)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:65)
             
             6) No implementation for edu.stanford.bmir.protege.web.shared.BrowserTextProvider was bound.
             while locating edu.stanford.bmir.protege.web.shared.BrowserTextProvider
             for parameter 1 at edu.stanford.bmir.protege.web.server.watches.WatchTriggeredHandlerImpl.<init>(WatchTriggeredHandlerImpl.java:42)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:65)
             
             7) No implementation for java.io.File annotated with @edu.stanford.bmir.protege.web.server.inject.DataDirectory() was bound.
             while locating java.io.File annotated with @edu.stanford.bmir.protege.web.server.inject.DataDirectory()
             for parameter 0 at edu.stanford.bmir.protege.web.server.inject.project.ProjectDirectoryProvider.<init>(ProjectDirectoryProvider.java:22)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:45)
             
             8) Could not find a suitable constructor in edu.stanford.bmir.protege.web.server.events.EventManager. Classes must have either one (and only one) constructor
             annotated with @Inject or a zero-argument constructor that is not private.
             at edu.stanford.bmir.protege.web.server.events.EventManager.class(EventManager.java:26)
             while locating edu.stanford.bmir.protege.web.server.events.EventManager<edu.stanford.bmir.protege.web.shared.event.ProjectEvent<?>>
             for parameter 5 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             8 errors
             
             Stack trace:
             
             com.google.gwt.user.client.rpc.SerializationException: Type 'com.google.inject.CreationException' was not included in the set of types which can be serialized
             by this SerializationPolicy or its Class object could not be loaded. For security purposes, this type will not be serialized.: instance =
             com.google.inject.CreationException: Guice creation errors:
             
             1) No implementation for edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLClass> was bound.
             while locating edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLClass>
             for parameter 1 at edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder.<init>(IndirectlyWatchedEntitiesFinder.java:35)
             while locating edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             2) No implementation for edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLDataProperty> was bound.
             while locating edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLDataProperty>
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder.<init>(IndirectlyWatchedEntitiesFinder.java:35)
             while locating edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             3) No implementation for edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLObjectProperty> was bound.
             while locating edu.stanford.bmir.protege.web.server.hierarchy.OWLObjectHierarchyProvider<org.semanticweb.owlapi.model.OWLObjectProperty>
             for parameter 2 at edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder.<init>(IndirectlyWatchedEntitiesFinder.java:35)
             while locating edu.stanford.bmir.protege.web.server.watches.IndirectlyWatchedEntitiesFinder
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             4) No implementation for edu.stanford.bmir.protege.web.server.logging.WebProtegeLogger was bound.
             while locating edu.stanford.bmir.protege.web.server.logging.WebProtegeLogger
             for parameter 2 at edu.stanford.bmir.protege.web.server.watches.WatchStoreImpl.<init>(WatchStoreImpl.java:46)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:64)
             
             5) No implementation for edu.stanford.bmir.protege.web.server.mail.SendMail was bound.
             while locating edu.stanford.bmir.protege.web.server.mail.SendMail
             for parameter 3 at edu.stanford.bmir.protege.web.server.watches.WatchTriggeredHandlerImpl.<init>(WatchTriggeredHandlerImpl.java:42)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:65)
             
             6) No implementation for edu.stanford.bmir.protege.web.shared.BrowserTextProvider was bound.
             while locating edu.stanford.bmir.protege.web.shared.BrowserTextProvider
             for parameter 1 at edu.stanford.bmir.protege.web.server.watches.WatchTriggeredHandlerImpl.<init>(WatchTriggeredHandlerImpl.java:42)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:65)
             
             7) No implementation for java.io.File annotated with @edu.stanford.bmir.protege.web.server.inject.DataDirectory() was bound.
             while locating java.io.File annotated with @edu.stanford.bmir.protege.web.server.inject.DataDirectory()
             for parameter 0 at edu.stanford.bmir.protege.web.server.inject.project.ProjectDirectoryProvider.<init>(ProjectDirectoryProvider.java:22)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:45)
             
             8) Could not find a suitable constructor in edu.stanford.bmir.protege.web.server.events.EventManager. Classes must have either one (and only one) constructor
             annotated with @Inject or a zero-argument constructor that is not private.
             at edu.stanford.bmir.protege.web.server.events.EventManager.class(EventManager.java:26)
             while locating edu.stanford.bmir.protege.web.server.events.EventManager<edu.stanford.bmir.protege.web.shared.event.ProjectEvent<?>>
             for parameter 5 at edu.stanford.bmir.protege.web.server.watches.WatchManagerImpl.<init>(WatchManagerImpl.java:43)
             at edu.stanford.bmir.protege.web.server.inject.project.ProjectModule.configure(ProjectModule.java:63)
             
             8 errors
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serialize(ServerSerializationStreamWriter.java:667)
             at com.google.gwt.user.client.rpc.impl.AbstractSerializationStreamWriter.writeObject(AbstractSerializationStreamWriter.java:130)
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter$ValueWriter$8.write(ServerSerializationStreamWriter.java:153)
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeValue(ServerSerializationStreamWriter.java:587)
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeClass(ServerSerializationStreamWriter.java:758)
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeImpl(ServerSerializationStreamWriter.java:797)
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serialize(ServerSerializationStreamWriter.java:669)
             at com.google.gwt.user.client.rpc.impl.AbstractSerializationStreamWriter.writeObject(AbstractSerializationStreamWriter.java:130)
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter$ValueWriter$8.write(ServerSerializationStreamWriter.java:153)
             at com.google.gwt.user.server.rpc.impl.ServerSerializationStreamWriter.serializeValue(ServerSerializationStreamWriter.java:587)
             at com.google.gwt.user.server.rpc.RPC.encodeResponse(RPC.java:631)
             at com.google.gwt.user.server.rpc.RPC.encodeResponseForFailure(RPC.java:419)
             at com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:605)
             at com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:333)
             at com.google.gwt.user.server.rpc.RemoteServiceServlet.processCall(RemoteServiceServlet.java:303)
             at edu.stanford.bmir.protege.web.server.WebProtegeRemoteServiceServlet.processCall(WebProtegeRemoteServiceServlet.java:115)
             at com.google.gwt.user.server.rpc.RemoteServiceServlet.processPost(RemoteServiceServlet.java:373)
             at com.google.gwt.user.server.rpc.AbstractRemoteServiceServlet.doPost(AbstractRemoteServiceServlet.java:62)
             at javax.servlet.http.HttpServlet.service(HttpServlet.java:646)
             at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
             at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
             at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
             at edu.stanford.bmir.protege.web.server.filter.WebProtegeWebAppFilter.doFilter(WebProtegeWebAppFilter.java:76)
             at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
             at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
             at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
             at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
             at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:501)
             at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
             at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:98)
             at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
             at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
             at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
             at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1040)
             at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
             at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:313)
             at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
             at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
             at java.lang.Thread.run(Thread.java:745)


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