webprotege_debugger issueshttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues2020-09-23T14:19:33Zhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/1Find solution regarding the purge behaviour of projects with running debuggin...2020-09-23T14:19:33ZWolfgang SchmidFind solution regarding the purge behaviour of projects with running debugging sessionThe project to be debugged is disposed after some time of inactivity.
Problems that arise: reasoner tasks can take longer than this inactivity time out.
TODO: evaluate the architecture and functionality behind the disposal idea and fin...The project to be debugged is disposed after some time of inactivity.
Problems that arise: reasoner tasks can take longer than this inactivity time out.
TODO: evaluate the architecture and functionality behind the disposal idea and find a solution to this problem for our Debugger.Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/2Front-end buttons with back-end status communication2020-09-02T12:31:59ZbodaweFront-end buttons with back-end status communicationThe status of buttons(Start, Stop, Execute) are depended of debugger session, therefore the result from back-end should contain the debugging status, with that the front-end can enable/disable the buttons.The status of buttons(Start, Stop, Execute) are depended of debugger session, therefore the result from back-end should contain the debugging status, with that the front-end can enable/disable the buttons.bodawebodawehttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/3Represent axioms in form Manchester Syntax2020-09-16T14:41:51ZbodaweRepresent axioms in form Manchester SyntaxThe axioms in queries, repairs and test cases should be represented in the form of Manchester Syntax.
For example:
![image](/uploads/cf4d43d810401d8fffe62f0970cd1dbe/image.png)The axioms in queries, repairs and test cases should be represented in the form of Manchester Syntax.
For example:
![image](/uploads/cf4d43d810401d8fffe62f0970cd1dbe/image.png)bodawebodawehttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/4Set views size dynamic2020-09-02T15:04:05ZbodaweSet views size dynamicThere are empty space the the debugger views, they should be delete.
![image](/uploads/7eb88a1fe03f8f57a3e4290989168eae/image.png)
To Do: set the dynamic size of debugger viewsThere are empty space the the debugger views, they should be delete.
![image](/uploads/7eb88a1fe03f8f57a3e4290989168eae/image.png)
To Do: set the dynamic size of debugger viewsbodawebodawehttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/5Waiting animated wheel for debugging processing2020-09-07T14:02:28ZbodaweWaiting animated wheel for debugging processingIf we have pressed a button and did not receive a response from the back-end (either through a result or an exception), the user should not be able to press any other buttons.
TODO: Animated wheel.
![image](/uploads/919a0ba2e63cd1510e...If we have pressed a button and did not receive a response from the back-end (either through a result or an exception), the user should not be able to press any other buttons.
TODO: Animated wheel.
![image](/uploads/919a0ba2e63cd1510e4edc43c778e184/image.png)bodawebodawehttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/6RuntimeException when debug Thesaurus ontology2020-09-23T14:19:34ZbodaweRuntimeException when debug Thesaurus ontologyFor debugging Thesaurus ontology, Start debugging return 3 axioms. But if I submit first axiom as true and second axiom as false, I get the following exception:
java.lang.RuntimeException: Debugging session is in unexpected state INIT an...For debugging Thesaurus ontology, Start debugging return 3 axioms. But if I submit first axiom as true and second axiom as false, I get the following exception:
java.lang.RuntimeException: Debugging session is in unexpected state INIT and thus query calculation is not allowed.
The whole exception from console is:
`edu.stanford.bmir.protege.web.shared.dispatch.ActionExecutionException: java.lang.RuntimeException: Debugging session is in unexpected state INIT and thus query calculation is not allowed.
at edu.stanford.bmir.protege.web.server.debugger.DebuggingSession.calculateQuery(DebuggingSession.java:127)
at edu.stanford.bmir.protege.web.server.debugger.DebuggingSessionManager.submitQuery(DebuggingSessionManager.java:62)
at edu.stanford.bmir.protege.web.server.debugger.SubmitDebuggingActionHandler.execute(SubmitDebuggingActionHandler.java:43)
at edu.stanford.bmir.protege.web.server.debugger.SubmitDebuggingActionHandler.execute(SubmitDebuggingActionHandler.java:17)
at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.execAction(DispatchServiceExecutorImpl.java:136)
at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.execute(DispatchServiceExecutorImpl.java:89)
at edu.stanford.bmir.protege.web.server.dispatch.DispatchServlet.executeAction(DispatchServlet.java:49)
at jdk.internal.reflect.GeneratedMethodAccessor59.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:564)
at com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:587)
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.app.WebProtegeRemoteServiceServlet.processCall(WebProtegeRemoteServiceServlet.java:64)
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:647)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:728)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:305)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:51)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at edu.stanford.bmir.protege.web.server.filter.WebProtegeWebAppFilter.doFilter(WebProtegeWebAppFilter.java:75)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:243)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:210)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:222)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:123)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:502)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:171)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:100)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:953)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:118)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:408)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1041)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:603)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:312)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1130)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:630)
at java.base/java.lang.Thread.run(Thread.java:832)
Caused by: java.lang.RuntimeException: Debugging session is in unexpected state INIT and thus query calculation is not allowed.
at edu.stanford.bmir.protege.web.server.debugger.DebuggingSession.calculateQuery(DebuggingSession.java:79)
... 39 common frames omitted
`https://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/7Debugging Session only possible for one user per project?2020-09-18T12:36:39ZbodaweDebugging Session only possible for one user per project?Discuss with Kostya and PatrickDiscuss with Kostya and PatrickWolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/8Reloading page action2020-10-06T13:56:30ZbodaweReloading page actionFind the entry point where the action is sent to the backend when a page reload occurs (currently empty list).
Hint: GetCommentedEntitiesAction used for Comments perspectiveFind the entry point where the action is sent to the backend when a page reload occurs (currently empty list).
Hint: GetCommentedEntitiesAction used for Comments perspectivebodawebodawehttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/9DebuggingSessionManager should be ApplicationSingleton and not ProjectSingleton2020-09-18T14:43:55ZWolfgang SchmidDebuggingSessionManager should be ApplicationSingleton and not ProjectSingletonFor each project a new DebuggingSessionManager instance is created, which is not the intented functionality. This is because it has @ProjectSingleton annotation but not @ApplicationSingleton.
The problem however is that when you switch ...For each project a new DebuggingSessionManager instance is created, which is not the intented functionality. This is because it has @ProjectSingleton annotation but not @ApplicationSingleton.
The problem however is that when you switch to ApplicationSingleton then the RevisionManager is not accessible.
Possibly the reason for the behaviour of issue #1Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/10Improved exception handling using popup windows2020-09-30T11:40:18ZWolfgang SchmidImproved exception handling using popup windowsIf an exception occurs in the backend this exception will be thrown as an *ActionExecutionException* which then pops up automatically in the frontend.
When the exception occurs then the backend stops the debugging session but the fronte...If an exception occurs in the backend this exception will be thrown as an *ActionExecutionException* which then pops up automatically in the frontend.
When the exception occurs then the backend stops the debugging session but the frontend has no information about the backend status and possibly shows queries to be answered and the user can then still click on buttons which will cause further exceptions. Therefore it would improve the interaction to inform the frontend about the occurence of an excption and the the current state of the backend (status, query, diagnosis, testcases etc.) instead of just throwing an exception.
As a solution we could extend the *DebuggingSessionStateResult* with a flag class which simply contains an OK/ERROR flag and an error message to be shown with a PopUp in case the flag is set to ERROR.
The flag then has to be checked by the frontend each time and in case of the ERROR the popup window is shown and addditionally the frontend has the information of what to show in the presenters (query, diagnoses, etc).
The protocol extension is to be discussed with @bodaweWolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/11Make DebuggingSession disposable2020-09-21T07:50:47ZWolfgang SchmidMake DebuggingSession disposableWhen a project gets purged the debugging session belonging to this project has to be disposed too and it's resources has to be cleaned up.When a project gets purged the debugging session belonging to this project has to be disposed too and it's resources has to be cleaned up.Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/12Find a proper lookup mechanism for query answering2020-09-22T14:33:02ZWolfgang SchmidFind a proper lookup mechanism for query answeringFind a bulletproof method for the lookup of those axioms whose answers are sent from the frontend.
Current solution with owlObjectRenderer.render(Axiom) does not always match with the string sent from frontend.
e.g.
Frontends (its the...Find a bulletproof method for the lookup of those axioms whose answers are sent from the frontend.
Current solution with owlObjectRenderer.render(Axiom) does not always match with the string sent from frontend.
e.g.
Frontends (its the string from the HTML):
KoalaWithPhD EquivalentTo Koala and hasDegree value PhD
vs.
owlObjectRenderer.render():
KoalaWithPhD EquivalentTo Koala and (hasDegree value PhD)
ManchesterSyntaxRenderer does not work.Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/13Implementation of RepairAction2020-10-06T13:54:21ZbodaweImplementation of RepairActionWolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/14Preferences/settings for debugger2021-05-02T20:05:26ZWolfgang SchmidPreferences/settings for debuggerBoda has the idea to add preferences/settings for the debugger.
possible settings are:
- selection of **reasoner** to be used
- **keep alive time** for a debugging session (currently it is hard coded to 10 minutes).
- debugger preferenc...Boda has the idea to add preferences/settings for the debugger.
possible settings are:
- selection of **reasoner** to be used
- **keep alive time** for a debugging session (currently it is hard coded to 10 minutes).
- debugger preferences for diagnosis engine and query calculation (not clear if all are useful) maybe:
- **max. size of diagnoses** (currently this preference is set to 0 which means compute all diagnoses)
- **query enrichment** (currently active, but can be expensive due to reasoner involvment)Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/15Add tooltips to buttons2020-10-29T15:58:25ZWolfgang SchmidAdd tooltips to buttonsSupport the user with tooltips for each button.
The text should be shown can be discussed.Support the user with tooltips for each button.
The text should be shown can be discussed.bodawebodawehttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/16Varying sizes of views2020-10-13T12:48:10ZWolfgang SchmidVarying sizes of viewsThe views in the Debugger presenter sometimes vary depending on the content shown and on the browser used.
For example, sometimes you have to scroll down to get to the diagnosis views.
This also depends on the used browser. The views in...The views in the Debugger presenter sometimes vary depending on the content shown and on the browser used.
For example, sometimes you have to scroll down to get to the diagnosis views.
This also depends on the used browser. The views in Chrome have a different layout behaviour as the views in Firefox.
It would be nice if the position and size of the views are fixed and you have to scroll down to see all content just within the views.
Example of an unfixed view in Chrome (you have to scroll down to see all of :
![image](/uploads/9c89bec324f7dd2a9353d4f2bbf86ade/image.png)
Firefox has this layout by default:
![image](/uploads/eff3fe78f20b21769f528837e06024ed/image.png)bodawebodawehttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/17Ontologychange during Debugging Session (Allow or Lock)2021-01-25T15:17:54ZWolfgang SchmidOntologychange during Debugging Session (Allow or Lock)Shall the ontology be locked while a debugging session is running?
Or:
Shall the debugging session be stopped as soon as a change happens.Shall the ontology be locked while a debugging session is running?
Or:
Shall the debugging session be stopped as soon as a change happens.Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/18View for Possibly Faulty and Correct Axioms2020-10-20T14:52:33ZWolfgang SchmidView for Possibly Faulty and Correct AxiomsThere is yet no view to see the set of logical axioms and if they are possibly faulty (by default all are) or assumed as correct.There is yet no view to see the set of logical axioms and if they are possibly faulty (by default all are) or assumed as correct.Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/19Extend Repair interface with a modify and undo operation2021-01-14T12:33:59ZWolfgang SchmidExtend Repair interface with a modify and undo operationUse of a popup window will become necessary.
This is an extension of issue #13Use of a popup window will become necessary.
This is an extension of issue #13Wolfgang SchmidWolfgang Schmidhttps://git-ainf.aau.at/interactive-KB-debugging/webprotege_debugger/-/issues/20Wrong order of diagnosis2020-10-13T14:57:56ZWolfgang SchmidWrong order of diagnosisWolfgang SchmidWolfgang Schmid