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[protege-dev] WebProtege 2.6 Release readiness

Raphael, Nicholas nraphael at hbs.edu
Thu Dec 3 14:42:09 PST 2015


Hi Tania:

I'm sorry to say that the method for importing ontologies does not appear to work, no doubt through some misconfiguration on my part or an uncertain rasp on the exact ontology syntax/semantics. Note that Protégé 5 loads the files correctly - with the appropriate catalog file, of course.

I have read this wiki entry, but I cannot say I understand where Webprotege stands on this matter.

I am including the information I have that might give an indication of the problem involved, I'd appreciate any help.

I am running webprotege-2.6.0-SNAPSHOT.war in tomcat7, java version "1.8.0_66", under Ubuntu 14.04LTS, Linux 3.13.0-68-generic x86_64

So, I have a zip archive that contains the following files:

    10085  2015-12-03 16:48   root-ontology.owl
    28053  2015-11-25 10:27   CommonSenseMapping.owl
    11490  2015-11-25 10:28   DLP_397.owl
    82227  2015-11-25 10:26   DOLCE-Lite.owl
   160681  2015-11-25 10:29   ExtendedDnS.owl
    19113  2015-11-25 10:29   FunctionalParticipation.owl
    40545  2015-11-25 10:29   InformationObjects.owl
   159337  2015-11-25 10:29   KYOTO3.3Middle.owl
    17911  2015-11-25 10:29   KYOTOtop3.owl
    12677  2015-11-25 10:30   ModalDescriptions.owl
    76088  2015-11-25 10:30   Plans.owl
    45610  2015-11-25 10:30   SocialUnits.owl
    12674  2015-11-25 10:30   SpatialRelations.owl
    12647  2015-11-25 10:30   TemporalRelations.owl

root-ontology.owl has the following import statement in its owl:Ontology element:

    <owl:Ontology rdf:about="http://data.hbs.edu/">
                <owl:imports rdf:resource="KYOTO3.3Middle.owl"/>
    </owl:Ontology>

KYOTO3.3Middle.owl has the following import statement in its owl:Ontology element:

    <owl:Ontology rdf:about="http://www.kyoto-project.eu/ontologies/KYOTO3/KYOTO3Middle">
        <dc:title>KYOTO3.3 Middle</dc:title>
        <owl:imports rdf:resource="KYOTOtop3.owl"/>
    </owl:Ontology>

And so on.

As you can see, the importing ontology (the root ontology) has an ontology URI  of http://data.hbs.edu/. If I do not make the URIs dereferenceable by making data.hbs.edu an alias of localhost and copying the dependent owl files into the root of my web server, the zip archive loads the root-ontology fine, but nothing else:

[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Received upload from 0:0:0:0:0:0:0:1
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Created server side file upload-6033798621410311058.  File size is 0 MB
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Saving first revision of project ProjectId{eb502240-b796-47cd-aafc-713dc83f75f8}
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Request for unloaded project. Loading eb502240-b796-47cd-aafc-713dc83f75f8.
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Loading existing project: ProjectId{eb502240-b796-47cd-aafc-713dc83f75f8}
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Loading root ontology imports closure.
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Ontology loading started: file:/data/webprotege/data-store/project-data/eb502240-b796-47cd-aafc-713dc83f75f8/ontology-data/root-ontology.binary
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Fetching imported ontology from <http://data.hbs.edu/KYOTO3.3Middle.owl>.
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Ontology loading started: http://data.hbs.edu/KYOTO3.3Middle.owl
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Ontology loading failed: http://data.hbs.edu/KYOTO3.3Middle.owl (Reason: java.io.FileNotFoundException: http://data.hbs.edu/KYOTO3.3Middle.owl)
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Missing import: http://data.hbs.edu/KYOTO3.3Middle.owl due to java.io.FileNotFoundException: http://data.hbs.edu/KYOTO3.3Middle.owl
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Ontology loading finished: file:/data/webprotege/data-store/project-data/eb502240-b796-47cd-aafc-713dc83f75f8/ontology-data/root-ontology.binary (Loaded:
             OntologyID(OntologyIRI(<http://data.hbs.edu/>)))
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Ontology loading completed in 9 ms.
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Change history loading complete.  Loaded 1 revisions in 0 ms
Runtime Warning: Parsers should load imported ontologies using the makeImportLoadRequest method.
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Project: eb502240-b796-47cd-aafc-713dc83f75f8
             Initialized notes manager in 88 ms
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Memory Usage: Using 85 MB of 495 MB (17.27%) [409 MB free]
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             1 projects are now being accessed
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Request to save meta-project received. Scheduling save task.
[WebProtege] Thu Dec 03 17:15:26 EST 2015
             Request to save meta-project received. Scheduling save task.
[WebProtege] Thu Dec 03 17:16:19 EST 2015
             Loading project: ProjectId{eb502240-b796-47cd-aafc-713dc83f75f8}
[WebProtege] Thu Dec 03 17:16:19 EST 2015
             .... loaded project in 0 ms
[WebProtege] Thu Dec 03 17:16:26 EST 2015
             Saving meta-project now.
[WebProtege] Thu Dec 03 17:16:26 EST 2015
             Saved meta-project in 132 ms


If I _do_ make the URIs derefenceable as I described above, the log output when I try to create a project by uploading the archive is the following listing (which appears to loop on the import of the first imported ontology):

INFO: Deploying web application directory /var/lib/tomcat7/webapps/ROOT
Dec 03, 2015 4:38:18 PM org.apache.coyote.AbstractProtocol start
INFO: Starting ProtocolHandler ["http-bio-8080"]
Dec 03, 2015 4:38:18 PM org.apache.catalina.startup.Catalina start
INFO: Server startup in 9983 ms
[WebProtege] Thu Dec 03 16:38:35 EST 2015
             Received upload from 0:0:0:0:0:0:0:1
[WebProtege] Thu Dec 03 16:38:35 EST 2015
             Created server side file upload-8176219319343690189.  File size is 0 MB
[WebProtege] Thu Dec 03 16:38:37 EST 2015
             Saving first revision of project ProjectId{80772396-cd55-4fb5-87da-fed3d0104c38}
[WebProtege] Thu Dec 03 16:38:37 EST 2015
             Cached imported ontology: OntologyID(OntologyIRI(<http://www.kyoto-project.eu/ontologies/KYOTO3/KYOTO3Middle>)) in 52709ef5-e517-4dba-a866-bdab3122bf13.binary
[WebProtege] Thu Dec 03 16:38:37 EST 2015
             Request for unloaded project. Loading 80772396-cd55-4fb5-87da-fed3d0104c38.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Loading existing project: ProjectId{80772396-cd55-4fb5-87da-fed3d0104c38}
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Cached import: OntologyID(OntologyIRI(<http://www.kyoto-project.eu/ontologies/KYOTO3/KYOTO3Middle>))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Loading root ontology imports closure.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading started: file:/data/webprotege/data-store/project-data/80772396-cd55-4fb5-87da-fed3d0104c38/ontology-data/root-ontology.binary
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Fetching imported ontology from <http://data.hbs.edu/KYOTO3.3Middle.owl>.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading started: http://data.hbs.edu/KYOTO3.3Middle.owl
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading finished: http://data.hbs.edu/KYOTO3.3Middle.owl (Loaded: OntologyID(Anonymous-13))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading finished: file:/data/webprotege/data-store/project-data/80772396-cd55-4fb5-87da-fed3d0104c38/ontology-data/root-ontology.binary (Loaded:
             OntologyID(Anonymous-10))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading completed in 40 ms.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Loading existing project: ProjectId{80772396-cd55-4fb5-87da-fed3d0104c38}
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Cached import: OntologyID(OntologyIRI(<http://www.kyoto-project.eu/ontologies/KYOTO3/KYOTO3Middle>))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Loading root ontology imports closure.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading started: file:/data/webprotege/data-store/project-data/80772396-cd55-4fb5-87da-fed3d0104c38/ontology-data/root-ontology.binary
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Fetching imported ontology from <http://data.hbs.edu/KYOTO3.3Middle.owl>.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading started: http://data.hbs.edu/KYOTO3.3Middle.owl
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading finished: http://data.hbs.edu/KYOTO3.3Middle.owl (Loaded: OntologyID(Anonymous-19))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading finished: file:/data/webprotege/data-store/project-data/80772396-cd55-4fb5-87da-fed3d0104c38/ontology-data/root-ontology.binary (Loaded:
             OntologyID(Anonymous-16))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading completed in 25 ms.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Loading existing project: ProjectId{80772396-cd55-4fb5-87da-fed3d0104c38}
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Cached import: OntologyID(OntologyIRI(<http://www.kyoto-project.eu/ontologies/KYOTO3/KYOTO3Middle>))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Loading root ontology imports closure.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading started: file:/data/webprotege/data-store/project-data/80772396-cd55-4fb5-87da-fed3d0104c38/ontology-data/root-ontology.binary
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Fetching imported ontology from <http://data.hbs.edu/KYOTO3.3Middle.owl>.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading started: http://data.hbs.edu/KYOTO3.3Middle.owl
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading finished: http://data.hbs.edu/KYOTO3.3Middle.owl (Loaded: OntologyID(Anonymous-25))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading finished: file:/data/webprotege/data-store/project-data/80772396-cd55-4fb5-87da-fed3d0104c38/ontology-data/root-ontology.binary (Loaded:
             OntologyID(Anonymous-22))
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Project: 80772396-cd55-4fb5-87da-fed3d0104c38
             Ontology loading completed in 20 ms.
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Loading existing project: ProjectId{80772396-cd55-4fb5-87da-fed3d0104c38}
[WebProtege] Thu Dec 03 16:38:38 EST 2015
             Cached import: OntologyID(OntologyIRI(<http://www.kyoto-project.eu/ontologies/KYOTO3/KYOTO3Middle>))

(snip more of same ....)

[WebProtege] Thu Dec 03 16:50:00 EST 2015
             ***** SEVERE *****
             An unexpected exception was thrown on the server

             Date and time: Thu Dec 03 16:50:00 EST 2015

             User: nraphael
             Request URI: /webprotege/webprotege/dispatchservice
             Remote address: 0:0:0:0:0:0:0:1
             Remote host: 0:0:0:0:0:0:0:1

             Headers:
             host: localhost:8080
             user-agent: Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:42.0) Gecko/20100101 Firefox/42.0
             accept: text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8
             accept-language: en-US,en;q=0.5
             accept-encoding: gzip, deflate
             content-type: text/x-gwt-rpc; charset=utf-8
             x-gwt-permutation: CC41E36EC5442639CE36990BE84FC7B8
             x-gwt-module-base: http://localhost:8080/webprotege/webprotege/
             referer: http://localhost:8080/webprotege/
             content-length: 655
             cookie: JSESSIONID=5C5ADB96EDEDB6FE9F88C8403932CBDB; workspacePreferencesId=WSP1
             connection: keep-alive
             pragma: no-cache
             cache-control: no-cache


             Message: Service method 'public abstract edu.stanford.bmir.protege.web.shared.dispatch.DispatchServiceResultContainer
             edu.stanford.bmir.protege.web.client.dispatch.DispatchService.executeAction(edu.stanford.bmir.protege.web.shared.dispatch.Action) throws
             edu.stanford.bmir.protege.web.client.dispatch.ActionExecutionException,edu.stanford.bmir.protege.web.shared.permissions.PermissionDeniedException' threw an
             unexpected exception: com.google.inject.internal.util.$ComputationException: java.lang.ArrayIndexOutOfBoundsException: 18176

             Stack trace:

             com.google.gwt.user.server.rpc.UnexpectedException: Service method 'public abstract
             edu.stanford.bmir.protege.web.shared.dispatch.DispatchServiceResultContainer
             edu.stanford.bmir.protege.web.client.dispatch.DispatchService.executeAction(edu.stanford.bmir.protege.web.shared.dispatch.Action) throws
             edu.stanford.bmir.protege.web.client.dispatch.ActionExecutionException,edu.stanford.bmir.protege.web.shared.permissions.PermissionDeniedException' threw an
             unexpected exception: com.google.inject.internal.util.$ComputationException: java.lang.ArrayIndexOutOfBoundsException: 18176
             at com.google.gwt.user.server.rpc.RPC.encodeResponseForFailure(RPC.java:415)
             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:85)
             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:1041)
             at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:607)
             at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:315)
             at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
             at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
             at java.lang.Thread.run(Thread.java:745)
             Caused by: com.google.inject.internal.util.$ComputationException: java.lang.ArrayIndexOutOfBoundsException: 18176
             at com.google.inject.internal.util.$MapMaker$StrategyImpl.compute(MapMaker.java:553)
             at com.google.inject.internal.util.$MapMaker$StrategyImpl.compute(MapMaker.java:419)
             at com.google.inject.internal.util.$CustomConcurrentHashMap$ComputingImpl.get(CustomConcurrentHashMap.java:2041)
             at com.google.inject.internal.util.$StackTraceElements.forMember(StackTraceElements.java:53)
             at com.google.inject.internal.Errors.formatInjectionPoint(Errors.java:716)
             at com.google.inject.internal.Errors.formatSource(Errors.java:678)
             at com.google.inject.internal.Errors.format(Errors.java:555)
             at com.google.inject.CreationException.getMessage(CreationException.java:48)
             at java.lang.Throwable.getLocalizedMessage(Throwable.java:391)
             at java.lang.Throwable.toString(Throwable.java:480)
             at java.lang.Throwable.<init>(Throwable.java:311)
             at java.lang.Exception.<init>(Exception.java:102)
             at java.lang.RuntimeException.<init>(RuntimeException.java:96)
             at edu.stanford.bmir.protege.web.client.dispatch.ActionExecutionException.<init>(ActionExecutionException.java:35)
             at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceExecutorImpl.execute(DispatchServiceExecutorImpl.java:41)
             at edu.stanford.bmir.protege.web.server.dispatch.impl.DispatchServiceImpl.executeAction(DispatchServiceImpl.java:40)
             at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
             at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
             at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
             at java.lang.reflect.Method.invoke(Method.java:497)
             at com.google.gwt.user.server.rpc.RPC.invokeAndEncodeResponse(RPC.java:587)
             ... 26 more
             Caused by: java.lang.ArrayIndexOutOfBoundsException: 18176
             at com.google.inject.internal.asm.$ClassReader.readClass(Unknown Source)
             at com.google.inject.internal.asm.$ClassReader.accept(Unknown Source)
             at com.google.inject.internal.asm.$ClassReader.accept(Unknown Source)
             at com.google.inject.internal.util.$LineNumbers.<init>(LineNumbers.java:62)
             at com.google.inject.internal.util.$StackTraceElements$1.apply(StackTraceElements.java:36)
             at com.google.inject.internal.util.$StackTraceElements$1.apply(StackTraceElements.java:33)
             at com.google.inject.internal.util.$MapMaker$StrategyImpl.compute(MapMaker.java:549)
             ... 46 more

Thank you,

Nick Raphael


From: protege-dev [mailto:protege-dev-bounces at lists.stanford.edu] On Behalf Of Tania Tudorache
Sent: Tuesday, November 10, 2015 1:39 PM
To: protege-dev at lists.stanford.edu
Subject: Re: [protege-dev] WebProtege 2.6 Release readiness

Sure, I hope it helps!

Tania
On 11/10/2015 08:13 AM, Raphael, Nicholas wrote:
Thank you and good Wiki entry.

Nick
From: protege-dev [mailto:protege-dev-bounces at lists.stanford.edu] On Behalf Of Tania Tudorache
Sent: Monday, November 09, 2015 6:55 PM
To: protege-dev at lists.stanford.edu<mailto:protege-dev at lists.stanford.edu>
Subject: Re: [protege-dev] WebProtege 2.6 Release readiness

Just a quick clarification, because my formulation in the previous email was not very clear: you need to rename the most importing ontology to root-ontology.owl.
The archive itself can be named in any way.

I have also created a wiki entry for this question, because it was missing in our user guide:
http://protegewiki.stanford.edu/wiki/WebProtegeUsersGuide#Ontologies_with_imports

Tania
On 11/09/2015 03:13 PM, Tania Tudorache wrote:
Hi Nick,

Just to clarify: are you trying to upload an ontology with local imports into WebProtege? Local imports meaning that they should be fetched locally, rather than from the Web?

If so, then WebProtege supports this, there is no need to change the import IRI in the ontology file.

You create a zip archive containing your most importing ontology (rename it to root-ontology.owl), and also add in this archive all the imported OWL files.
WebProtege will then read the top ontology together with all its local imports, and should be handling it correctly.

Cheers,
Tania


On 11/09/2015 02:06 PM, Raphael, Nicholas wrote:

Hello Tania:



Thank you very much. I have loaded WebProtege 2.6 into our Tomcat7 container and have run some basic tests on the upload and merge facility and so far it suits my needs precisely.



Unfortunately, the next requirement for our work involves our base owl document. It all loads well into Protégé thanks to its catalog file, but of course it will not load in WebProtege.



The first problem is that WebProtege cannot resolve the URLs after it loads the driver file up to its server location.



I edited the import URLs so that the imports load from my local, but then I run into a different problem. Would you be interested in the package of files? At any rate, I am attaching the log output and the stack dump. There is so much repetition in the loading, the load seems to be caught in a loop.



Thank you,



Nick Raphael



-----Original Message-----

From: protege-dev [mailto:protege-dev-bounces at lists.stanford.edu] On Behalf Of Tania Tudorache

Sent: Wednesday, November 04, 2015 1:05 PM

To: protege-dev at lists.stanford.edu<mailto:protege-dev at lists.stanford.edu>

Subject: Re: [protege-dev] WebProtege 2.6 Release readiness



Hi Nick,



We hope to have the next WebProtege release soon, sometimes this month.



Meanwhile, you may test the current snapshot from here:

http://protege.stanford.edu/download/webprotege/candidate/webprotege-2.6.0-SNAPSHOT.war



If you have any issues with it, please let us know.



Cheers,

Tania



On 10/29/2015 07:45 AM, nraphael wrote:

Hi:



After learning of the feature from a previous post, I realize I

actually currently need the ontology merge facility in WebProtege 2.6,

specifically for batch incremental updates. Is there a published date

for the 2.6 release? If not, is there a latest stable pre-release that I could use?



Thank you,



Nick Raphael

Tech Lead, Semantic Infrastructure

Baker Library

Harvard Business School







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