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[protege-discussion] Help : Protege 4 client server (Bleeding edge version)

Dinbandhu Laxman Gauda Dinbandhu_Gauda at infosys.com
Thu Nov 8 01:42:32 PST 2012


Hi,



I am now able to deploy , start and connect Protege4 server.  Thanks for all your help and support.



I have couple of more issues

1) After uploading owl file to server, it saves it as a .history file. This file seems to be a flat file. In the final release, will this file have the same extension.?

2) When I try to open .history(already uploaded file) file from server I see the class hierarchy structure seems to be not correct. Some classes are missing. Though individual looks file.



Attached is a screen shot with more details

Owl file :



[cid:image001.png at 01CDBDC3.7990D660]



>From Server:



[cid:image002.png at 01CDBDC3.33113310]



Thanks

-Dinu



-----Original Message-----
From: protege-discussion-bounces at lists.stanford.edu [mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of protege-discussion-request at lists.stanford.edu
Sent: Wednesday, November 07, 2012 1:55 AM
To: protege-discussion at lists.stanford.edu
Subject: protege-discussion Digest, Vol 76, Issue 7



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Today's Topics:



   1. Re: Help : Protege 4 client server (Bleeding edge version)

      (Timothy Redmond)





----------------------------------------------------------------------



Message: 1

Date: Tue, 06 Nov 2012 12:24:51 -0800

From: Timothy Redmond <tredmond at stanford.edu<mailto:tredmond at stanford.edu>>

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

Subject: Re: [protege-discussion] Help : Protege 4 client server

                (Bleeding edge version)

Message-ID: <50997213.5090404 at stanford.edu<mailto:50997213.5090404 at stanford.edu>>

Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"





I set the logging level to debug for the service starter (do svn update).  This seems like a good default because the logging information is not that voluminous and might have just the information that we need.



-Timothy





On 11/6/12 11:19 AM, Timothy Redmond wrote:

> On 11/5/12 11:35 PM, Dinbandhu Laxman Gauda wrote:

>> Hi,

>>

>> Thanks for looking into this Prot?g? 4 item and for a quick reply.  Below is a log from commons-daemon log file and ant log which gives some more information on the error. Attached is ant log as well for more details..

>>

>> Couple of things I would like to know

>> 1) I do not see any executales or ant targets to run client.

>

> The main way to run the client is to

>

>  1. download the latest Protege 4.2 distribution [2]  2. add the two

> files from the client installation page to the plugins

>     directory of the Protege 4.2 distribution location (usually

>     something like C:\Program Files\Protege_4.2_beta by default).

>

> Then you will be able to run the client as shown in the first video

> [3].  This should have been there before but our documentation is

> still getting worked out.

>

> We also have some command-line capabilities that allow you to use the

> server with tools other than Protege but I haven't written the windows

> scripts yet.

>

>> 2) I have created plugins folder under C:\Program Files\Protege OWL Server\, just want to know this is a correct place.

>

> Don't put anything there yet.  As of now we don't have any Protege OWL

> server plugins though the support is all there already.

>> 3) even I tried to start server using this command line statement "OWLDocService //ES//OWLServer"  , but I do not see server in running mode in both services or in taskmanager/services, both are showing Stopped.

>

> Yes you are gathering all the right data and this is very useful. This

> error message - "Failed creating java" - is frustratingly

> uninformative.  Not too long ago I spent a whole weekend banging my

> head against a very similar error message only to realize that I was

> using a 32-bit executable and an incompatible memory setting.  (This

> is why I thought that it might be a memory problem before).

>

> At the moment, I only have one theory and one workaround which I think

> will work.  I am wondering if you are using the java that came with

> Windows or if you installed Oracle's java.  I know from past messages

> that the java that comes with windows can cause problems.

>

> If you are using Oracle's java then, hopefully today, I will add a

> .bat run script that I am pretty sure will work.  This approach has

> the disadvantage that you will have to start the server manually on

> each reboot but it should remove some of the variables that are giving

> us trouble.  I will also keep thinking about what else might be wrong.

> Finally I will look into seeing if we can run a public server over

> here which would allow you to try out the client.

>

> Thank you for the help debugging and apologies for the wrinkles that

> we have not yet worked out.

>

> -Timothy

>

> [1]http://protegewiki.stanford.edu/wiki/Protege4ClientServer#Installat

> ion_details [2]http://protege.stanford.edu/download/download.html

> [3]http://protegewiki.stanford.edu/wiki/Protege4ClientServer#Videoss

>> Commons-Daemon log:

>> [2012-11-06 12:44:26] [info]  Commons Daemon procrun (1.0.10.0

>> 32-bit) started

>> [2012-11-06 12:44:26] [info]  Running 'OWLServer' Service...

>> [2012-11-06 12:44:26] [info]  Starting service...

>> [2012-11-06 12:44:26] [error] Failed creating java

>> [2012-11-06 12:44:26] [error] ServiceStart returned 1

>> [2012-11-06 12:44:26] [info]  Run service finished.

>> [2012-11-06 12:44:26] [info]  Commons Daemon procrun finished

>> [2012-11-06 12:55:53] [info]  Commons Daemon procrun (1.0.10.0

>> 32-bit) started

>> [2012-11-06 12:55:53] [info]  Service OWLServer name OWLServer

>> [2012-11-06 12:55:53] [info]  Service 'OWLServer' installed

>> [2012-11-06 12:55:53] [info]  Commons Daemon procrun finished

>> [2012-11-06 12:55:53] [info]  Commons Daemon procrun (1.0.10.0

>> 32-bit) started

>> [2012-11-06 12:55:53] [info]  Starting service 'OWLServer' ...

>> [2012-11-06 12:55:53] [info]  Commons Daemon procrun (1.0.10.0

>> 32-bit) started

>> [2012-11-06 12:55:53] [info]  Running 'OWLServer' Service...

>> [2012-11-06 12:55:53] [info]  Starting service...

>> [2012-11-06 12:55:53] [error] Failed creating java

>> [2012-11-06 12:55:53] [error] ServiceStart returned 1

>> [2012-11-06 12:55:53] [info]  Run service finished.

>> [2012-11-06 12:55:53] [info]  Commons Daemon procrun finished

>> [2012-11-06 12:55:54] [error] Failed to start 'OWLServer' service

>> [2012-11-06 12:55:54] [error] The data area passed to a system call is too small.

>> [2012-11-06 12:55:54] [info]  Start service finished.

>> [2012-11-06 12:55:54] [error] Commons Daemon procrun failed with exit

>> value: 5 (Failed to start service)

>> [2012-11-06 12:55:55] [error] The data area passed to a system call is too small.

>>

>> Ant Log:

>> deploy.windows:

>>       [echo] Deploying windows Protege OWL Server

>>       [echo] Will run as protege : C:/Program Files/Protege OWL Server/logs

>>       [exec] Current OS is Windows 7

>>       [exec] Executing 'C:\Program Files\Protege OWL Server\bin\OWLDocService.exe' with arguments:

>>       [exec] '//IS//OWLServer'

>>       [exec] '--Install=C:\Program Files\Protege OWL Server\bin\OWLDocService.exe'

>>       [exec] '--Jvm=auto'

>>       [exec] '--Description=Protege-OWL-Document-Service'

>>       [exec] '--DisplayName=OWLServer'

>>       [exec] '--LogPath=C:/Program Files/Protege OWL Server/logs'

>>       [exec] '--StdOutput=auto'

>>       [exec] '--StdError=auto'

>>       [exec] '--Startup=auto'

>>       [exec] '--Classpath=bin/winsvc.jar;lib/felix.jar;lib/ProtegeLauncher.jar'

>>       [exec] '--JvmMx=700'

>>       [exec] '++JvmOptions=-DentityExpansionLimit=100000000'

>>       [exec] '++JvmOptions=-Dfile.encoding=UTF-8'

>>       [exec] '++JvmOptions=-Djava.rmi.server.hostname=dinu'

>>       [exec] '++JvmOptions=-Dorg.protege.owl.server.configuration=metaproject.owl'

>>       [exec] '++JvmOptions=-Djava.util.logging.config.file=logging.properties'

>>       [exec] '--StartPath=C:\Program Files\Protege OWL Server'

>>       [exec] '--StartMode=jvm'

>>       [exec] '--StartClass=org.protege.owl.server.deploy.windows.WindowsOWLServer'

>>       [exec] '--StartParams=start'

>>       [exec] '--StopPath=C:\Program Files\Protege OWL Server'

>>       [exec] '--StopMode=jvm'

>>       [exec] '--StopClass=org.protege.owl.server.deploy.windows.WindowsOWLServer'

>>       [exec] '--StopParams=stop'

>>       [exec]

>>       [exec] The ' characters around the executable and arguments are

>>       [exec] not part of the command.

>>       [echo] prefix C:\Program Files\Protege OWL Server\bin\OWLDocService.exe

>>       [exec] Current OS is Windows 7

>>       [exec] Executing 'C:\Program Files\Protege OWL Server\bin\OWLDocService.exe' with arguments:

>>       [exec] '//ES//OWLServer'

>>       [exec]

>>       [exec] The ' characters around the executable and arguments are

>>       [exec] not part of the command.

>>        [ant] Exiting D:\work\workspace\protegeserver4\org.protege.owl.server.deploy\build.xml.

>>

>> BUILD FAILED

>> D:\work\workspace\protegeserver4\build.xml:35: The following error occurred while executing this line:

>> D:\work\workspace\protegeserver4\org.protege.owl.server.deploy\build.xml:339: exec returned: 5

>>           at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:646)

>>           at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:672)

>>           at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:498)

>>           at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)

>>           at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)

>>           at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

>>           at java.lang.reflect.Method.invoke(Method.java:597)

>>

>>

>> Thanks

>> -Dinu

>>

>> -----Original Message-----

>> From:protege-discussion-bounces at lists.stanford.edu

>> [mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf

>> Ofprotege-discussion-request at lists.stanford.edu<mailto:Ofprotege-discussion-request at lists.stanford.edu>

>> Sent: Tuesday, November 06, 2012 5:10 AM

>> To:protege-discussion at lists.stanford.edu

>> Subject: protege-discussion Digest, Vol 76, Issue 4

>>

>> Send protege-discussion mailing list submissions to

>>           protege-discussion at lists.stanford.edu<mailto:protege-discussion at lists.stanford.edu>

>>

>> To subscribe or unsubscribe via the World Wide Web, visit

>>           https://mailman.stanford.edu/mailman/listinfo/protege-discussion

>> or, via email, send a message with subject or body 'help' to

>>           protege-discussion-request at lists.stanford.edu<mailto:protege-discussion-request at lists.stanford.edu>

>>

>> You can reach the person managing the list at

>>           protege-discussion-owner at lists.stanford.edu<mailto:protege-discussion-owner at lists.stanford.edu>

>>

>> When replying, please edit your Subject line so it is more specific than "Re: Contents of protege-discussion digest..."

>>

>>

>> Today's Topics:

>>

>>     1. Re: Help : Protege 4 client server (Bleeding edge version)

>>        (Timothy Redmond)

>>

>>

>> ---------------------------------------------------------------------

>> -

>>

>> Message: 1

>> Date: Mon, 05 Nov 2012 15:39:22 -0800

>> From: Timothy Redmond<tredmond at stanford.edu<mailto:tredmond at stanford.edu>>

>> To:protege-discussion at lists.stanford.edu

>> Subject: Re: [protege-discussion] Help : Protege 4 client server

>>           (Bleeding edge version)

>> Message-ID:<50984E2A.9020408 at stanford.edu<mailto:50984E2A.9020408 at stanford.edu>>

>> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

>>

>>

>> I am running 32-bit windows in a virtualbox and have replicated a

>> problem with your symptoms.   The windows error messages are aweful!  I

>> will have to see if there is anything that I can do about this as I refine this process.

>>

>> I also realized that there is an important step that is not yet documented - to be able to interact with the server you need to install the Protege client jars.  When the Protege OWL server is released, these will be included in the Protege distribution.  In the meantime, I have attached two jar files that you can put in the Protege plugins directory.

>>

>> First do an svn update on the server directory - I have fixed a couple of typos.  Second, I have determined that if the server has been deployed then if the deploy target is called it will fail with exactly the "exec returned: 8" error message.  The solution is to run "ant undeploy" to clean up and then run "ant deploy" to put the service back.

>>

>> I hope that this fixes the problem for you but if it doesn't I will soon write a .bat script that will let you manually start running the server.  This script would not resume running on a reboot but it will allow you to proceed even if my scripts to configure the apache daemon don't work.

>>

>> You can monitor if the OWL server has been installed by looking at the Services application.  You can find this by going to the "Start" menu and searching for "services".  When you run this program it will show all the installed services and the OWL Server will show up as "OWLServer".  This is shown in the diagram that I have included below.

>>

>> -Timothy.

>>

>>

>>

>>

>>

>>

>> On 11/1/12 12:27 PM, Timothy Redmond wrote:

>>> I am sorry for the delay on looking at this.  I am trying to get my

>>> hands on a 32-bit windows image for testing.  But I did have one

>>> thought.  Make sure that the memory.mb setting in the

>>> local.properties file is less than 2048 because a 32-bit windows

>>> process can't handle more than 2 gig of memory.  When I was testing

>>> this before I noticed that some of the errors under windows are a bit obscure.

>>>

>>> -Timothy

>>>

>>>

>>> On 10/31/12 5:04 AM, Dinbandhu Laxman Gauda wrote:

>>>> The below issue  is resolved by fixing this line in build.xml file.

>>>>

>>>>

>>>> <target name="install.windows32.files" depends="jar, install.noarch.files" if="is.windows32">

>>>>                     <!--copy file="${service64.src}"  tofile="${service}"/>   -->

>>>>     <copy file="${service32.src}"  tofile="${service}"/>

>>>>     </target>

>>>>

>>>> But I am seeing other issues like..  Attached is a ant log file..

>>>>

>>>> BUILD FAILED

>>>> D:\work\workspace\protege-server-4\build.xml:35: The following error occurred while executing this line:

>>>> D:\work\workspace\protege-server-4\org.protege.owl.server.deploy\build.xml:310: exec returned: 8

>>>>     at org.apache.tools.ant.taskdefs.ExecTask.runExecute(ExecTask.java:646)

>>>>     at org.apache.tools.ant.taskdefs.ExecTask.runExec(ExecTask.java:672)

>>>>     at org.apache.tools.ant.taskdefs.ExecTask.execute(ExecTask.java:498)

>>>>     at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)

>>>>     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)

>>>>     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

>>>>     at java.lang.reflect.Method.invoke(Method.java:597)

>>>>     at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)

>>>>     at org.apache.tools.ant.Task.perform(Task.java:348)

>>>>     at org.apache.tools.ant.Target.execute(Target.java:392)

>>>>     at org.apache.tools.ant.Target.performTasks(Target.java:413)

>>>>     at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)

>>>>     at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)

>>>>     at org.apache.tools.ant.Project.executeTargets(Project.java:1251)

>>>>     at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:442)

>>>>     at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:291)

>>>>     at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)

>>>>     at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)

>>>>     at java.lang.reflect.Method.invoke(Method.java:597)

>>>>     at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)

>>>>     at org.apache.tools.ant.Task.perform(Task.java:348)

>>>>     at org.apache.tools.ant.Target.execute(Target.java:392)

>>>>     at org.apache.tools.ant.Target.performTasks(Target.java:413)

>>>>     at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1399)

>>>>     at org.apache.tools.ant.Project.executeTarget(Project.java:1368)

>>>>     at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)

>>>>     at org.apache.tools.ant.Project.executeTargets(Project.java:1251)

>>>>     at org.apache.tools.ant.Main.runBuild(Main.java:811)

>>>>     at org.apache.tools.ant.Main.startAnt(Main.java:217)

>>>>     at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)

>>>>     at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)

>>>>

>>>>

>>>>

>>>> -----Original Message-----

>>>> From: Dinbandhu Laxman Gauda

>>>> Sent: Wednesday, October 31, 2012 4:38 PM

>>>> To: 'protege-discussion at lists.stanford.edu'

>>>> Subject: RE: [protege-discussion] Help : Protege 4 client server

>>>> (Bleeding edge version)

>>>>

>>>> Hi,

>>>>

>>>> I am not able to deploy Prot?g? 4 server  on Windows 7 (32 bit) even though exe is installed for x32 bit.

>>>>

>>>> Similar issue is with clean.full as well

>>>>

>>>> Attached is a log from ant build.

>>>>

>>>> Thanks

>>>> -Dinu

>>>>

>>>> -----Original Message-----

>>>> From:protege-discussion-bounces at lists.stanford.edu

>>>> [mailto:protege-discussion-bounces at lists.stanford.edu] On Behalf Of

>>>> Timothy Redmond

>>>> Sent: Wednesday, 31 October, 2012 12:52

>>>> To:protege-discussion at lists.stanford.edu

>>>> Subject: Re: [protege-discussion] Help : Protege 4 client server

>>>> (Bleeding edge version)

>>>>

>>>> On 10/30/2012 10:08 PM, Dinbandhu Laxman Gauda wrote:

>>>>> Hi Timothy,

>>>>>

>>>>> Attached is a log text file.  I looked at

>>>>> org.protege.owl.server.jar file and looks like

>>>>> SetMetaprojectDataDir.class file is missing. I infact .java file

>>>>> is also missing from

>>>>> org.protege.owl.server\src\main\java\org\protege\owl\server\comman

>>>>> d

>>>>> folder

>>>>>

>>>>> Thanks

>>>>> -Dinu

>>>>>

>>>> Thanks very much for the help.  This problem was completely my

>>>> mistake - actually I made several mistakes to make this happen.  It

>>>> has been broken for a bit and I didn't notice.  If you update and

>>>> try again I think that it will work.  (I just ran the installer in

>>>> both linux and

>>>> windows.)

>>>>

>>>> One of the things that I changed to fix this was to change the ant clean target and add a clean.full target.  The clean target now just cleans up the built artifacts in the checked out directories.  The clean.full target will also clean up the Protege OWL server files that have been installed in the system directories.

>>>>

>>>> You have also helped me see that I can simplify this process when the server is ready for release.  The current version involves two projects (the server project and the server deployer project) that get built.  If anything goes wrong in either one then the build fails.  But really all we need to distribute is the deployer project together with a built copy of the server.

>>>>

>>>> -Timothy

>>>>

>>>>

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