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

Dinbandhu Laxman Gauda Dinbandhu_Gauda at infosys.com
Tue Oct 30 22:08:23 PDT 2012


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\command folder

Thanks
-Dinu

-----Original Message-----
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Sent: Tuesday, October 30, 2012 9:46 PM
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Today's Topics:

   1. An Earth Science Ontology Dialog - miniseries session-4 - Thu
      2012.11.01 - "A Review of Ontologies for Earth Sciences" -
      Co-chairs: Dalia Varanka & Mark Schildhauer (Peter Yim)
   2. Re: Help : Protege 4 client server (Bleeding	edge version)
      (Dinbandhu Laxman Gauda)
   3. Re: Help : Protege 4 client server (Bleeding edge version)
      (Timothy Redmond)


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

Message: 1
Date: Mon, 29 Oct 2012 18:13:05 -0700
From: Peter Yim <peter.yim at cim3.com>
To: protege-discussion at mailman.stanford.edu
Subject: [protege-discussion] An Earth Science Ontology Dialog -
	miniseries session-4 - Thu 2012.11.01 - "A Review of Ontologies for
	Earth Sciences" - Co-chairs: Dalia Varanka & Mark Schildhauer
Message-ID:
	<CAGdcwD060BcHKyoXbOvOnHReEA2of_HKzXV9W7_=UrcRL2NXmA at mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Re: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_11_01


Dear Colleagues,


You are cordially invited to participate at the 4th "Earth Science Ontology Dialog" mini-series of virtual panel sessions, which is coming up this Thursday, 1-Nov-2012.

The mini-series (dubbed: "EarthScienceOntolog") is designed to explore the current status and application of multi-level ontologies towards developing a semantically enabled cyberinfrastructure for the Earth Science Community. In addition, one key mission of the mini-series is to bring together members of both communities (Earth Science and
Ontology/Semantics) into a meaningful dialog. We anticipate that the sharing of requirements and use cases, geo-science problems and issues, ontological engineering architectures and approaches, and prospective tools, will enable collaborative understanding of the challenges and potential value in the application of ontology and semantics in Earth Science.

This mini-series of virtual events are co-organized/supported by members of the EarthCube community, Ontolog community, SOCoP community and the IAOA community.


****************** Headlines ***********************


Please join us this Thursday (Nov-1) at this "EarthScienceOntolog"
mini-series session:

*Thu 1 Nov 2012* - "A Review of Ontologies for Earth Sciences" -
Co-chairs: Dr. Dalia Varanka (USGS) and Dr. Mark Schildhauer (NCEAS, UC Santa Barbara) - see details on the session page at:
http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_11_01
 ... *RSVP now*!

The event will be 2-hour virtual panel sessions starting at: 9:30am PDT / 12:30pm EDT / 5:30pm CET / 16:30 UTC
- see worldclock:
http://www.timeanddate.com/worldclock/fixedtime.html?month=11&day=1&year=2012&hour=9&min=30&sec=0&p1=224

*Register your attendance* by emailing <peter.yim at cim3.com> off-line or register yourself directly to the wiki session page (if you are already a part of the Ontolog community). Please include your affiliation and specify the date of the session(s) when you are writing in to register and specify date of the session you plan to attend.


Five virtual panel sessions have been scheduled for the mini-series - see details under:
http://ontolog.cim3.net/cgi-bin/wiki.pl?EarthScienceOntolog#nid3CWE


********************* Details ************************

EarthScienceOntolog: Panel Session-04 - Thu 2012-11-01

Mini-Series Theme: An Earth Science Ontology Dialog

Session Topic: A Review of Ontologies for Earth Sciences

Session Co-chairs:
 Dr. Dalia Varanka (USGS) and Dr. Mark Schildhauer (NCEAS, UCSB)

Panelists / Briefings:

* Dr. Luis Bermudez (OGC)
  - "Use of Ontologies within the Open Geospatial Consortium (OGC)"

* Dr. Boyan Brodaric (Geological Survey of Canada)
  - "Toward an integrated surface and subsurface water ontology"

* Dr. Norman Morrison (U of Manchester, UK)
  - "The Environment Ontology: What sort of a place was it?"

* Dr. Thomas Huang (JPL/NASA)
  - "From Modeling the Earth to Terrain Simulation"

* Dr. Mark Schildhauer (UC Santa Barbara)
  - "Where do we go from here with Earth and Environmental Science
      Ontologies?" (a joint work by Mark Schildhauer & Ben Adams)

---

This, and the rest of the mini-series sessions, like all Ontolog virtual events, are open and free of charge. Anyone who is interested, or (better still) who may have something to contribute, is welcome.
Please refer to event details on the session pages, to which the hyperlink is given above, where you will find session agenda, conference call dial-in, slides and other pertinent information. Feel free to pass this invitation along to colleagues who may also find these sessions to be of interest.

*RSVP* by emailing Peter Yim at <peter.yim at cim3.com> offline (or add yourself directly to the session page if you are already an Ontolog community member) so that we can prepare enough resources to support everyone. [Please state clearly the date of the session you are registering for in your email.]

These sessions will be recorded and made available in a publicly accessible archive. Therefore, before participating, please make sure you are cognizant of our IPR policy (ref:
http://ontolog.cim3.net/cgi-bin/wiki.pl?WikiHomePage#nid32).


Regards. =ppy

For and on behalf of

the Session-4 co-chairs,
  Dalia Varanka & Dr. Mark Schildhauer

and the EarthScienceOntolog mini-series Organizing Committee,
  Dalia Varanka
  Gary Berg-Cross
  Krishna Sinha
  Krzysztof Janowicz
  Leo Obrst
  Mark Schildhauer
  Mike Dean
  Naicong Li
  Nancy Wiegand
  Pascal Hitzler
  Peter Yim

http://ontolog.cim3.net/cgi-bin/wiki.pl?EarthScienceOntolog


p.s. The full proceedings from past 3 sessions (including abstracts, slides, audio recording, in-session chat-transcript, etc.) are available online now, for those who have missed the session, or those who desire to revisit the materials and study them in greater detail - please look under the "Archives" section on the respective session pages at:
- s01: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_08_23
- s02: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_09_06
- s03: http://ontolog.cim3.net/cgi-bin/wiki.pl?ConferenceCall_2012_10_11
--


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

Message: 2
Date: Tue, 30 Oct 2012 10:16:07 +0000
From: Dinbandhu Laxman Gauda <Dinbandhu_Gauda at infosys.com>
To: "protege-discussion at lists.stanford.edu"
	<protege-discussion at lists.stanford.edu>
Subject: Re: [protege-discussion] Help : Protege 4 client server
	(Bleeding	edge version)
Message-ID:
	<337E541B074A3C42B29E8238923CDA7B47DD0F at blrkecmbx15.ad.infosys.com>
Content-Type: text/plain; charset="iso-8859-1"

Hi,

Were you guys able to install and deploy Prot?g? 4 client - Server in windows environment ?

I am seeing this error when try to run using "ant deploy" target.  Is this supported on windows yet? Am I missing something?

configure.metaproject:
     [java] java.lang.NoClassDefFoundError: org/protege/owl/server/command/SetMetaprojectDataDir
     [java] Caused by: java.lang.ClassNotFoundException: org.protege.owl.server.command.SetMetaprojectDataDir
     [java]     at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
     [java]     at java.security.AccessController.doPrivileged(Native Method)
     [java]     at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
     [java]     at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
     [java]     at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
     [java]     at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
     [java] Could not find the main class: org.protege.owl.server.command.SetMetaprojectDataDir.  Program will exit.
     [java] Exception in thread "main"

BUILD FAILED
D:\work\workspace\protege4\build.xml:35: The following error occurred while executing this line:
D:\work\workspace\protege4\org.protege.owl.server.deploy\build.xml:112: Java returned: 1


Thanks
-Dinu

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Message: 3
Date: Tue, 30 Oct 2012 09:15:54 -0700
From: Timothy Redmond <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: <508FFD3A.7030409 at stanford.edu>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"

On 10/30/2012 03:16 AM, Dinbandhu Laxman Gauda wrote:
>
> Hi,
>
> Were you guys able to install and deploy Prot?g? 4 client -- Server in 
> windows environment ?
>

Yes - we have this working here.  The one thing that is unfortunate about the windows deploy is that the Protege server runs with full privileges which is non-optimal.

> I am seeing this error when try to run using "ant deploy" target.  Is 
> this supported on windows yet? Am I missing something?
>

We haven't quite released it yet but it would be good to know what is happening and get it to work.  My first guess, from your error is that the org.protege.owl.server build failed but for some reason the build continued running until it hit the problem that you describe below.  The class that you are missing should have been found in the org.protege.owl.server.jar file that should have been built by the time you reach this stage.

Could you send me the full logs from the ant deploy run?  It looks like you can do this in windows with the following magic incantation:

       ant deploy > log.txt 2>&1


It might actually be useful to also have a verbose log of the run:


       ant -v deploy > log-with-everything.txt 2>&1



-Timothy



> configure.metaproject:
>
>      [java] java.lang.NoClassDefFoundError: 
> org/protege/owl/server/command/SetMetaprojectDataDir
>
>      [java] Caused by: java.lang.ClassNotFoundException: 
> org.protege.owl.server.command.SetMetaprojectDataDir
>
>      [java] at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
>
>      [java] at java.security.AccessController.doPrivileged(Native 
> Method)
>
>      [java] at 
> java.net.URLClassLoader.findClass(URLClassLoader.java:190)
>
>      [java] at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
>
>      [java] at
> sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
>
>      [java] at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
>
>      [java] Could not find the main class: 
> org.protege.owl.server.command.SetMetaprojectDataDir. Program will exit.
>
>      [java] Exception in thread "main"
>
> BUILD FAILED
>
> D:\work\workspace\protege4\build.xml:35: The following error occurred 
> while executing this line:
>
> D:\work\workspace\protege4\org.protege.owl.server.deploy\build.xml:112
> : Java
> returned: 1
>
> Thanks
>
> -Dinu
>
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