Fwd: WebProtege

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Fwd: WebProtege

Matthew Lange
I am getting a whole host of errors that I don't understand, including a fail to build in Eclipse.  
I am following the build instructions here.  Upon attempting to build, I get the workspace build message:
"
Building workspace has encountered a problem.
Errors occurred during the build.
Errors running builder 'Google App Engine Project Change Notifier' on project 'WebProtegeICF'.
NO_MODIFICATION_ALLOWED_ERR: An attempt is made to modify an object where modifications are not allowed."

Further errors are attached.
I am using jars from protege 3.5.1 beta as instructed in linked webpage above. WebProtege is from trunk on SVN.
All files except the junit jar are in my personal directory with read/write access.

Thanks in advance for your help.
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Re: Fwd: WebProtege

Tania Tudorache
Hi Matthew,

We have recently changed the location of SVN for WebProtege 1.0 (the one that works with Protege 3.x). This is the new SVN location that you should check out:

https://smi-protege.stanford.edu/repos/protege/icat/trunk

Sorry, I thought I have updated the wiki description, but obviously, I haven't. I just did now..

The SVN version will work also with the latest Protege 3.x release, so you can use newer versions of Protege 3.x. It also works with GWT 2.4.

There is a newer version of WebProtege 2.0 that works with the OWL-API, and that has a reimplemented backend (which is what you have checked-out). That version is not yet ready for plugins or development, as we are still cleaning it up.

Let us know if you still have problems.

Cheers,
Tania



On 11/08/2012 11:51 PM, matthew lange wrote:
I am getting a whole host of errors that I don't understand, including a fail to build in Eclipse.  
I am following the build instructions here.  Upon attempting to build, I get the workspace build message:
"
Building workspace has encountered a problem.
Errors occurred during the build.
Errors running builder 'Google App Engine Project Change Notifier' on project 'WebProtegeICF'.
NO_MODIFICATION_ALLOWED_ERR: An attempt is made to modify an object where modifications are not allowed."

Further errors are attached.
I am using jars from protege 3.5.1 beta as instructed in linked webpage above. WebProtege is from trunk on SVN.
All files except the junit jar are in my personal directory with read/write access.

Thanks in advance for your help.

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Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03


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Re: Fwd: WebProtege

Matthew Lange
I don't mind hacking on the bleeding edge--can stick with what I have,
and be including libraries from the more recent OWL Protege Servers? I
am more interested in OWL compliance anyway...

On Fri, Nov 9, 2012 at 3:01 PM, Tania Tudorache <[hidden email]> wrote:

> Hi Matthew,
>
> We have recently changed the location of SVN for WebProtege 1.0 (the one
> that works with Protege 3.x). This is the new SVN location that you should
> check out:
>
> https://smi-protege.stanford.edu/repos/protege/icat/trunk
>
> Sorry, I thought I have updated the wiki description, but obviously, I
> haven't. I just did now..
>
> The SVN version will work also with the latest Protege 3.x release, so you
> can use newer versions of Protege 3.x. It also works with GWT 2.4.
>
> There is a newer version of WebProtege 2.0 that works with the OWL-API, and
> that has a reimplemented backend (which is what you have checked-out). That
> version is not yet ready for plugins or development, as we are still
> cleaning it up.
>
> Let us know if you still have problems.
>
> Cheers,
> Tania
>
>
>
>
> On 11/08/2012 11:51 PM, matthew lange wrote:
>
> I am getting a whole host of errors that I don't understand, including a
> fail to build in Eclipse.
> I am following the build instructions here.  Upon attempting to build, I get
> the workspace build message:
> "
> Building workspace has encountered a problem.
> Errors occurred during the build.
> Errors running builder 'Google App Engine Project Change Notifier' on
> project 'WebProtegeICF'.
> NO_MODIFICATION_ALLOWED_ERR: An attempt is made to modify an object where
> modifications are not allowed."
>
> Further errors are attached.
> I am using jars from protege 3.5.1 beta as instructed in linked webpage
> above. WebProtege is from trunk on SVN.
> All files except the junit jar are in my personal directory with read/write
> access.
>
> Thanks in advance for your help.
>
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>
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Re: Fwd: WebProtege

Tania Tudorache
OK, your risk :) We warned you :)

You will still need to include the libs that are documented on the wiki
that depend on Protege 3 because we have both backends still in place.
We are gradually cleaning up the code, and these dependencies will be
gone eventually. Try to include all the jars you find, including the
ones in WEB-INF/lib. It should at least compile.

The new OWL server is not working with WebProtege, yet. Currently it
uses a different mechanism and a binary (and super fast!) backend for
storing the changes and supporting concurrency that Matthew implemented.

In any case, we don't recommend that you do any development (at least
backend side) with WebProtege 2.0 because we might change it significantly.

Good luck!

Tania



On 11/09/2012 08:09 PM, matthew lange wrote:

> I don't mind hacking on the bleeding edge--can stick with what I have,
> and be including libraries from the more recent OWL Protege Servers? I
> am more interested in OWL compliance anyway...
>
> On Fri, Nov 9, 2012 at 3:01 PM, Tania Tudorache <[hidden email]> wrote:
>> Hi Matthew,
>>
>> We have recently changed the location of SVN for WebProtege 1.0 (the one
>> that works with Protege 3.x). This is the new SVN location that you should
>> check out:
>>
>> https://smi-protege.stanford.edu/repos/protege/icat/trunk
>>
>> Sorry, I thought I have updated the wiki description, but obviously, I
>> haven't. I just did now..
>>
>> The SVN version will work also with the latest Protege 3.x release, so you
>> can use newer versions of Protege 3.x. It also works with GWT 2.4.
>>
>> There is a newer version of WebProtege 2.0 that works with the OWL-API, and
>> that has a reimplemented backend (which is what you have checked-out). That
>> version is not yet ready for plugins or development, as we are still
>> cleaning it up.
>>
>> Let us know if you still have problems.
>>
>> Cheers,
>> Tania
>>
>>
>>
>>
>> On 11/08/2012 11:51 PM, matthew lange wrote:
>>
>> I am getting a whole host of errors that I don't understand, including a
>> fail to build in Eclipse.
>> I am following the build instructions here.  Upon attempting to build, I get
>> the workspace build message:
>> "
>> Building workspace has encountered a problem.
>> Errors occurred during the build.
>> Errors running builder 'Google App Engine Project Change Notifier' on
>> project 'WebProtegeICF'.
>> NO_MODIFICATION_ALLOWED_ERR: An attempt is made to modify an object where
>> modifications are not allowed."
>>
>> Further errors are attached.
>> I am using jars from protege 3.5.1 beta as instructed in linked webpage
>> above. WebProtege is from trunk on SVN.
>> All files except the junit jar are in my personal directory with read/write
>> access.
>>
>> Thanks in advance for your help.
>>
>> _______________________________________________
>> protege-discussion mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03
>>
>>

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Re: Fwd: WebProtege

Matthew Horridge
Yes, this is a fair warning.  So, be warned!  :)

In particular, the back end format *will* change in the near future - there's a chance the old format will still work, but we won't promise this.  We are also revising some of the core data structures - so expect to have to make some changes for any front end stuff you're developing as well.

Cheers,

Matthew


On 12 Nov 2012, at 14:22, Tania Tudorache wrote:

> OK, your risk :) We warned you :)
>
> You will still need to include the libs that are documented on the wiki that depend on Protege 3 because we have both backends still in place. We are gradually cleaning up the code, and these dependencies will be gone eventually. Try to include all the jars you find, including the ones in WEB-INF/lib. It should at least compile.
>
> The new OWL server is not working with WebProtege, yet. Currently it uses a different mechanism and a binary (and super fast!) backend for storing the changes and supporting concurrency that Matthew implemented.
>
> In any case, we don't recommend that you do any development (at least backend side) with WebProtege 2.0 because we might change it significantly.
>
> Good luck!
>
> Tania
>
>
>
> On 11/09/2012 08:09 PM, matthew lange wrote:
>> I don't mind hacking on the bleeding edge--can stick with what I have,
>> and be including libraries from the more recent OWL Protege Servers? I
>> am more interested in OWL compliance anyway...
>>
>> On Fri, Nov 9, 2012 at 3:01 PM, Tania Tudorache <[hidden email]> wrote:
>>> Hi Matthew,
>>>
>>> We have recently changed the location of SVN for WebProtege 1.0 (the one
>>> that works with Protege 3.x). This is the new SVN location that you should
>>> check out:
>>>
>>> https://smi-protege.stanford.edu/repos/protege/icat/trunk
>>>
>>> Sorry, I thought I have updated the wiki description, but obviously, I
>>> haven't. I just did now..
>>>
>>> The SVN version will work also with the latest Protege 3.x release, so you
>>> can use newer versions of Protege 3.x. It also works with GWT 2.4.
>>>
>>> There is a newer version of WebProtege 2.0 that works with the OWL-API, and
>>> that has a reimplemented backend (which is what you have checked-out). That
>>> version is not yet ready for plugins or development, as we are still
>>> cleaning it up.
>>>
>>> Let us know if you still have problems.
>>>
>>> Cheers,
>>> Tania
>>>
>>>
>>>
>>>
>>> On 11/08/2012 11:51 PM, matthew lange wrote:
>>>
>>> I am getting a whole host of errors that I don't understand, including a
>>> fail to build in Eclipse.
>>> I am following the build instructions here.  Upon attempting to build, I get
>>> the workspace build message:
>>> "
>>> Building workspace has encountered a problem.
>>> Errors occurred during the build.
>>> Errors running builder 'Google App Engine Project Change Notifier' on
>>> project 'WebProtegeICF'.
>>> NO_MODIFICATION_ALLOWED_ERR: An attempt is made to modify an object where
>>> modifications are not allowed."
>>>
>>> Further errors are attached.
>>> I am using jars from protege 3.5.1 beta as instructed in linked webpage
>>> above. WebProtege is from trunk on SVN.
>>> All files except the junit jar are in my personal directory with read/write
>>> access.
>>>
>>> Thanks in advance for your help.
>>>
>>> _______________________________________________
>>> protege-discussion mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>>>
>>> Instructions for unsubscribing:
>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>>
>>>
>
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

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Re: Fwd: WebProtege

Safran, Tracy (NIH/NCI) [C]
In reply to this post by Tania Tudorache

I checked out webprotege from the icat/trunk location you’ve specified and  added the jars per the instructions here http://protegewiki.stanford.edu/wiki/WebProtege#Developer.27s_Guide.  I am pointing to my Protégé_3.4.8 installation for the User Libraries and most everything works except this:

 

 

The method exportWithNativeWriter(OWLModel, URI, Collection) is undefined for the type JenaExportPlugin

                AdminServiceImpl.java

                /webprotege/src/edu/stanford/bmir/protege/web/server

                line 259 Java Problem

 

 

 

Tracy M. Safran  (Contractor)

Programmer Analyst

EVS support

SAIC-Frederick, Inc.

Frederick National Laboratory for Cancer Research (FNLCR)

301-402-1537

 

From: Tania Tudorache [mailto:[hidden email]]
Sent: Friday, November 09, 2012 6:01 PM
To: [hidden email]; User support for Core Protege and the Protege-Frames editor
Subject: Re: [protege-discussion] Fwd: WebProtege

 

Hi Matthew,

We have recently changed the location of SVN for WebProtege 1.0 (the one that works with Protege 3.x). This is the new SVN location that you should check out:

https://smi-protege.stanford.edu/repos/protege/icat/trunk

Sorry, I thought I have updated the wiki description, but obviously, I haven't. I just did now..

The SVN version will work also with the latest Protege 3.x release, so you can use newer versions of Protege 3.x. It also works with GWT 2.4.

There is a newer version of WebProtege 2.0 that works with the OWL-API, and that has a reimplemented backend (which is what you have checked-out). That version is not yet ready for plugins or development, as we are still cleaning it up.

Let us know if you still have problems.

Cheers,
Tania



On 11/08/2012 11:51 PM, matthew lange wrote:

I am getting a whole host of errors that I don't understand, including a fail to build in Eclipse.  
I am following the build instructions here.  Upon attempting to build, I get the workspace build message:
"
Building workspace has encountered a problem.
Errors occurred during the build.
Errors running builder 'Google App Engine Project Change Notifier' on project 'WebProtegeICF'.
NO_MODIFICATION_ALLOWED_ERR: An attempt is made to modify an object where modifications are not allowed."

Further errors are attached.
I am using jars from protege 3.5.1 beta as instructed in linked webpage above. WebProtege is from trunk on SVN.
All files except the junit jar are in my personal directory with read/write access.

Thanks in advance for your help.


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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-discussion
 
Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03

 


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Re: Fwd: WebProtege

Kamales Mandal
I am facing the same issue - The method exportWithNativeWriter(OWLModel, URI, Collection) is undefined for the type JenaExportPlugin.

Any resolution?
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Re: Fwd: WebProtege

Tania Tudorache
Indeed, the WebProtege code has evolved since we made the Protege 3.4.8
release, and it compiles against the protege sources from our SVN.

There are a few solutions:
1. You comment out the code that calls the exportWithNativeWriter method
in WebProtege code. Or,
2. You replace the protege-owl.jar in your Protege installation with
this one:
http://www.stanford.edu/~ttania/share/protege-owl.jar

Or,
3. You check out the protege-owl source code from our SVN, and use that
one, instead of the jar that comes with the distribution.

Solution 2 is the easiest.

Once we make the Protege 3.5 release and WebProtege 1.0 release, these
changes will not be needed anymore.

Tania


On 02/12/2013 08:33 AM, Kamales Mandal wrote:

> I am facing the same issue - The method exportWithNativeWriter(OWLModel, URI,
> Collection) is undefined for the type JenaExportPlugin.
>
> Any resolution?
>
>
>
> --
> View this message in context: http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nabble.com/Fwd-WebProtege-tp4656595p4657210.html
> Sent from the Protege-Frames Support mailing list archive at Nabble.com.
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03
>
>

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Re: Fwd: WebProtege

Kamales Mandal
Thanks a ton Tania!

I was trying out the third option. Option 2 has made life simpler.  Thanks once again.

Regards,
Kamales

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Tania Tudorache
Sent: Wednesday, February 13, 2013 6:41 AM
To: [hidden email]
Subject: Re: [protege-discussion] Fwd: WebProtege

Indeed, the WebProtege code has evolved since we made the Protege 3.4.8 release, and it compiles against the protege sources from our SVN.

There are a few solutions:
1. You comment out the code that calls the exportWithNativeWriter method in WebProtege code. Or, 2. You replace the protege-owl.jar in your Protege installation with this one:
http://www.stanford.edu/~ttania/share/protege-owl.jar

Or,
3. You check out the protege-owl source code from our SVN, and use that one, instead of the jar that comes with the distribution.

Solution 2 is the easiest.

Once we make the Protege 3.5 release and WebProtege 1.0 release, these changes will not be needed anymore.

Tania


On 02/12/2013 08:33 AM, Kamales Mandal wrote:

> I am facing the same issue - The method
> exportWithNativeWriter(OWLModel, URI,
> Collection) is undefined for the type JenaExportPlugin.
>
> Any resolution?
>
>
>
> --
> View this message in context:
> http://protege-ontology-editor-knowledge-acquisition-system.136.n4.nab
> ble.com/Fwd-WebProtege-tp4656595p4657210.html
> Sent from the Protege-Frames Support mailing list archive at Nabble.com.
> _______________________________________________
> protege-discussion mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-discussion
>
> Instructions for unsubscribing:
> http://protege.stanford.edu/doc/faq.html#01a.03
>
>

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