[protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

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[protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Hicklin, Austin
Using Protege-OWL, we end up with a partially saved/corrupted owl file every few days, and the non-Beta Protege-OWL 3.2 continues to have the same problems. Our ontology has about 1500 classes, which I wouldn't expect to be a problem in sheer size.
- Are there functions that we should avoid?
- What are appropriate java stack sizes?
- Are there reasonable mitigation methods?

Until Protege-OWL is made more stable, has there been any discussion of automatic backups for Protege?

Austin Hicklin
hicklin - at - mitretek.org


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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Tania Tudorache
Austin,

If you give us a more detailed description of file corruption and the
steps to reproduce it, we will be able to fix it. Are you using SWRL?

What do you mean by automatic backups of Protege? Do you mean backups of
the files? You can use the archiving functionality for that. This is
manual, but I can imagine that it must be pretty easy to automate it, if
you use it with the Scripts Tab. Just an idea.

Tania


Hicklin, Austin wrote:

> Using Protege-OWL, we end up with a partially saved/corrupted owl file every few days, and the non-Beta Protege-OWL 3.2 continues to have the same problems. Our ontology has about 1500 classes, which I wouldn't expect to be a problem in sheer size.
> - Are there functions that we should avoid?
> - What are appropriate java stack sizes?
> - Are there reasonable mitigation methods?
>
> Until Protege-OWL is made more stable, has there been any discussion of automatic backups for Protege?
>
> Austin Hicklin
> hicklin - at - mitretek.org
>
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>
>  

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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Hicklin, Austin
What happens is that saving takes a very long time, then results in java exceptions on the console, and only a portion of the file is saved (truncated at a random point in the OWL file).

Unfortunately, we have not been able to attribute this to a cause, or reproduce the problems. We are not using any of the add-on tabs - we are just adding/editing a number of classes.

I'll look at archiving through the scripts tab - thanks!

-austin


-----Original Message-----
From: Tania Tudorache [mailto:[hidden email]]
Sent: Thu 11/9/2006 3:54 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)
 
Austin,

If you give us a more detailed description of file corruption and the
steps to reproduce it, we will be able to fix it. Are you using SWRL?

What do you mean by automatic backups of Protege? Do you mean backups of
the files? You can use the archiving functionality for that. This is
manual, but I can imagine that it must be pretty easy to automate it, if
you use it with the Scripts Tab. Just an idea.

Tania


Hicklin, Austin wrote:

> Using Protege-OWL, we end up with a partially saved/corrupted owl file every few days, and the non-Beta Protege-OWL 3.2 continues to have the same problems. Our ontology has about 1500 classes, which I wouldn't expect to be a problem in sheer size.
> - Are there functions that we should avoid?
> - What are appropriate java stack sizes?
> - Are there reasonable mitigation methods?
>
> Until Protege-OWL is made more stable, has there been any discussion of automatic backups for Protege?
>
> Austin Hicklin
> hicklin - at - mitretek.org
>
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>
>  







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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Tania Tudorache
Austin,

Can you please send the stack trace from the console?

I suspect that you got an out of memory exception and if so, the fix for
this is to increase the heap size allocated to Protege.

Tania


Hicklin, Austin wrote:

> What happens is that saving takes a very long time, then results in java exceptions on the console, and only a portion of the file is saved (truncated at a random point in the OWL file).
>
> Unfortunately, we have not been able to attribute this to a cause, or reproduce the problems. We are not using any of the add-on tabs - we are just adding/editing a number of classes.
>
> I'll look at archiving through the scripts tab - thanks!
>
> -austin
>
>
> -----Original Message-----
> From: Tania Tudorache [mailto:[hidden email]]
> Sent: Thu 11/9/2006 3:54 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)
>  
> Austin,
>
> If you give us a more detailed description of file corruption and the
> steps to reproduce it, we will be able to fix it. Are you using SWRL?
>
> What do you mean by automatic backups of Protege? Do you mean backups of
> the files? You can use the archiving functionality for that. This is
> manual, but I can imagine that it must be pretty easy to automate it, if
> you use it with the Scripts Tab. Just an idea.
>
> Tania
>
>
> Hicklin, Austin wrote:
>  
>> Using Protege-OWL, we end up with a partially saved/corrupted owl file every few days, and the non-Beta Protege-OWL 3.2 continues to have the same problems. Our ontology has about 1500 classes, which I wouldn't expect to be a problem in sheer size.
>> - Are there functions that we should avoid?
>> - What are appropriate java stack sizes?
>> - Are there reasonable mitigation methods?
>>
>> Until Protege-OWL is made more stable, has there been any discussion of automatic backups for Protege?
>>
>> Austin Hicklin
>> hicklin - at - mitretek.org
>>
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>>
>>  
>>    
>
>
>
>
>
>
>
>
>  

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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Daniel Elenius
In reply to this post by Tania Tudorache
I have also encountered corrupted files, saved changes that were later
"forgotten", and owl files being completely zeroed out on many occasions
(but mostly in the last month or so). Unfortunately, we have not been
able to track down what causes these things. The most recent betas seem
to have at least reduced the frequency of these problems.

We are using SWRL a lot. Is that known to cause problems?


Tania Tudorache wrote:

> Austin,
>
> If you give us a more detailed description of file corruption and the
> steps to reproduce it, we will be able to fix it. Are you using SWRL?
>
> What do you mean by automatic backups of Protege? Do you mean backups of
> the files? You can use the archiving functionality for that. This is
> manual, but I can imagine that it must be pretty easy to automate it, if
> you use it with the Scripts Tab. Just an idea.
>
> Tania
>
>
> Hicklin, Austin wrote:
>  
>> Using Protege-OWL, we end up with a partially saved/corrupted owl file every few days, and the non-Beta Protege-OWL 3.2 continues to have the same problems. Our ontology has about 1500 classes, which I wouldn't expect to be a problem in sheer size.
>> - Are there functions that we should avoid?
>> - What are appropriate java stack sizes?
>> - Are there reasonable mitigation methods?
>>
>> Until Protege-OWL is made more stable, has there been any discussion of automatic backups for Protege?
>>
>> Austin Hicklin
>> hicklin - at - mitretek.org
>>
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>>
>>  
>>    
>
> _______________________________________________
> protege-owl mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>
> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>  

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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Hicklin, Austin
In reply to this post by Tania Tudorache
Tania -
I will send a stack trace the next time it happens. What do you recommend for heap size? I assume you set this in the -Xmx100000000 commandline directive? (I would have thought 100M should be plenty...)
-austin


-----Original Message-----
From: Tania Tudorache [mailto:[hidden email]]
Sent: Thu 11/9/2006 5:41 PM
To: User support for the Protege-OWL editor
Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)
 
Austin,

Can you please send the stack trace from the console?

I suspect that you got an out of memory exception and if so, the fix for
this is to increase the heap size allocated to Protege.

Tania


Hicklin, Austin wrote:

> What happens is that saving takes a very long time, then results in java exceptions on the console, and only a portion of the file is saved (truncated at a random point in the OWL file).
>
> Unfortunately, we have not been able to attribute this to a cause, or reproduce the problems. We are not using any of the add-on tabs - we are just adding/editing a number of classes.
>
> I'll look at archiving through the scripts tab - thanks!
>
> -austin
>
>
> -----Original Message-----
> From: Tania Tudorache [mailto:[hidden email]]
> Sent: Thu 11/9/2006 3:54 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)
>  
> Austin,
>
> If you give us a more detailed description of file corruption and the
> steps to reproduce it, we will be able to fix it. Are you using SWRL?
>
> What do you mean by automatic backups of Protege? Do you mean backups of
> the files? You can use the archiving functionality for that. This is
> manual, but I can imagine that it must be pretty easy to automate it, if
> you use it with the Scripts Tab. Just an idea.
>
> Tania
>
>
> Hicklin, Austin wrote:
>  
>> Using Protege-OWL, we end up with a partially saved/corrupted owl file every few days, and the non-Beta Protege-OWL 3.2 continues to have the same problems. Our ontology has about 1500 classes, which I wouldn't expect to be a problem in sheer size.
>> - Are there functions that we should avoid?
>> - What are appropriate java stack sizes?
>> - Are there reasonable mitigation methods?
>>
>> Until Protege-OWL is made more stable, has there been any discussion of automatic backups for Protege?
>>
>> Austin Hicklin
>> hicklin - at - mitretek.org
>>
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>>
>>  
>>    
>
>
>
>
>
>
>
>
>  




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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Tania Tudorache
Austin,

100MB as heap size is the default setting for Protege. However, if your
ontologies are large you will need to set it higher. For example, for
loading the whole NCI Thesaurus into memory (around 50.000 classes and
3-40.000 restrictions), I use 700MB heap size. The larger the ontology,
the more heap size you need, if you want to load it all into memory.
However, if your ontology gets very large, it is recommended that you
use the OWL Database backend, which only loads into memory the part of
the ontology that the user is working on. With the OWL Database backend,
you don't need much heap size. You could load the NCI Thesaurus with
only 100MB of heap.

We have a wiki page about the scalability and performance tuning of
Protege that might be of interest to you:
http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning

Tania


Hicklin, Austin wrote:

> Tania -
> I will send a stack trace the next time it happens. What do you recommend for heap size? I assume you set this in the -Xmx100000000 commandline directive? (I would have thought 100M should be plenty...)
> -austin
>
>
> -----Original Message-----
> From: Tania Tudorache [mailto:[hidden email]]
> Sent: Thu 11/9/2006 5:41 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)
>  
> Austin,
>
> Can you please send the stack trace from the console?
>
> I suspect that you got an out of memory exception and if so, the fix for
> this is to increase the heap size allocated to Protege.
>
> Tania
>
>
> Hicklin, Austin wrote:
>  
>> What happens is that saving takes a very long time, then results in java exceptions on the console, and only a portion of the file is saved (truncated at a random point in the OWL file).
>>
>> Unfortunately, we have not been able to attribute this to a cause, or reproduce the problems. We are not using any of the add-on tabs - we are just adding/editing a number of classes.
>>
>> I'll look at archiving through the scripts tab - thanks!
>>
>> -austin
>>
>>
>> -----Original Message-----
>> From: Tania Tudorache [mailto:[hidden email]]
>> Sent: Thu 11/9/2006 3:54 PM
>> To: User support for the Protege-OWL editor
>> Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)
>>  
>> Austin,
>>
>> If you give us a more detailed description of file corruption and the
>> steps to reproduce it, we will be able to fix it. Are you using SWRL?
>>
>> What do you mean by automatic backups of Protege? Do you mean backups of
>> the files? You can use the archiving functionality for that. This is
>> manual, but I can imagine that it must be pretty easy to automate it, if
>> you use it with the Scripts Tab. Just an idea.
>>
>> Tania
>>
>>
>> Hicklin, Austin wrote:
>>  
>>    
>>> Using Protege-OWL, we end up with a partially saved/corrupted owl file every few days, and the non-Beta Protege-OWL 3.2 continues to have the same problems. Our ontology has about 1500 classes, which I wouldn't expect to be a problem in sheer size.
>>> - Are there functions that we should avoid?
>>> - What are appropriate java stack sizes?
>>> - Are there reasonable mitigation methods?
>>>
>>> Until Protege-OWL is made more stable, has there been any discussion of automatic backups for Protege?
>>>
>>> Austin Hicklin
>>> hicklin - at - mitretek.org
>>>
>>>
>>> _______________________________________________
>>> protege-owl mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>
>>> Instructions for unsubscribing: http://protege.stanford.edu/doc/faq.html#01a.03 
>>>
>>>  
>>>    
>>>      
>>
>>
>>
>>
>>
>>
>>  
>>    
>
>
>
>
>
>  

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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Tania Tudorache
In reply to this post by Daniel Elenius
It seems that these problems are caused by namespace prefixes. We are
investigating this now. SWRL is indirectly affected by this. If the SWRL
Tab is initialized in a certain way, its prefix is stored as "j:0"
instead of "swrl", which seems to cause confusion to parts of the code.
We are looking into this issue now.

However, if you have a concrete example, when file corruption occurs,
please report it, so that we can fix it.

Thanks,
Tania

Daniel Elenius wrote:

> I have also encountered corrupted files, saved changes that were later
> "forgotten", and owl files being completely zeroed out on many
> occasions (but mostly in the last month or so). Unfortunately, we have
> not been able to track down what causes these things. The most recent
> betas seem to have at least reduced the frequency of these problems.
>
> We are using SWRL a lot. Is that known to cause problems?
>
>
> Tania Tudorache wrote:
>> Austin,
>>
>> If you give us a more detailed description of file corruption and the
>> steps to reproduce it, we will be able to fix it. Are you using SWRL?
>>
>> What do you mean by automatic backups of Protege? Do you mean backups
>> of the files? You can use the archiving functionality for that. This
>> is manual, but I can imagine that it must be pretty easy to automate
>> it, if you use it with the Scripts Tab. Just an idea.
>>
>> Tania
>>
>>
>> Hicklin, Austin wrote:
>>  
>>> Using Protege-OWL, we end up with a partially saved/corrupted owl
>>> file every few days, and the non-Beta Protege-OWL 3.2 continues to
>>> have the same problems. Our ontology has about 1500 classes, which I
>>> wouldn't expect to be a problem in sheer size. - Are there functions
>>> that we should avoid? - What are appropriate java stack sizes? - Are
>>> there reasonable mitigation methods?
>>>
>>> Until Protege-OWL is made more stable, has there been any discussion
>>> of automatic backups for Protege?
>>> Austin Hicklin
>>> hicklin - at - mitretek.org
>>>
>>>
>>> _______________________________________________
>>> protege-owl mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>
>>> Instructions for unsubscribing:
>>> http://protege.stanford.edu/doc/faq.html#01a.03
>>>      
>>
>> _______________________________________________
>> protege-owl mailing list
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>
>> Instructions for unsubscribing:
>> http://protege.stanford.edu/doc/faq.html#01a.03   
>
>

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Re: [protege-owl] Stability of Protege-OWL 3.2 (saving corrupted files)

Hicklin, Austin
In reply to this post by Tania Tudorache
Tania - Thank you!  We'll set the max heap to 1G, and if we still have
problems will switch to the OWL Database backend.

- Austin

Austin Hicklin
[hidden email]
703-610-1995


-----Original Message-----
From: Tania Tudorache [mailto:[hidden email]]
Sent: Friday, November 10, 2006 3:34 PM
To: User support for the Protege-OWL editor
Cc: Hicklin, Austin; Oz, Noam
Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving
corrupted files)

Austin,

100MB as heap size is the default setting for Protege. However, if your
ontologies are large you will need to set it higher. For example, for
loading the whole NCI Thesaurus into memory (around 50.000 classes and
3-40.000 restrictions), I use 700MB heap size. The larger the ontology,
the more heap size you need, if you want to load it all into memory.
However, if your ontology gets very large, it is recommended that you
use the OWL Database backend, which only loads into memory the part of
the ontology that the user is working on. With the OWL Database backend,

you don't need much heap size. You could load the NCI Thesaurus with
only 100MB of heap.

We have a wiki page about the scalability and performance tuning of
Protege that might be of interest to you:
http://protege.cim3.net/cgi-bin/wiki.pl?ScalabilityAndTuning

Tania


Hicklin, Austin wrote:
> Tania -
> I will send a stack trace the next time it happens. What do you
recommend for heap size? I assume you set this in the -Xmx100000000
commandline directive? (I would have thought 100M should be plenty...)
> -austin
>
>
> -----Original Message-----
> From: Tania Tudorache [mailto:[hidden email]]
> Sent: Thu 11/9/2006 5:41 PM
> To: User support for the Protege-OWL editor
> Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving
corrupted files)
>  
> Austin,
>
> Can you please send the stack trace from the console?
>
> I suspect that you got an out of memory exception and if so, the fix
for
> this is to increase the heap size allocated to Protege.
>
> Tania
>
>
> Hicklin, Austin wrote:
>  
>> What happens is that saving takes a very long time, then results in
java exceptions on the console, and only a portion of the file is saved
(truncated at a random point in the OWL file).
>>
>> Unfortunately, we have not been able to attribute this to a cause, or
reproduce the problems. We are not using any of the add-on tabs - we are
just adding/editing a number of classes.

>>
>> I'll look at archiving through the scripts tab - thanks!
>>
>> -austin
>>
>>
>> -----Original Message-----
>> From: Tania Tudorache [mailto:[hidden email]]
>> Sent: Thu 11/9/2006 3:54 PM
>> To: User support for the Protege-OWL editor
>> Subject: Re: [protege-owl] Stability of Protege-OWL 3.2 (saving
corrupted files)
>>  
>> Austin,
>>
>> If you give us a more detailed description of file corruption and the

>> steps to reproduce it, we will be able to fix it. Are you using SWRL?
>>
>> What do you mean by automatic backups of Protege? Do you mean backups
of
>> the files? You can use the archiving functionality for that. This is
>> manual, but I can imagine that it must be pretty easy to automate it,
if
>> you use it with the Scripts Tab. Just an idea.
>>
>> Tania
>>
>>
>> Hicklin, Austin wrote:
>>  
>>    
>>> Using Protege-OWL, we end up with a partially saved/corrupted owl
file every few days, and the non-Beta Protege-OWL 3.2 continues to have
the same problems. Our ontology has about 1500 classes, which I wouldn't
expect to be a problem in sheer size.
>>> - Are there functions that we should avoid?
>>> - What are appropriate java stack sizes?
>>> - Are there reasonable mitigation methods?
>>>
>>> Until Protege-OWL is made more stable, has there been any discussion
of automatic backups for Protege?

>>>
>>> Austin Hicklin
>>> hicklin - at - mitretek.org
>>>
>>>
>>> _______________________________________________
>>> protege-owl mailing list
>>> [hidden email]
>>> https://mailman.stanford.edu/mailman/listinfo/protege-owl
>>>
>>> Instructions for unsubscribing:
http://protege.stanford.edu/doc/faq.html#01a.03 

>>>
>>>  
>>>    
>>>      
>>
>>
>>
>>
>>
>>
>>  
>>    
>
>
>
>
>
>  

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[protege-owl] Protege cannot open ontologies created by Jena

Kostas Vavliakis
Hello,

Protégé cannot open a file that is created from Jena when I am saving an
OntModel to an .owl file, all I do is loading it and saving it with Jena.
For example I used the popular pizza ontology that comes with Protégé. The
code is:

        OntModel base = ModelFactory.createOntologyModel();
       
base.read("file:///C:/Borland/Projects/pizza/unclassified/pizza.owl");
        RDFWriter writer = base.getWriter("RDF/XML");
        OutputStream out = new FileOutputStream("pizzaJena.owl");
        writer.write(base, out, "http://test/");


I read about a possible bug here:
http://article.gmane.org/gmane.comp.misc.ontology.protege.owl/18773/matc\
h=reading+inferred+properties


Is there anything I can do in my code, or if actually there is a bug in
protégé, do you plan to fix it in a recent release?

Thank you for your time,

Kostas


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Re: [protege-owl] Protege cannot open ontologies created by Jena

Tania Tudorache
Kostas,

Please send the stacktrace from the console. The bug you are referring
to has been fixed in the Protege 3.2 release (b355).

And also please send the snippet of code you are calling to load the OWL
file using the Protege API.

Thanks,
Tania

Vavliakis Kostas wrote:

> Hello,
>
> Protégé cannot open a file that is created from Jena when I am saving an
> OntModel to an .owl file, all I do is loading it and saving it with Jena.
> For example I used the popular pizza ontology that comes with Protégé. The
> code is:
>
> OntModel base = ModelFactory.createOntologyModel();
>
> base.read("file:///C:/Borland/Projects/pizza/unclassified/pizza.owl");
> RDFWriter writer = base.getWriter("RDF/XML");
> OutputStream out = new FileOutputStream("pizzaJena.owl");
> writer.write(base, out, "http://test/");
>
>
> I read about a possible bug here:
> http://article.gmane.org/gmane.comp.misc.ontology.protege.owl/18773/matc\
> h=reading+inferred+properties
>
>
> Is there anything I can do in my code, or if actually there is a bug in
> protégé, do you plan to fix it in a recent release?
>
> Thank you for your time,
>
> Kostas
>
>
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