Question on some old classes/methods

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Question on some old classes/methods

Mark Feblowitz
I was wondering what became of these two classes in Protege:

         edu.stanford.smi.protege.ui.ProjectView - specifically
detachCurrentTab()

         edu.stanford.smi.protege.plugin.DefaultEntry

Have these been moved, removed or replaced? What would be the new equivalents?

Thanks,

Mark
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Re: Question on some old classes/methods

Mark Feblowitz
Add to that

         edu.stanford.smi.protege.util.FileHandler


At 05:05 PM 10/13/2006, Mark Feblowitz wrote:

>I was wondering what became of these two classes in Protege:
>
>          edu.stanford.smi.protege.ui.ProjectView - specifically
>detachCurrentTab()
>
>          edu.stanford.smi.protege.plugin.DefaultEntry
>
>Have these been moved, removed or replaced? What would be the new equivalents?
>
>Thanks,
>
>Mark
>_______________________________________________
>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: Question on some old classes/methods

Tania Tudorache
Mark,

We are very careful not to delete or move public classes or methods.

The

edu.stanford.smi.protege.util.FileHandler

is in the same place :)

In which version did Protege have a detachCurrentTab() method in
ProjectView? I think the method you are looking for is the
detachCurrentView().

The DefaultEntry is still in the same place:

edu.stanford.smi.protege.plugin. DefaultEntry

Are you using the right jars?

Tania




Mark Feblowitz wrote:

> Add to that
>
>          edu.stanford.smi.protege.util.FileHandler
>
>
> At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
>  
>> I was wondering what became of these two classes in Protege:
>>
>>          edu.stanford.smi.protege.ui.ProjectView - specifically
>> detachCurrentTab()
>>
>>          edu.stanford.smi.protege.plugin.DefaultEntry
>>
>> Have these been moved, removed or replaced? What would be the new equivalents?
>>
>> Thanks,
>>
>> Mark
>> _______________________________________________
>> 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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Using multiple necessary and sufficient blocks

Alan March
Hi all.

Could someone please explain the reasons for using multiple necessary and
sufficient blocks? And probably provide an example?

Many thanks!

Alan

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Re: Using multiple necessary and sufficient blocks

Leonardo Jacques da Silva
Hi Alan,

You use necessary and sufficient conditions to define that any class that
satisfy the conditions present in this block belong to this class where the
block was defined.
In the case of necessary block any class can satisfy the conditions present
in this block, but not necessarily belong to the class.

Example: Pizza Ontology

The class CheesyPizza has a necessary and sufficient condition that specify
that any class that "hasTopping some CheeseTopping" ought to be considered a
cheesy pizza.

The class CheesyPizza has a necessary condition inherited from the class
Pizza that specify that any class  that "hasBase some PizzaBase" can be or
not a cheesy pizza.

I'm not sure if my explanation is clear to you.


On 10/15/06, Alan March <[hidden email]> wrote:

>
> Hi all.
>
> Could someone please explain the reasons for using multiple necessary and
> sufficient blocks? And probably provide an example?
>
> Many thanks!
>
> Alan
>
> _______________________________________________
> 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
>



--
Leonardo Jacques
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Re: Using multiple necessary and sufficient blocks

Alan March
Hi Leonardo, and thanks for your advice.

I think I understand the use of a single necessary and sufficient blocks but
fail to grasp the conditions under which *multiple* necessary and sufficient
blocks are required.

My hunch is that one case would be when a class may be fully defined by two
different combinations of properties. For example: suppose InterestingPizza
could by fully defined as in pizza.owl, but I decide that it could also be
defined as a "a pizza which is sold at least 30 times per day". Should I
place these conditions (say: Pizza as parent class and hasSalesPerWeek min
30) in a separate N&S block to do the trick? Or am I entirely failing to
understand the concept?

Many thanks. As a sideline, congratulations to the developers of Protégé.
It's undoubtedly the best ontology management tool available, much better
and powerful than commercial software out there.

> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On
> Behalf Of Leonardo Jacques da Silva
> Sent: Monday, October 16, 2006 10:13 AM
> To: User support for Core Protege and the Protege-Frames editor
> Subject: Re: [protege-discussion] Using multiple necessary
> and sufficient blocks
>
> Hi Alan,
>
> You use necessary and sufficient conditions to define that
> any class that satisfy the conditions present in this block
> belong to this class where the block was defined.
> In the case of necessary block any class can satisfy the
> conditions present in this block, but not necessarily belong
> to the class.
>
> Example: Pizza Ontology
>
> The class CheesyPizza has a necessary and sufficient
> condition that specify that any class that "hasTopping some
> CheeseTopping" ought to be considered a cheesy pizza.
>
> The class CheesyPizza has a necessary condition inherited
> from the class Pizza that specify that any class  that
> "hasBase some PizzaBase" can be or not a cheesy pizza.
>
> I'm not sure if my explanation is clear to you.
>
>
> On 10/15/06, Alan March <[hidden email]> wrote:
> >
> > Hi all.
> >
> > Could someone please explain the reasons for using multiple
> necessary
> > and sufficient blocks? And probably provide an example?
> >
> > Many thanks!
> >
> > Alan
> >
> > _______________________________________________
> > 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
> >
>
>
>
> --
> Leonardo Jacques
> _______________________________________________
> 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: Question on some old classes/methods

Mark Feblowitz
In reply to this post by Tania Tudorache
I'm trying to get the Mayo
<http://informatics.mayo.edu/LexGrid/index.php?page=protege>LexGrid<http://informatics.mayo.edu/LexGrid/index.php?page=protege>
Protege in Eclipse (July 2004) running for the current Protege
Beta.  Remarkably, virtually all of it works with no modification.

Not so remarkably, the Metadata Tab does not.

The two exceptions noted at startup are:

Can't load log handler "edu.stanford.smi.protege.util.FileHandler"
java.lang.ClassNotFoundException: edu.stanford.smi.protege.util.FileHandler
java.lang.ClassNotFoundException: edu.stanford.smi.protege.util.FileHandler
at java.net.URLClassLoader.findClass(URLClassLoader.java:492)
at java.lang.ClassLoader.loadClass(ClassLoader.java:560)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:327)
at java.lang.ClassLoader.loadClass(ClassLoader.java:517)
...
and
WARNING: java.lang.NullPointerException
at
edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.createOntologyBrowserHeader(Unknown
Source)
at
edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.<init>(Unknown
Source)
at
edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.createMainPanel(Unknown
Source)
at
edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.initialize(Unknown
Source)
at
edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown
Source)
at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
at edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Source)
at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
at
org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingFrameAccess.init(LgProtegeEditor.java:180)

at
org.lexgrid.ui.extension.protege.LgProtegeEditor.getSwingFrame(LgProtegeEditor.java:338)

at
org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingInitThread.run(LgProtegeEditor.java:266)

The only change needed to remove compilation errors was to replace
detachCurrentTab() with detachCurrentView().

I understand that the Metadata tab has changed significantly from
2004. Any suggestions as to how I might resolve this issue?

Also, when navigating the Instances tab, I see the words "LOST
GENERATOR" pop up on the console. I'm not sure what the significance
of this is.

Thanks,

Mark



At 06:24 PM 10/13/2006, you wrote:

>Mark,
>
>We are very careful not to delete or move public classes or methods.
>
>The
>
>edu.stanford.smi.protege.util.FileHandler
>
>is in the same place :)
>
>In which version did Protege have a detachCurrentTab() method in
>ProjectView? I think the method you are looking for is the
>detachCurrentView().
>
>The DefaultEntry is still in the same place:
>
>edu.stanford.smi.protege.plugin. DefaultEntry
>
>Are you using the right jars?
>
>Tania
>
>
>
>
>Mark Feblowitz wrote:
> > Add to that
> >
> >          edu.stanford.smi.protege.util.FileHandler
> >
> >
> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
> >
> >> I was wondering what became of these two classes in Protege:
> >>
> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
> >> detachCurrentTab()
> >>
> >>          edu.stanford.smi.protege.plugin.DefaultEntry
> >>
> >> Have these been moved, removed or replaced? What would be the
> new equivalents?
> >>
> >> Thanks,
> >>
> >> Mark
> >> _______________________________________________
> >> 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
> >
> >
>
>_______________________________________________
>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: Using multiple necessary and sufficient blocks

Thomas Russ
In reply to this post by Alan March
Should be on the OWL list, but...

On Oct 14, 2006, at 7:04 PM, Alan March wrote:

> Hi all.
>
> Could someone please explain the reasons for using multiple  
> necessary and
> sufficient blocks? And probably provide an example?

Triangle ==  Polygon and exactly 3 angles
Triangle ==  Polygon and exactly 3 sides

Two sets of necessary and sufficient conditions.




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Build Questions (was Re: Question on some old classes/methods)

Mark Feblowitz
In reply to this post by Tania Tudorache
My prior questions had to do with my efforts to update the LexGrid
"Protege in Eclipse" project. All seems to be well, with the
exception of the Protege Owl Plugin's Metadata Tab.

I'm trying to debug and have the need to debug the source of Protege.
I've imported the Protege core, but have a persistent problem with
two build errors:

         The project was not built since its build path is
incomplete. Cannot find the class file for
javax.swing.plaf.metal.DefaultMetalTheme.
The type javax.swing.plaf.metal.DefaultMetalTheme cannot be resolved.
It is indirectly referenced from required .class files
Protege/src/edu/stanford/smi/protege/util  ProtegePlasticTheme.java
I'm using the IBM 1.5 JRE. When I switch to the Sun 1.5 JRE, I get 4
errors about
"Parser cannot be resolved to at type"
and 42 errors about
jThe declared package "javax.swing.plaf.metal" does not match the
expected package "edu.stanford.smi.protege.util"

I'm doing this work within ecplise 3.2.0

What should I be using for my JRE? Any additional jars in the build
path needed to reference javax.swing.plaf.metal.DefaultMetalTheme?

Thanks,

Mark


At 06:24 PM 10/13/2006, Tania Tudorache wrote:

>Mark,
>
>We are very careful not to delete or move public classes or methods.
>
>The
>
>edu.stanford.smi.protege.util.FileHandler
>
>is in the same place :)
>
>In which version did Protege have a detachCurrentTab() method in
>ProjectView? I think the method you are looking for is the
>detachCurrentView().
>
>The DefaultEntry is still in the same place:
>
>edu.stanford.smi.protege.plugin. DefaultEntry
>
>Are you using the right jars?
>
>Tania
>
>
>
>
>Mark Feblowitz wrote:
> > Add to that
> >
> >          edu.stanford.smi.protege.util.FileHandler
> >
> >
> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
> >
> >> I was wondering what became of these two classes in Protege:
> >>
> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
> >> detachCurrentTab()
> >>
> >>          edu.stanford.smi.protege.plugin.DefaultEntry
> >>
> >> Have these been moved, removed or replaced? What would be the
> new equivalents?
> >>
> >> Thanks,
> >>
> >> Mark
> >> _______________________________________________
> >> 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
> >
> >
>
>_______________________________________________
>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: Question on some old classes/methods

Tania Tudorache
In reply to this post by Mark Feblowitz
Mark,

The Lexgrid Protege in Eclipse uses an ancient version of Protege (2.1),
and it is no wonder that certain things are not working, when replacing
the old jars with the new ones. We have made significant changes in the
Protege core code since 2.1 release.

I suppose the sources of the Eclipse plugin must be recompiled against
the new Protege sources and everything should work.

Tania


Mark Feblowitz wrote:

> I'm trying to get the Mayo LexGrid
> <http://informatics.mayo.edu/LexGrid/index.php?page=protege> Protege
> in Eclipse
> <http://informatics.mayo.edu/LexGrid/index.php?page=protege>(July
> 2004) running for the current Protege Beta.  Remarkably, virtually all
> of it works with no modification.
>
> Not so remarkably, the Metadata Tab does not.
>
> The two exceptions noted at startup are:
>
>     Can't load log handler "edu.stanford.smi.protege.util.FileHandler"
>     _java.lang.ClassNotFoundException_ :
>     edu.stanford.smi.protege.util.FileHandler
>     _java.lang.ClassNotFoundException_ :
>     edu.stanford.smi.protege.util.FileHandler
>     at java.net.URLClassLoader.findClass( _URLClassLoader.java:492_ )
>     at java.lang.ClassLoader.loadClass( _ClassLoader.java:560_ )
>     at sun.misc.Launcher$AppClassLoader.loadClass( _Launcher.java:327_ )
>     at java.lang.ClassLoader.loadClass( _ClassLoader.java:517_ )
>     ...
>
> and
>
>     WARNING: _java.lang.NullPointerException_
>     at
>     edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.createOntologyBrowserHeader(Unknown
>     Source)
>     at
>     edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.<init>(Unknown
>     Source)
>     at
>     edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.createMainPanel(Unknown
>     Source)
>     at
>     edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.initialize(Unknown
>     Source)
>     at
>     edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown
>     Source)
>     at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
>     at
>     edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown
>     Source)
>     at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
>     at
>     org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingFrameAccess.init(
>     _LgProtegeEditor.java:180_ )
>     at org.lexgrid.ui.extension.protege.LgProtegeEditor.getSwingFrame(
>     _LgProtegeEditor.java:338_ )
>     at
>     org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingInitThread.run(
>     _LgProtegeEditor.java:266_ )
>
> The only change needed to remove compilation errors was to replace
> detachCurrentTab() with detachCurrentView().
>
> I understand that the Metadata tab has changed significantly from
> 2004. Any suggestions as to how I might resolve this issue?
>
> Also, when navigating the Instances tab, I see the words "LOST
> GENERATOR" pop up on the console. I'm not sure what the significance
> of this is.
>
> Thanks,
>
> Mark
>
>
>
> At 06:24 PM 10/13/2006, you wrote:
>> Mark,
>>
>> We are very careful not to delete or move public classes or methods.
>>
>> The
>>
>> edu.stanford.smi.protege.util.FileHandler
>>
>> is in the same place :)
>>
>> In which version did Protege have a detachCurrentTab() method in
>> ProjectView? I think the method you are looking for is the
>> detachCurrentView().
>>
>> The DefaultEntry is still in the same place:
>>
>> edu.stanford.smi.protege.plugin. DefaultEntry
>>
>> Are you using the right jars?
>>
>> Tania
>>
>>
>>
>>
>> Mark Feblowitz wrote:
>> > Add to that
>> >
>> >          edu.stanford.smi.protege.util.FileHandler
>> >
>> >
>> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
>> >  
>> >> I was wondering what became of these two classes in Protege:
>> >>
>> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
>> >> detachCurrentTab()
>> >>
>> >>          edu.stanford.smi.protege.plugin.DefaultEntry
>> >>
>> >> Have these been moved, removed or replaced? What would be the new
>> equivalents?
>> >>
>> >> Thanks,
>> >>
>> >> Mark
>> >> _______________________________________________
>> >> 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
>> >
>> >  
>>
>> _______________________________________________
>> 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: Build Questions (was Re: Question on some old classes/methods)

Tania Tudorache
In reply to this post by Mark Feblowitz
Mark,

If you use the latest Protege 3.2 beta, than you should use Java 1.5.

The Parser class is automatically generated by the Protege build script.
The instructions for building Protege out of the svn repository or
source code distribution are here:
http://protege.stanford.edu/doc/readme.html

However, I don't think that you need to recompile Protege. I suppose,
you can use the Protege jars and only recompile the Eclipse plugin code.

Tania


Mark Feblowitz wrote:

> My prior questions had to do with my efforts to update the LexGrid
> "Protege in Eclipse" project. All seems to be well, with the exception
> of the Protege Owl Plugin's Metadata Tab.
>
> I'm trying to debug and have the need to debug the source of Protege.
> I've imported the Protege core, but have a persistent problem with two
> build errors:
>
>         The project was not built since its build path is incomplete.
> Cannot find the class file for javax.swing.plaf.metal.DefaultMetalTheme.
>
>     The type javax.swing.plaf.metal.DefaultMetalTheme cannot be
>     resolved. It is indirectly referenced from required .class files
>     Protege/src/edu/stanford/smi/protege/util   ProtegePlasticTheme.java
>
> I'm using the IBM 1.5 JRE. When I switch to the Sun 1.5 JRE, I get 4
> errors about
>
>     "Parser cannot be resolved to at type"
>
> and 42 errors about
>
>     jThe declared package "javax.swing.plaf.metal" does not match the
>     expected package "edu.stanford.smi.protege.util"      
>
> I'm doing this work within ecplise 3.2.0
>
> What should I be using for my JRE? Any additional jars in the build
> path needed to reference javax.swing.plaf.metal.DefaultMetalTheme?
>
> Thanks,
>
> Mark
>
>
> At 06:24 PM 10/13/2006, Tania Tudorache wrote:
>> Mark,
>>
>> We are very careful not to delete or move public classes or methods.
>>
>> The
>>
>> edu.stanford.smi.protege.util.FileHandler
>>
>> is in the same place :)
>>
>> In which version did Protege have a detachCurrentTab() method in
>> ProjectView? I think the method you are looking for is the
>> detachCurrentView().
>>
>> The DefaultEntry is still in the same place:
>>
>> edu.stanford.smi.protege.plugin. DefaultEntry
>>
>> Are you using the right jars?
>>
>> Tania
>>
>>
>>
>>
>> Mark Feblowitz wrote:
>> > Add to that
>> >
>> >          edu.stanford.smi.protege.util.FileHandler
>> >
>> >
>> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
>> >  
>> >> I was wondering what became of these two classes in Protege:
>> >>
>> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
>> >> detachCurrentTab()
>> >>
>> >>          edu.stanford.smi.protege.plugin.DefaultEntry
>> >>
>> >> Have these been moved, removed or replaced? What would be the new
>> equivalents?
>> >>
>> >> Thanks,
>> >>
>> >> Mark
>> >> _______________________________________________
>> >> 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
>> >
>> >  
>>
>> _______________________________________________
>> 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: Build Questions (was Re: Question on some old classes/methods)

Mark Feblowitz
One more thing -

Where can I find information on building the Protege Owl source?

I see the source, but it doesn't include the corresponding build.xml  file.

Mark



At 02:48 PM 10/17/2006, Tania Tudorache wrote:

>Mark,
>
>If you use the latest Protege 3.2 beta, than you should use Java 1.5.
>
>The Parser class is automatically generated by the Protege build
>script. The instructions for building Protege out of the svn
>repository or source code distribution are here:
>http://protege.stanford.edu/doc/readme.html
>
>However, I don't think that you need to recompile Protege. I
>suppose, you can use the Protege jars and only recompile the Eclipse
>plugin code.
>
>Tania
>
>
>Mark Feblowitz wrote:
>>My prior questions had to do with my efforts to update the LexGrid
>>"Protege in Eclipse" project. All seems to be well, with the
>>exception of the Protege Owl Plugin's Metadata Tab.
>>
>>I'm trying to debug and have the need to debug the source of
>>Protege. I've imported the Protege core, but have a persistent
>>problem with two build errors:
>>
>>         The project was not built since its build path is
>> incomplete. Cannot find the class file for
>> javax.swing.plaf.metal.DefaultMetalTheme.
>>
>>     The type javax.swing.plaf.metal.DefaultMetalTheme cannot be
>>     resolved. It is indirectly referenced from required .class files
>>     Protege/src/edu/stanford/smi/protege/util   ProtegePlasticTheme.java
>>I'm using the IBM 1.5 JRE. When I switch to the Sun 1.5 JRE, I get
>>4 errors about
>>
>>     "Parser cannot be resolved to at type"
>>and 42 errors about
>>
>>     jThe declared package "javax.swing.plaf.metal" does not match the
>>     expected package "edu.stanford.smi.protege.util"
>>
>>I'm doing this work within ecplise 3.2.0
>>
>>What should I be using for my JRE? Any additional jars in the build
>>path needed to reference javax.swing.plaf.metal.DefaultMetalTheme?
>>
>>Thanks,
>>
>>Mark
>>
>>
>>At 06:24 PM 10/13/2006, Tania Tudorache wrote:
>>>Mark,
>>>
>>>We are very careful not to delete or move public classes or methods.
>>>
>>>The
>>>
>>>edu.stanford.smi.protege.util.FileHandler
>>>
>>>is in the same place :)
>>>
>>>In which version did Protege have a detachCurrentTab() method in
>>>ProjectView? I think the method you are looking for is the
>>>detachCurrentView().
>>>
>>>The DefaultEntry is still in the same place:
>>>
>>>edu.stanford.smi.protege.plugin. DefaultEntry
>>>
>>>Are you using the right jars?
>>>
>>>Tania
>>>
>>>
>>>
>>>
>>>Mark Feblowitz wrote:
>>> > Add to that
>>> >
>>> >          edu.stanford.smi.protege.util.FileHandler
>>> >
>>> >
>>> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
>>> >
>>> >> I was wondering what became of these two classes in Protege:
>>> >>
>>> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
>>> >> detachCurrentTab()
>>> >>
>>> >>          edu.stanford.smi.protege.plugin.DefaultEntry
>>> >>
>>> >> Have these been moved, removed or replaced? What would be the
>>> new equivalents?
>>> >>
>>> >> Thanks,
>>> >>
>>> >> Mark
>>> >> _______________________________________________
>>> >> 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
>>> >
>>> >
>>>
>>>_______________________________________________
>>>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: Build Questions (was Re: Question on some old classes/methods)

Jennifer Vendetti
Administrator

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Re: Build Questions (was Re: Question on some old classes/methods)

Jennifer Vendetti
Administrator
In reply to this post by Mark Feblowitz

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Re: Build Questions (was Re: Question on some old classes/methods)

Jennifer Vendetti
Administrator
In reply to this post by Mark Feblowitz
Mark,

There is an Ant build file that you can download from our Subversion
repository in the following location:

http://smi-protege.stanford.edu/repos/protege/owl/trunk/build.xml

Jennifer

Mark Feblowitz wrote:
> One more thing -
>
> Where can I find information on building the Protege Owl source?
>
> I see the source, but it doesn't include the corresponding build.xml  file.
>
> Mark
>  
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Re: Build Questions (was Re: Question on some old classes/methods)

Mark Feblowitz
In reply to this post by Tania Tudorache
I'm trying to do source level debugging to the point of failure,
which is in the method. I can't do that in eclipse without having
generated line number in the jar for the debug. So I'm trying to
build the protege.jar from either the source distribution or the
Subversion repository (the latter seems to work better.

I've been able to get the protege core and protege owl plugin to
compile without errors (with a little extra help from ant where
eclipse isn't doing the tric.

One thing I noticed is that the build file for protege does not
correctly identify javacc.home. Is that a known problem or just
something I had needed to handle?

Also, when trying to run the constructed protege.jar, an exception is
thrown that makes me wonder whether I have all of the right parts in the jar:

Exception in thread
"org.lexgrid.ui.extension.protege.LgProtegeEditor"
java.lang.NoClassDefFoundError: com/hp/hpl/jena/rdf/arp/StatementHandler
at
edu.stanford.smi.protegex.owl.jena.JenaKnowledgeBaseFactory.createKnowledgeBase(JenaKnowledgeBaseFactory.java:77)
at edu.stanford.smi.protege.model.Project.createDomainKB(Project.java:323)
at
edu.stanford.smi.protege.model.Project.createDomainKnowledgeBase(Project.java:341)
at edu.stanford.smi.protege.model.Project.<init>(Project.java:253)
at edu.stanford.smi.protege.model.Project.<init>(Project.java:237)
at edu.stanford.smi.protege.model.Project.<init>(Project.java:273)
at edu.stanford.smi.protege.model.Project.<init>(Project.java:262)
at
org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingFrameAccess.init(LgProtegeEditor.java:166)
at
org.lexgrid.ui.extension.protege.LgProtegeEditor.getSwingFrame(LgProtegeEditor.java:338)
at
org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingInitThread.run(LgProtegeEditor.java:266)

Do I need anything else other than the protege core and protege owl
plugin (and the jars they reference)?

Thanks,

Mark


At 02:48 PM 10/17/2006, Tania Tudorache wrote:

>Mark,
>
>If you use the latest Protege 3.2 beta, than you should use Java 1.5.
>
>The Parser class is automatically generated by the Protege build
>script. The instructions for building Protege out of the svn
>repository or source code distribution are here:
>http://protege.stanford.edu/doc/readme.html
>
>However, I don't think that you need to recompile Protege. I
>suppose, you can use the Protege jars and only recompile the Eclipse
>plugin code.
>
>Tania
>
>
>Mark Feblowitz wrote:
>>My prior questions had to do with my efforts to update the LexGrid
>>"Protege in Eclipse" project. All seems to be well, with the
>>exception of the Protege Owl Plugin's Metadata Tab.
>>
>>I'm trying to debug and have the need to debug the source of
>>Protege. I've imported the Protege core, but have a persistent
>>problem with two build errors:
>>
>>         The project was not built since its build path is
>> incomplete. Cannot find the class file for
>> javax.swing.plaf.metal.DefaultMetalTheme.
>>
>>     The type javax.swing.plaf.metal.DefaultMetalTheme cannot be
>>     resolved. It is indirectly referenced from required .class files
>>     Protege/src/edu/stanford/smi/protege/util   ProtegePlasticTheme.java
>>I'm using the IBM 1.5 JRE. When I switch to the Sun 1.5 JRE, I get
>>4 errors about
>>
>>     "Parser cannot be resolved to at type"
>>and 42 errors about
>>
>>     jThe declared package "javax.swing.plaf.metal" does not match the
>>     expected package "edu.stanford.smi.protege.util"
>>
>>I'm doing this work within ecplise 3.2.0
>>
>>What should I be using for my JRE? Any additional jars in the build
>>path needed to reference javax.swing.plaf.metal.DefaultMetalTheme?
>>
>>Thanks,
>>
>>Mark
>>
>>
>>At 06:24 PM 10/13/2006, Tania Tudorache wrote:
>>>Mark,
>>>
>>>We are very careful not to delete or move public classes or methods.
>>>
>>>The
>>>
>>>edu.stanford.smi.protege.util.FileHandler
>>>
>>>is in the same place :)
>>>
>>>In which version did Protege have a detachCurrentTab() method in
>>>ProjectView? I think the method you are looking for is the
>>>detachCurrentView().
>>>
>>>The DefaultEntry is still in the same place:
>>>
>>>edu.stanford.smi.protege.plugin. DefaultEntry
>>>
>>>Are you using the right jars?
>>>
>>>Tania
>>>
>>>
>>>
>>>
>>>Mark Feblowitz wrote:
>>> > Add to that
>>> >
>>> >          edu.stanford.smi.protege.util.FileHandler
>>> >
>>> >
>>> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
>>> >
>>> >> I was wondering what became of these two classes in Protege:
>>> >>
>>> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
>>> >> detachCurrentTab()
>>> >>
>>> >>          edu.stanford.smi.protege.plugin.DefaultEntry
>>> >>
>>> >> Have these been moved, removed or replaced? What would be the
>>> new equivalents?
>>> >>
>>> >> Thanks,
>>> >>
>>> >> Mark
>>> >> _______________________________________________
>>> >> 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
>>> >
>>> >
>>>
>>>_______________________________________________
>>>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: Build Questions (was Re: Question on some old classes/methods)

Mark Feblowitz
In reply to this post by Tania Tudorache
Ok -

Forget all of my prior questions :-) Using ant instead of eclipse,
I've been able to debug and diagnose the problem I'm having.

You were right on the money!

The LexGrid Protege in Eclipse code creates a project and project
views, but does not set the current project.

The problem comes when trying to get the current project.

I assume that the LG code is using some outdated means of loading a
project. Below is the method that appears to be flawed.

Can you point me to something the does this correctly?

Thanks!

Mark

from LgProtegeEditor.java:
...
public void init() throws SwingInitException {
         try {
                 final IFileEditorInput input = (IFileEditorInput)
getEditorInput();
                 if (input != null) {
                         Collection errs = new ArrayList();
                         p = new
Project(((org.eclipse.core.internal.resources.File)
input.getStorage()).getRawLocation().toString(), errs);
                         if (!disposed) {
                                 if (!errs.isEmpty()) {
                                         for (Iterator errIt =
errs.iterator(); errIt.hasNext(); )
                                                 Plugin.log(IStatus.ERROR,
errIt.next().toString());
                                         display.syncExec(new Runnable() {
                                                 public void run() {
                                                         MessageDialog.openError(getSite().getShell(),
"Error",
                                                                 "Errors
occurred initializing the Protege project. Refer to the error log for
additional information.");
                                                 }
                                         });
                                 }
                                 if (p.hasCompleteSources()) {
                                         // Create the Swing-based canvas ...
                                                                                 pv
= new ProjectView(p);
                                         f.setLayout(new
java.awt.BorderLayout());
                                         f.add(pv, "Center");
                                         f.addWindowListener(new
WindowAdapter() {
                                                 public void
windowClosing(WindowEvent event) {
                                                         dispose();
                                                 }
                                         });
                                         // Fresh starting point for
edit tracking ...
                                         p.clearIsDirty();
                                 } else {
                                         throw new SwingInitException();
                                 }
                         }
                 }
...


At 04:50 PM 10/17/2006, Tania Tudorache wrote:

>Mark,
>
>I can't tell you what's going on, if I don't know in which line the
>exception occurred. I suppose it occurred in
>
>String projName =
>ProjectManager.getProjectManager().getCurrentProject().getName();
>
>which probably means that the project manager was not initialized
>correctly, or that the project was not yet created.
>
>Maybe some things have also changed in Eclipse initialization as
>well. I know that they support only partially Swing applications.
>
>Tania
>
>
>
>Mark Feblowitz wrote:
>>I am using Java 1.5, either the IBM version or the Sun version.
>>
>>I'll see if I can get some help here in using eclipse to do the build.
>>
>>I'm bringing in the Protege source to debug what's happening in
>>Protege. It's a problem with rendering the Metadata Tab, but looks
>>like it occurs in the Protege code. Here's the exception:
>>
>>WARNING: _java.lang.NullPointerException
>>_at
>>edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.createOntologyBrowserHeader(Unknown
>>Source)
>>at
>>edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.<init>(Unknown
>>Source)
>>at
>>edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.createMainPanel(Unknown
>>Source)
>>at
>>edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.initialize(Unknown
>>Source)
>>at
>>edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Unknown Source)
>>at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
>>at edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Source)
>>at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
>>at
>>org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingFrameAccess.init(
>>_LgProtegeEditor.java:180_ )
>>at org.lexgrid.ui.extension.protege.LgProtegeEditor.getSwingFrame(
>>_LgProtegeEditor.java:338_ )
>>at
>>org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingInitThread.run
>>( _LgProtegeEditor.java:266_ )
>>
>>Mark
>>
>>
>>
>>At 02:48 PM 10/17/2006, you wrote:
>>>Mark,
>>>
>>>If you use the latest Protege 3.2 beta, than you should use Java 1.5.
>>>
>>>The Parser class is automatically generated by the Protege build
>>>script. The instructions for building Protege out of the svn
>>>repository or source code distribution are here:
>>>http://protege.stanford.edu/doc/readme.html
>>>
>>>However, I don't think that you need to recompile Protege. I
>>>suppose, you can use the Protege jars and only recompile the
>>>Eclipse plugin code.
>>>
>>>Tania
>>>
>>>
>>>Mark Feblowitz wrote:
>>>>My prior questions had to do with my efforts to update the
>>>>LexGrid "Protege in Eclipse" project. All seems to be well, with
>>>>the exception of the Protege Owl Plugin's Metadata Tab.
>>>>
>>>>I'm trying to debug and have the need to debug the source of
>>>>Protege. I've imported the Protege core, but have a persistent
>>>>problem with two build errors:
>>>>
>>>>         The project was not built since its build path is
>>>> incomplete. Cannot find the class file for
>>>> javax.swing.plaf.metal.DefaultMetalTheme.
>>>>
>>>>     The type javax.swing.plaf.metal.DefaultMetalTheme cannot be
>>>>     resolved. It is indirectly referenced from required .class files
>>>>     Protege/src/edu/stanford/smi/protege/util
>>>>ProtegePlasticTheme.java
>>>>I'm using the IBM 1.5 JRE. When I switch to the Sun 1.5 JRE, I
>>>>get 4 errors about
>>>>
>>>>     "Parser cannot be resolved to at type"
>>>>and 42 errors about
>>>>
>>>>     jThe declared package "javax.swing.plaf.metal" does not match the
>>>>     expected package "edu.stanford.smi.protege.util"
>>>>
>>>>I'm doing this work within ecplise 3.2.0
>>>>
>>>>What should I be using for my JRE? Any additional jars in the
>>>>build path needed to reference javax.swing.plaf.metal.DefaultMetalTheme?
>>>>
>>>>Thanks,
>>>>
>>>>Mark
>>>>
>>>>
>>>>At 06:24 PM 10/13/2006, Tania Tudorache wrote:
>>>>>Mark,
>>>>>
>>>>>We are very careful not to delete or move public classes or methods.
>>>>>
>>>>>The
>>>>>
>>>>>edu.stanford.smi.protege.util.FileHandler
>>>>>
>>>>>is in the same place :)
>>>>>
>>>>>In which version did Protege have a detachCurrentTab() method in
>>>>>ProjectView? I think the method you are looking for is the
>>>>>detachCurrentView().
>>>>>
>>>>>The DefaultEntry is still in the same place:
>>>>>
>>>>>edu.stanford.smi.protege.plugin. DefaultEntry
>>>>>
>>>>>Are you using the right jars?
>>>>>
>>>>>Tania
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>Mark Feblowitz wrote:
>>>>> > Add to that
>>>>> >
>>>>> >          edu.stanford.smi.protege.util.FileHandler
>>>>> >
>>>>> >
>>>>> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
>>>>> > >> I was wondering what became of these two classes in Protege:
>>>>> >>
>>>>> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
>>>>> >> detachCurrentTab()
>>>>> >>
>>>>> >>          edu.stanford.smi.protege.plugin.DefaultEntry
>>>>> >>
>>>>> >> Have these been moved, removed or replaced? What would be
>>>>> the new equivalents?
>>>>> >>
>>>>> >> Thanks,
>>>>> >>
>>>>> >> Mark
>>>>> >> _______________________________________________
>>>>> >> 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
>>>>> >
>>>>> >
>>>>>_______________________________________________
>>>>>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: Build Questions (was Re: Question on some old classes/methods)

Mark Feblowitz
And a follow-up  -

I've found a few references to ProtegeOWL.createJenaOWLModelFromURI()

If this is the right way to solve my problem, then perhaps you could
help me figure out why my code gives me a
java.lang.NoClassDefFoundError: edu/stanford/smi/protegex/owl/ProtegeOWL

I'm using the code

         JenaOWLModel owlModel =
ProtegeOWL.createJenaOWLModelFromURI(fileName);

with the import

         import edu.stanford.smi.protegex.owl.*;

It seems to compile ok but the class is not found att runtime.


Thanks,

Mark

At 10:09 AM 10/20/2006, Mark Feblowitz wrote:

>Ok -
>
>Forget all of my prior questions :-) Using ant instead of eclipse,
>I've been able to debug and diagnose the problem I'm having.
>
>You were right on the money!
>
>The LexGrid Protege in Eclipse code creates a project and project
>views, but does not set the current project.
>
>The problem comes when trying to get the current project.
>
>I assume that the LG code is using some outdated means of loading a
>project. Below is the method that appears to be flawed.
>
>Can you point me to something the does this correctly?
>
>Thanks!
>
>Mark
>
>from LgProtegeEditor.java:
>...
>public void init() throws SwingInitException {
>          try {
>                  final IFileEditorInput input = (IFileEditorInput)
>getEditorInput();
>                  if (input != null) {
>                          Collection errs = new ArrayList();
>                          p = new
>Project(((org.eclipse.core.internal.resources.File)
>input.getStorage()).getRawLocation().toString(), errs);
>                          if (!disposed) {
>                                  if (!errs.isEmpty()) {
>                                          for (Iterator errIt =
>errs.iterator(); errIt.hasNext(); )
>                                                  Plugin.log(IStatus.ERROR,
>errIt.next().toString());
>                                          display.syncExec(new Runnable() {
>                                                  public void run() {
>
>MessageDialog.openError(getSite().getShell(),
>"Error",
>                                                                  "Errors
>occurred initializing the Protege project. Refer to the error log for
>additional information.");
>                                                  }
>                                          });
>                                  }
>                                  if (p.hasCompleteSources()) {
>                                          // Create the Swing-based canvas ...
>
>pv
>= new ProjectView(p);
>                                          f.setLayout(new
>java.awt.BorderLayout());
>                                          f.add(pv, "Center");
>                                          f.addWindowListener(new
>WindowAdapter() {
>                                                  public void
>windowClosing(WindowEvent event) {
>                                                          dispose();
>                                                  }
>                                          });
>                                          // Fresh starting point for
>edit tracking ...
>                                          p.clearIsDirty();
>                                  } else {
>                                          throw new SwingInitException();
>                                  }
>                          }
>                  }
>...
>
>
>At 04:50 PM 10/17/2006, Tania Tudorache wrote:
> >Mark,
> >
> >I can't tell you what's going on, if I don't know in which line the
> >exception occurred. I suppose it occurred in
> >
> >String projName =
> >ProjectManager.getProjectManager().getCurrentProject().getName();
> >
> >which probably means that the project manager was not initialized
> >correctly, or that the project was not yet created.
> >
> >Maybe some things have also changed in Eclipse initialization as
> >well. I know that they support only partially Swing applications.
> >
> >Tania
> >
> >
> >
> >Mark Feblowitz wrote:
> >>I am using Java 1.5, either the IBM version or the Sun version.
> >>
> >>I'll see if I can get some help here in using eclipse to do the build.
> >>
> >>I'm bringing in the Protege source to debug what's happening in
> >>Protege. It's a problem with rendering the Metadata Tab, but looks
> >>like it occurs in the Protege code. Here's the exception:
> >>
> >>WARNING: _java.lang.NullPointerException
> >>_at
> >>edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.crea
> teOntologyBrowserHeader(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.<ini
> t>(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.create
> MainPanel(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.initia
> lize(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Un
> known Source)
> >>at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
> >>at edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Source)
> >>at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
> >>at
> >>org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingFrameAccess.init(
> >>_LgProtegeEditor.java:180_ )
> >>at org.lexgrid.ui.extension.protege.LgProtegeEditor.getSwingFrame(
> >>_LgProtegeEditor.java:338_ )
> >>at
> >>org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingInitThread.run
> >>( _LgProtegeEditor.java:266_ )
> >>
> >>Mark
> >>
> >>
> >>
> >>At 02:48 PM 10/17/2006, you wrote:
> >>>Mark,
> >>>
> >>>If you use the latest Protege 3.2 beta, than you should use Java 1.5.
> >>>
> >>>The Parser class is automatically generated by the Protege build
> >>>script. The instructions for building Protege out of the svn
> >>>repository or source code distribution are here:
> >>>http://protege.stanford.edu/doc/readme.html
> >>>
> >>>However, I don't think that you need to recompile Protege. I
> >>>suppose, you can use the Protege jars and only recompile the
> >>>Eclipse plugin code.
> >>>
> >>>Tania
> >>>
> >>>
> >>>Mark Feblowitz wrote:
> >>>>My prior questions had to do with my efforts to update the
> >>>>LexGrid "Protege in Eclipse" project. All seems to be well, with
> >>>>the exception of the Protege Owl Plugin's Metadata Tab.
> >>>>
> >>>>I'm trying to debug and have the need to debug the source of
> >>>>Protege. I've imported the Protege core, but have a persistent
> >>>>problem with two build errors:
> >>>>
> >>>>         The project was not built since its build path is
> >>>> incomplete. Cannot find the class file for
> >>>> javax.swing.plaf.metal.DefaultMetalTheme.
> >>>>
> >>>>     The type javax.swing.plaf.metal.DefaultMetalTheme cannot be
> >>>>     resolved. It is indirectly referenced from required .class files
> >>>>     Protege/src/edu/stanford/smi/protege/util
> >>>>ProtegePlasticTheme.java
> >>>>I'm using the IBM 1.5 JRE. When I switch to the Sun 1.5 JRE, I
> >>>>get 4 errors about
> >>>>
> >>>>     "Parser cannot be resolved to at type"
> >>>>and 42 errors about
> >>>>
> >>>>     jThe declared package "javax.swing.plaf.metal" does not match the
> >>>>     expected package "edu.stanford.smi.protege.util"
> >>>>
> >>>>I'm doing this work within ecplise 3.2.0
> >>>>
> >>>>What should I be using for my JRE? Any additional jars in the
> >>>>build path needed to reference javax.swing.plaf.metal.DefaultMetalTheme?
> >>>>
> >>>>Thanks,
> >>>>
> >>>>Mark
> >>>>
> >>>>
> >>>>At 06:24 PM 10/13/2006, Tania Tudorache wrote:
> >>>>>Mark,
> >>>>>
> >>>>>We are very careful not to delete or move public classes or methods.
> >>>>>
> >>>>>The
> >>>>>
> >>>>>edu.stanford.smi.protege.util.FileHandler
> >>>>>
> >>>>>is in the same place :)
> >>>>>
> >>>>>In which version did Protege have a detachCurrentTab() method in
> >>>>>ProjectView? I think the method you are looking for is the
> >>>>>detachCurrentView().
> >>>>>
> >>>>>The DefaultEntry is still in the same place:
> >>>>>
> >>>>>edu.stanford.smi.protege.plugin. DefaultEntry
> >>>>>
> >>>>>Are you using the right jars?
> >>>>>
> >>>>>Tania
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>Mark Feblowitz wrote:
> >>>>> > Add to that
> >>>>> >
> >>>>> >          edu.stanford.smi.protege.util.FileHandler
> >>>>> >
> >>>>> >
> >>>>> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
> >>>>> > >> I was wondering what became of these two classes in Protege:
> >>>>> >>
> >>>>> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
> >>>>> >> detachCurrentTab()
> >>>>> >>
> >>>>> >>          edu.stanford.smi.protege.plugin.DefaultEntry
> >>>>> >>
> >>>>> >> Have these been moved, removed or replaced? What would be
> >>>>> the new equivalents?
> >>>>> >>
> >>>>> >> Thanks,
> >>>>> >>
> >>>>> >> Mark
> >>>>> >> _______________________________________________
> >>>>> >> 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
> >>>>> >
> >>>>> >
> >>>>>_______________________________________________
> >>>>>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: Build Questions (was Re: Question on some old classes/methods)

Mark Feblowitz
In reply to this post by Mark Feblowitz
Since there's been radio silence on this, I'll restate my request as
I currently understand it.

What is the best way to load a project, such that currentProject is
set correctly?  It seems like simply issuing a "new
Project(...)"  doesn't do the trick.

(Is that a bug or simply an incomplete creation/loading of the project?)

It would help to see some code that loads a project (that is an Owl project).

Thanks,

Mark


At 10:09 AM 10/20/2006, Mark Feblowitz wrote:

>Ok -
>
>Forget all of my prior questions :-) Using ant instead of eclipse,
>I've been able to debug and diagnose the problem I'm having.
>
>You were right on the money!
>
>The LexGrid Protege in Eclipse code creates a project and project
>views, but does not set the current project.
>
>The problem comes when trying to get the current project.
>
>I assume that the LG code is using some outdated means of loading a
>project. Below is the method that appears to be flawed.
>
>Can you point me to something the does this correctly?
>
>Thanks!
>
>Mark
>
>from LgProtegeEditor.java:
>...
>public void init() throws SwingInitException {
>          try {
>                  final IFileEditorInput input = (IFileEditorInput)
>getEditorInput();
>                  if (input != null) {
>                          Collection errs = new ArrayList();
>                          p = new
>                         Project(((org.eclipse.core.internal.resources.File)
>
>input.getStorage()).getRawLocation().toString(), errs);
>                          if (!disposed) {
>                                  if (!errs.isEmpty()) {
>                                          for (Iterator errIt =
>                                         errs.iterator(); errIt.hasNext(); )
>                                                  Plugin.log(IStatus.ERROR,
>                                                 errIt.next().toString());
>                                              display.syncExec(new
> Runnable() {
>                                                  public void run() {
>
>MessageDialog.openError(getSite().getShell(),
>                                         "Error",
>
>"Errors occurred initializing the Protege project. Refer to the
>error log for  additional information.");
>                                                  }
>                                          });
>                                  }
>                                  if (p.hasCompleteSources()) {
>                                          // Create the Swing-based canvas ...
>                                          pv = new ProjectView(p);
>                                          f.setLayout(new
> java.awt.BorderLayout());
>                                          f.add(pv, "Center");
>                                          f.addWindowListener(new
> WindowAdapter() {
>                                                  public void
> windowClosing(WindowEvent event) {
>                                                          dispose();
>                                                  }
>                                          });
>                                          // Fresh starting point
> for edit tracking ...
>                                          p.clearIsDirty();
>                                  } else {
>                                          throw new SwingInitException();
>                                  }
>                          }
>                  }
>...
>
>
>At 04:50 PM 10/17/2006, Tania Tudorache wrote:
> >Mark,
> >
> >I can't tell you what's going on, if I don't know in which line the
> >exception occurred. I suppose it occurred in
> >
> >String projName =
> >ProjectManager.getProjectManager().getCurrentProject().getName();
> >
> >which probably means that the project manager was not initialized
> >correctly, or that the project was not yet created.
> >
> >Maybe some things have also changed in Eclipse initialization as
> >well. I know that they support only partially Swing applications.
> >
> >Tania
> >
> >
> >
> >Mark Feblowitz wrote:
> >>I am using Java 1.5, either the IBM version or the Sun version.
> >>
> >>I'll see if I can get some help here in using eclipse to do the build.
> >>
> >>I'm bringing in the Protege source to debug what's happening in
> >>Protege. It's a problem with rendering the Metadata Tab, but looks
> >>like it occurs in the Protege code. Here's the exception:
> >>
> >>WARNING: _java.lang.NullPointerException
> >>_at
> >>edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.crea
> teOntologyBrowserHeader(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protegex.owl.ui.importstree.ImportsTreePanel.<ini
> t>(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.create
> MainPanel(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protegex.owl.ui.metadatatab.OWLMetadataTab.initia
> lize(Unknown
> >>Source)
> >>at
> >>edu.stanford.smi.protege.widget.WidgetUtilities.createTabWidget(Un
> known Source)
> >>at edu.stanford.smi.protege.ui.ProjectView.addTab(Unknown Source)
> >>at edu.stanford.smi.protege.ui.ProjectView.createTabbedPane(Unknown Source)
> >>at edu.stanford.smi.protege.ui.ProjectView.<init>(Unknown Source)
> >>at
> >>org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingFrameAccess.init(
> >>_LgProtegeEditor.java:180_ )
> >>at org.lexgrid.ui.extension.protege.LgProtegeEditor.getSwingFrame(
> >>_LgProtegeEditor.java:338_ )
> >>at
> >>org.lexgrid.ui.extension.protege.LgProtegeEditor$SwingInitThread.run
> >>( _LgProtegeEditor.java:266_ )
> >>
> >>Mark
> >>
> >>
> >>
> >>At 02:48 PM 10/17/2006, you wrote:
> >>>Mark,
> >>>
> >>>If you use the latest Protege 3.2 beta, than you should use Java 1.5.
> >>>
> >>>The Parser class is automatically generated by the Protege build
> >>>script. The instructions for building Protege out of the svn
> >>>repository or source code distribution are here:
> >>>http://protege.stanford.edu/doc/readme.html
> >>>
> >>>However, I don't think that you need to recompile Protege. I
> >>>suppose, you can use the Protege jars and only recompile the
> >>>Eclipse plugin code.
> >>>
> >>>Tania
> >>>
> >>>
> >>>Mark Feblowitz wrote:
> >>>>My prior questions had to do with my efforts to update the
> >>>>LexGrid "Protege in Eclipse" project. All seems to be well, with
> >>>>the exception of the Protege Owl Plugin's Metadata Tab.
> >>>>
> >>>>I'm trying to debug and have the need to debug the source of
> >>>>Protege. I've imported the Protege core, but have a persistent
> >>>>problem with two build errors:
> >>>>
> >>>>         The project was not built since its build path is
> >>>> incomplete. Cannot find the class file for
> >>>> javax.swing.plaf.metal.DefaultMetalTheme.
> >>>>
> >>>>     The type javax.swing.plaf.metal.DefaultMetalTheme cannot be
> >>>>     resolved. It is indirectly referenced from required .class files
> >>>>     Protege/src/edu/stanford/smi/protege/util
> >>>>ProtegePlasticTheme.java
> >>>>I'm using the IBM 1.5 JRE. When I switch to the Sun 1.5 JRE, I
> >>>>get 4 errors about
> >>>>
> >>>>     "Parser cannot be resolved to at type"
> >>>>and 42 errors about
> >>>>
> >>>>     jThe declared package "javax.swing.plaf.metal" does not match the
> >>>>     expected package "edu.stanford.smi.protege.util"
> >>>>
> >>>>I'm doing this work within ecplise 3.2.0
> >>>>
> >>>>What should I be using for my JRE? Any additional jars in the
> >>>>build path needed to reference javax.swing.plaf.metal.DefaultMetalTheme?
> >>>>
> >>>>Thanks,
> >>>>
> >>>>Mark
> >>>>
> >>>>
> >>>>At 06:24 PM 10/13/2006, Tania Tudorache wrote:
> >>>>>Mark,
> >>>>>
> >>>>>We are very careful not to delete or move public classes or methods.
> >>>>>
> >>>>>The
> >>>>>
> >>>>>edu.stanford.smi.protege.util.FileHandler
> >>>>>
> >>>>>is in the same place :)
> >>>>>
> >>>>>In which version did Protege have a detachCurrentTab() method in
> >>>>>ProjectView? I think the method you are looking for is the
> >>>>>detachCurrentView().
> >>>>>
> >>>>>The DefaultEntry is still in the same place:
> >>>>>
> >>>>>edu.stanford.smi.protege.plugin. DefaultEntry
> >>>>>
> >>>>>Are you using the right jars?
> >>>>>
> >>>>>Tania
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>Mark Feblowitz wrote:
> >>>>> > Add to that
> >>>>> >
> >>>>> >          edu.stanford.smi.protege.util.FileHandler
> >>>>> >
> >>>>> >
> >>>>> > At 05:05 PM 10/13/2006, Mark Feblowitz wrote:
> >>>>> > >> I was wondering what became of these two classes in Protege:
> >>>>> >>
> >>>>> >>          edu.stanford.smi.protege.ui.ProjectView - specifically
> >>>>> >> detachCurrentTab()
> >>>>> >>
> >>>>> >>          edu.stanford.smi.protege.plugin.DefaultEntry
> >>>>> >>
> >>>>> >> Have these been moved, removed or replaced? What would be
> >>>>> the new equivalents?
> >>>>> >>
> >>>>> >> Thanks,
> >>>>> >>
> >>>>> >> Mark
> >>>>> >> _______________________________________________
> >>>>> >> 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
> >>>>> >
> >>>>> >
> >>>>>_______________________________________________
> >>>>>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: Build Questions (was Re: Question on some old classes/methods)

Thomas Russ

On Oct 23, 2006, at 1:15 PM, Mark Feblowitz wrote:

> Since there's been radio silence on this, I'll restate my request as
> I currently understand it.
>
> What is the best way to load a project, such that currentProject is
> set correctly?  It seems like simply issuing a "new
> Project(...)"  doesn't do the trick.

ProjectManager.setCurrentProject  perhaps?

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12