Display problem with trees in Protege 4.3

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Display problem with trees in Protege 4.3

Johannes Scharf
Hello!
 
I'm using Protege 4.3 with Java 1.7 Update 51 on Windows 7 x86.
For unknown reason ALL trees at the GUI have a display error. They just contain crap (see attachment).
 
To track down the cause I've already tried to use a different Java version and also an earlier version of Protege - same results.
Please help me! Any ideas what's wrong here?
 
Thanks!
 
Kind regards,
Johannes

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Re: Display problem with trees in Protege 4.3

Jennifer Vendetti
Administrator
I'm running Protege 4.3 on Windows 7 with the same version of Java and I can't reproduce this display problem.  Could you send us the contents of your Protege log file?  On Windows it will be in your /Users/<your-username>/.Protege/logs directory.

Jennifer


On 4/14/2014 4:11 AM, Johannes Scharf wrote:
Hello!
 
I'm using Protege 4.3 with Java 1.7 Update 51 on Windows 7 x86.
For unknown reason ALL trees at the GUI have a display error. They just contain crap (see attachment).
 
To track down the cause I've already tried to use a different Java version and also an earlier version of Protege - same results.
Please help me! Any ideas what's wrong here?
 
Thanks!
 
Kind regards,
Johannes


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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Display problem with trees in Protege 4.3

Johannes Scharf
Hello!
 
Of course - I've switched logging to DEBUG level and attached the file.
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....
 
Kind regards,
Johannes
 
Gesendet: Montag, 14. April 2014 um 20:08 Uhr
Von: "Jennifer Vendetti" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
I'm running Protege 4.3 on Windows 7 with the same version of Java and I can't reproduce this display problem.  Could you send us the contents of your Protege log file?  On Windows it will be in your /Users/<your-username>/.Protege/logs directory.

Jennifer

 
On 4/14/2014 4:11 AM, Johannes Scharf wrote:
Hello!
 
I'm using Protege 4.3 with Java 1.7 Update 51 on Windows 7 x86.
For unknown reason ALL trees at the GUI have a display error. They just contain crap (see attachment).
 
To track down the cause I've already tried to use a different Java version and also an earlier version of Protege - same results.
Please help me! Any ideas what's wrong here?
 
Thanks!
 
Kind regards,
Johannes
 
 
 
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Re: Display problem with trees in Protege 4.3

Altaf
In reply to this post by Jennifer Vendetti
Respected Sir / Madam

Please find the log files as an attachment.

Best Regards

Altaf


On Mon, Apr 14, 2014 at 8:08 PM, Jennifer Vendetti <[hidden email]> wrote:
I'm running Protege 4.3 on Windows 7 with the same version of Java and I can't reproduce this display problem.  Could you send us the contents of your Protege log file?  On Windows it will be in your /Users/<your-username>/.Protege/logs directory.

Jennifer


On 4/14/2014 4:11 AM, Johannes Scharf wrote:
Hello!
 
I'm using Protege 4.3 with Java 1.7 Update 51 on Windows 7 x86.
For unknown reason ALL trees at the GUI have a display error. They just contain crap (see attachment).
 
To track down the cause I've already tried to use a different Java version and also an earlier version of Protege - same results.
Please help me! Any ideas what's wrong here?
 
Thanks!
 
Kind regards,
Johannes


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user




--

Altaf 


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protege-3.log (16K) Download Attachment
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Re: Display problem with trees in Protege 4.3

Jennifer Vendetti
Administrator
In reply to this post by Johannes Scharf
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:



Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer


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Re: Display problem with trees in Protege 4.3

Altaf
Respected Madam 

Hoping that you will be fine.

I would like to thank you for guiding me to resolve the protege problem. First I uninstall the old protege and deleted the .Protege folder under user directory. Then re install the protege as you instructed however the problem still persist. Please see the log file attached as well as the example pizza.owl. I would be very thankful for your kind guidance and help in advance.

Best Regards

Altaf Ahmad 


On Tue, Apr 15, 2014 at 12:12 AM, Jennifer Vendetti <[hidden email]> wrote:
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:



Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user




--

Altaf 


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protege-0.log (55K) Download Attachment
protege-1.log (7K) Download Attachment
protege-2.log (14K) Download Attachment
pizza.owl (18K) Download Attachment
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Re: Display problem with trees in Protege 4.3

Johannes Scharf
In reply to this post by Jennifer Vendetti
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Display problem with trees in Protege 4.3

Tania Tudorache
This is interesting.

Is it just the trees that look weird, or also other things? For example, do the menus look OK?

I don't have access to a windows machine at this time, but here are a few things you can try:

1. File menu -> Preferences -> press on the Reset preferences button at the bottom of the window.

Restart Protege, see how it looks. If it doesn't work, then:

2. Delete manually the Java preferences for Protege. See here how: 

Hopefully this will do it. If not:

3. Try to run Protege using the run.bat file. I assume there is a run.bat in the Protege installation folder. Open a command terminal, cd to the Protege installation folder, and start run.bat. You may need to adjust the java path if "java" is not on your system path.

If this still doesn't work (probably it won't), then try the last desperate step:

4. Try to install Protege 3.5, and see if the problem also appears there:

Feel free to uninstall it after the test, and please report the result.

Tania




From: "Johannes Scharf" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Sent: Tuesday, April 15, 2014 12:58:26 AM
Subject: Re: [protege-user] Display problem with trees in Protege 4.3

Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


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Re: Display problem with trees in Protege 4.3

Altaf
In reply to this post by Johannes Scharf
Respected Madam / sir

Hoping that you will be fine.

I have tried to install Protege 4.3 64 bit and run the example on Ubuntu 13.10 64 bit. There was no error like the null pointer as I am experiencing in windows 7. However when I put the object property restriction on MargheritaPizza "hasTopping only (MozzerallaTopping or TomatoTopping)" there is no problem. However as mentioned in the "A Practical Guide To Building OWL Ontologies Using Protege 4 and CO-ODE Tools Edition 1.3" when I put the restriction on MargheritaPizza "hasTopping some MozzerallaTopping" then the reasoner put MargheritaPizza under Nothing. I am unable to understand this problem and could not resolve the problem. Please help me in this regards where I am wrong I am send the example I am working on as attachment.

Best Regards


On Tue, Apr 15, 2014 at 9:58 AM, Johannes Scharf <[hidden email]> wrote:
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr

Von: "Jennifer Vendetti" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

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--

Altaf 


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Re: Display problem with trees in Protege 4.3

Johannes Scharf
In reply to this post by Tania Tudorache
Suggestion 1) did it - I just reset the preferenced in Protege 4.3 and it worked like a charm. Moreover after the reset Protege 4.0 started to work again as well - do they share the same ressources in registry?
 
Thank you very much!
Kind regards,
 
Johannes
 
 
 
Gesendet: Dienstag, 15. April 2014 um 11:09 Uhr
Von: "Tania Tudorache" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
This is interesting.
 
Is it just the trees that look weird, or also other things? For example, do the menus look OK?
 
I don't have access to a windows machine at this time, but here are a few things you can try:
 
1. File menu -> Preferences -> press on the Reset preferences button at the bottom of the window.
 
Restart Protege, see how it looks. If it doesn't work, then:
 
2. Delete manually the Java preferences for Protege. See here how: 
 
Hopefully this will do it. If not:
 
3. Try to run Protege using the run.bat file. I assume there is a run.bat in the Protege installation folder. Open a command terminal, cd to the Protege installation folder, and start run.bat. You may need to adjust the java path if "java" is not on your system path.
 
If this still doesn't work (probably it won't), then try the last desperate step:
 
4. Try to install Protege 3.5, and see if the problem also appears there:
 
Feel free to uninstall it after the test, and please report the result.
 
Tania
 
 
 

From: "Johannes Scharf" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Sent: Tuesday, April 15, 2014 12:58:26 AM
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
 
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
 
_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Display problem with trees in Protege 4.3

Johannes Scharf
In reply to this post by Tania Tudorache
Update: I found the cause of the problem: When I configure Graphviz 2.28 the problem occured again in Protege 4.0 and Protege 4.3 - any hints?
 
Thanks.
 
Gesendet: Dienstag, 15. April 2014 um 11:09 Uhr
Von: "Tania Tudorache" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
This is interesting.
 
Is it just the trees that look weird, or also other things? For example, do the menus look OK?
 
I don't have access to a windows machine at this time, but here are a few things you can try:
 
1. File menu -> Preferences -> press on the Reset preferences button at the bottom of the window.
 
Restart Protege, see how it looks. If it doesn't work, then:
 
2. Delete manually the Java preferences for Protege. See here how: 
 
Hopefully this will do it. If not:
 
3. Try to run Protege using the run.bat file. I assume there is a run.bat in the Protege installation folder. Open a command terminal, cd to the Protege installation folder, and start run.bat. You may need to adjust the java path if "java" is not on your system path.
 
If this still doesn't work (probably it won't), then try the last desperate step:
 
4. Try to install Protege 3.5, and see if the problem also appears there:
 
Feel free to uninstall it after the test, and please report the result.
 
Tania
 
 
 

From: "Johannes Scharf" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Sent: Tuesday, April 15, 2014 12:58:26 AM
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
 
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
 
_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user

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[hidden email]
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Re: Display problem with trees in Protege 4.3

Csongor Nyulas
Administrator
How did you configure Graphviz 2.28?

Csongor

On 04/15/2014 05:58 AM, Johannes Scharf wrote:
Update: I found the cause of the problem: When I configure Graphviz 2.28 the problem occured again in Protege 4.0 and Protege 4.3 - any hints?
 
Thanks.
 
Gesendet: Dienstag, 15. April 2014 um 11:09 Uhr
Von: "Tania Tudorache" [hidden email]
An: "User support for WebProtege and Protege Desktop" [hidden email]
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
This is interesting.
 
Is it just the trees that look weird, or also other things? For example, do the menus look OK?
 
I don't have access to a windows machine at this time, but here are a few things you can try:
 
1. File menu -> Preferences -> press on the Reset preferences button at the bottom of the window.
 
Restart Protege, see how it looks. If it doesn't work, then:
 
2. Delete manually the Java preferences for Protege. See here how: 
 
Hopefully this will do it. If not:
 
3. Try to run Protege using the run.bat file. I assume there is a run.bat in the Protege installation folder. Open a command terminal, cd to the Protege installation folder, and start run.bat. You may need to adjust the java path if "java" is not on your system path.
 
If this still doesn't work (probably it won't), then try the last desperate step:
 
4. Try to install Protege 3.5, and see if the problem also appears there:
 
Feel free to uninstall it after the test, and please report the result.
 
Tania
 
 
 

From: "Johannes Scharf" [hidden email]
To: "User support for WebProtege and Protege Desktop" [hidden email]
Sent: Tuesday, April 15, 2014 12:58:26 AM
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
 
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" [hidden email]
An: "User support for WebProtege and Protege Desktop" [hidden email]
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user

_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
 
_______________________________________________ protege-user mailing list [hidden email] https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
protege-user mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user


_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user
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Re: Display problem with trees in Protege 4.3

Johannes Scharf
I've just set the path under Preferences of Protege to Dot.exe and hit "OK".
I did some further research and found out that not GraphViz seems to cause the weird rendering of the trees but the preferences dialog seems to write a bunch of options into registry after hitting "OK". One of the preferences seems to interfer - I removed all of them except the OWLViz configuration including GraphViz and suddenly Protege 4.0 started rendering the trees again correctly! Moreover GraphViz seems to work as well. I hadn't enough time to try this wiht Protege 4.3 as well.
 
I conclude that the preferences must write some options to the registry which seem to interfer with a component of my system? Never saw such a strange behaviour before....
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 19:46 Uhr
Von: "Csongor Nyulas" <[hidden email]>
An: [hidden email]
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
How did you configure Graphviz 2.28?

Csongor

On 04/15/2014 05:58 AM, Johannes Scharf wrote:
Update: I found the cause of the problem: When I configure Graphviz 2.28 the problem occured again in Protege 4.0 and Protege 4.3 - any hints?
 
Thanks.
 
Gesendet: Dienstag, 15. April 2014 um 11:09 Uhr
Von: "Tania Tudorache" <tudorache@...>
An: "User support for WebProtege and Protege Desktop" <protege-user@...>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
This is interesting.
 
Is it just the trees that look weird, or also other things? For example, do the menus look OK?
 
I don't have access to a windows machine at this time, but here are a few things you can try:
 
1. File menu -> Preferences -> press on the Reset preferences button at the bottom of the window.
 
Restart Protege, see how it looks. If it doesn't work, then:
 
2. Delete manually the Java preferences for Protege. See here how: 
 
Hopefully this will do it. If not:
 
3. Try to run Protege using the run.bat file. I assume there is a run.bat in the Protege installation folder. Open a command terminal, cd to the Protege installation folder, and start run.bat. You may need to adjust the java path if "java" is not on your system path.
 
If this still doesn't work (probably it won't), then try the last desperate step:
 
4. Try to install Protege 3.5, and see if the problem also appears there:
 
Feel free to uninstall it after the test, and please report the result.
 
Tania
 
 
 

From: "Johannes Scharf" <johannes.scharf@...>
To: "User support for WebProtege and Protege Desktop" <protege-user@...>
Sent: Tuesday, April 15, 2014 12:58:26 AM
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
 
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" <vendetti@...>
An: "User support for WebProtege and Protege Desktop" <protege-user@...>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

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Re: Display problem with trees in Protege 4.3

Csongor Nyulas
Administrator
This is really strange, indeed. It must be something particular to your system setup (or the applications installed), because this is the first time this problem is reported over the many years of providing support for Protege.
I would be curious to know if changing any preferences (something not related to Graphviz) once things work normally would also write garbage in your preferences?

It would be great if you could figure out what is going wrong and report back, maybe there is something we can fix in the Protege code.
Unfortunately, we can't do too much to help you debug this issue.

Csongor


On 04/15/2014 11:30 AM, Johannes Scharf wrote:
I've just set the path under Preferences of Protege to Dot.exe and hit "OK".
I did some further research and found out that not GraphViz seems to cause the weird rendering of the trees but the preferences dialog seems to write a bunch of options into registry after hitting "OK". One of the preferences seems to interfer - I removed all of them except the OWLViz configuration including GraphViz and suddenly Protege 4.0 started rendering the trees again correctly! Moreover GraphViz seems to work as well. I hadn't enough time to try this wiht Protege 4.3 as well.
 
I conclude that the preferences must write some options to the registry which seem to interfer with a component of my system? Never saw such a strange behaviour before....
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 19:46 Uhr
Von: "Csongor Nyulas" [hidden email]
An: [hidden email]
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
How did you configure Graphviz 2.28?

Csongor

On 04/15/2014 05:58 AM, Johannes Scharf wrote:
Update: I found the cause of the problem: When I configure Graphviz 2.28 the problem occured again in Protege 4.0 and Protege 4.3 - any hints?
 
Thanks.
 
Gesendet: Dienstag, 15. April 2014 um 11:09 Uhr
Von: "Tania Tudorache" <tudorache@...>
An: "User support for WebProtege and Protege Desktop" <protege-user@...>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
This is interesting.
 
Is it just the trees that look weird, or also other things? For example, do the menus look OK?
 
I don't have access to a windows machine at this time, but here are a few things you can try:
 
1. File menu -> Preferences -> press on the Reset preferences button at the bottom of the window.
 
Restart Protege, see how it looks. If it doesn't work, then:
 
2. Delete manually the Java preferences for Protege. See here how: 
 
Hopefully this will do it. If not:
 
3. Try to run Protege using the run.bat file. I assume there is a run.bat in the Protege installation folder. Open a command terminal, cd to the Protege installation folder, and start run.bat. You may need to adjust the java path if "java" is not on your system path.
 
If this still doesn't work (probably it won't), then try the last desperate step:
 
4. Try to install Protege 3.5, and see if the problem also appears there:
 
Feel free to uninstall it after the test, and please report the result.
 
Tania
 
 
 

From: "Johannes Scharf" <johannes.scharf@...>
To: "User support for WebProtege and Protege Desktop" <protege-user@...>
Sent: Tuesday, April 15, 2014 12:58:26 AM
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
 
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" <vendetti@...>
An: "User support for WebProtege and Protege Desktop" <protege-user@...>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

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Re: Display problem with trees in Protege 4.3

Johannes Scharf
I did some tests with a clean install of Protege 4.0 and the following results:
 
1) Changing the path of GraphViz to a non-existing location and hitting "OK" destroyed the trees again.
 
2) Also just opening the preferences dialog and hitting "OK" without chaning any settings killed the trees again.
 
What's wrong here? I worked with Protege on a Windows XP machine before and never experienced similar problems.
 
Kind regards,
Johannes

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Re: Display problem with trees in Protege 4.3

Tania Tudorache
Protege uses Java preferences to store the different preferences and customizations.

I am not sure how they can get corrupted. If you want to investigate further, it may be that the key/values in the "org.protege.editor.owl.ui.renderer.OWLRendererPreferences" are somehow being corrupted (see below). You can inspect them before and after saving and see what has changed.

It is hard for us to debug this problem, because we can't reproduce it.

I also suggest that you use the latest Protege 4.3, because Protege 4.0 only worked with OWL 1.1, and if I remember well, it can output invalid OWL syntax. Protege 4.3 also contains several bug fixes and improvements, and is OWL 2.0 compliant, unlike Protege 4.0.

Tania






On 04/15/2014 01:33 PM, Johannes Scharf wrote:
I did some tests with a clean install of Protege 4.0 and the following results:
 
1) Changing the path of GraphViz to a non-existing location and hitting "OK" destroyed the trees again.
 
2) Also just opening the preferences dialog and hitting "OK" without chaning any settings killed the trees again.
 
What's wrong here? I worked with Protege on a Windows XP machine before and never experienced similar problems.
 
Kind regards,
Johannes


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Re: Display problem with trees in Protege 4.3

Csongor Nyulas
Administrator
In reply to this post by Altaf
Dear Altaf,

The problem is that you mixed up the domain and range of the isToppingOf property in your ontology. It should have domain PizzaTopping, and range Pizza not the other way around. In other words:
PizzaTopping isToppingOf Pizza.
You can "debug" the problems in your ontology if you click on the question mark icon on right of a given axiom, which is "suspicious" or unexpected. For example, if you would select MargheritaPizza that is classified under owl:Nothing in the inferred class hierarchy, and you would click on the question mark icon on the inferred "Equivalent to" owl:Nothing line, you would see several explanation that would involve the axiom "hasTopping inverse of isToppingOf" and an axiom about the range or domain of either hasTopping or isToppingOf.

Note: If you have other questions in the future, please do not post your question as a reply to an email thread that is on a different topic, because it gets very difficult to follow the different issues if they are not labeled appropriately. Obviously your question was not related at all to Johannes' "Display problem with trees in Protege 4.3" thread.

Cheers,
Csongor

On 04/15/2014 02:15 AM, Altaf wrote:
Respected Madam / sir

Hoping that you will be fine.

I have tried to install Protege 4.3 64 bit and run the example on Ubuntu 13.10 64 bit. There was no error like the null pointer as I am experiencing in windows 7. However when I put the object property restriction on MargheritaPizza "hasTopping only (MozzerallaTopping or TomatoTopping)" there is no problem. However as mentioned in the "A Practical Guide To Building OWL Ontologies Using Protege 4 and CO-ODE Tools Edition 1.3" when I put the restriction on MargheritaPizza "hasTopping some MozzerallaTopping" then the reasoner put MargheritaPizza under Nothing. I am unable to understand this problem and could not resolve the problem. Please help me in this regards where I am wrong I am send the example I am working on as attachment.

Best Regards


On Tue, Apr 15, 2014 at 9:58 AM, Johannes Scharf <[hidden email]> wrote:
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes



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Re: Display problem with trees in Protege 4.3

lesego phoshane
In reply to this post by Johannes Scharf

Hi,

Pls remove me from your mail list. I don't use protege anymore.

Thanx

On 15 Apr 2014 04:11, "Johannes Scharf" <[hidden email]> wrote:
Suggestion 1) did it - I just reset the preferenced in Protege 4.3 and it worked like a charm. Moreover after the reset Protege 4.0 started to work again as well - do they share the same ressources in registry?
 
Thank you very much!
Kind regards,
 
Johannes
 
 
 
Gesendet: Dienstag, 15. April 2014 um 11:09 Uhr
Von: "Tania Tudorache" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
This is interesting.
 
Is it just the trees that look weird, or also other things? For example, do the menus look OK?
 
I don't have access to a windows machine at this time, but here are a few things you can try:
 
1. File menu -> Preferences -> press on the Reset preferences button at the bottom of the window.
 
Restart Protege, see how it looks. If it doesn't work, then:
 
2. Delete manually the Java preferences for Protege. See here how: 
 
Hopefully this will do it. If not:
 
3. Try to run Protege using the run.bat file. I assume there is a run.bat in the Protege installation folder. Open a command terminal, cd to the Protege installation folder, and start run.bat. You may need to adjust the java path if "java" is not on your system path.
 
If this still doesn't work (probably it won't), then try the last desperate step:
 
4. Try to install Protege 3.5, and see if the problem also appears there:
 
Feel free to uninstall it after the test, and please report the result.
 
Tania
 
 
 

From: "Johannes Scharf" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Sent: Tuesday, April 15, 2014 12:58:26 AM
Subject: Re: [protege-user] Display problem with trees in Protege 4.3
 
Hello!
 
I've already tried using the bundled Java that ships with Protege - same results.
 
In the meantime I uninstalled all of my Java version on my machine and installed the latest JDK 1.7.0_51. Unfortunately that hasn't changed anything.
 
However I concluded that this is NOT a problem with Java. As I already mentioned I've observed the same problem running with Java 1.6. In fact if you look closely the NoSuchMethodException points at some missing method of a Java class from Protege (e.g. NewAction) itself and NOT Swing.
Moreover all my other Java programs run fine on the same machine... What's really strange is that the error appears in Protege 4.0 and 4.3. I've already tried to use another Look and Feel inside Protege - I thought the Plastic LaF could be the problem...
 
Any further ideas?
Thanks!
 
Kind regards,
Johannes
 
Gesendet: Dienstag, 15. April 2014 um 00:12 Uhr
Von: "Jennifer Vendetti" <[hidden email]>
An: "User support for WebProtege and Protege Desktop" <[hidden email]>
Betreff: Re: [protege-user] Display problem with trees in Protege 4.3
On 4/14/2014 12:14 PM, Johannes Scharf wrote:
 
Of course - I've switched logging to DEBUG level and attached the file.

Thank you for sending the log file.  I noticed a lot of java.lang.NoSuchMethodException error messages for methods from the javax.swing package, e.g.:

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting a menu itemjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuItem(javax.swing.JMenuItem)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

DEBUG Action org.protege.editor.core.ui.action.NewAction@f2a691 is not requesting its parentjava.lang.NoSuchMethodException: org.protege.editor.core.ui.action.NewAction.setMenuParent(javax.swing.JComponent)  org.protege.editor.core.ui.menu.MenuBuilder[FelixDispatchQueue]

I'm wondering if there's something wrong with your Java installation.  Could you try installing a version of Protege 4.3 with a VM already bundled?  For example, go to the Protege website Products page (http://protege.stanford.edu/products.php#desktop-protege) and click the Download for Windows button.  In the resulting download dialog, choose an installer file marked with the text "(with VM)", e.g., "Protege Desktop for Windows 64bit (with Java VM)", or "Protege Desktop for Windows (with Java VM)".  During the installation process, make sure to choose "Use the Java VM installed with this application":



When you run Protege this way, you should see in the console that it uses Java 6:



Do you still have the same display issues when you run Protege this way?

Alternatively, you could try reinstalling Java 7.  As I mentioned previously, I can run Protege w/out display issues with the same version of Java 7 that you have installed:


 
Btw... Protege 4.3 needs to startup about 5 (!) minutes on my i5 quad-core machine.... Protege 4.0 starts up in 2 secs....

There are a number of error messages in the log from Protege's auto-update functionality complaining about connectivity issues:

java.io.IOException: Server returned HTTP response code: 503 for URL: http://sourceforge.net/p/owllink-owlapi/code/
    at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1626)

DEBUG Examining node http://smi-protege/repos/protege/protege4/plugins/org.protege.osgi.jdbc/trunk/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
java.net.UnknownHostException: smi-protege

DEBUG Examining node https://raw.githubusercontent.com/protegeproject/dlquery/master/etc/update.properties  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
DEBUG Cannot open remote plugin file/registry  org.protege.editor.core.update.PluginRegistryImpl$Calculator[Auto-update]
javax.net.ssl.SSLProtocolException: handshake alert:  unrecognized_name

I'm able to hit all of these URLs w/out issue.  Try going to File | Preferences... | Plugins, and uncheck the option to "Automatically check for plugins at start up", then restart Protege.  Do you see the same performance issue?

Jennifer

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Re: Display problem with trees in Protege 4.3

Johannes Scharf
In reply to this post by Tania Tudorache
Hello!
 
Unfoftunately I have to stay with Protege 4.0 for the moment because of an old plugin with doesn't run with Protege 4.3.
 
The good news are that I think I've isolated the problem. The "illegal" preference belongs to the registry key "HKEY_CURRENT_USER\Software\JavaSoft\Prefs\/P/R/O/T/E/G/E_/P/R/E/F/E/R/E/N/C/E/S\application_preferences\org.protege.editor.owl.ui.renderer./O/W/L/Renderer/Preferences" and is named "/F/O/N/T_/N/A/M/E" (see attachment).
 
It contains value "18th/Century" - after deleting this single entry Protege 4.0 renders the trees correctly. I guess Protege 4.3 would work as well - I will check if I have some time left.
 
I still can't get it why this entries seems to interfer with my system? Maybe the font isn't installed? On my machine only "Century Standard", "Century Gothic" and "18thCentury" (note the slightly different spelling compared to the registry entry value) seem to be available.
 
Any ideas? I bet the solution of that mystery is just around the corner.. ;)
 
Kind regards,
Johannes

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Re: Display problem with trees in Protege 4.3

Tania Tudorache
Yes, that was my thought from the beginning that it was a problem with the font. It happens because you use Protege 4.0, which used to allow users to set the font in the UI. We removed that feature in Protege 4.3 because it caused to many problems.

So, Protege 4.0 writes the "bad" font to the registry, and Protege 4.3 seems to still read it, although we need to check if that is still needed. I would think that it is not. The method for setting the font in Protege 4 has been deprecated for some while now.

At least now we understand the weird behavior. There have been numerous fixes in Protege 4.3 wrt to Protege 4.0, and the fonts was one of them, so, we won't fix this issue.

I will add an issue in our tracker, to see if reading the fonts from the registry is necessary, and ideally, take that out.

Thanks for the report!
Tania

On 04/16/2014 12:30 AM, Johannes Scharf wrote:
Hello!
 
Unfoftunately I have to stay with Protege 4.0 for the moment because of an old plugin with doesn't run with Protege 4.3.
 
The good news are that I think I've isolated the problem. The "illegal" preference belongs to the registry key "HKEY_CURRENT_USER\Software\JavaSoft\Prefs\/P/R/O/T/E/G/E_/P/R/E/F/E/R/E/N/C/E/S\application_preferences\org.protege.editor.owl.ui.renderer./O/W/L/Renderer/Preferences" and is named "/F/O/N/T_/N/A/M/E" (see attachment).
 
It contains value "18th/Century" - after deleting this single entry Protege 4.0 renders the trees correctly. I guess Protege 4.3 would work as well - I will check if I have some time left.
 
I still can't get it why this entries seems to interfer with my system? Maybe the font isn't installed? On my machine only "Century Standard", "Century Gothic" and "18thCentury" (note the slightly different spelling compared to the registry entry value) seem to be available.
 
Any ideas? I bet the solution of that mystery is just around the corner.. ;)
 
Kind regards,
Johannes


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