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Reasoner not Working

Michael DeBellis-2
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"

I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 

This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 

Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.

There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 

The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 

I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 

Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 

The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   

ReasonerProb1.PNG

ReasonerProb2.PNG

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ProtegeLog-12-13-19.txt (7K) Download Attachment
FrequencyExample2.owl (51K) Download Attachment
DOSLog-12-13-19.txt (16K) Download Attachment
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Re: Reasoner not Working

Lorenz Buehmann

Hi Michael,

Linux user here, openjdk version "1.8.0_222"

On 13.12.19 21:46, Michael DeBellis wrote:
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"

I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 

This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined.
This is also the case for me.

Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed.
for the individual "Always" 4 object property assertions for "isMoreFrequentThan" are inferred and shown.
Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either.

Here I can see a difference between Pellet and HermiT reasoner:

Pellet: Michael suggestArtist REM, Michael suggestArtist Mahler

HermiT: Michael suggestArtist REM

So one inferred axiom is missing, which indicates a bug in one of the reasoner.

The explanation for "Michael suggestArtist Mahler" with Pellet is

Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either.
hasPreference values are inferred for me
As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.

There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 

The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 

I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 

Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 

The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   

ReasonerProb1.PNG

ReasonerProb2.PNG

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Re: Reasoner not Working

Igor Toujilov-2
In reply to this post by Michael DeBellis-2

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Michael DeBellis-2
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."

Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 

Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.

Two questions:

1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 

2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 

I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 

Thanks for the help,
Michael

On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: Reasoner not Working

Igor Toujilov-2

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Michael DeBellis-2
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 

1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 

Cheers,
Michael

On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Igor Toujilov-2

Hi Michael,

The answers are here.

1-2. Do not delete the common Java installation as it is required for Eclipse and other applications.

3. Just deleting the Protégé folder should be fine.

4. I would stop automatic updates, but be able to decide whether to run the new update or skip it depending on the situation. Do not allow an update just for the sake of update. Run an update if you really need it for your work. There is an exception: security updates should be always applied straight away.

Good luck!

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 12:15 AM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 
 
1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 
 
Cheers,
Michael
 
On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Igor Toujilov-2

Michael,

This is an additional observation. Your Protégé log tells it’s running JVM 1.8.0_121-b13, which is the embedded Java environment, the same as in my Protégé installation. This is different from what you see in your Windows Java: Version 8 Update 231. (build 1.8.0_231-b11). This means you have the Protégé installation with the embedded Java, and this making me scratching my head: How on earth the Windows update managed to break your Protégé?

My hypothesis is: perhaps Protégé still uses some additional dependencies, which are outside of the embedded Java environment.

Let us ask the Protégé developers.

 

Cheers,

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 11:33 AM
From: "Igor Toujilov" <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Reasoner not Working

Hi Michael,

The answers are here.

1-2. Do not delete the common Java installation as it is required for Eclipse and other applications.

3. Just deleting the Protégé folder should be fine.

4. I would stop automatic updates, but be able to decide whether to run the new update or skip it depending on the situation. Do not allow an update just for the sake of update. Run an update if you really need it for your work. There is an exception: security updates should be always applied straight away.

Good luck!

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 12:15 AM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 
 
1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 
 
Cheers,
Michael
 
On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Michael DeBellis-2
Igor, thanks for the help. I finally got back to this and I tried uninstalling and re-installing Protege and unfortunately I still have the same results. Here is the log from when I start Protege from this new fresh installation:

   INFO  13:17:00  ------------------------------------ Protege -----------------------------------
   INFO  13:17:00  Protege Desktop
   INFO  13:17:00  Version 5.5.0, Build
   INFO  13:17:00  
   INFO  13:17:00  
   INFO  13:17:00  ----------------------------------- Platform -----------------------------------
   INFO  13:17:00  Java: JVM 1.8.0_121-b13  Memory: 466M
   INFO  13:17:00  Language: en, Country: US
   INFO  13:17:00  Framework: Apache Software Foundation (1.8)
   INFO  13:17:00  OS: windows10 (10.0)
   INFO  13:17:00  Processor: x86-64

That seems to not be the embedded version (not what I want) correct? Just to be clear I went to this page: https://protege.stanford.edu/products.php#desktop-protege  and clicked on the big grey box that says:  

"Dowload for Windows
Protege Desktop v.5.5.0"

Beneath it there is text that says: 
"Download platform independent version (requires a Java Runtime Environment)" 

I didn't click on that. 

All I can think of to do now is to uninstall Java and then reinstall Protege and see if that works. I'm not worried about not being able to run Eclipse. I don't have any serious work that I would lose anyway, I could always uninstall it and get Protege working and then install Java and see if Eclipse still runs. If anyone has alternative ideas please let me know. BTW, I mentioned this in an earlier message but I also tried running the old version of Protege: Protege-5.2.0-win  and that had the same erroneous behavior (and it worked fine in the past). I didn't delete that when I installed the new version. Perhaps I'll try that first, delete the version I just installed and then the old one and try re-installing the new one again. I doubt it will make a difference but it will just take a few minutes and since the old version isn't working anyway, I have nothing to lose. If that doesn't work I think I'll try uninstalling Java and then installing the bundled version. Or I could try installing the platform independent version and just see if it picks up the JRE from my version of Java and perhaps that will work.

One more thing (I'm just grasping at straws here) I have a folder on my desktop called Protege and I put each new release into that folder where the zip file creates a directory structure under that starting with  Protege-5.5.0-win or  Protege-5.2.0-win  I'm assuming that where I put the Protege application doesn't make a difference, let me know if that is incorrect. 

Any additional help would be greatly appreciated. 

Cheers,
Michael

On Tue, Dec 17, 2019 at 8:40 AM Igor Toujilov <[hidden email]> wrote:

Michael,

This is an additional observation. Your Protégé log tells it’s running JVM 1.8.0_121-b13, which is the embedded Java environment, the same as in my Protégé installation. This is different from what you see in your Windows Java: Version 8 Update 231. (build 1.8.0_231-b11). This means you have the Protégé installation with the embedded Java, and this making me scratching my head: How on earth the Windows update managed to break your Protégé?

My hypothesis is: perhaps Protégé still uses some additional dependencies, which are outside of the embedded Java environment.

Let us ask the Protégé developers.

 

Cheers,

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 11:33 AM
From: "Igor Toujilov" <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Reasoner not Working

Hi Michael,

The answers are here.

1-2. Do not delete the common Java installation as it is required for Eclipse and other applications.

3. Just deleting the Protégé folder should be fine.

4. I would stop automatic updates, but be able to decide whether to run the new update or skip it depending on the situation. Do not allow an update just for the sake of update. Run an update if you really need it for your work. There is an exception: security updates should be always applied straight away.

Good luck!

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 12:15 AM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 
 
1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 
 
Cheers,
Michael
 
On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Igor Toujilov-2

Hi Michael,

Answering your question: “That seems to not be the embedded version (not what I want) correct?”.

You have installed the Protégé version with the embedded Java, which I recommend. I think Protégé developers recommend it as well, as it is shown as a prominent button on the web-page.

I suggest leaving your Protégé installations along (do not delete them). Uninstall your Windows Java, if it is possible, and try running Protégé.

You can install as many Protégé versions as you want, and they should work independently. You can try the platform independent version as well.

Regards,

Igor

 
 
Sent: Friday, December 20, 2019 at 9:44 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor, thanks for the help. I finally got back to this and I tried uninstalling and re-installing Protege and unfortunately I still have the same results. Here is the log from when I start Protege from this new fresh installation:
 
   INFO  13:17:00  ------------------------------------ Protege -----------------------------------
   INFO  13:17:00  Protege Desktop
   INFO  13:17:00  Version 5.5.0, Build
   INFO  13:17:00  
   INFO  13:17:00  
   INFO  13:17:00  ----------------------------------- Platform -----------------------------------
   INFO  13:17:00  Java: JVM 1.8.0_121-b13  Memory: 466M
   INFO  13:17:00  Language: en, Country: US
   INFO  13:17:00  Framework: Apache Software Foundation (1.8)
   INFO  13:17:00  OS: windows10 (10.0)
   INFO  13:17:00  Processor: x86-64
 
That seems to not be the embedded version (not what I want) correct? Just to be clear I went to this page: https://protege.stanford.edu/products.php#desktop-protege  and clicked on the big grey box that says:  
 
"Dowload for Windows
Protege Desktop v.5.5.0"
 
Beneath it there is text that says: 
"Download platform independent version (requires a Java Runtime Environment)" 
 
I didn't click on that. 
 
All I can think of to do now is to uninstall Java and then reinstall Protege and see if that works. I'm not worried about not being able to run Eclipse. I don't have any serious work that I would lose anyway, I could always uninstall it and get Protege working and then install Java and see if Eclipse still runs. If anyone has alternative ideas please let me know. BTW, I mentioned this in an earlier message but I also tried running the old version of Protege: Protege-5.2.0-win  and that had the same erroneous behavior (and it worked fine in the past). I didn't delete that when I installed the new version. Perhaps I'll try that first, delete the version I just installed and then the old one and try re-installing the new one again. I doubt it will make a difference but it will just take a few minutes and since the old version isn't working anyway, I have nothing to lose. If that doesn't work I think I'll try uninstalling Java and then installing the bundled version. Or I could try installing the platform independent version and just see if it picks up the JRE from my version of Java and perhaps that will work.
 
One more thing (I'm just grasping at straws here) I have a folder on my desktop called Protege and I put each new release into that folder where the zip file creates a directory structure under that starting with  Protege-5.5.0-win or  Protege-5.2.0-win  I'm assuming that where I put the Protege application doesn't make a difference, let me know if that is incorrect. 
 
Any additional help would be greatly appreciated. 
 
Cheers,
Michael
 
On Tue, Dec 17, 2019 at 8:40 AM Igor Toujilov <[hidden email]> wrote:

Michael,

This is an additional observation. Your Protégé log tells it’s running JVM 1.8.0_121-b13, which is the embedded Java environment, the same as in my Protégé installation. This is different from what you see in your Windows Java: Version 8 Update 231. (build 1.8.0_231-b11). This means you have the Protégé installation with the embedded Java, and this making me scratching my head: How on earth the Windows update managed to break your Protégé?

My hypothesis is: perhaps Protégé still uses some additional dependencies, which are outside of the embedded Java environment.

Let us ask the Protégé developers.

 

Cheers,

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 11:33 AM
From: "Igor Toujilov" <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Reasoner not Working

Hi Michael,

The answers are here.

1-2. Do not delete the common Java installation as it is required for Eclipse and other applications.

3. Just deleting the Protégé folder should be fine.

4. I would stop automatic updates, but be able to decide whether to run the new update or skip it depending on the situation. Do not allow an update just for the sake of update. Run an update if you really need it for your work. There is an exception: security updates should be always applied straight away.

Good luck!

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 12:15 AM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 
 
1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 
 
Cheers,
Michael
 
On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Michael DeBellis-2
Igor, Unfortunately I already tried uninstalling all my Protege installations and then re-installing the most recent one (the recommended one) before I read your message. I did that without removing the version of Java I have installed, I was hoping I could avoid that so I wouldn't have problems with Eclipse and the Java code I've written so far. 

But it still didn't work. So then I tried uninstalling the latest one and installing the platform independent version. It ran so I think it was seeing my version of Java but it still had the same problem where the Reasoner was not doing basic inferences on properties. I thought I would try that first because that way I wouldn't have to worry about problems with Eclipse. I'm going to try uninstalling Java today and then re-installing the bundled version, hopefully that will work. I haven't had great luck with this Windows machine. One other time something (not related to Protege) got corrupted and it interfered with the whole system in a serious way and the only advise I could get from the support people was to reset the desktop to the factory settings and then re-install all my applications. That's my worst case scenario. Hopefully uninstalling Java will work but I do want to go back and use Eclipse and Java for development at some point. But first I just want to get Protege working again. Thanks to all for the help, as always any additional suggestions would be welcome. 

Cheers,
Michael

On Sat, Dec 21, 2019 at 3:12 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

Answering your question: “That seems to not be the embedded version (not what I want) correct?”.

You have installed the Protégé version with the embedded Java, which I recommend. I think Protégé developers recommend it as well, as it is shown as a prominent button on the web-page.

I suggest leaving your Protégé installations along (do not delete them). Uninstall your Windows Java, if it is possible, and try running Protégé.

You can install as many Protégé versions as you want, and they should work independently. You can try the platform independent version as well.

Regards,

Igor

 
 
Sent: Friday, December 20, 2019 at 9:44 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor, thanks for the help. I finally got back to this and I tried uninstalling and re-installing Protege and unfortunately I still have the same results. Here is the log from when I start Protege from this new fresh installation:
 
   INFO  13:17:00  ------------------------------------ Protege -----------------------------------
   INFO  13:17:00  Protege Desktop
   INFO  13:17:00  Version 5.5.0, Build
   INFO  13:17:00  
   INFO  13:17:00  
   INFO  13:17:00  ----------------------------------- Platform -----------------------------------
   INFO  13:17:00  Java: JVM 1.8.0_121-b13  Memory: 466M
   INFO  13:17:00  Language: en, Country: US
   INFO  13:17:00  Framework: Apache Software Foundation (1.8)
   INFO  13:17:00  OS: windows10 (10.0)
   INFO  13:17:00  Processor: x86-64
 
That seems to not be the embedded version (not what I want) correct? Just to be clear I went to this page: https://protege.stanford.edu/products.php#desktop-protege  and clicked on the big grey box that says:  
 
"Dowload for Windows
Protege Desktop v.5.5.0"
 
Beneath it there is text that says: 
"Download platform independent version (requires a Java Runtime Environment)" 
 
I didn't click on that. 
 
All I can think of to do now is to uninstall Java and then reinstall Protege and see if that works. I'm not worried about not being able to run Eclipse. I don't have any serious work that I would lose anyway, I could always uninstall it and get Protege working and then install Java and see if Eclipse still runs. If anyone has alternative ideas please let me know. BTW, I mentioned this in an earlier message but I also tried running the old version of Protege: Protege-5.2.0-win  and that had the same erroneous behavior (and it worked fine in the past). I didn't delete that when I installed the new version. Perhaps I'll try that first, delete the version I just installed and then the old one and try re-installing the new one again. I doubt it will make a difference but it will just take a few minutes and since the old version isn't working anyway, I have nothing to lose. If that doesn't work I think I'll try uninstalling Java and then installing the bundled version. Or I could try installing the platform independent version and just see if it picks up the JRE from my version of Java and perhaps that will work.
 
One more thing (I'm just grasping at straws here) I have a folder on my desktop called Protege and I put each new release into that folder where the zip file creates a directory structure under that starting with  Protege-5.5.0-win or  Protege-5.2.0-win  I'm assuming that where I put the Protege application doesn't make a difference, let me know if that is incorrect. 
 
Any additional help would be greatly appreciated. 
 
Cheers,
Michael
 
On Tue, Dec 17, 2019 at 8:40 AM Igor Toujilov <[hidden email]> wrote:

Michael,

This is an additional observation. Your Protégé log tells it’s running JVM 1.8.0_121-b13, which is the embedded Java environment, the same as in my Protégé installation. This is different from what you see in your Windows Java: Version 8 Update 231. (build 1.8.0_231-b11). This means you have the Protégé installation with the embedded Java, and this making me scratching my head: How on earth the Windows update managed to break your Protégé?

My hypothesis is: perhaps Protégé still uses some additional dependencies, which are outside of the embedded Java environment.

Let us ask the Protégé developers.

 

Cheers,

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 11:33 AM
From: "Igor Toujilov" <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Reasoner not Working

Hi Michael,

The answers are here.

1-2. Do not delete the common Java installation as it is required for Eclipse and other applications.

3. Just deleting the Protégé folder should be fine.

4. I would stop automatic updates, but be able to decide whether to run the new update or skip it depending on the situation. Do not allow an update just for the sake of update. Run an update if you really need it for your work. There is an exception: security updates should be always applied straight away.

Good luck!

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 12:15 AM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 
 
1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 
 
Cheers,
Michael
 
On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Igor Toujilov-2

Michael,

Another thought has come to my mind. During Eclipse installation, the common Java path might be configured to point to the common Java environment. This might redirect some Java components inside the Protégé Java environment to load some libraries from the common Java environment, which is not good for Protégé. When you uninstall the common Java environment, and try running Protégé, it might shine a light on this if this is the case.

 

Regards,

Igor

Sent: Sunday, December 22, 2019 at 7:21 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor, Unfortunately I already tried uninstalling all my Protege installations and then re-installing the most recent one (the recommended one) before I read your message. I did that without removing the version of Java I have installed, I was hoping I could avoid that so I wouldn't have problems with Eclipse and the Java code I've written so far. 
 
But it still didn't work. So then I tried uninstalling the latest one and installing the platform independent version. It ran so I think it was seeing my version of Java but it still had the same problem where the Reasoner was not doing basic inferences on properties. I thought I would try that first because that way I wouldn't have to worry about problems with Eclipse. I'm going to try uninstalling Java today and then re-installing the bundled version, hopefully that will work. I haven't had great luck with this Windows machine. One other time something (not related to Protege) got corrupted and it interfered with the whole system in a serious way and the only advise I could get from the support people was to reset the desktop to the factory settings and then re-install all my applications. That's my worst case scenario. Hopefully uninstalling Java will work but I do want to go back and use Eclipse and Java for development at some point. But first I just want to get Protege working again. Thanks to all for the help, as always any additional suggestions would be welcome. 
 
Cheers,
Michael
 
On Sat, Dec 21, 2019 at 3:12 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

Answering your question: “That seems to not be the embedded version (not what I want) correct?”.

You have installed the Protégé version with the embedded Java, which I recommend. I think Protégé developers recommend it as well, as it is shown as a prominent button on the web-page.

I suggest leaving your Protégé installations along (do not delete them). Uninstall your Windows Java, if it is possible, and try running Protégé.

You can install as many Protégé versions as you want, and they should work independently. You can try the platform independent version as well.

Regards,

Igor

 
 
Sent: Friday, December 20, 2019 at 9:44 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor, thanks for the help. I finally got back to this and I tried uninstalling and re-installing Protege and unfortunately I still have the same results. Here is the log from when I start Protege from this new fresh installation:
 
   INFO  13:17:00  ------------------------------------ Protege -----------------------------------
   INFO  13:17:00  Protege Desktop
   INFO  13:17:00  Version 5.5.0, Build
   INFO  13:17:00  
   INFO  13:17:00  
   INFO  13:17:00  ----------------------------------- Platform -----------------------------------
   INFO  13:17:00  Java: JVM 1.8.0_121-b13  Memory: 466M
   INFO  13:17:00  Language: en, Country: US
   INFO  13:17:00  Framework: Apache Software Foundation (1.8)
   INFO  13:17:00  OS: windows10 (10.0)
   INFO  13:17:00  Processor: x86-64
 
That seems to not be the embedded version (not what I want) correct? Just to be clear I went to this page: https://protege.stanford.edu/products.php#desktop-protege  and clicked on the big grey box that says:  
 
"Dowload for Windows
Protege Desktop v.5.5.0"
 
Beneath it there is text that says: 
"Download platform independent version (requires a Java Runtime Environment)" 
 
I didn't click on that. 
 
All I can think of to do now is to uninstall Java and then reinstall Protege and see if that works. I'm not worried about not being able to run Eclipse. I don't have any serious work that I would lose anyway, I could always uninstall it and get Protege working and then install Java and see if Eclipse still runs. If anyone has alternative ideas please let me know. BTW, I mentioned this in an earlier message but I also tried running the old version of Protege: Protege-5.2.0-win  and that had the same erroneous behavior (and it worked fine in the past). I didn't delete that when I installed the new version. Perhaps I'll try that first, delete the version I just installed and then the old one and try re-installing the new one again. I doubt it will make a difference but it will just take a few minutes and since the old version isn't working anyway, I have nothing to lose. If that doesn't work I think I'll try uninstalling Java and then installing the bundled version. Or I could try installing the platform independent version and just see if it picks up the JRE from my version of Java and perhaps that will work.
 
One more thing (I'm just grasping at straws here) I have a folder on my desktop called Protege and I put each new release into that folder where the zip file creates a directory structure under that starting with  Protege-5.5.0-win or  Protege-5.2.0-win  I'm assuming that where I put the Protege application doesn't make a difference, let me know if that is incorrect. 
 
Any additional help would be greatly appreciated. 
 
Cheers,
Michael
 
On Tue, Dec 17, 2019 at 8:40 AM Igor Toujilov <[hidden email]> wrote:

Michael,

This is an additional observation. Your Protégé log tells it’s running JVM 1.8.0_121-b13, which is the embedded Java environment, the same as in my Protégé installation. This is different from what you see in your Windows Java: Version 8 Update 231. (build 1.8.0_231-b11). This means you have the Protégé installation with the embedded Java, and this making me scratching my head: How on earth the Windows update managed to break your Protégé?

My hypothesis is: perhaps Protégé still uses some additional dependencies, which are outside of the embedded Java environment.

Let us ask the Protégé developers.

 

Cheers,

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 11:33 AM
From: "Igor Toujilov" <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Reasoner not Working

Hi Michael,

The answers are here.

1-2. Do not delete the common Java installation as it is required for Eclipse and other applications.

3. Just deleting the Protégé folder should be fine.

4. I would stop automatic updates, but be able to decide whether to run the new update or skip it depending on the situation. Do not allow an update just for the sake of update. Run an update if you really need it for your work. There is an exception: security updates should be always applied straight away.

Good luck!

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 12:15 AM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 
 
1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 
 
Cheers,
Michael
 
On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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Re: Reasoner not Working

Michael DeBellis-2
Thanks Igor. Good news! Protege is working again! I uninstalled Java and then re-installed the bundled version and it works now. If you have any additional ideas on things I could do to understand what went wrong (e.g., check path variables in DOS or in initialization files) please let me know. Are there any guidelines for how I should set (or not set) paths if I re-install Java? Are there any guidelines in general for people who want to use Eclipse and Protege on the same machine? My understanding is that Eclipse needs its own version of Java and can't just use the same version that comes bundled with Protege but I could be wrong about that, is that the case?

Thanks again to you and everyone who helped me to get it working again. 

Cheers,
Michael

On Sun, Dec 22, 2019 at 3:20 PM Igor Toujilov <[hidden email]> wrote:

Michael,

Another thought has come to my mind. During Eclipse installation, the common Java path might be configured to point to the common Java environment. This might redirect some Java components inside the Protégé Java environment to load some libraries from the common Java environment, which is not good for Protégé. When you uninstall the common Java environment, and try running Protégé, it might shine a light on this if this is the case.

 

Regards,

Igor

Sent: Sunday, December 22, 2019 at 7:21 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor, Unfortunately I already tried uninstalling all my Protege installations and then re-installing the most recent one (the recommended one) before I read your message. I did that without removing the version of Java I have installed, I was hoping I could avoid that so I wouldn't have problems with Eclipse and the Java code I've written so far. 
 
But it still didn't work. So then I tried uninstalling the latest one and installing the platform independent version. It ran so I think it was seeing my version of Java but it still had the same problem where the Reasoner was not doing basic inferences on properties. I thought I would try that first because that way I wouldn't have to worry about problems with Eclipse. I'm going to try uninstalling Java today and then re-installing the bundled version, hopefully that will work. I haven't had great luck with this Windows machine. One other time something (not related to Protege) got corrupted and it interfered with the whole system in a serious way and the only advise I could get from the support people was to reset the desktop to the factory settings and then re-install all my applications. That's my worst case scenario. Hopefully uninstalling Java will work but I do want to go back and use Eclipse and Java for development at some point. But first I just want to get Protege working again. Thanks to all for the help, as always any additional suggestions would be welcome. 
 
Cheers,
Michael
 
On Sat, Dec 21, 2019 at 3:12 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

Answering your question: “That seems to not be the embedded version (not what I want) correct?”.

You have installed the Protégé version with the embedded Java, which I recommend. I think Protégé developers recommend it as well, as it is shown as a prominent button on the web-page.

I suggest leaving your Protégé installations along (do not delete them). Uninstall your Windows Java, if it is possible, and try running Protégé.

You can install as many Protégé versions as you want, and they should work independently. You can try the platform independent version as well.

Regards,

Igor

 
 
Sent: Friday, December 20, 2019 at 9:44 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor, thanks for the help. I finally got back to this and I tried uninstalling and re-installing Protege and unfortunately I still have the same results. Here is the log from when I start Protege from this new fresh installation:
 
   INFO  13:17:00  ------------------------------------ Protege -----------------------------------
   INFO  13:17:00  Protege Desktop
   INFO  13:17:00  Version 5.5.0, Build
   INFO  13:17:00  
   INFO  13:17:00  
   INFO  13:17:00  ----------------------------------- Platform -----------------------------------
   INFO  13:17:00  Java: JVM 1.8.0_121-b13  Memory: 466M
   INFO  13:17:00  Language: en, Country: US
   INFO  13:17:00  Framework: Apache Software Foundation (1.8)
   INFO  13:17:00  OS: windows10 (10.0)
   INFO  13:17:00  Processor: x86-64
 
That seems to not be the embedded version (not what I want) correct? Just to be clear I went to this page: https://protege.stanford.edu/products.php#desktop-protege  and clicked on the big grey box that says:  
 
"Dowload for Windows
Protege Desktop v.5.5.0"
 
Beneath it there is text that says: 
"Download platform independent version (requires a Java Runtime Environment)" 
 
I didn't click on that. 
 
All I can think of to do now is to uninstall Java and then reinstall Protege and see if that works. I'm not worried about not being able to run Eclipse. I don't have any serious work that I would lose anyway, I could always uninstall it and get Protege working and then install Java and see if Eclipse still runs. If anyone has alternative ideas please let me know. BTW, I mentioned this in an earlier message but I also tried running the old version of Protege: Protege-5.2.0-win  and that had the same erroneous behavior (and it worked fine in the past). I didn't delete that when I installed the new version. Perhaps I'll try that first, delete the version I just installed and then the old one and try re-installing the new one again. I doubt it will make a difference but it will just take a few minutes and since the old version isn't working anyway, I have nothing to lose. If that doesn't work I think I'll try uninstalling Java and then installing the bundled version. Or I could try installing the platform independent version and just see if it picks up the JRE from my version of Java and perhaps that will work.
 
One more thing (I'm just grasping at straws here) I have a folder on my desktop called Protege and I put each new release into that folder where the zip file creates a directory structure under that starting with  Protege-5.5.0-win or  Protege-5.2.0-win  I'm assuming that where I put the Protege application doesn't make a difference, let me know if that is incorrect. 
 
Any additional help would be greatly appreciated. 
 
Cheers,
Michael
 
On Tue, Dec 17, 2019 at 8:40 AM Igor Toujilov <[hidden email]> wrote:

Michael,

This is an additional observation. Your Protégé log tells it’s running JVM 1.8.0_121-b13, which is the embedded Java environment, the same as in my Protégé installation. This is different from what you see in your Windows Java: Version 8 Update 231. (build 1.8.0_231-b11). This means you have the Protégé installation with the embedded Java, and this making me scratching my head: How on earth the Windows update managed to break your Protégé?

My hypothesis is: perhaps Protégé still uses some additional dependencies, which are outside of the embedded Java environment.

Let us ask the Protégé developers.

 

Cheers,

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 11:33 AM
From: "Igor Toujilov" <[hidden email]>
To: [hidden email]
Subject: Re: [protege-user] Reasoner not Working

Hi Michael,

The answers are here.

1-2. Do not delete the common Java installation as it is required for Eclipse and other applications.

3. Just deleting the Protégé folder should be fine.

4. I would stop automatic updates, but be able to decide whether to run the new update or skip it depending on the situation. Do not allow an update just for the sake of update. Run an update if you really need it for your work. There is an exception: security updates should be always applied straight away.

Good luck!

Igor

 

 
 
Sent: Tuesday, December 17, 2019 at 12:15 AM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Thanks Igor, I'm almost positive that when I originally loaded Protege I downloaded the version with the embedded JVM not the platform independent version.  But as you said perhaps the Java update still messed things up or there is a slight chance I accidentally loaded the platform independent version.. A few more questions before I reload Protege: 
 
1) Should I delete the version of Java I currently have on my computer or is the embedded version supposed to just ignore other versions of Java that are on the machine? 
2) If I do that (delete Java) do you think Eclipse will be able to use the VM and SDK bundled with Protege? 
3) Is there anything I should do to uninstall the current version of Protege or can I just move all the files to the trash?
4) If the answer to 1 is no (keep the version of Java I have installed independent of Protege) should I stop loading Java updates?
Just FYI, it's more important for me to get Protege working than to worry about not having Eclipse working. Thanks again for the help I appreciate it. 
 
Cheers,
Michael
 
On Mon, Dec 16, 2019 at 12:24 PM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

When you go to the Protégé download page and see the button to download Protégé for Windows, this is what should be pressed to get the installation pack with embedded JVM including SDK. There is another link on this page: Download platform independent version (requires a Java Runtime Environment), which does not include JVM; in this case Protégé will use a common JVM and SDK installed on you machine.

If you run the platform independent version, it’s pretty clear what happened: Windows automatically installed JVM and/or SDK, which is buggy and/or not compatible with Protégé.

If you run the embedded Java, it’s unclear how but still likely Windows Java update has broken your Protégé installation.

Anyway try uninstalling Protégé and installing the Windows-specific vertion.

 

Regards,

Igor

 

 
 
Sent: Monday, December 16, 2019 at 4:00 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: Re: [protege-user] Reasoner not Working
Igor said: " Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? 
I recommend the later, because the  former makes Protégé very vulnerable to common Java updates."
 
Thanks, Igor, I think that may be my problem, I wasn't aware of that. I have Java installed on my machine and I regularly
update when there is one. When I go to the Java application in Windows and do an About it says Version 8 Update 231. (build 1.8.0_231-b11)  I'm not sure but I think I did an update of Java fairly recently. 
 
Also, I tried using Protege version 5.2.0 and that didn't work either, which makes me think that you are probably right about Java as I think even the old version of Protege would just use the most recent update of Java.
 
Two questions:
 
1) Is there a way to revert this so that I just use the JVM embedded in Protege? As far as I know, I haven't done anything to tell Protege to use a different version of Java but I assume it's just taking the newer version I have installed on my machine. Is that correct? I did modify the Protege.l4j.ini to tell it to use more memory but I'm assuming that would have no effect on what version of Java was being used. 
 
2) I also use Eclipse once in a while and for that my understanding is I need the Java SDK because I use things like Swing. Is there a way I can use the JVM embedded with Protege but still have the SDK for Eclipse? 
 
I really appreciate any additional feedback. I'm pretty clueless when it comes to things like the JVM and the SDK but it's kind of a pain right now not being able to use Protege. 
 
Thanks for the help,
Michael
 
On Sat, Dec 14, 2019 at 4:05 AM Igor Toujilov <[hidden email]> wrote:

Hi Michael,

On Ubuntu with Protégé 5.5.0, Java JVM 1.8.0_121-b13 (embedded in the Protégé installation), Pellet Reasoner Plug-in 2.2.0 everything works fine as you expect (I have no problems you described).

Do you run a common JVM, installed in your system, or the JVM embedded in the Protégé installation? I recommend the later, because the former makes Protégé very vulnerable to common Java updates.

 

Regards,

Igor

 

 
 
Sent: Friday, December 13, 2019 at 8:46 PM
From: "Michael DeBellis" <[hidden email]>
To: "User support for WebProtege and Protege Desktop" <[hidden email]>
Subject: [protege-user] Reasoner not Working
The reasoner seems to have stopped working correctly for me. I'm working in Windows 10 Home version 1903 Build 18362.535  I'm running Version 8 Update 231 of Java. My desktop has a 64-bit OS and chip. I'm using version 5.5.0 of Protege and 2.2.0 of Pellet. In the About screen it says "Max memory set to 444MB (via Java -Xmx setting)  Currently using 86MB"
 
I just loaded a Windows update recently and it hasn't worked since then although I'm not sure if it was the update that made a difference since I haven't done any work in Protege for a while (about 2-3 weeks ago when things were working fine). I noticed it yesterday when I was debugging some SWRL rules to help someone. I had a rule that I was sure should work but it didn't and then I noticed that an inverse relation wasn't working but when I sent my revision to the person I was working with the inverse and rule worked for her. 
 
This morning I tried restarting Windows and then without starting any other programs starting Protege. I loaded the small ontology FrequencyExample2 and ran Pellet. In that ontology the property isLessFrequentThan is defined as the inverse of isMoreFrequentThan (see screen snapshot 1 below) but as you can see from the second screen snapshot the domain and range for isLessFrequentThan are still undefined. 
 
Also, the property is defined as transitive so there should be a bunch of values that should be computed automatically on the instances of Frequency  but those property values are not computed. Also, there is one SWRL rule that should be asserting recommendations for the Customers based on their Preferences and it's not working either. Also, hasPreference and isPreferenceFor are inverse relations and those values aren't being computed either. As I think of it this may be a problem just with the properties because none of the SWRL rules in this ontology or the other one I had would work without the appropriate inverse assertions.
 
There is a DL axiom for the definition of the MusicLover class (some Customer who listens to any Artist Always) and that is working. Also, when I was helping someone else debug a different problem yesterday the reasoner was working correctly in identifying errors caused by inconsistent disjoint class definitions. 
 
The reasoner is active and I've checked Reasoner>Configure and all boxes are checked. I've attached the file for this ontology but my guess is it will work fine when others test it, it was working fine before. I also tried stopping Pellet and starting Hermit and got the same result. 
 
I've also attached the log file from Protege and the DOS log from the DOS window (I think that's what it is, the black window titled C:\WINDOWS\system32\cmd.exe)   I usually start Protege by double clicking the run.bat file. In the past that was the only way it would work and I just got in the habit of starting that way although I just tried quitting and clicking on the Protege.exe file and that does work to start Protege but I still have the same problem. 
 
Also, I received an email last night from someone who was working through my SWRL tutorial and something really basic wasn't working. I'm not sure if they are having the same problem though, they are in a different time zone and I asked them to try a few things and haven't heard back yet. 
 
The only thing I can think of is to uninstall and reinstall Protege but wanted to see if anyone else has ideas before I do that.   
 
ReasonerProb1.PNG
 
ReasonerProb2.PNG
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