Protege locking up

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Protege locking up

Ken Keefe
I've recently been trying to learn Protege and I'm running into a very annoying issue. When I try to open an owl ontology, the protege tool locks up. It does this in OSX and in Ubuntu linux. I have sent the ontology files to a colleague and it opens right up for him without any trouble. I have even opened protege, saved the default empty ontology that it starts with, closed protege, started protege, and attempted to open that blank ontology. It still locks up. I am not seeing any errors in the terminal window (in Ubuntu linux), except for a warning about being unable to flush the user prefs: java.util.prefs.BackingStoreException

Sometimes it will eventually open the ontology I've selected, but it takes over 10 minutes, during which the tool is locked up. I should stress that these ontologies that I am trying to open are very small.

Can you offer any suggestions for how I can debug this problem?

Thanks,
Ken Keefe

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Re: Protege locking up

Ken Keefe
After some fiddling, I've discovered that it only seems to lock up (take a long time to load) if the ontology file is located in my home directory. Does this shed any light on the problem? I created a new subdirectory in my home directory called "ontologies" and moved the same files I was having trouble opening into this directory. Protege was able to open those immediately. The permissions on my home directory and ontologies are identical.

Any thoughts?

Ken


On Mon, Feb 24, 2014 at 2:02 PM, Ken Keefe <[hidden email]> wrote:
I've recently been trying to learn Protege and I'm running into a very annoying issue. When I try to open an owl ontology, the protege tool locks up. It does this in OSX and in Ubuntu linux. I have sent the ontology files to a colleague and it opens right up for him without any trouble. I have even opened protege, saved the default empty ontology that it starts with, closed protege, started protege, and attempted to open that blank ontology. It still locks up. I am not seeing any errors in the terminal window (in Ubuntu linux), except for a warning about being unable to flush the user prefs: java.util.prefs.BackingStoreException

Sometimes it will eventually open the ontology I've selected, but it takes over 10 minutes, during which the tool is locked up. I should stress that these ontologies that I am trying to open are very small.

Can you offer any suggestions for how I can debug this problem?

Thanks,
Ken Keefe


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Re: Protege locking up

Ken Keefe
I had my colleague try it and his protege locks up when he tries to open an ontology file that is located in his home directory. Do I need to do anything else besides send this email to submit a bug report?

Ken


On Mon, Feb 24, 2014 at 2:31 PM, Ken Keefe <[hidden email]> wrote:
After some fiddling, I've discovered that it only seems to lock up (take a long time to load) if the ontology file is located in my home directory. Does this shed any light on the problem? I created a new subdirectory in my home directory called "ontologies" and moved the same files I was having trouble opening into this directory. Protege was able to open those immediately. The permissions on my home directory and ontologies are identical.

Any thoughts?

Ken


On Mon, Feb 24, 2014 at 2:02 PM, Ken Keefe <[hidden email]> wrote:
I've recently been trying to learn Protege and I'm running into a very annoying issue. When I try to open an owl ontology, the protege tool locks up. It does this in OSX and in Ubuntu linux. I have sent the ontology files to a colleague and it opens right up for him without any trouble. I have even opened protege, saved the default empty ontology that it starts with, closed protege, started protege, and attempted to open that blank ontology. It still locks up. I am not seeing any errors in the terminal window (in Ubuntu linux), except for a warning about being unable to flush the user prefs: java.util.prefs.BackingStoreException

Sometimes it will eventually open the ontology I've selected, but it takes over 10 minutes, during which the tool is locked up. I should stress that these ontologies that I am trying to open are very small.

Can you offer any suggestions for how I can debug this problem?

Thanks,
Ken Keefe



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Re: Protege locking up

Timothy Redmond
In reply to this post by Ken Keefe
On 02/24/2014 12:31 PM, Ken Keefe wrote:
After some fiddling, I've discovered that it only seems to lock up (take a long time to load) if the ontology file is located in my home directory. Does this shed any light on the problem? I created a new subdirectory in my home directory called "ontologies" and moved the same files I was having trouble opening into this directory. Protege was able to open those immediately. The permissions on my home directory and ontologies are identical.

Yes - this probably explains exactly what is happening.  You have hit a known bug.  Protege parses the contents of the current directory and its descendants to determine how to handle imports (e.g., can an import be loaded off the disk or does Protege need to go to the internet).  It puts the results of this analysis in the catalog-v001.xml file.  Sometimes this runs very slowly and the usual reason is that it has hit some xml file with dtd content.  Unfortunately dtd content can cause a huge problem with the performance of an xml parser and Protege should be turning xml validation off.

It is also possible, but I am guessing not the case, that you have so many files under your home directory that analyzing the possibility that they are imports takes too long.

-Timothy



Any thoughts?

Ken


On Mon, Feb 24, 2014 at 2:02 PM, Ken Keefe <[hidden email]> wrote:
I've recently been trying to learn Protege and I'm running into a very annoying issue. When I try to open an owl ontology, the protege tool locks up. It does this in OSX and in Ubuntu linux. I have sent the ontology files to a colleague and it opens right up for him without any trouble. I have even opened protege, saved the default empty ontology that it starts with, closed protege, started protege, and attempted to open that blank ontology. It still locks up. I am not seeing any errors in the terminal window (in Ubuntu linux), except for a warning about being unable to flush the user prefs: java.util.prefs.BackingStoreException

Sometimes it will eventually open the ontology I've selected, but it takes over 10 minutes, during which the tool is locked up. I should stress that these ontologies that I am trying to open are very small.

Can you offer any suggestions for how I can debug this problem?

Thanks,
Ken Keefe



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


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Re: Protege locking up

Matthew Horridge-2
Administrator
In reply to this post by Ken Keefe
Hi Ken,

Thanks for the extra info.  This does shed a lot of light on the matter.

When Protege loads an ontology it searches the directory where the ontology is loaded from for imports.  Do you have a lot of files in your home directory?  If so, the problem is most likely due to the logic used here.

It could do with some kind of progress monitor and lazy search.

Cheers,

Matthew

On 24 Feb 2014, at 12:31, Ken Keefe <[hidden email]> wrote:

After some fiddling, I've discovered that it only seems to lock up (take a long time to load) if the ontology file is located in my home directory. Does this shed any light on the problem? I created a new subdirectory in my home directory called "ontologies" and moved the same files I was having trouble opening into this directory. Protege was able to open those immediately. The permissions on my home directory and ontologies are identical.

Any thoughts?

Ken


On Mon, Feb 24, 2014 at 2:02 PM, Ken Keefe <[hidden email]> wrote:
I've recently been trying to learn Protege and I'm running into a very annoying issue. When I try to open an owl ontology, the protege tool locks up. It does this in OSX and in Ubuntu linux. I have sent the ontology files to a colleague and it opens right up for him without any trouble. I have even opened protege, saved the default empty ontology that it starts with, closed protege, started protege, and attempted to open that blank ontology. It still locks up. I am not seeing any errors in the terminal window (in Ubuntu linux), except for a warning about being unable to flush the user prefs: java.util.prefs.BackingStoreException

Sometimes it will eventually open the ontology I've selected, but it takes over 10 minutes, during which the tool is locked up. I should stress that these ontologies that I am trying to open are very small.

Can you offer any suggestions for how I can debug this problem?

Thanks,
Ken Keefe

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


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