Is there a way to bypass a DOT error on load of Protege?

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Is there a way to bypass a DOT error on load of Protege?

sizedam
Ever since I added a Visualization tab with Graphviz window I cannot launch Protege (ver 5.0.5-beta-17). I get a popup error saying "A DOT error has occurred. This is probably because OWLViz could not find the DOT application. OWLViz requires that Graphviz is insalled an the path to the DOt application is set properly (in options)".

Is there a way to load Protege in some sort of 'safe mode' so I can get rid of that tab and remove the dependency? I don't see any reference to it in an editable XML log4j.xml or config.xml. Or do I just have to reinstall Protege?

There does not seem to be a Yosemite version of Graphviz available so I would just as soon just do without it for now: http://www.graphviz.org/Download_macos.php
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Re: Is there a way to bypass a DOT error on load of Protege?

Tania Tudorache

One solution is to update to Protege 5.1.0, the latest release, which handles the missing dot error more gracefully, it won't show it as a popup, but rather as a message in the console.


Alternatively, you can also delete the Protege preferences, if you want to keep using your current version:

http://protegewiki.stanford.edu/wiki/ClearingP4Preferences


Tania


From: protege-user <[hidden email]> on behalf of sizedam <[hidden email]>
Sent: Tuesday, March 14, 2017 8:29:30 AM
To: [hidden email]
Subject: [protege-user] Is there a way to bypass a DOT error on load of Protege?
 
Ever since I added a Visualization tab with Graphviz window I cannot launch
Protege (ver 5.0.5-beta-17). I get a popup error saying "A DOT error has
occurred. This is probably because OWLViz could not find the DOT
application. OWLViz requires that Graphviz is insalled an the path to the
DOt application is set properly (in options)".

Is there a way to load Protege in some sort of 'safe mode' so I can get rid
of that tab and remove the dependency? I don't see any reference to it in an
editable XML log4j.xml or config.xml. Or do I just have to reinstall
Protege?

There does not seem to be a Yosemite version of Graphviz available so I
would just as soon just do without it for now:
http://www.graphviz.org/Download_macos.php



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Re: Is there a way to bypass a DOT error on load of Protege?

sizedam
Thank you Tania Tudorache. Great tips ...

Upgrading is not an easy option for me given I'm in a corporate environment. I tried deleting Protege preferences in ~/Library/Preferences/com.apple.java.util.prefs.plist using XCode. I even tried deleting that plist altogether. But Protege still freezes when I try to open it.

ProtegePreferences.png

I did notice a number of other plists in that folder prefixed with 'protege'. Would they be of any interest in overcoming this issue?

protege_preferences.annotation_prefs_set.hidden_annoations_uris.plist
protege_preferences.application_preferences.custom_tabs.plist
protege_preferences.application_preferences.file_preferences_key.plist
protege_preferences.application_preferences.look_and_feel_key.plist
protege_preferences.application_preferences.ontologypreferences.plist
protege_preferences.application_preferences.org.protege.editor.core.ui.workspace.workspaceframe.plist
protege_preferences.application_preferences.org.protege.editor.core.update.pluginmanager.plist
protege_preferences.application_preferences.org.protege.editor.owl.finder.plist
protege_preferences.application_preferences.org.protege.editor.owl.ui.renderer.owlrendererpreferences.plist
protege_preferences.application_preferences.tabs.plist
protege_preferences.application_preferences.viewlayoutpreferences.plist
protege_preferences.application_preferences.xmlwriterprefs.plist
protege_preferences.code_generation_preferences.org.protege.editor.owl.codegeneration.generateprotegeowljavacodeaction.plist
protege_preferences.inference_prefs_set.org.protege.editor.owl.model.inference.reasonerpreferences.plist
protege_preferences.uk.ac.man.cs.mig.coode.owlviz.owlvizprefs.plist

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Re: Is there a way to bypass a DOT error on load of Protege?

Tania Tudorache

You need to delete all of the Protege related properties. I suggest to use one of the methods that I sent in the previous email:

http://protegewiki.stanford.edu/wiki/ClearingP4Preferences


Delete everything under PROTEGE_PREFERENCES


Also, for the upgrade, you don't need admin rights, you just need to be able to write to any folder on your filesystem.


Tania


From: protege-user <[hidden email]> on behalf of sizedam <[hidden email]>
Sent: Tuesday, March 14, 2017 5:08:44 PM
To: [hidden email]
Subject: Re: [protege-user] Is there a way to bypass a DOT error on load of Protege?
 
Thank you Tania Tudorache. Great tips ...

Upgrading is not an easy option for me given I'm in a corporate environment.
I tried deleting Protege preferences in
~/Library/Preferences/com.apple.java.util.prefs.plist using XCode. I even
tried deleting that plist altogether. But Protege still freezes when I try
to open it.

ProtegePreferences.png
<http://protege-project.136.n4.nabble.com/file/n4667820/ProtegePreferences.png

I did notice a number of other plists in that folder prefixed with
'protege'. Would they be of any interest in overcoming this issue?

protege_preferences.annotation_prefs_set.hidden_annoations_uris.plist
protege_preferences.application_preferences.custom_tabs.plist
protege_preferences.application_preferences.file_preferences_key.plist
protege_preferences.application_preferences.look_and_feel_key.plist
protege_preferences.application_preferences.ontologypreferences.plist
protege_preferences.application_preferences.org.protege.editor.core.ui.workspace.workspaceframe.plist
protege_preferences.application_preferences.org.protege.editor.core.update.pluginmanager.plist
protege_preferences.application_preferences.org.protege.editor.owl.finder.plist
protege_preferences.application_preferences.org.protege.editor.owl.ui.renderer.owlrendererpreferences.plist
protege_preferences.application_preferences.tabs.plist
protege_preferences.application_preferences.viewlayoutpreferences.plist
protege_preferences.application_preferences.xmlwriterprefs.plist
protege_preferences.code_generation_preferences.org.protege.editor.owl.codegeneration.generateprotegeowljavacodeaction.plist
protege_preferences.inference_prefs_set.org.protege.editor.owl.model.inference.reasonerpreferences.plist
protege_preferences.uk.ac.man.cs.mig.coode.owlviz.owlvizprefs.plist





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Re: Is there a way to bypass a DOT error on load of Protege?

sizedam
This post was updated on .
Thanks for all your help, Tania. Still no luck.

I deleted everything under PROTEGE_PREFERENCES in ~/Library/Preferences/com.apple.java.util.prefs.plist. I even deleted the 'org.protege.editor.owl.recenteditorkits' entry in my screenshot. I noticed some of those other plists I listed have PROTEGE_PREFERENCES sections. Not sure if that's relevant.

I tried modifying 'protege_preferences.application_preferences.custom_tabs.plist' and 'protege_preferences.application_preferences.tabs.plist' to get rid of the custom tabs I added just before the crash. Still no relief.

I have to use XCode because our corporation doesn't have JPUI packaged for Mac, but I can't imagine that would make a difference.

I do not have write access to my Applications folder, so I presume I cannot do the upgrade without admin assistance. Besides we have rigorous application packaging procedures at our company.

Below is my console output just before I freeze. Any clues there? Is there a way I can repoint my 'active ontology' in a config or open Protege at the command line with a different ontology?

Rebuilding entity indices...
... rebuilt in 3 ms
Setting active ontology to OntologyID(OntologyIRI(<http://www.semanticweb.org/u522971/ontologies/2017/2/untitled-ontology-18>))
Rebuilding entity indices...
... rebuilt in 3 ms
... active ontology changed
Cannot generate ontology catalog for ontology at http://www.semanticweb.org/u522971/ontologies/2017/2/untitled-ontology-18
Setting active ontology to OntologyID(OntologyIRI(<http://www.semanticweb.org/u522971/ontologies/2017/2/untitled-ontology-18>))
Rebuilding entity indices...
... rebuilt in 1 ms
... active ontology changed
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Re: Is there a way to bypass a DOT error on load of Protege?

Tania Tudorache
In reply to this post by sizedam

You are right, Protege seems pretty stubborn with deleting the preferences. I reproduced the bug, and filed an issue:


Hopefully, we can fix this soon.


The message about not being able to regenerate the catalog is harmless. You can start Protege with an existing OWL file, by right-clicking on the OWL file -> Open with -> Protege. But I don't think that will help in your situation.


Can you describe what you mean by "freeze"?


Is the Protege UI coming up or not? Can you describe more of the behavior?


Thanks,

Tania


From: protege-user <[hidden email]> on behalf of sizedam <[hidden email]>
Sent: Tuesday, March 14, 2017 5:08:44 PM
To: [hidden email]
Subject: Re: [protege-user] Is there a way to bypass a DOT error on load of Protege?
 
Thank you Tania Tudorache. Great tips ...

Upgrading is not an easy option for me given I'm in a corporate environment.
I tried deleting Protege preferences in
~/Library/Preferences/com.apple.java.util.prefs.plist using XCode. I even
tried deleting that plist altogether. But Protege still freezes when I try
to open it.

ProtegePreferences.png
<http://protege-project.136.n4.nabble.com/file/n4667820/ProtegePreferences.png

I did notice a number of other plists in that folder prefixed with
'protege'. Would they be of any interest in overcoming this issue?

protege_preferences.annotation_prefs_set.hidden_annoations_uris.plist
protege_preferences.application_preferences.custom_tabs.plist
protege_preferences.application_preferences.file_preferences_key.plist
protege_preferences.application_preferences.look_and_feel_key.plist
protege_preferences.application_preferences.ontologypreferences.plist
protege_preferences.application_preferences.org.protege.editor.core.ui.workspace.workspaceframe.plist
protege_preferences.application_preferences.org.protege.editor.core.update.pluginmanager.plist
protege_preferences.application_preferences.org.protege.editor.owl.finder.plist
protege_preferences.application_preferences.org.protege.editor.owl.ui.renderer.owlrendererpreferences.plist
protege_preferences.application_preferences.tabs.plist
protege_preferences.application_preferences.viewlayoutpreferences.plist
protege_preferences.application_preferences.xmlwriterprefs.plist
protege_preferences.code_generation_preferences.org.protege.editor.owl.codegeneration.generateprotegeowljavacodeaction.plist
protege_preferences.inference_prefs_set.org.protege.editor.owl.model.inference.reasonerpreferences.plist
protege_preferences.uk.ac.man.cs.mig.coode.owlviz.owlvizprefs.plist





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Re: Is there a way to bypass a DOT error on load of Protege?

sizedam
Here is a more detailed description: The UI comes up, with the same culprit 'Visualization' tab I tried to remove, and the DOT modal. When I click on 'OK' to dismiss the modal, and then try to click on any tabs or menu items, the UI does not respond. Eventually, the apple spinner shows up and I ultimately have to force-quit Protege to do anything on my machine at all.

 ProtegeDOTError.png
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Re: Is there a way to bypass a DOT error on load of Protege?

Tania Tudorache

OK, thank you for the details.


One quick temporary workaround is to remove OWLViz from your plugins.


Go to the Protege installation folder -> Right click on the Protege.app -> Show package contents -> Contents -> Java -> plugins


and delete the owlviz.jar.


Tania




From: protege-user <[hidden email]> on behalf of sizedam <[hidden email]>
Sent: Wednesday, March 15, 2017 5:44:57 AM
To: [hidden email]
Subject: Re: [protege-user] Is there a way to bypass a DOT error on load of Protege?
 
Here is a more detailed description: The UI comes up, with the same culprit
'Visualization' tab I tried to remove, and the DOT modal. When I click on
'OK' to dismiss the modal, and then try to click on any tabs or menu items,
the UI does not respond. Eventually, the apple spinner shows up and I
ultimately have to force-quit Protege to do anything on my machine at all.

  ProtegeDOTError.png
<http://protege-project.136.n4.nabble.com/file/n4667840/ProtegeDOTError.png



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Re: Is there a way to bypass a DOT error on load of Protege?

sizedam
I do not have a Protege.app in my installation folder. I start Protege by double-clicking run.command. I have org.coode.owlviz.jar in my plug-ins folder. No owlviz.jar.

I was able to get past this today by throwing my entire installation folder into the trash, along with any suspect plists (com.apple.java.util.prefs.plist & everything prefixed with protege), then have our tech support push Protege to my Mac again. Oddly enough, when I reopened Protege from a fresh install, the bad custom tabs were still there ... but at least I was able to click on them and delete them this time.

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Re: Is there a way to bypass a DOT error on load of Protege?

Tania Tudorache

OK, great. Yes, you had an earlier installation of Protege, so deleting the org.coode.owlviz.jar would have worked. You probably had the platform independent installation rather than the Mac OSX one.


But, if you now the latest release, it is even better.


You can follow the progress on the Reset preferences issue on GitHub.


Tania




From: protege-user <[hidden email]> on behalf of sizedam <[hidden email]>
Sent: Wednesday, March 15, 2017 2:16:56 PM
To: [hidden email]
Subject: Re: [protege-user] Is there a way to bypass a DOT error on load of Protege?
 
I do not have a Protege.app in my installation folder. I start Protege by
double-clicking run.command. I have org.coode.owlviz.jar in my plug-ins
folder. No owlviz.jar.

I was able to get past this today by throwing my entire installation folder
into the trash, along with any suspect plists
(com.apple.java.util.prefs.plist & everything prefixed with protege), then
have our tech support push Protege to my Mac again. Oddly enough, when I
reopened Protege from a fresh install, the bad custom tabs were still there
... but at least I was able to click on them and delete them this time.





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Sent from the Protege User mailing list archive at Nabble.com.
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