Protege 5.2.0 Remove Temp File Freeze

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Protege 5.2.0 Remove Temp File Freeze

Johannes K.
Dear all,

I started using protege some days ago. Since today an odd program freeze
occurs. When I start Protege and open an existing file or create a new one
the program freezes. I started the program from the terminal. I seems that
the program hangs when trying to delete a temporary file from the /tmp
folder (see log below). Unfortunately I did not find any solution to this
problem in the forum here. I tried the following things

+ Remove the program and install it again
+ Install the linux version and the platform independent version

Does anybody have a clue how the problem can be solved?
The system configuration is as given in the log below.

Thank you in advance for your help!
Johannes

johannes@johannes:~$ cd Protege-5.2.0/
johannes@johannes:~/Protege-5.2.0$ bash run.sh
CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
********************************************************************************
 **                                  Protege                                  
**
********************************************************************************
 
----------------- Initialising and Starting the OSGi Framework
-----------------
FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory
 
The OSGi framework has been initialised
------------------------------- Starting Bundles
-------------------------------
Starting bundle org.protege.common
Starting bundle org.eclipse.equinox.common
Starting bundle org.eclipse.equinox.supplement
Starting bundle org.eclipse.equinox.registry
Starting bundle org.protege.editor.core.application
Starting bundle com.google.inject
Starting bundle org.eclipse.equinox.registry
Starting bundle ch.qos.logback.classic
Starting bundle jul.to.slf4j
Not starting bundle com.google.inject.assistedinject explicitly because it
is a fragment bundle.
Starting bundle com.google.guava
Starting bundle log4j.over.slf4j
Starting bundle org.protege.editor.owl
Starting bundle org.protege.common
Not starting bundle com.google.inject.multibindings explicitly because it is
a fragment bundle.
Starting bundle org.eclipse.equinox.common
Starting bundle org.apache.servicemix.bundles.javax-inject
Starting bundle slf4j.api
Starting bundle org.protege.editor.core.application
Starting bundle ch.qos.logback.core
Starting bundle org.apache.servicemix.bundles.aopalliance
Starting bundle org.jsr-305
Starting bundle org.apache.commons.io
Starting bundle org.eclipse.equinox.supplement
Starting bundle org.semanticweb.owl.owlapi
Starting bundle swrltab-plugin
Starting bundle org.protege.ontograf
Starting bundle code-generation
Starting bundle org.coode.owlviz                                                                                                                                                                                                
Starting bundle org.protege.owl.rdf                                                                                                                                                                                              
Starting bundle org.protege.editor.owl.rdf                                                                                                                                                                                      
Starting bundle existentialquery                                                                                                                                                                                                
Starting bundle org.semanticweb.hermit                                                                                                                                                                                          
Starting bundle uk.ac.manchester.cs.owl.explanation                                                                                                                                                                              
Starting bundle org.coode.dlquery                                                                                                                                                                                                
Starting bundle org.coode.browser                                                                                                                                                                                                
Starting bundle cellfie                                                                                                                                                                                                          
The OSGi framework has been started                                                                                                                                                                                              
                                                                                                                                                                                                                                 
------------------------------------ Protege
-----------------------------------                                                                                                                                                
Protege Desktop                                                                                                                                                                                                                  
Version 5.2.0, Build                                                                                                                                                                                                            
                                                                                                                                                                                                                                 
 
----------------------------------- Platform
-----------------------------------
Java: JVM 1.8.0_40-b26  Memory: 466M
Language: de, Country: AT
Framework: Apache Software Foundation (1.7)  
OS: linux (4.9.0-3-amd64)
Processor: x86-64
 
 
------------------------------------ Plugins
-----------------------------------
Plugin: SWRLTab Protege 5.0+ Plugin (1.0.3)
Plugin: OntoGraf (2.0.3)
Plugin: OWL Code Generation Plug-in (2.0.0)
Plugin: OWLViz (5.0.3)
Plugin: OWLAPI RDF Library (2.0.2)
Plugin: Protege SPARQL Plugin (2.0.1)
Plugin: Existential Query (2.0.0)
Plugin: HermiT (1.3.8.413)
Plugin: Explanation Workbench (3.0.0)
Plugin: DL Query (4.0.1)
Plugin: Browser View (OWLDoc) (3.0.3)
Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)
 
Creating and setting up empty (default) editor kit
OWL API Version: 4.2.8.20170104-2310
Cannot generate ontology catalog for ontology at
http://www.semanticweb.org/johannes/ontologies/untitled-ontology-61 
------------------------------- Auto-update Check
------------------------------
Auto-update last performed: Tue Dec 26 14:23:39 CET 2017
Auto-update has been performed today.  Not performing it again.
 
### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
------------------------ Saving Workspace and Ontologies
-----------------------
Will prompt 'Save As' for the active ontology because it was not loaded from
a local file
Saving untitled-ontology-61
Saving ontology to temp file: /tmp/temp-ontology330251554964919013
Copying ontology from temp file (/tmp/temp-ontology330251554964919013) to
actual destination (/home/johannes/test.owl)
Removing temp file: /tmp/temp-ontology330251554964919013




--
Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
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Re: Protege 5.2.0 Remove Temp File Freeze

Matthew Horridge-2
Administrator
Hi Johannes,

I’m not sure of the cause of this problem.  The deletion of the file uses standard Java calls under the hood.  Can you confirm that the temporary file does not get deleted?  Also, do you see a progress window when you save the file and if so does this disappear at all?

Cheers,

Matthew



> On 7 Jan 2018, at 14:24, Johannes K. <[hidden email]> wrote:
>
> Dear all,
>
> I started using protege some days ago. Since today an odd program freeze
> occurs. When I start Protege and open an existing file or create a new one
> the program freezes. I started the program from the terminal. I seems that
> the program hangs when trying to delete a temporary file from the /tmp
> folder (see log below). Unfortunately I did not find any solution to this
> problem in the forum here. I tried the following things
>
> + Remove the program and install it again
> + Install the linux version and the platform independent version
>
> Does anybody have a clue how the problem can be solved?
> The system configuration is as given in the log below.
>
> Thank you in advance for your help!
> Johannes
>
> johannes@johannes:~$ cd Protege-5.2.0/
> johannes@johannes:~/Protege-5.2.0$ bash run.sh
> CompilerOracle: exclude javax/swing/text/GlyphView.getBreakSpot
> ********************************************************************************
> **                                  Protege                                  
> **
> ********************************************************************************
>
> ----------------- Initialising and Starting the OSGi Framework
> -----------------
> FrameworkFactory Class: org.apache.felix.framework.FrameworkFactory
>
> The OSGi framework has been initialised
> ------------------------------- Starting Bundles
> -------------------------------
> Starting bundle org.protege.common
> Starting bundle org.eclipse.equinox.common
> Starting bundle org.eclipse.equinox.supplement
> Starting bundle org.eclipse.equinox.registry
> Starting bundle org.protege.editor.core.application
> Starting bundle com.google.inject
> Starting bundle org.eclipse.equinox.registry
> Starting bundle ch.qos.logback.classic
> Starting bundle jul.to.slf4j
> Not starting bundle com.google.inject.assistedinject explicitly because it
> is a fragment bundle.
> Starting bundle com.google.guava
> Starting bundle log4j.over.slf4j
> Starting bundle org.protege.editor.owl
> Starting bundle org.protege.common
> Not starting bundle com.google.inject.multibindings explicitly because it is
> a fragment bundle.
> Starting bundle org.eclipse.equinox.common
> Starting bundle org.apache.servicemix.bundles.javax-inject
> Starting bundle slf4j.api
> Starting bundle org.protege.editor.core.application
> Starting bundle ch.qos.logback.core
> Starting bundle org.apache.servicemix.bundles.aopalliance
> Starting bundle org.jsr-305
> Starting bundle org.apache.commons.io
> Starting bundle org.eclipse.equinox.supplement
> Starting bundle org.semanticweb.owl.owlapi
> Starting bundle swrltab-plugin
> Starting bundle org.protege.ontograf
> Starting bundle code-generation
> Starting bundle org.coode.owlviz                                                                                                                                                                                                
> Starting bundle org.protege.owl.rdf                                                                                                                                                                                              
> Starting bundle org.protege.editor.owl.rdf                                                                                                                                                                                      
> Starting bundle existentialquery                                                                                                                                                                                                
> Starting bundle org.semanticweb.hermit                                                                                                                                                                                          
> Starting bundle uk.ac.manchester.cs.owl.explanation                                                                                                                                                                              
> Starting bundle org.coode.dlquery                                                                                                                                                                                                
> Starting bundle org.coode.browser                                                                                                                                                                                                
> Starting bundle cellfie                                                                                                                                                                                                          
> The OSGi framework has been started                                                                                                                                                                                              
>
> ------------------------------------ Protege
> -----------------------------------                                                                                                                                                
> Protege Desktop                                                                                                                                                                                                                  
> Version 5.2.0, Build                                                                                                                                                                                                            
>
>
> ----------------------------------- Platform
> -----------------------------------
> Java: JVM 1.8.0_40-b26  Memory: 466M
> Language: de, Country: AT
> Framework: Apache Software Foundation (1.7)  
> OS: linux (4.9.0-3-amd64)
> Processor: x86-64
>
>
> ------------------------------------ Plugins
> -----------------------------------
> Plugin: SWRLTab Protege 5.0+ Plugin (1.0.3)
> Plugin: OntoGraf (2.0.3)
> Plugin: OWL Code Generation Plug-in (2.0.0)
> Plugin: OWLViz (5.0.3)
> Plugin: OWLAPI RDF Library (2.0.2)
> Plugin: Protege SPARQL Plugin (2.0.1)
> Plugin: Existential Query (2.0.0)
> Plugin: HermiT (1.3.8.413)
> Plugin: Explanation Workbench (3.0.0)
> Plugin: DL Query (4.0.1)
> Plugin: Browser View (OWLDoc) (3.0.3)
> Plugin: Cellfie Protege 5.0+ Plugin (2.1.0)
>
> Creating and setting up empty (default) editor kit
> OWL API Version: 4.2.8.20170104-2310
> Cannot generate ontology catalog for ontology at
> http://www.semanticweb.org/johannes/ontologies/untitled-ontology-61 
> ------------------------------- Auto-update Check
> ------------------------------
> Auto-update last performed: Tue Dec 26 14:23:39 CET 2017
> Auto-update has been performed today.  Not performing it again.
>
> ### Excluding compile: javax.swing.text.GlyphView::getBreakSpot
> ------------------------ Saving Workspace and Ontologies
> -----------------------
> Will prompt 'Save As' for the active ontology because it was not loaded from
> a local file
> Saving untitled-ontology-61
> Saving ontology to temp file: /tmp/temp-ontology330251554964919013
> Copying ontology from temp file (/tmp/temp-ontology330251554964919013) to
> actual destination (/home/johannes/test.owl)
> Removing temp file: /tmp/temp-ontology330251554964919013
>
>
>
>
> --
> Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
> _______________________________________________
> protege-user mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-user

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