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[p4-feedback] Protege 4.1 import URI resolution

Timothy Redmond tredmond at
Mon Apr 19 14:43:32 PDT 2010

On 04/19/2010 12:56 PM, Samson Tu wrote:
> Hi,
> I have a collection of OWL ontologies that load without any problem in 
> Protege 4.0x, but when I tried to load it with Protege 4.1, I got 
> "file not found error."
> I see that the file of an imported ontology study_examples has been 
> resolved to "file:/Users/tu/Dropbox/OCRE/trunk/study_examples.owl" 
> which is the correct file path for my Mac at home. However, I am using 
> a Windows workstation. Where is Protege 4.1 getting the path 
> information, and why does Protege 4.0 behaves correctly but Protege 
> 4.1 doesn't?

This is a bug that has been fixed in the latest svn but perhaps not in 
the latest update.  I need to send another update in soon anyway because 
there have been several improvements.  (Actually I think that I will 
push for a new build when Jennifer gets back.)

I believe that the invalid path information is coming from a catalog.xml 
file (which is like the old .repository files except it is a 
standard).   My guess is that you are synchronizing the two machines 
using some kind of synchronization software?  Unfortunately I was 
putting absolute addresses in the catalog.xml file when I didn't need to 
and I was not checking for files that had been deleted.  I will try to 
push an update soon but deleting  the calalog.xml will probably fix the 
problem.  I will have to think about whether there are other problems 
with synchronization that I will have to solve.

This is new to Protege 4.1 because it is an attempt to deal with the 
change from import by name to import  by location change in OWL 2.0.  
XML catalogs are an industry standard way of redirecting references made 
by an xml catalog to external resources.


> Thank you.
> With best regards,
> Samson
> C:\Program Files\Protege_4.1>java -Dlog4j.configuration=file:log4j.xml 
> -DentityE
> xpansionLimit=100000000 -Dfile.encoding=utf-8 
> -Dorg.protege.plugin.dir=plugins -
> classpath bin/felix.jar org.apache.felix.main.Main
> Welcome to Felix
> ================
> Starting Protege 4 OWL Editor (Version 4.1.0, Build = 102)
> Platform:
>     Java: JVM 1.6.0_06-b02 Memory: 954M
>     Language: en, Country: US
>     Framework: Apache Software Foundation (1.5)
>     OS: win (5.2)
>     Processor: x86-64
> Installed plugin Dlquery
> Installed plugin Owlviz Plug-in
> Installed plugin The Protege 4 OWL Editor
> Installed plugin HermiT Reasoner
> Installed plugin The OWL API
> Using OWL API version
> Rebuilding entity indices...
> ... rebuilt in 16 ms
> loading Anonymous-1 from 
> file:/C:/My%20Dropbox/OCRE/trunk/OCRe-Start-Here.owl
> Mapping (from automapping): Folder: C:\My Dropbox\OCRE\trunk): 
> et/OCRe/study_examples.owl -> 
> file:/Users/tu/Dropbox/OCRE/trunk/study_examples.o
> wl
> loading <> from 
> file:/Users/tu/Dropbo
> x/OCRE/trunk/study_examples.owl

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