Protege 5.5.0 beta 5 fails on Java Exception: "URI has an authority component"

[metro]

This is unfortunately a newbie question along the lines of "Please do not press this button again".

I've tried 5.5.0 beta 4 and it worked just fine for at least 2 weeks.

Then I did two things, one of which has sealed my fate.

The first was attempt to load the Matrix plug-in, which may have been an incompatible version, but I don't think that was the reason.

The other thing I changed was the default location from a web URI/URL (http://semanticweb.org...) to a local file path on some Configuration/Preferences dialog.

I can’t tell you which dialog ‘cos I can’t get the thing to start again.

In the next restart 5.5.0 beta 4 stopped on:

"java.lang.IllegalArgumentException: URI has an authority component"

"at java.io.File.<init>(File.java:423) ~[na:1.8.0_40]"

In the log file it says:

"Cannot generate ontology catalog for ontology at file:.... URI has an authority component"

It doesn’t display the GUI, it just stops.

• Deleting the entire install directory and replacing it with a fresh install of beta 4 and beta 5 doesn't work
• Same result with the protege.exe and run.bat.
• I searched the archives for "authority component" and got no hits and "IllegalArgumentException" got 99 hits, but nothing looked close.

My diagnosis:

Protege seems to be remembering the setting of that URI as a 'user default’ or ‘preference' across installs in a place I can't find, so I can't delete it.

It isn't in an obvious place like "C:\Users\<user name>", like the log file is. It isn’t in the install directory because I delete it completely between installs.

• Where can I look for that configuration setting and can I manually edit it?
• What should I change it to?
• Does it fiddle with the Registry?

 

Windows 10, 64bit

java version "1.8.0_191"

Java(TM) SE Runtime Environment (build 1.8.0_191-b12)

 

Thanks in advance....BTW a truly impressive tool.

 

- Demmy

Architecture & Security Team

Information Technology Services

Victoria University of Wellington

 

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[metro]

I got no response to my query of 15/11/2018 so I had another deeper look
through the registry, guessed at something and I think solved my immediate
problem.

I found a registry key:
Computer\HKEY_USERS\...\Software\JavaSoft\Prefs\/P/R/O/T/E/G/E_/P/R/E/F/E/R/E/N/C/E/S\application_preferences\/Ontology/Preferences
Which was set to (what I thought was) a valid File/URI reference.

After I set the key value to null, Protégé started up no problems.

I believe the parameter I clobbered that led to the java error, was accessed
via:
File->Preferences->New Ontologies->’Default ontology IRI base’ field.
It now displays as ‘null’ after Protégé starts, but I believe had
‘http://semanticweb.org’ or similar at first for some reason I don’t
understand.

Can someone tell me what the ‘Default ontology IRI base’ field is for?
Why was it pointed at ‘http://semanticweb.org’?
Can I get by with it set to null?
What functionality will I lose?
I didn’t get very far searching the Wiki for "IRI".

Thanks in advance…

- Demmy
Architecture & Security Team
Information Technology Services
Victoria University of Wellington





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[Liliana Andres]

Hi,

any updates about this :(


Best,



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[samsontu]

Hi,

On Nov 19, 2018, at 4:25 PM, metro <[hidden email]> wrote:

I got no response to my query of 15/11/2018 so I had another deeper look
through the registry, guessed at something and I think solved my immediate
problem.

I found a registry key:
Computer\HKEY_USERS\...\Software\JavaSoft\Prefs\/P/R/O/T/E/G/E_/P/R/E/F/E/R/E/N/C/E/S\application_preferences\/Ontology/Preferences
Which was set to (what I thought was) a valid File/URI reference.

After I set the key value to null, Protégé started up no problems.

I believe the parameter I clobbered that led to the java error, was accessed
via:
File->Preferences->New Ontologies->’Default ontology IRI base’ field.
It now displays as ‘null’ after Protégé starts, but I believe had
‘http://semanticweb.org’ or similar at first for some reason I don’t
understand.

Can someone tell me what the ‘Default ontology IRI base’ field is for?
Why was it pointed at ‘http://semanticweb.org’?
Can I get by with it set to null?
What functionality will I lose?
I didn’t get very far searching the Wiki for "IRI”.

 ‘Default ontology IRI base’ is the ontology IRI base Protege uses to create a new ontology. Initially it’s set as http://semanticweb.org because … that IRI base is as good as any.   As you found out, you can set the default IRI base in the “New ontologies” tab of Protege preference. If you leave the value blank in the preference tab, Protege will use something like “urn:absolute” as the base. Probably not a good idea. The idea is that once you created your ontology you can change the ontology IRI to be the IRI you want, overriding the default.

With best regards,

Samson

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