[protege-discussion] [POSSIBLE VIRUS:###] please advise. Thanks

[Jones, Josette F.]

Greetings we keep running into some errors. Please advise on how we can correct. Thanks.
The errors are described below.
System Configuration:

Windows Vista Home Basic sp1 32 bit
Dell Vostro 1400 Intel Core2 Duo 1.4GHz 2Gb RAM
Java(TM) 6 Update 10 (11/3/2008)

Protege v3.4 beta with following tabs enabled: Classes, Slots, Forms, Instances, Queries, UMLS, Jambalaya, Knowledge Tree, Prompt, Changes, DataMaster v1.3.1, String Search, XML Tab.
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Issue 1: The following package could not be imported while creating custom SWRL built-in.

Could not resolve:
import edu.stanford.smi.protegex.owl.swrl.bridge.exceptions.*;
public class SWRLBuiltInLibraryImpl  extends AbstractSWRLBuiltInLibrary{

However, the following could be resolved:
import edu.stanford.smi.protegex.owl.swrl.bridge.*;
import edu.stanford.smi.protegex.owl.swrl.bridge.builtins.*;
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Issue 2: Converting project to OWL using "File -> Export to Format -> OWL" fails with the following message in a pop -up window:

"Export Failed: edu.stanford.smi.protege.util.MessageError at f16070"

The following exception is seen in the console (please check the attachment Export_Console.txt for complete log):

SEVERE: Failed to save file file:/C:/Users/bugsnspikes/Documents/IUPU/RA/Ontolog
y/scans_oct30_1.owl using Protege2Jena. -- com.hp.hpl.jena.shared.BadURIExceptio
n: Only well-formed absolute URIrefs can be included in RDF/XML output: <E> Code
: 58/REQUIRED_COMPONENT_MISSING in SCHEME: A component that is required by the
scheme is missing.

Disabled all tabs except Classes, Instances, Slots and tried again. But the error persists.
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Issue 3: Converting project using "File -> Convert Project to Format .." turns non-responsive (has been running for about 10 minutes) with numerous plugin exceptions, out of memory exceptions after running high CPU (100% on one of my Dual core) and java.exe consuming > 268,000k memory. Please check Convert_Console.txt for complete log.

Resolution: The logs indicated problem with Jambalaya, UMLS. Disabled all the tabs except Classes, Instances, Slots and the conversion worked fine.
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Issue 4: Enabling SWRL tab after resolving issue#3 does not converge. Runs on high CPU(100%) and memory (> 271,000k) for several minutes. Then the Protege display goes blank and CPU usage falls to zero for the process. Please check SWRLTab_Console.txt for the complete log.

NOTE: This problem is not seen while working with a OWL project. Its only seen after converting to OWL from RDF format.
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Have a gentle day!
Josette
Josette Jones, RN, PhD
Assistant Professor School of Informatics and School of Nursing
Indiana University, Indianapolis
535 Michigan Avenue
Room 491
Indianapolis, IN 46202
Phone:  (317) 274-8059
Fax:      (317) 278-7669
Email: jofjones at iupui.edu<mailto:jofjones at iupui.edu>
Webpage: http://informatics.iupui.edu/people/jofjones

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