[protege-discussion] PAL ValidationErrorImpl errors when using API but not GUI

[Bertram Stuart]

Hi,

I've just checked in the JAR and all the entries appear to be in the 
manifest file. Diffing the files said that they were different, despite 
the fact that I copied them from my Protege install yesterday. I've 
recopied them and diff is reporting no differences, but validation is 
still failing with the same errors.

As for JVMs, I checked and I had Protege modified to force it to run on 
the Sun JDK while everything else ran on the Sun OpenJDK (both v1.6). 
The only reason I had done that was to try to get Jambalaya to work, so 
I've reverted it and Protege validation still works while code-based 
validation on the same ontology from matching JARs still fails.

Thanks,

Stuart


Samson Tu wrote:
> Open your pal.jar file with Winzip and verify that the manifest.mf file 
> has entries like:
> 
> Name: edu/stanford/smi/protegex/pal/predicates/LessThanP.class
> PAL-Predicate: True
> 
> Make sure that your are using the same jar files and jvm 
> programmatically as Protege GUI.
> 
> I am not aware of any change made to PAL in recent years.
> 
> Samson
> 
> 
> Bertram Stuart wrote:
>> Hi,
>>
>> I have an application that uses a Protege ontology (pprj format) and a 
>> number of PAL rules for validation. Those PAL rules are called through 
>> the API, looping over each constraint and calling the following:
>>
>>
>> EvaluationPolicy evalPolicy = new EvaluationPolicy();
>> evalPolicy.setFindAllCounterExamples(true);
>> ConstraintEvaluationEngine evalEngine = new 
>> ConstraintEvaluationEngine(evalPolicy, kb);
>> ConstraintEngineResponse response = 
>> evalEngine.checkSingleStatement(palConstraint);
>> Collection<ConstraintViolation> constraintResult = null;
>>
>> if (response.areThereValidationErrors())
>> {
>> 	for (Object obj : response.getValidationErrors(palConstraint))
>> 	{
>> 		log.warn(obj.toString());
>> 	}
>> }
>> else if (response.areThereConstraintViolations())
>> {
>> 	constraintResult = response.getConstraintViolations(palConstraint);
>> 	log.info("Number of violations of " + palConstraint.getBrowserText() + 
>> " = " + constraintResult.size());
>> }
>> else
>> {
>> 	log.info("No constraint violations for " + palConstraint.getBrowserText());
>> }
>>
>>
>> palConstraint is an Instance that is the constraint and kb is the 
>> KnowledgeBase that the palConstraint was taken from and should be 
>> checked against. log is just a Log4J logger.
>>
>> This has worked perfectly fine until recently, when it has started 
>> failing to parse the PAL rules and instead returning ValidationErrorImpl 
>> errors. The rules themselves are perfectly fine, as I can run them from 
>> within Protege and they pass/fail as appropriate. The problem is only 
>> from API calls, which get messages like the following:
>>
>> 	Predicate named < is referenced but not defined.
>> 	Predicate named > is referenced but not defined.
>> 	Function named number-of-own-slot-values is referenced but not defined.
>> 	Function named coerce-to-string is referenced but not defined.
>>
>> Given that the predicates and functions are core functionality, I am at 
>> a loss as to how they can not be defined. I have the protege.jar (3.3.1 
>> and 3.2.1 have been tested), lax.jar and looks-2.1.3.jar files from the 
>> Protege folder, plus antlr.jar and pal.jar from the plugins all included 
>> in my project.
>>
>> Any suggestions on what might be causing core predicates and functions 
>> to fail as "not defined", especially when it works from the Protege app 
>> and worked as API calls until recently?
> 
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