Re: [OWLAPI-developer] Class label issue when parsing DL query to class expression

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Matthew's diagnosis was correct.  You need to setup the OWLEntityChecker 
correctly.

I was struck by the fact that this works in Protege 4 so it seemed a bit 
less likely that this was an OWL api bug.  I made a test (attached) and 
it parsed your expression without any trouble.

-Timothy

On 07/30/2012 02:13 AM, Dani Welter wrote:
> Query that works in Protege but not in code: 'GWAS study' and 
> has_publication_date some dateTime[< 
> "2009-01-01T00:00:00+00:00"^^dateTime]
>
> Query that works in both cases: chromosome and  has_part value 
> band_10p15.1
>
> Exception for first query:
> org.semanticweb.owlapi.expression.ParserException: Encountered 'GWAS 
> study' at line 1 column 1. Expected one of:
>     Class name
>     Object property name
>     Data property name
>     not
>     inverse
>     (
>     {
>
>     at 
> org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.createException(ManchesterOWLSyntaxEditorParser.java:2969)
>     at 
> org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseNonNaryClassExpression(ManchesterOWLSyntaxEditorParser.java:801)
>     at 
> org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseUnion(ManchesterOWLSyntaxEditorParser.java:687)
>     at 
> org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseIntersection(ManchesterOWLSyntaxEditorParser.java:662)
>     at 
> org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxEditorParser.parseClassExpression(ManchesterOWLSyntaxEditorParser.java:649)
>     at 
> org.coode.owlapi.manchesterowlsyntax.ManchesterOWLSyntaxClassExpressionParser.parse(ManchesterOWLSyntaxClassExpressionParser.java:72)
>     at 
> uk.ac.ebi.fgpt.StuffTester.DLQueryTester.main(DLQueryTester.java:134)
>
>
> Code used for the parser:
>
> List<OWLAnnotationProperty> properties = Arrays.asList(df.getRDFSLabel());
> AnnotationValueShortFormProvider annoSFP = new 
> AnnotationValueShortFormProvider(
>                     properties, new HashMap<OWLAnnotationProperty, 
> List<String>>(), manager);
> ShortFormEntityChecker checker = new ShortFormEntityChecker(new 
> BidirectionalShortFormProviderAdapter(manager, 
> manager.getOntologies(), annoSFP));
> ManchesterOWLSyntaxClassExpressionParser parser = new 
> ManchesterOWLSyntaxClassExpressionParser(df, checker);
> String query1 = "'GWAS study' and  has_publication_date some 
> dateTime[< \"2009-01-01T00:00:00+00:00\"^^dateTime]";
> OWLClassExpression pre2009 = parser.parse(query1);
>
>
> Thanks
> Dani
>
>
> On 27/07/12 19:30, Ignazio Palmisano wrote:
>>
>>
>> On Jul 27, 2012 3:01 PM, "Dani Welter" <dw...@eb... 
>> <mailto:dw...@eb...>> wrote:
>> >
>> > Hi,
>> >
>> > I'm trying to parse DL queries in Manchester syntax into class
>> > expressions using the ManchesterOWLSyntaxClassExpressionParser but fail
>> > at the following problem: most of my class labels have a space in them
>> > (e.g. 'GWAS study', 'cytogenetic band' etc). In the DL query tab in
>> > Protege, this is easily solved by surrounding the name with single
>> > quotes but in my program, for some reason, this is interpreted as the
>> > label starting with a single quote, which throws a ParserException. 
>> I've
>> > tried various combinations of double quotes and + or %20 to replace
>> > space etc but no success. The rest of the code is definitely correct as
>> > the query parser works fine if the query starts with a single-word 
>> class
>> > name.
>> >
>> > Any suggestions for fixes/work-arounds (other than manually build the
>> > query)?
>>
>> It's clearly a bug with that parser. I'm not sure if there is another 
>> parser that you can use to work around the issue. Can you post an 
>> example query that works in protégé and gives you troubles in code? 
>> It makes it easier to write junit  tests.
>>
>> I.
>>
>> >
>> > Thanks
>> > Dani
>> >
>> > 
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