Re: is this query in scope for sparql-exists

Thank you so much for your attention.
I have filed a bug with the implementor.

Jeremy 



> On Sep 27, 2016, at 5:13 AM, Peter F. Patel-Schneider <pfpschneider@gmail.com> wrote:
> 
> It appears that the SPARQL implementation that you are using is somehow losing
> the binding for ?MDxReport_B.  As far as I can tell, this is a bug in the
> implementation and not a problem with the SPARQL specification.  Therefore
> this is not in scope for the CG.
> 
> 
> peter
> 
> 
> On 09/26/2016 10:39 PM, Jeremy J Carroll wrote:
>> Questions:
>> with my example (1) below:
>> A) is this an example of the defect that this group is addressing
>> B) is my workaround (3) appropriate:
>>   In particular, I would like this to be as ‘standards
>> conferment’/interoperable as possible, given a bug in the spec.
>> 
>> This query is matching cancer patients to potential experimental therapies
>> matching their genetic profile.
>> 
>> If A is answered in the affirmative, please feel free to use this query in any
>> documentation you are developing.
>> 
>> thanks
>> 
>> Jeremy
>> Senior Principal Architect, Syapse Inc.
>> 
>> 
>> I have had an issue with the scope of the ?MDxReport_B variable in the
>> following double negation (for all, expressed, as NOT EXISTS NOT)
>> 
>> (1) 
>> 
>> SELECT *
>> WHERE {
>>  ?Therapy_A rdf:type foo:Therapy .
>>  ?MDxReport_B rdf:type foo:fooMolecularResultsReport .
>>  ?MDxReport_B foo:hasPatient ?Patient_A .
>> 
>>  ?Patient_A rdf:type foo:Patient .
>>  ?MDxReport_B foo:hasNegativeFinding/foo:gene $j__4 .
>>  ?Therapy_A foo:hasGeneEligibilityCriteria/foo:hasNegativeFinding/foo:gene  $j__4
>>  FILTER NOT EXISTS { 
>>    ?hasGeneEligibilityCriteria_A rdf:type foo:GeneEligibilityCriteria .
>>    ?Therapy_A foo:hasGeneEligibilityCriteria ?hasGeneEligibilityCriteria_A .
>>    ?hasGeneEligibilityCriteria_A foo:isRequiredCriteria True .
>>    ?hasGeneEligibilityCriteria_A foo:criteriaType 'Inclusion'
>>    FILTER NOT EXISTS { 
>>      ?MDxReport_B foo:hasNegativeFinding/foo:gene $j__5 .
>>      ?hasGeneEligibilityCriteria_A foo:hasNegativeFinding/foo:gene  $j__5
>>    }
>>  }
>>  }
>> 
>> 
>> This is being executed as if it were:
>> 
>> 
>> (2)
>> 
>> SELECT *
>> WHERE {
>>  ?Therapy_A rdf:type foo:Therapy .
>>  ?MDxReport_B rdf:type foo:fooMolecularResultsReport .
>>  ?MDxReport_B foo:hasPatient ?Patient_A .
>> 
>>  ?Patient_A rdf:type foo:Patient .
>>  ?MDxReport_B foo:hasNegativeFinding/foo:gene $j__4 .
>>  ?Therapy_A foo:hasGeneEligibilityCriteria/foo:hasNegativeFinding/foo:gene  $j__4
>>  FILTER NOT EXISTS { 
>>    ?hasGeneEligibilityCriteria_A rdf:type foo:GeneEligibilityCriteria .
>>    ?Therapy_A foo:hasGeneEligibilityCriteria ?hasGeneEligibilityCriteria_A .
>>    ?hasGeneEligibilityCriteria_A foo:isRequiredCriteria True .
>>    ?hasGeneEligibilityCriteria_A foo:criteriaType 'Inclusion'
>>    FILTER NOT EXISTS { 
>>      ?A_different_MDxReport_B foo:hasNegativeFinding/foo:gene $j__5 .
>>      ?hasGeneEligibilityCriteria_A foo:hasNegativeFinding/foo:gene  $j__5
>>    }
>>  }
>>  }
>> 
>> 
>> 
>> where the variable in the doubly-nested EXISTS is not treated as the same variable as in the outer graph pattern
>> 
>> 
>> It seems I can fix this by simply repeating the type triple:
>> 
>> 
>> (3)
>> 
>> 
>> SELECT *
>> WHERE {
>>  ?Therapy_A rdf:type foo:Therapy .
>>  ?MDxReport_B rdf:type foo:fooMolecularResultsReport .
>>  ?MDxReport_B foo:hasPatient ?Patient_A .
>> 
>>  ?Patient_A rdf:type foo:Patient .
>>  ?MDxReport_B foo:hasNegativeFinding/foo:gene $j__4 .
>>  ?Therapy_A foo:hasGeneEligibilityCriteria/foo:hasNegativeFinding/foo:gene  $j__4
>>  FILTER NOT EXISTS { 
>> 
>>    ?MDxReport_B rdf:type foo:fooMolecularResultsReport .
>> 
>>    ?hasGeneEligibilityCriteria_A rdf:type foo:GeneEligibilityCriteria .
>>    ?Therapy_A foo:hasGeneEligibilityCriteria ?hasGeneEligibilityCriteria_A .
>>    ?hasGeneEligibilityCriteria_A foo:isRequiredCriteria True .
>>    ?hasGeneEligibilityCriteria_A foo:criteriaType 'Inclusion'
>>    FILTER NOT EXISTS { 
>>      ?MDxReport_B foo:hasNegativeFinding/foo:gene $j__5 .
>>      ?hasGeneEligibilityCriteria_A foo:hasNegativeFinding/foo:gene  $j__5
>>    }
>>  }
>>  }
>> 
>> 
>> and then the SPARQL implementation I am using does seem to see that all
>> instances of ?MDxReport_B
>> are one and the same variable.
>> 
>> 
>> 
>> 
>> 
>>

Received on Tuesday, 27 September 2016 16:15:28 UTC