is this query in scope for sparql-exists

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.