Hi,

I’ve encountered problems constructing nested Boolean expressions in Drools 5.0 using the prefixOr syntax.  We’re using Drools to build a genome annotation system at the Venter Institute.     The following example rule assigns an annotation if there is a blast hit to a gene GB|AAQ16631.1, or either a blast hit to gene GB|AAQ16631.1, or to any gene within 500 bases of a gene with an HMM hit to TIGR00905.  I’ve left off some details to focus on how we are structuring the syntax of our prefixOr and prefixAnd expressions.

The Drools parser throws errors when it encounters the 2^nd “blast_hit” statement in the example below.  Our prefixOr and prefixAnd expressions work as expected when we use similar syntax, at least until we attempt to use nested or expressions.

rule "2645|lysine decarboxylase CadA"

when

      (or

            (and

                  blast_hit : BlastHit( hitId=='GB|AAQ16631.1')

                  gene1 : Feature( featureId == blast_hit.queryId )

            )

            (or

                  (and

                        blast_hit : BlastHit( hitId=='GB|AAQ16631.1' )

                        gene1 : Feature( featureId == blast_hit.queryId )

                  )

                  (and

                        hmm_hit1 : HmmHit( hitId=='TIGR00905' )

                        gene1 : Feature( featureId == hmm_hit1.queryId )

                        gene2 : Feature( eval(gene2.isWithin(gene1, 500)) )

                  )

            )

      )

then

      Annotation a = new Annotation("lysine decarboxylase CadA");

      gene1.addAnnotation(a);

end

Any suggestions are much appreciated.

Thanks,

Nelson