PATCH: optimize generate-result

Pursuant to comment https://github.com/MOZI-AI/annotation-scheme/issues/98#issuecomment-571891078 and similar to issue #103 the speed of biogrid annotation can be more than doubled, with the code below. Viz, before, the patch, perf is this:

Time: 2945.8490 secs. calls: 75 avg: 39277986.8 usec/call for find-output-interactors
Time: 2067.2802 secs. calls: 46366 avg:  44586.1 usec/call for generate-result

after patching, its this:

Time: 1409.3709 secs. calls: 75 avg: 18791612.0 usec/call for find-output-interactors
Time: 330.18767 secs. calls: 45971 avg:   7182.5 usec/call for generate-result

The patch is this (i'm not making a pull req, because it requires additional cleanup for production code) Also, plenty more optimization opportunities are readily available in this code-block.

(define-public (xgenerate-result gene-a gene-b prot go)
      (let* (
            [output (find-pubmed-id gene-a gene-b)]
            [res (filter
               (lambda (ggg) (not (reported-genes ggg)))
               (list gene-a gene-b))]
            [pairs (reported-grid-pairs (Set gene-a gene-b))]

            [interaction (if (= 1 (string->number (cog-name prot)))
                (ListLink
                  (build-interaction gene-a gene-b output "interacts_with")
                  (build-interaction (find-protein-form gene-a) (find-protein-form gene-b) output "inferred_interaction"))
                (build-interaction gene-a gene-b output "interacts_with"))]
            [namespace (if (null? (cog-outgoing-set go)) '() (car (cog-outgoing-set go)))]
            [parent (if (null? (cog-outgoing-set go)) '() (cadr (cog-outgoing-set go)))]
          )

and the rest of the function is more-or-less same as before, except:

delete biogrid-pairs and biogrid-genes they are not needed

delete GeneNode its already an atom. So this gives:

      (if (null? interaction)
        (ListLink)
      )
      (match res
          ((a b)
              (begin
                  (if (= 1 (string->number (cog-name prot)))
                    (let ([coding-prot-a (find-protein-form a)]
                          [coding-prot-b (find-protein-form b)])
                    (if (or (equal? coding-prot-a (ListLink)) (equal? coding-prot-b (ListLink)))
                      (ListLink)
                      (ListLink
                        interaction
                        (Evaluation (Predicate "expresses") (ListLink a coding-prot-a))
                        (node-info a)
                        (node-info coding-prot-a)
                        (locate-node coding-prot-a)
                        (EvaluationLink (PredicateNode "expresses") (ListLink b coding-prot-b))
                        (node-info b)
                        (node-info coding-prot-b)
                        (locate-node coding-prot-b))  ;;; <<< bug fix here
                    ))
                  (ListLink
                      interaction
                      (node-info a)
                      (locate-node  a)
                      (node-info b)
                      (locate-node  b)
                      (if (not (null? namespace))
                      (ListLink
                        (ConceptNode "gene-go-annotation")
                        ; bug fix here!!! 
                        (find-go-term a (string-split (cog-name namespace) #\ ) (string->number (cog-name parent)))
                        (find-go-term b (string-split (cog-name namespace) #\ ) (string->number (cog-name parent)))
                        (ListLink (ConceptNode "biogrid-interaction-annotation"))
                        )
                        '() )
                  )
              ))
          )
          ((a)
              (begin
                  (if (= 1 (string->number (cog-name prot)))
                    (let ([coding-prot (find-protein-form a)])
                    (if (equal? coding-prot (ListLink))
                      (ListLink)
                      (ListLink
                        interaction
                        (EvaluationLink (PredicateNode "expresses") (ListLink a coding-prot))
                        (node-info a)
                        (node-info coding-prot)
                        (locate-node coding-prot))
                    ))
                  (ListLink
                      interaction
                      (node-info a)
                      (locate-node  a)
                      (if (not (null? namespace))
                      (ListLink (ConceptNode "gene-go-annotation")
                         (find-go-term a
                         (string-split (cog-name namespace) #\ )
                         (string->number (cog-name parent)))
                      (ListLink (ConceptNode "biogrid-interaction-annotation"))
                      )
                      '()
                      ))
              ))
          )
          (()
              (if pairs
                (ListLink)
                (ListLink
                      interaction
                  )
              )
          )
      )
  )
)

Note that the above also contains three bug fixes: two to find-go-term and one to (locate-node coding-prot-b)) ;;; <<< bug fix here

MOZI-AI / annotation-scheme

PATCH: optimize generate-result #106

135 contains one bug fix mentioned above.