#! Run from base dir with

. .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm

and with some extra paths

. .guix-shell ruby --expose=/home/wrk/iwrk/opensource/code/genetics/gemma-wrapper/=/gemma-wrapper --expose=/home/wrk/iwrk/opensource/code/genetics/gemma/=/gemma -- env TMPDIR=tmp guile -L . -s ./scripts/precompute/precompute-hits.scm

You may want to forward a mysql port if there is no DB locally

ssh -L 3306:127.0.0.1:3306 -f -N tux02.genenetwork.org

!#

(use-modules (dbi dbi)
             (gn db mysql)
             (gn data dataset)
             (gn data hits)
             (gn data strains)
             (gn util convert)
             (gn runner gemma)
             ; (rnrs base)
             (ice-9 match)
             (srfi srfi-1)
             )


;; potentially you want to test connection with mysql client:
;;
;;    mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;"
;;
;; for now update Locus_old with
;;
;;    update ProbeSetXRef set Locus_old=NULL;

(call-with-db
 (lambda (db)
   (begin
     ;(newline)
     ; (dbi-query db "SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = 1 AND Used_for_mapping='Y' ORDER BY StrainId;")
     ; (let [(row (get-row db))]
     ;  (display row)
     ;  )
     ;(let [(result (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))]
     ;  (display (car result)))

     ;; ---- fetch all known BXD sample/individual/strain names
     (define bxd-strains (bxd-strain-id-names #:map? #t))
     ;(display (assoc 64728 bxd-strains))
     ;(newline)
     ;(newline)
     ;(dbi-query db "SELECT * FROM ProbeSetXRef LIMIT 3")
     ;(let [(row (get-row db))]
     ;  (display row)
     ;  )
     ;(db-check2 db)
     ;(newline)
     ;; ---- get first available dataset for precompute:
     ;; @@ order by dataid - recurse

     (define (get-trait db probeset-id)
       (dbi-query db (string-append "select Id,Chr,Mb,Name,Symbol,description from ProbeSet where Id=" (int-to-string probeset-id) " limit 1"))
       (get-row db)
   )

     (define (run-precompute db prev-id)
       (let [(hit (get-precompute-hit db prev-id))]
         (if hit
             (let* [(data-id (assoc-ref hit "DataId"))
                    (data-id-str (int-to-string data-id))
                    (probesetfreeze-id (assoc-ref hit "ProbeSetFreezeId"))
                    (probeset-id (assoc-ref hit "ProbeSetId"))
                    (trait (get-trait db probeset-id))
                    (trait-name (assoc-ref trait "Name"))
                    (name (dataset-name db probesetfreeze-id))
                    ]
               (display hit)
               (display data-id)
               (newline)
               ;; ---- Get strains and phenotypes for this dataset
               (dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" data-id-str))
               (define id_traits (get-rows-apply db
                                                 (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "value")))
                                                 '()))
               ;; ---- Now we need to make sure that all strains belong to BXD
               (define non-bxd (fold
                                (lambda (strain lst)
                                  (let* [(id (car strain))
                                         (name (assoc id bxd-strains))]
                                    (if name
                                        lst
                                        (append lst `(,name)))))

                                '()
                                id_traits))
               (define traits (map
                               (lambda (t)
                                 (match t
                                   ((id . value) (cons (assoc-ref bxd-strains id) value)
                                    )))
                               id_traits))
               ;; (display traits)
               ;; (if (= 0 (length non-bxd))
               (if (eq? non-bxd '())
                   (begin
                     (set-precompute-hit-status! db data-id-str "GEMMA-START")
                     (run-gemma "BXD" data-id probeset-id probesetfreeze-id name trait-name traits)
                     (set-precompute-hit-status! db data-id-str "GEMMA-DONE"))
                   ;; disable precompute if non-bxd, for now, so it won't try again
                   (set-precompute-hit-status! db data-id-str "NON-BXD"))
               (run-precompute db data-id) ;; next round
               ))))
         (run-precompute db 0) ;; start precompute
)))