#! Step p1 lists traits that need to be computed. This is a script that fetches trait IDs from the GN database directly. The direct database calls are used right now and ought to be turned into a REST API. Run from base dir with . .guix-shell -- guile -L . -s ./scripts/precompute/list-traits-to-compute.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 test connection with mysql client: mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;" to create a clean slate, for now, update Locus_old with update ProbeSetXRef set Locus_old=NULL; you should see MariaDB [db_webqtl]> select count(Locus_old) from ProbeSetXRef where Locus_old != NULL limit 5; +------------------+ | count(Locus_old) | +------------------+ | 0 | +------------------+ Now list the next 1000 trait IDs: . .guix-shell -- guile -L . -s ./scripts/precompute/list-traits-to-compute.scm --next 1000 !# (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) ) (call-with-db (lambda (db) (begin (define bxd-strains (bxd-strain-id-names #:used-for-mapping? #t)) (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-list-traits-to-compute db prev-id count) (let [(hits (get-precompute-hits db prev-id count))] (for-each (lambda (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) (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)) #t)) hits))) (run-list-traits-to-compute db 0 5) ;; start precompute )))