diff options
| -rw-r--r-- | gn/data/dataset.scm | 23 | ||||
| -rw-r--r-- | gn/data/hits.scm | 2 | ||||
| -rwxr-xr-x | scripts/precompute/precompute-hits.scm | 22 |
3 files changed, 42 insertions, 5 deletions
diff --git a/gn/data/dataset.scm b/gn/data/dataset.scm new file mode 100644 index 0000000..5e81d1e --- /dev/null +++ b/gn/data/dataset.scm @@ -0,0 +1,23 @@ +(define-module (gn data dataset) + #:use-module (json) + #:use-module (ice-9 match) + #:use-module (ice-9 format) + #:use-module (ice-9 iconv) + #:use-module (ice-9 receive) + #:use-module (ice-9 string-fun) + ;; #:use-module (gn db sparql) + #:use-module (dbi dbi) + #:use-module (gn db mysql) + #:use-module (gn data group) + #:use-module (gn util convert) + #:use-module (web gn-uri) + + #:export ( + dataset-name + )) + +(define (dataset-name db probesetfreeze-id) + (dbi-query db + (string-append + "select Name2 from ProbeSetFreeze where Id=" (int-to-string probesetfreeze-id) " limit 1;")) + (assoc-ref (get-row db) "Name2")) diff --git a/gn/data/hits.scm b/gn/data/hits.scm index a66eee5..f0a24f3 100644 --- a/gn/data/hits.scm +++ b/gn/data/hits.scm @@ -17,5 +17,5 @@ )) (define (get-next-hit-for-precompute db prev-id) - (dbi-query db (string-append "select Locus, DataId, ProbeSetId from ProbeSetXRef where DataId>" (int-to-string prev-id) " AND Locus_old is NULL ORDER BY DataId LIMIT 1")) + (dbi-query db (string-append "select Locus, DataId, ProbeSetId, ProbeSetFreezeId from ProbeSetXRef where DataId>" (int-to-string prev-id) " AND Locus_old is NULL ORDER BY DataId LIMIT 1")) (get-row db)) diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm index 0088431..d8170db 100755 --- a/scripts/precompute/precompute-hits.scm +++ b/scripts/precompute/precompute-hits.scm @@ -6,6 +6,7 @@ (use-modules (dbi dbi) (gn db mysql) + (gn data dataset) (gn data hits) (gn data strains) (gn util convert) @@ -35,7 +36,7 @@ ;(newline) (define bxd-strains (bxd-strain-id-names #:map? #t)) - ;(display (assoc 64728 bxd-strains)) + ;(display (assoc 64728 bxd-strains)) ;(newline) ;(newline) ;(dbi-query db "SELECT * FROM ProbeSetXRef LIMIT 3") @@ -47,15 +48,26 @@ ;; ---- get first available dataset for precompute: ;; @@ order by dataid - recurse + (define (get-trait-name db probeset-id) + (dbi-query db (string-append "select Name,Symbol from ProbeSet where Id=" (int-to-string probeset-id) " limit 1")) + (get-row db) + ) (define (run-precompute db prev-id) (let* [(hit (get-next-hit-for-precompute db prev-id)) - (data-id (assoc-ref hit "DataId"))] + (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-name db probeset-id)) + (trait-name (assoc-ref trait "Name")) + ] (display hit) (display data-id) (newline) + (define name (dataset-name db probesetfreeze-id)) ;; ---- Get strains and phenotypes for this dataset - (dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" (int-to-string data-id))) + (dbi-query db (string-append "SELECT StrainId,value from ProbeSetData WHERE Id=" data-id-str)) (define traits (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "value"))) '())) @@ -71,10 +83,12 @@ traits)) (if (= 0 (length non-bxd)) (begin - (display "WE HAVE OUR BXD DATASET for precompute!\n") + (if name + (display (string-append "WE HAVE OUR BXD DATASET " name " and trait " trait-name " for precompute!\n"))) (display data-id) (display traits) (newline) + )) (run-precompute db data-id) )) |