diff options
| -rw-r--r-- | gn/data/hits.scm | 6 | ||||
| -rwxr-xr-x | scripts/precompute/list-traits-to-compute.scm | 34 |
2 files changed, 24 insertions, 16 deletions
diff --git a/gn/data/hits.scm b/gn/data/hits.scm index 88dee11..a7ba45a 100644 --- a/gn/data/hits.scm +++ b/gn/data/hits.scm @@ -20,20 +20,22 @@ update-precompute! hit-data-id hit-probeset-id + hit-probesetfreeze-id )) (define-record-type <hit> - (make-hit data-id probeset-id) + (make-hit data-id probeset-id probesetfreeze-id) hit? (data-id hit-data-id) (probeset-id hit-probeset-id) + (probesetfreeze-id hit-probesetfreeze-id) ) (define (get-precompute-hits db first-id num) (dbi-query db (string-append "select Locus, DataId, ProbeSetId, ProbeSetFreezeId from ProbeSetXRef where DataId>" (int-to-string first-id) " AND Locus_old is NULL ORDER BY DataId LIMIT " (format #f "~d" num))) (map (lambda (r) - (make-hit (assoc-ref r "DataId") (assoc-ref r "ProbeSetId"))) + (make-hit (assoc-ref r "DataId") (assoc-ref r "ProbeSetId") (assoc-ref r "ProbeSetFreezeId"))) (get-rows db '()) )) diff --git a/scripts/precompute/list-traits-to-compute.scm b/scripts/precompute/list-traits-to-compute.scm index 199f457..9a548b7 100755 --- a/scripts/precompute/list-traits-to-compute.scm +++ b/scripts/precompute/list-traits-to-compute.scm @@ -108,17 +108,20 @@ The following is produced by gemma-wrapper as metadata !# -(define (write-json-ld id dataset-id recs) +(define (write-json-ld id name trait trait-name probeset-id recs) ;; see also https://www.w3.org/2018/jsonld-cg-reports/json-ld/ (display id) (display ":") - (display dataset-id) + (display name) + (display ":") + (display trait-name) (newline) (let* [(traits (map (lambda (r) (match r [(strain-id . value) (cons (bxd-name strain-id) value)] )) (reverse recs))) + (uri (format #f "https://genenetwork.org/show_trait?trait_id=~a&dataset=~a" trait-name name)) (sha256 (sha-256->string (sha-256 (string->utf8 (scm->json-string traits))))) (json-data `(("@context" . "https://genenetwork.org/resource") (type . traits) @@ -128,8 +131,11 @@ The following is produced by gemma-wrapper as metadata (time . ,(date->string (time-utc->date (current-time)))))) (data . ((,id . - ((dataset . ,dataset-id) - (traits . ,traits)))))))] + ((probeset-id . ,probeset-id) + (name . ,name) + (trait-name . ,trait-name) + (traits . ,traits) + (uri . ,uri)))))))] (call-with-output-file (string-append (number->string id) ".json") (lambda (port) (put-string port (scm->json-string json-data)))) @@ -172,19 +178,19 @@ The following is produced by gemma-wrapper as metadata id-traits) ;; --- create the json output as a file (for-each (lambda (r h) - ;; (let* [;; (probeset-id (assoc-ref hit "ProbeSetId")) - ;; (data-id (assoc-ref hit "DataId")) - ;; (data-id-str (int-to-string data-id)) - ;; (probesetfreeze-id (assoc-ref hit "ProbeSetFreezeId")) - ;; (trait (get-trait db probeset-id)) - ;; (trait-name (assoc-ref trait "Name")) - ;; (name (dataset-name db probesetfreeze-id)) - ;; ] + (let* [ + (probeset-id (hit-probeset-id h)) + ;; (data-id-str (int-to-string id)) + (probesetfreeze-id (hit-probesetfreeze-id h)) + (name (dataset-name db probesetfreeze-id)) + (trait (get-trait db probeset-id)) + (trait-name (assoc-ref trait "Name")) + ] (match r ((id . recs) (if (has-bxd? recs) - (write-json-ld id (hit-probeset-id h) recs) + (write-json-ld id name trait trait-name probeset-id recs) )) - )) nrecs hits) + ))) nrecs hits) (if (> rest 0) (run-list-traits-to-compute db rest (first (reverse data-ids)))) ;; start precompute ))) |