From 91ed2e9f0f1c5bd96b4378db0cdfe88fdbb4d01a Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sun, 5 May 2024 14:06:55 +0200
Subject: Trait IDs fetch in batch

---
 gn/data/hits.scm                              |  8 ++-
 scripts/precompute/list-traits-to-compute.scm | 80 +++++++++++++--------------
 2 files changed, 43 insertions(+), 45 deletions(-)

diff --git a/gn/data/hits.scm b/gn/data/hits.scm
index 94b4749..f7ce49e 100644
--- a/gn/data/hits.scm
+++ b/gn/data/hits.scm
@@ -13,14 +13,18 @@
   #:use-module (web gn-uri)
 
   #:export (
+            get-precompute-hits
             get-precompute-hit
             set-precompute-hit-status!
             update-precompute!
             ))
 
+(define (get-precompute-hits db prev-id num)
+  (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 " (format #f "~d" num)))
+  (get-rows db '()))
+
 (define (get-precompute-hit db prev-id)
-  (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))
+  (car (get-precompute-hits db prev-id 1)))
 
 (define (set-precompute-hit-status! db data-id-str status-str)
   "Set status of precompute record - typically from NULL to 'GEMMA-START' or 'NON-BXD'.
diff --git a/scripts/precompute/list-traits-to-compute.scm b/scripts/precompute/list-traits-to-compute.scm
index 3cba292..68f0711 100755
--- a/scripts/precompute/list-traits-to-compute.scm
+++ b/scripts/precompute/list-traits-to-compute.scm
@@ -59,47 +59,41 @@ Now list the next 1000 trait IDs:
        (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 [(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)
-               (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))
-               (if (eq? non-bxd '())
-                   (set-precompute-hit-status! db data-id-str "GEMMA-START")
-                   ;; disable precompute if non-bxd, for now, so it won't try again
-                   (set-precompute-hit-status! db data-id-str "NON-BXD"))
-               (if (> count 0)
-                   (run-list-traits-to-compute db data-id (- count 1)) ;; next round
-                   )
-               ))))
+       (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
-)))
+       )))
-- 
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