From 8e8263c374f84fb9cbd6c3a0da7b7f17e6e06c72 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 9 May 2024 10:33:53 +0200
Subject: Full test for whether a data-id belongs to the BXD

---
 gn/data/strains.scm | 54 ++++++++++++++++++++++++++++++++++++++---------------
 1 file changed, 39 insertions(+), 15 deletions(-)

(limited to 'gn/data')

diff --git a/gn/data/strains.scm b/gn/data/strains.scm
index 4a251d4..7854cfe 100644
--- a/gn/data/strains.scm
+++ b/gn/data/strains.scm
@@ -1,20 +1,23 @@
 (define-module (gn data strains)
-  #: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 cache memoize)
   #:use-module (gn data group)
   #:use-module (gn db mysql)
   #:use-module (gn util convert)
+  #:use-module (ice-9 format)
+  #:use-module (ice-9 iconv)
+  #:use-module (ice-9 match)
+  #:use-module (ice-9 receive)
+  #:use-module (ice-9 string-fun)
+  #:use-module (json)
   #:use-module (web gn-uri)
 
   #:export (
             strain-id-names
+            is-a-bxd?
+            has-bxd?
             bxd-strain-id-names
+            memo-bxd-strain-id-names
             ))
 
 (define* (strain-id-names inbred-set #:key (used-for-mapping? #t))
@@ -27,20 +30,41 @@ used-for-mapping? will say whether the strains/individuals are used for mapping.
    (lambda (db)
      (dbi-query db (string-append "SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = " (int-to-string inbred-set)
                                   (if used-for-mapping?
-                                      ;; " AND Used_for_mapping='Y'"
+                                      " AND Used_for_mapping='Y'"
                                       "")
                                   " ORDER BY StrainId;"))
       (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))))
 
+
+
 (define* (bxd-strain-id-names #:key (used-for-mapping? #f))
   "Return assoc list of tuples of strain id + names. Same as strain-id-names, but just for the BXD
 
 used-for-mapping? will say whether the strains/individuals are used for mapping. Always True, FIXME"
   (filter (lambda (l) l)
-  (map (lambda (l)
-         (let [(id (car l))
-               (name (cdr l))]
-           (if (or (< id 42) (string-contains name "BXD"))
-               l
-               #f))
-         ) (strain-id-names 1 #:used-for-mapping? used-for-mapping?))))
+            (map (lambda (l)
+                   (let [(id (car l))
+                         (name (cdr l))]
+                     (if (or (< id 42) (string-contains name "BXD"))
+                         l
+                         #f))
+                   ) (strain-id-names 1 #:used-for-mapping? used-for-mapping?))))
+
+(define memo-bxd-strain-id-names
+  (memoize bxd-strain-id-names))
+
+(define (is-a-bxd? strain-id)
+  "Is a strain a member of the BXD? For speed we memoize tuples from the DB. Note that we check the DB list, as
+well as the name. This won't work for the parents. We do it this way because the GN table is wrong."
+  (match (assoc strain-id (memo-bxd-strain-id-names))
+    [(id . name) (string-contains name "BXD")]
+    ))
+
+(define (has-bxd? trait-values)
+  "Walk tuples of trait strain-id and value. Check we have at least one BXD. Stops at the first match"
+  (match trait-values
+    [(trait . rest) (match trait
+                      [(strain-id . value) (if (is-a-bxd? strain-id)
+                                               #t
+                                               (has-bxd? rest))])]
+    [() #f]))
-- 
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