From b1db013cc01c94e27edf982be9b027a2b0bb9712 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 18 Nov 2023 12:33:22 +0100
Subject: Get first BXD dataset for precompute

---
 gn/data/strains.scm |  5 +++--
 gn/db/mysql.scm     |  2 +-
 gn/util/convert.scm | 14 ++++++++++++++
 3 files changed, 18 insertions(+), 3 deletions(-)
 create mode 100644 gn/util/convert.scm

(limited to 'gn')

diff --git a/gn/data/strains.scm b/gn/data/strains.scm
index 241ecda..39fe71e 100644
--- a/gn/data/strains.scm
+++ b/gn/data/strains.scm
@@ -7,8 +7,9 @@
   #: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 db mysql)
+  #:use-module (gn util convert)
   #:use-module (web gn-uri)
 
   #:export (
@@ -24,7 +25,7 @@ map? will say whether the strains/individuals are used for mapping.
 "
   (call-with-db
    (lambda (db)
-     (dbi-query db (string-append "SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = " (format #f "~d" inbred-set)
+     (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 map?
                                       " AND Used_for_mapping='Y'"
                                       "")
diff --git a/gn/db/mysql.scm b/gn/db/mysql.scm
index 4e2b280..fb7093a 100644
--- a/gn/db/mysql.scm
+++ b/gn/db/mysql.scm
@@ -50,7 +50,7 @@
   (dbi-get_row db))
 
 (define (get-rows db list)
-  "After running dbi-query we can fetch all rows and return them as a list of records, which are assoc list:
+  "After running dbi-query we can fetch all rows and return them as a list of records, which is an alist:
 
     (dbi-query db \"SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = 1 ORDER BY StrainId;\")
     (db-check db)
diff --git a/gn/util/convert.scm b/gn/util/convert.scm
new file mode 100644
index 0000000..ff943e0
--- /dev/null
+++ b/gn/util/convert.scm
@@ -0,0 +1,14 @@
+(define-module (gn util convert)
+  #: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)
+
+  #:export (
+            int-to-string
+            ))
+
+(define (int-to-string i)
+  (format #f "~d" i))
-- 
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