Move procedures into mysql.scm and add documentation

2 files changed, 44 insertions, 28 deletions

diff --git a/gn/db/mysql.scm b/gn/db/mysql.scm
index e35cc69..f6513af 100644
--- a/gn/db/mysql.scm
+++ b/gn/db/mysql.scm
@@ -14,10 +14,13 @@
 
   #:export (
             db-check
+            db-display-rows
+            db-get-rows
+            db-get-rows-apply
             ))
 
 (define (db-check db)
-  "Use DBI-style handle to report an error"
+  "Use DBI-style handle to report an error. On error the program will stop."
   (match (dbi-get_status db)
     ((stat . msg) (if (= stat 0)
                      #t
@@ -25,3 +28,37 @@
                        (display msg)
                        (newline)
                        (assert stat))))))
+
+(define (db-display-rows db)
+  (let [(row  (dbi-get_row db))]
+    (if row
+        (begin
+          (display row)
+          (get-rows db)
+          )
+        #t)))
+
+(define (db-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:
+
+    (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)
+    (display (db-get-rows db '()))
+
+    (((StrainId . 4) (Name . BXD1)) ((StrainId . 5) (Name . BXD2))...
+"
+  (let [(row (dbi-get_row db))]
+    (if row
+        (db-get-rows db (append list `(,row)))
+        list)))
+
+(define (db-get-rows-apply db func list)
+  "Similar to db-get-rows with a function that gets applied on every record, e.g.
+
+    (define ids (db-get-rows-apply db (lambda (r) `(,(assoc-ref r \"StrainId\") . ,(assoc-ref r \"Name\"))) '()))
+
+"
+  (let [(row (dbi-get_row db))]
+    (if row
+        (db-get-rows-apply db func (append list `(,(func row))))
+        list)))
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index 22bf2d7..cc26a9a 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -26,31 +26,10 @@
 (dbi-query db "SELECT StrainId,Strain.Name FROM Strain, StrainXRef WHERE StrainXRef.StrainId = Strain.Id AND StrainXRef.InbredSetId = 1 AND Used_for_mapping='Y' ORDER BY StrainId;")
 (db-check db)
 
-(define (display-rows db)
-  (let [(row  (dbi-get_row db))]
-    (if row
-        (begin
-          (display row)
-          (get-rows db)
-          )
-        #f
-        )
-  ))
+(define ids (db-get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))
 
-(define (get-rows db list)
-  (let [(row (dbi-get_row db))]
-    (if row
-        (get-rows db (append list `(,row)))
-        list
-        )))
-
-(define (get-rows-apply db func list)
-  (let [(row (dbi-get_row db))]
-    (if row
-        (get-rows-apply db func (append list `(,(func row))))
-        list
-        )))
-
-; (display (get-rows db '()))
-
-(display (get-rows-apply db (lambda (r) `(,(assoc-ref r "StrainId") . ,(assoc-ref r "Name"))) '()))
+(newline)
+(display (car ids))
+(newline)
+(display (assoc 5 ids))
+(newline)