Return list of BXD

5 files changed, 58 insertions, 13 deletions

diff --git a/.guix-shell b/.guix-shell
index 645b8c6..502f4b1 100755
--- a/.guix-shell
+++ b/.guix-shell
@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-#  . .guix-shell -- guile -L .. --fresh-auto-compile --listen=1970
+#  . .guix-shell -- guile -L . --fresh-auto-compile --listen=1970
 
 echo "Create a shell to run tools. In the container"
 
diff --git a/gn/db/mysql.scm b/gn/db/mysql.scm
index c84605d..e35cc69 100644
--- a/gn/db/mysql.scm
+++ b/gn/db/mysql.scm
@@ -1,3 +1,7 @@
+#!
+  Module for handling SQL DB primitives. Note that GN queries should go into gn/data
+!#
+
 (define-module (gn db mysql)
   #:use-module (json)
   #:use-module (ice-9 match)
@@ -5,11 +9,19 @@
   #:use-module (ice-9 iconv)
   #:use-module (ice-9 receive)
   #:use-module (ice-9 string-fun)
+  #:use-module (rnrs base)
+  #:use-module (dbi dbi)
 
   #:export (
-            open-db
-            )
-)
+            db-check
+            ))
 
-(define open-db
-  #t)
+(define (db-check db)
+  "Use DBI-style handle to report an error"
+  (match (dbi-get_status db)
+    ((stat . msg) (if (= stat 0)
+                     #t
+                     (begin
+                       (display msg)
+                       (newline)
+                       (assert stat))))))
diff --git a/gn/db/sparql.scm b/gn/db/sparql.scm
index c413b9a..b7d94f3 100644
--- a/gn/db/sparql.scm
+++ b/gn/db/sparql.scm
@@ -1,3 +1,12 @@
+#!
+
+Module for handling SPARQL primitives.
+
+Note that GN queries should go into gn/data - this is currently not
+the case.
+
+!#
+
 (define-module (gn db sparql)
   #:use-module (json)
   #:use-module (ice-9 match)
diff --git a/scripts/precompute/README.md b/scripts/precompute/README.md
index c1f2efc..4c4dc87 100644
--- a/scripts/precompute/README.md
+++ b/scripts/precompute/README.md
@@ -5,3 +5,7 @@ Some work on precompute is documented [here](https://issues.genenetwork.org/topi
 # Install and run
 
 See the header of [precompute-hits.scm](precompute-hits.scm).
+
+# Development
+
+My preferred way of developing is tunneling mysql from a remote, running guile3 in a separate guix shell and geiser-connect from emacs. See my [guix-shell](../../.guix-shell).
diff --git a/scripts/precompute/precompute-hits.scm b/scripts/precompute/precompute-hits.scm
index 7986f6a..fed05ba 100755
--- a/scripts/precompute/precompute-hits.scm
+++ b/scripts/precompute/precompute-hits.scm
@@ -1,20 +1,40 @@
 #! Run from base dir with
 
-. .guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
+.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
 !#
 
 (use-modules (dbi dbi)
              (gn db mysql)
+             (rnrs base)
+             (ice-9 match)
              )
 
 ;; potentially you want to test connection with mysql client:
 ;;
-;;    mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306
+;;    mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;"
 ;;
-(define db_webqtl (dbi-open "mysql" "webqtlout:webqtlout:db_webqtl:tcp:127.0.0.1:3306"))
-(dbi-query db_webqtl "SELECT * FROM ProbeSetXRef LIMIT 3")
-(display (dbi-get_status db_webqtl))
-(let [(row  (dbi-get_row db_webqtl))]
+(define db (dbi-open "mysql" "webqtlout:webqtlout:db_webqtl:tcp:127.0.0.1:3306"))
+(db-check db)
+(dbi-query db "SELECT * FROM ProbeSetXRef LIMIT 3")
+(db-check db)
+; (display (dbi-get_status db_webqtl))
+(let [(row  (dbi-get_row db))]
   (display row)
-)
+  )
+
+(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 (get-rows db)
+  (let [(row  (dbi-get_row db))]
+    (if row
+        (begin
+          (display row)
+          (get-rows db)
+          )
+        #f
+        )
+  ))
+
+(get-rows db)