From b1c2e3a1d5e7756c774515cc3bc55447591e8cf1 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 16 May 2024 03:43:49 -0500
Subject: Write json file for traits

---
 README.md                                     |  2 ++
 scripts/precompute/list-traits-to-compute.scm | 18 ++++++++++++------
 2 files changed, 14 insertions(+), 6 deletions(-)

diff --git a/README.md b/README.md
index 7c5a47c..6005264 100644
--- a/README.md
+++ b/README.md
@@ -18,10 +18,12 @@ GNU Guile allows you to develop against a live running web server using emacs-ge
 
 ```sh
 cd web
+unset GUIX_PROFILE
 . .guix-shell -- guile --listen=1970 -e main ./webserver.scm 8091
 ```
 
 Note the leading dot. The .guix-shell is defined in `genenetwork3/gn3-guile/web` and loads required packages using GNU Guix.
+If you are on Debian you may need to unset GUIX_PROFILE first.
 
 Next fire up emacs with `emacs-geiser-guile` and connect to the running web server with `M-x geiser-connect` and the port `1970`. Now you can not only inspect procedures, but also update any prodedure on the live server using `C-M-x` and get updated output from the webserver!
 
diff --git a/scripts/precompute/list-traits-to-compute.scm b/scripts/precompute/list-traits-to-compute.scm
index ea3a013..75e121a 100755
--- a/scripts/precompute/list-traits-to-compute.scm
+++ b/scripts/precompute/list-traits-to-compute.scm
@@ -19,6 +19,10 @@ test connection with mysql client:
 
     mysql -uwebqtlout -pwebqtlout -A -h 127.0.0.1 -P 3306 db_webqtl -e "show tables;"
 
+you can ignore the IPv6 message:
+
+    bind [::1]:3306: Cannot assign requested address
+
 to create a clean slate, for now, update Locus_old with
 
     update ProbeSetXRef set Locus_old=NULL;
@@ -69,6 +73,7 @@ When that is the case we might as well write the phenotype file because we have
              ; (rnrs base)
              (ice-9 getopt-long)
              (ice-9 match)
+             (ice-9 textual-ports)
              (json)
              (srfi srfi-1)
              )
@@ -77,12 +82,13 @@ When that is the case we might as well write the phenotype file because we have
 (define (write-json id recs)
   (display id)
   (newline)
-  (write (scm->json-string (map (lambda (r)
-                                  (match (pk r)
-                                    [(strain-id . value) (cons (bxd-name strain-id) value)]
-                                 ))
-                           (reverse recs))))
-  (newline)
+  (call-with-output-file (string-append (number->string id) ".json")
+    (lambda (port)
+      (put-string port (scm->json-string (map (lambda (r)
+                                                (match r
+                                                  [(strain-id . value) (cons (bxd-name strain-id) value)]
+                                                  ))
+                                              (reverse recs))))))
   )
 
 (define (write-phenotypes first-id num batch-size)
-- 
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