Precompute will run gemma and update the DB status

2 files changed, 18 insertions, 3 deletions

diff --git a/gn/data/hits.scm b/gn/data/hits.scm
index 5108bd0..29d377b 100644
--- a/gn/data/hits.scm
+++ b/gn/data/hits.scm
@@ -15,6 +15,7 @@
   #:export (
             get-precompute-hit
             set-precompute-hit-status!
+            update-precompute!
             ))
 
 (define (get-precompute-hit db prev-id)
@@ -22,9 +23,19 @@
   (get-row db))
 
 (define (set-precompute-hit-status! db data-id-str status-str)
-  "Set status of precompute record - typically 'RUN' or 'NON-BXD'.
+  "Set status of precompute record - typically from NULL to 'GEMMA-START' or 'NON-BXD'.
+On completion it is set to 'GEMMA-DONE'.
 This is a temporary measure to get precompute going.
 Note we are counting on automated MariaDB transactions to not compete."
   (dbi-query db (string-append "UPDATE ProbeSetXRef SET Locus_old=\"" status-str "\" WHERE DataId=" data-id-str " AND Locus_old is NULL"))
   (ensure db)
   )
+
+;; MariaDB [db_webqtl]> UPDATE ProbeSetXRef SET Locus_old=Locus,LRS_old=LRS,Locus="new",LRS=9.9,pValue=1.0,additive=1.0 WHERE ProbeSetFreezeId=1 AND DataId=2 AND Locus_old="GEMMA-START" ;
+
+(define (update-precompute! db data-id-str status-str locus lrs pvalue, additive)
+  "Once precompute is run we can update the table moving old values and plugging in the new.
+"
+  (dbi-query db (string-append "UPDATE ProbeSetXRef SET Locus_old=Locus,LRS_old=LRS,Locus=\"" locus "\",LRS=" lrs ",pValue=" pvalue ",additive=" additive " WHERE DataId=" data-id-str " AND Locus_old is \"GEMMA-START\""))
+  (ensure db)
+  )
diff --git a/gn/runner/gemma.scm b/gn/runner/gemma.scm
index 2edb7b2..a31846a 100644
--- a/gn/runner/gemma.scm
+++ b/gn/runner/gemma.scm
@@ -13,10 +13,11 @@
             ))
 
 (define (run-gemma population data-id name trait-name traits)
+  "Run gemma-wrapper to compute GRM and GWA. On failure the run will stop(!)"
   (define bxd-inds (geno-inds-bxd "BXD.json"))
   (assert (= 235 (length bxd-inds)))
   (if name
-      (display (string-append "WE HAVE OUR BXD DATASET " name " and trait " trait-name " for precompute!\n")))
+      (display (string-append "WE HAVE OUR " population " DATASET " name " and trait " trait-name " for precompute!\n")))
   (display data-id)
   (display traits)
   (newline)
@@ -38,7 +39,9 @@
                         (newline)
                         (display outvalue port)
                         (newline port))))
-                  bxd-inds)))
+                  bxd-inds)
+        (close port)
+       ))
 
     ;; set up with ./.guix-shell -- guile -L . -s ./scripts/precompute/precompute-hits.scm
 
@@ -56,4 +59,5 @@
     (delete-file k-json-fn)
     (rmdir tmpdir)
     )
+  #t
   )