for-each can take multiple lists, nice!

1 files changed, 29 insertions, 6 deletions

diff --git a/scripts/precompute/list-traits-to-compute.scm b/scripts/precompute/list-traits-to-compute.scm
index 08ed48d..5c3dfa3 100755
--- a/scripts/precompute/list-traits-to-compute.scm
+++ b/scripts/precompute/list-traits-to-compute.scm
@@ -81,6 +81,26 @@ When that is the case we might as well write the phenotype file because we have
              (srfi srfi-19) ; time
              )
 
+#!
+
+The following is produced by gemma-wrapper as metadata
+
+  "meta": {
+    "type": "gemma-wrapper",
+    "version": "0.99.7-pre1",
+    "population": "BXD",
+    "name": "HC_U_0304_R",
+    "trait": "101500_at",
+    "url": "https://genenetwork.org/show_trait?trait_id=101500_at&dataset=HC_U_0304_R",
+    "archive_GRM": "46bfba373fe8c19e68be6156cad3750120280e2e-gemma-cXX.tar.xz",
+    "archive_GWA": "779a54a59e4cd03608178db4068791db4ca44ab3-gemma-GWA.tar.xz",
+    "dataid": 75629,
+    "probesetid": 1097,
+    "probesetfreezeid": 7
+    }
+
+!#
+
 
 (define (write-json-ld id dataset-id recs)
   ;; see also https://www.w3.org/2018/jsonld-cg-reports/json-ld/
@@ -131,6 +151,7 @@ When that is the case we might as well write the phenotype file because we have
                 ]
            (display query)
            (dbi-query db query)
+           ;; ---- Walk each resulting trait
            (let [(id-traits (get-rows db '()))
                  (nrecs '())]
              (for-each (lambda (r)
@@ -144,12 +165,14 @@ When that is the case we might as well write the phenotype file because we have
                                 )]
                       (set! nrecs (assoc-set! nrecs data-id lst))))
                        id-traits)
-             (for-each (lambda (r)
-                         (match r
-                           ((id . recs) (if (has-bxd? recs)
-                                              (write-json-ld id (findit data-ids) recs)
-                                            ))
-                            )) nrecs)
+             ;; --- create the json output as a file
+             (for-each (lambda (r hit)
+                         (let [(probeset-id (assoc-ref hit "ProbeSetId"))]
+                           (match r
+                             ((id . recs) (if (has-bxd? recs)
+                                              (write-json-ld id probeset-id recs)
+                                              ))
+                             ))) nrecs hits)
              (if (> rest 0)
                  (run-list-traits-to-compute db rest (first (reverse data-ids)))) ;; start precompute
            )))