Need to get at dataset-id - next to trait-idHEADmain

1 files changed, 11 insertions, 7 deletions

diff --git a/scripts/precompute/list-traits-to-compute.scm b/scripts/precompute/list-traits-to-compute.scm
index 2c48d83..08ed48d 100755
--- a/scripts/precompute/list-traits-to-compute.scm
+++ b/scripts/precompute/list-traits-to-compute.scm
@@ -82,9 +82,11 @@ When that is the case we might as well write the phenotype file because we have
              )
 
 
-(define (write-json-ld id recs)
+(define (write-json-ld id dataset-id recs)
   ;; see also https://www.w3.org/2018/jsonld-cg-reports/json-ld/
   (display id)
+  (display ":")
+  (display dataset-id)
   (newline)
   (let* [(traits (map (lambda (r)
                         (match r
@@ -98,8 +100,10 @@ When that is the case we might as well write the phenotype file because we have
                                (steps . ())
                                (sha256 . ((input-traits . ,sha256)))
                                (time . ,(date->string (time-utc->date (current-time))))))
-                      (traits .
-                      ((,id . ,traits)))))]
+                      (data .
+                            ((,id .
+                                  ((dataset . ,dataset-id)
+                                   (traits . ,traits)))))))]
     (call-with-output-file (string-append (number->string id) ".json")
       (lambda (port)
         (put-string port (scm->json-string json-data))))
@@ -110,6 +114,7 @@ When that is the case we might as well write the phenotype file because we have
    (lambda (db)
    (begin
      ;; (let [(bxd-strains (memo-bxd-strain-id-names #:used-for-mapping? #t))]
+       (display "writing-phenotypes...")
        (define (run-list-traits-to-compute db num prev-id)
          (let* [(count (if (< batch-size num)
                            batch-size
@@ -117,15 +122,14 @@ When that is the case we might as well write the phenotype file because we have
                 (rest (- num count))
                 (hits (get-precompute-hits db prev-id count))
                 (data-ids (map (lambda (hit)
-                                 (let* [(data-id (assoc-ref hit "DataId"))
-                                        ; (data-id-str (int-to-string data-id))
-                                        ]
+                                 (let* [(data-id (assoc-ref hit "DataId"))]
                                    data-id))
                                hits))
                 (data-str-ids (map (lambda (id) (string-append "Id=" (int-to-string id))) data-ids))
                 (data-ids-query (string-join data-str-ids " OR "))
                 (query (string-append "SELECT Id,StrainId,value FROM ProbeSetData WHERE " data-ids-query))
                 ]
+           (display query)
            (dbi-query db query)
            (let [(id-traits (get-rows db '()))
                  (nrecs '())]
@@ -143,7 +147,7 @@ When that is the case we might as well write the phenotype file because we have
              (for-each (lambda (r)
                          (match r
                            ((id . recs) (if (has-bxd? recs)
-                                              (write-json-ld id recs)
+                                              (write-json-ld id (findit data-ids) recs)
                                             ))
                             )) nrecs)
              (if (> rest 0)