Added provenance processing and storage to datomic DB for gene/update…

…-other-names REST API calls #304
WormBase · Jul 10, 2020 · 29bdc50 · 29bdc50
1 parent fc6a6d4
commit 29bdc50
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/resources/schema/seed-data.edn b/resources/schema/seed-data.edn
@@ -70,6 +70,8 @@
   #:db{:ident :event/new-gene}
   #:db{:ident :event/new-unnamed-gene}
   #:db{:ident :event/update-gene}
+  #:db{:ident :event/add-gene-other-names}
+  #:db{:ident :event/retract-gene-other-names}
   #:db{:ident :event/merge-genes}
   #:db{:ident :event/undo-merge-genes}
   #:db{:ident :event/split-gene}

diff --git a/src/wormbase/names/entity.clj b/src/wormbase/names/entity.clj
@@ -196,7 +196,7 @@
                  (format "%s '%s' does not exist" ent-ns (last lur)))))))))))
 
 (defn update-multi-card
-  [identify-fn uiident dt-transact-fn attr]
+  [identify-fn uiident event dt-transact-fn attr]
   (fn handle-multi-card [request identifier]
     (let [{conn :conn payload :body-params} request
           ent-ns (namespace uiident)
@@ -206,10 +206,12 @@
         (let [build-tx (fn [id attr ^String val] (vec [dt-transact-fn id attr val]))
               ;;retriev db-id to add values to
               db-id (:db/id entity)
+              ;;retrieve provenance
+              prov (wnp/assoc-provenance request payload event)
               ;;build transaction statements to make
               txes (map #(build-tx db-id attr %) data)
               ;;transact data to datomic
-              tx-result @(d/transact-async conn txes)]
+              tx-result @(d/transact-async conn (conj txes prov))]
           (when-let [db-after (:db-after tx-result)]
             (if-let [updated (wdb/pull db-after [attr uiident] lur)]
               (ok (or (attr updated) []))

diff --git a/src/wormbase/names/gene.clj b/src/wormbase/names/gene.clj
@@ -455,7 +455,7 @@
                         (assoc bad-request {:schema ::wsv/error-response})
                         (wnu/response-map))
          :handler (fn [request]
-                    (let [add-other-names (wne/update-multi-card identify :gene/id :db/add ':gene/other-names)]
+                    (let [add-other-names (wne/update-multi-card identify :gene/id :event/add-gene-other-names :db/add ':gene/other-names)]
                       (add-other-names request identifier)))}
         :delete
         {:summary "Delete a set of other-names from a gene."
@@ -467,7 +467,7 @@
                         (assoc bad-request {:schema ::wsv/error-response})
                         (wnu/response-map))
          :handler (fn [request]
-                    (let [delete-other-names (wne/update-multi-card identify :gene/id :db/retract ':gene/other-names)]
+                    (let [delete-other-names (wne/update-multi-card identify :gene/id :event/retract-gene-other-names :db/retract ':gene/other-names)]
                       (delete-other-names request identifier)))}}))
     (sweet/context "/merge/:from-identifier" [from-identifier]
       (sweet/resource