Fix codesystem concept extract

Co-authored-by: @ghrpp <[email protected]>
zen-lang · Sep 29, 2021 · 9bafce8 · 9bafce8
1 parent 242cfaa
commit 9bafce8
Showing 1 changed file with 45 additions and 12 deletions.
diff --git a/src/zen/fhir/core.clj b/src/zen/fhir/core.clj
@@ -332,24 +332,57 @@
       :zen.fhir/resource (dissoc res :zen.fhir/file :zen.fhir/package :zen.fhir/package-ns :zen.fhir/header)})))
 
 
-(defn extract-concepts [codesystem]
-  (let [zen-fhir-keys (select-keys codesystem [:zen.fhir/file :zen.fhir/package :zen.fhir/package-ns :zen.fhir/header])
-        concept-part (-> {:resourceType "Concept"
-                          :system       (:url codesystem)
-                          :valueset     (some-> (:valueSet codesystem) vector)}
-                         utils/strip-nils)]
-    (map (fn [concept]
-           (let [res (-> (merge concept-part concept)
-                         (assoc :id (str (:id codesystem) "/" (:code concept))))]
-             (assoc (merge res zen-fhir-keys) :zen.fhir/resource res)))
-         (:concept codesystem))))
+(defn build-designation [ds]
+  (reduce (fn [acc d]
+            (assoc-in acc [(or (get-in d [:use :code]) "display")
+                           (or (:language d) "en")]
+                      (:value d)))
+          {} ds))
+
+(defn get-value [m]
+  (let [k (->> (keys m)
+               (filter #(str/starts-with? (name %) "value"))
+               (first))]
+    (get m k)))
+
+(defn build-property [code-system-id ps]
+  (reduce (fn [acc p]
+            (assoc-in acc [code-system-id (:code p)] (get-value p)))
+          {} ps))
+
+
+(defn reduce-concept [acc cid sys parents c]
+  (let [con (-> c
+                (select-keys [:code :display :definition])
+                (assoc :id (str cid "/" (:code c))
+                       :system sys
+                       :resourceType "Concept")
+                (cond-> (:designation c) (assoc :designation (build-designation (:designation c)))
+                        (not (empty? parents)) (assoc :hierarchy parents)
+                        (:property c)    (assoc :property (build-property cid (:property c)))))
+        acc (conj acc con)]
+    (if-let [cs (:concept c)]
+      (reduce (fn [acc c']
+                (reduce-concept acc cid sys (conj parents (:code con)) c'))
+              acc cs)
+      acc)))
+
+(defn codesystem->concepts [{:as codesystem, cid :id, sys :url, cs :concept}]
+  (let [zen-fhir-keys (select-keys codesystem [:zen.fhir/file :zen.fhir/package :zen.fhir/package-ns :zen.fhir/header])]
+    (->> cs
+         (reduce (fn [acc c] (reduce-concept acc cid sys [] c))
+                 [])
+         (map (fn [concept]
+                (-> concept
+                    (merge zen-fhir-keys)
+                    (assoc :zen.fhir/resource concept)))))))
 
 
 (defmethod process-on-load :CodeSystem
   [res]
   (merge
    (dissoc res :concept)
-   {:fhir/concepts (into {} (map (juxt :id identity)) (extract-concepts res))}
+   {:fhir/concepts (into {} (map (juxt :id identity)) (codesystem->concepts res))}
    {:zen.fhir/resource (dissoc res :concept :zen.fhir/file :zen.fhir/package :zen.fhir/package-ns :zen.fhir/header)}))