[WIP] Implement ValueSet References

Closes: #110

.clj-kondo/root/config.edn

@@ -80,6 +80,7 @@
     blaze.middleware.fhir.db db
     blaze.rest-api.header header
     blaze.scheduler sched
+    blaze.terminology-service ts
     blaze.test-util tu
     blaze.util u
     buddy.auth auth

.github/scripts/value-set-expand/expand.sh

@@ -0,0 +1,21 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/../util.sh"
+
+BASE="http://localhost:8080/fhir"
+
+expand() {
+  curl -sH "Accept: application/fhir+json" "$BASE/ValueSet/\$expand?url=$1" | jq -r '[.expansion.contains[].code] | join(",")'
+}
+
+test "Abrechnungsart" "$(expand "http://fhir.de/ValueSet/dkgev/Abrechnungsart")" "AOP,HSA,PIA,SPZ,ASV,KIA,DRG,PEPP,VNSB,AP,SPB,WLU,WLA,PS,SZ,KV,BG,SL,KEK,IA,MVZ,IV,DMP,REHA,PSY"
+test "AbrechnungsDiagnoseProzedur" "$(expand "http://fhir.de/ValueSet/AbrechnungsDiagnoseProzedur")" "hospital-main-diagnosis,principle-DRG,secondary-DRG"
+test "Diagnosesubtyp" "$(expand "http://fhir.de/ValueSet/Diagnosesubtyp")" "surgery-diagnosis,department-main-diagnosis,infection-control-diagnosis,cause-of-death,AD,DD"
+
+test "mii-vs-fall-diagnosis-use" "$(expand "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/ValueSet/mii-vs-fall-diagnosis-use")" "referral-diagnosis,treatment-diagnosis,surgery-diagnosis,department-main-diagnosis,infection-control-diagnosis,cause-of-death,AD,DD,CC,CM,pre-op,post-op,billing"
+test "identifier-type-codes" "$(expand "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/ValueSet/identifier-type-codes")" "ACSN,BRN,DL,DR,EN,FILL,JHN,MCN,MD,MR,NIIP,PLAC,PPN,PRN,SB,SNO,TAX,UDI,VN"
+test "location-physical-type" "$(expand "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/ValueSet/location-physical-type")" "wa,ro,bd"
+test "mii-vs-consent-answer" "$(expand "https://www.medizininformatik-initiative.de/fhir/modul-consent/ValueSet/mii-vs-consent-answer")" "2.16.840.1.113883.3.1937.777.24.5.2.3,2.16.840.1.113883.3.1937.777.24.5.2.2,2.16.840.1.113883.3.1937.777.24.5.2.1"
+test "mii-vs-consent-policy" "$(expand "https://www.medizininformatik-initiative.de/fhir/modul-consent/ValueSet/mii-vs-consent-policy")" "2.16.840.1.113883.3.1937.777.24.5.3.1,2.16.840.1.113883.3.1937.777.24.5.3.44,2.16.840.1.113883.3.1937.777.24.5.3.48,2.16.840.1.113883.3.1937.777.24.5.3.10,2.16.840.1.113883.3.1937.777.24.5.3.14,2.16.840.1.113883.3.1937.777.24.5.3.18,2.16.840.1.113883.3.1937.777.24.5.3.24,2.16.840.1.113883.3.1937.777.24.5.3.50,2.16.840.1.113883.3.1937.777.24.5.3.54,2.16.840.1.113883.3.1937.777.24.5.3.26,2.16.840.1.113883.3.1937.777.24.5.3.30,2.16.840.1.113883.3.1937.777.24.5.3.32,2.16.840.1.113883.3.1937.777.24.5.3.35"
+test "mii-vs-consent-signaturetypes" "$(expand "https://www.medizininformatik-initiative.de/fhir/modul-consent/ValueSet/mii-vs-consent-signaturetypes")" "1.2.840.10065.1.12.1.7,1.2.840.10065.1.12.1.11"

.github/scripts/value-set-expand/upload.sh

@@ -0,0 +1,17 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+
+BASE="http://localhost:8080/fhir"
+
+# Upload CodeSystem resources
+for file in "$SCRIPT_DIR"/CodeSystem-*.json; do
+  echo "Uploading $file..."
+  curl -H "Content-Type: application/fhir+json" -H "Prefer: return=minimal" -d @"$file" "$BASE/CodeSystem"
+done
+
+# Upload ValueSet resources
+for file in "$SCRIPT_DIR"/ValueSet-*.json; do
+  echo "Uploading $file..."
+  curl -H "Content-Type: application/fhir+json" -H "Prefer: return=minimal" -d @"$file" "$BASE/ValueSet"
+done

.github/workflows/build.yml

@@ -1222,6 +1222,40 @@ jobs:
     - name: Docker Stats
       run: docker stats --no-stream
 
+  integration-test-value-set-expand:
+    needs: build
+    runs-on: ubuntu-24.04
+
+    steps:
+    - name: Check out Git repository
+      uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+
+    - name: Setup .NET Core SDK
+      uses: actions/setup-dotnet@v4
+      with:
+        dotnet-version: 8.0.x
+
+    - name: Install Firely Terminal
+      run: dotnet tool install -g firely.terminal
+
+    - name: Install Consent
+      run: fhir install de.medizininformatikinitiative.kerndatensatz.consent 1.0.7
+
+    - name: Download Blaze Image
+      uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4
+      with:
+        name: blaze-image
+        path: /tmp
+
+    - name: Load Blaze Image
+      run: docker load --input /tmp/blaze.tar
+
+    - name: Run Blaze
+      run: docker run --name blaze -d -e JAVA_TOOL_OPTIONS=-Xmx2g -p 8080:8080 --read-only --tmpfs /tmp:exec -v blaze-data:/app/data blaze:latest
+
+    - name: Wait for Blaze
+      run: .github/scripts/wait-for-url.sh http://localhost:8080/health
+
   not-enforcing-referential-integrity-test:
     needs: build
     runs-on: ubuntu-24.04
@@ -2001,6 +2035,7 @@ jobs:
     - integration-test
     - integration-test-synthea-1000
     - integration-test-patient-purge
+    - integration-test-value-set-expand
     - not-enforcing-referential-integrity-test
     - admin-api-test
     - small-transactions-test

deps.edn

@@ -13,6 +13,9 @@
   blaze/interaction
   {:local/root "modules/interaction"}
 
+  blaze/openid-auth
+  {:local/root "modules/openid-auth"}
+
   blaze.operation/compact
   {:local/root "modules/operation-compact"}
 
@@ -31,8 +34,8 @@
   blaze.operation/totals
   {:local/root "modules/operation-totals"}
 
-  blaze/openid-auth
-  {:local/root "modules/openid-auth"}
+  blaze.operation/value-set-expand
+  {:local/root "modules/operation-value-set-expand"}
 
   blaze/page-store-cassandra
   {:local/root "modules/page-store-cassandra"}
@@ -46,6 +49,9 @@
   blaze/server
   {:local/root "modules/server"}
 
+  blaze/terminology-service
+  {:local/root "modules/terminology-service"}
+
   blaze/thread-pool-executor-collector
   {:local/root "modules/thread-pool-executor-collector"}
 

docs/api.md

@@ -193,6 +193,7 @@ The following Operations are implemented:
 * [Measure $evaluate-measure](api/operation-measure-evaluate-measure.md)
 * [Patient $everything](api/operation-patient-everything.md)
 * [Patient $purge](api/operation-patient-purge.md)
+* [ValueSet $expand](api/operation-value-set-expand.md)
 
 ## Asynchronous Requests
 

docs/api/operation-value-set-expand.md

@@ -0,0 +1,15 @@
+# Operation \$expand on ValueSet
+
+> [!CAUTION]
+> The operation \$expand on ValueSet is currently **beta**. Only a basic functionality is implemented.
+
+The \$expand operation can be used to expand all codes of a ValueSet.
+
+```
+GET [base]/ValueSet/$expand
+GET [base]/ValueSet/[id]/$expand
+```
+
+The official documentation can be found [here][1].
+
+[1]: <http://hl7.org/fhir/R4/valueset-operation-expand.html>

docs/conformance/cql.md

@@ -32,8 +32,8 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 3.8.  | ConceptRef    | ✓          |                          |       |
 | 3.9.  | Quantity      | ✓          |                          |       |
 | 3.10. | Ratio         | ✓          |                          |       |
-| 3.11. | ValueSetDef   | ✗          |                          |       |
-| 3.12. | ValueSetRef   | ✗          |                          |       |
+| 3.11. | ValueSetDef   | ✓          |                          |       |
+| 3.12. | ValueSetRef   | ✓          |                          |       |
 
 ### 4. Type Specifiers
 
@@ -373,7 +373,7 @@ The section numbers refer to the documentation of the [ELM Specification](https:
 | 23.5.  | Equal           | ✓          |
 | 23.6.  | Equivalent      | ✓          |
 | 23.7.  | InCodeSystem    | ✗          |
-| 23.8.  | InValueSet      | ✗          |
+| 23.8.  | InValueSet      | ✓          |
 | 23.9.  | ExpandValueSet  | ✗          |
 | 23.10. | Not Equal       | ✓          |
 | 23.11. | SubsumedBy      | ✗          |

modules/cql/deps.edn

@@ -4,6 +4,9 @@
  {blaze/db
   {:local/root "../db"}
 
+  blaze/terminology-service
+  {:local/root "../terminology-service"}
+
   com.fasterxml.jackson.module/jackson-module-jaxb-annotations
   {:mvn/version "2.18.1"
    :exclusions [javax.xml.bind/jaxb-api]}

modules/cql/src/blaze/elm/compiler/clinical_operators.clj

@@ -4,9 +4,12 @@
   Section numbers are according to
   https://cql.hl7.org/04-logicalspecification.html."
   (:require
+   [blaze.elm.compiler.clinical-operators.impl :as impl]
    [blaze.elm.compiler.core :as core]
    [blaze.elm.compiler.macros :refer [reify-expr]]
-   [blaze.elm.protocols :as p]))
+   [blaze.elm.concept :as concept]
+   [blaze.elm.protocols :as p]
+   [blaze.elm.value-set :as value-set]))
 
 ;; 23.3. CalculateAge
 ;;
@@ -42,3 +45,30 @@
     (when-let [date (core/compile* context date)]
       (let [chrono-precision (some-> precision core/to-chrono-unit)]
         (calculate-age-at-op birth-date date chrono-precision precision)))))
+
+;; 23.8. InValueSet
+(defn- in-value-set [code value-set]
+  (reify-expr core/Expression
+    (-attach-cache [_ cache]
+      (core/attach-cache-helper in-value-set cache code value-set))
+    (-resolve-refs [_ expression-defs]
+      (core/resolve-refs-helper in-value-set expression-defs code value-set))
+    (-resolve-params [_ parameters]
+      (core/resolve-params-helper in-value-set parameters code value-set))
+    (-optimize [_ db]
+      (core/optimize-helper in-value-set db code value-set))
+    (-eval [_ context resource scope]
+      (let [value-set (core/-eval value-set context resource scope)
+            code (core/-eval code context resource scope)]
+        (cond
+          (string? code) (contains? (into #{} (map :code) value-set) code)
+          (concept/concept? code) (impl/contains-any? value-set (:codes code))
+          :else (contains? value-set (value-set/from-code code)))))
+    (-form [_]
+      (list 'in-value-set (core/-form code) (core/-form value-set)))))
+
+(defmethod core/compile* :elm.compiler.type/in-value-set
+  [context {:keys [code] value-set :valueset}]
+  (let [code (core/compile* context code)]
+    (when-let [value-set (core/compile* context value-set)]
+      (in-value-set code value-set))))

modules/cql/src/blaze/elm/compiler/clinical_operators/impl.clj

@@ -0,0 +1,9 @@
+(ns blaze.elm.compiler.clinical-operators.impl
+  (:require
+   [blaze.elm.value-set :as value-set]))
+
+(defn contains-any? [value-set [code & codes]]
+  (cond
+    (nil? code) false
+    (contains? value-set (value-set/from-code code)) true
+    :else (recur value-set codes)))

modules/cql/src/blaze/elm/compiler/clinical_values.clj

@@ -7,10 +7,14 @@
    [blaze.anomaly :as ba :refer [throw-anom]]
    [blaze.elm.code :as code]
    [blaze.elm.compiler.core :as core]
+   [blaze.elm.compiler.macros :refer [reify-expr]]
    [blaze.elm.concept :refer [concept]]
    [blaze.elm.date-time :as date-time]
    [blaze.elm.quantity :refer [quantity]]
-   [blaze.elm.ratio :refer [ratio]]))
+   [blaze.elm.ratio :refer [ratio]]
+   [blaze.elm.value-set :as value-set]
+   [blaze.fhir.spec.type :as type]
+   [blaze.terminology-service :as ts]))
 
 (defn- find-code-system-def
   "Returns the code-system-def with `name` from `library` or nil if not found."
@@ -113,5 +117,31 @@
 ;; Not needed because it's not an expression.
 
 ;; 3.12. ValueSetRef
-;;
-;; TODO
+(defn- find-value-set-def
+  "Returns the value-set-def with `name` from `library` or nil if not found."
+  {:arglists '([library name])}
+  [{{value-set-defs :def} :valueSets} name]
+  (some #(when (= name (:name %)) %) value-set-defs))
+
+(defn- to-code [{:keys [system code]}]
+  (value-set/->Code (type/value system) (type/value code)))
+
+(defn- value-set [{{:keys [contains]} :expansion}]
+  (into #{} (map to-code) contains))
+
+(defn- expand-value-set [terminology-service request]
+  (try
+    @(ts/expand-value-set terminology-service request)
+    (catch Exception e
+      (throw (ex-cause e)))))
+
+(defmethod core/compile* :elm.compiler.type/value-set-ref
+  [{:keys [library terminology-service]} {:keys [name]}]
+  (when-let [{:keys [id]} (find-value-set-def library name)]
+    (reify-expr core/Expression
+      (-optimize [_ db]
+        (value-set (expand-value-set terminology-service {:db db :url id})))
+      (-eval [_ _ _ _]
+        (throw-anom (ba/fault "Can't eval value-set expression without optimization.")))
+      (-form [_]
+        (list 'value-set id)))))

modules/cql/src/blaze/elm/compiler/core.clj

@@ -5,7 +5,7 @@
    [blaze.fhir.spec.type.system :as system]
    [clojure.string :as str])
   (:import
-   [clojure.lang IReduceInit]
+   [clojure.lang IPersistentSet IReduceInit]
    [java.time.temporal ChronoUnit]))
 
 (set! *warn-on-reflection* true)
@@ -200,7 +200,25 @@
   (-eval [expr _ _ _]
     expr)
   (-form [expr]
-    (mapv -form expr)))
+    (mapv -form expr))
+
+  IPersistentSet
+  (-static [_]
+    true)
+  (-attach-cache [expr _]
+    [(fn [] [expr])])
+  (-patient-count [_]
+    nil)
+  (-resolve-refs [expr _]
+    expr)
+  (-resolve-params [expr _]
+    expr)
+  (-optimize [expr _]
+    expr)
+  (-eval [expr _ _ _]
+    expr)
+  (-form [expr]
+    `(~'set ~@(mapv -form expr))))
 
 (defmulti compile*
   "Compiles `expression` in `context`.

modules/cql/src/blaze/elm/compiler/external_data.clj

@@ -44,6 +44,8 @@
                                                            data-type clauses)]
       (reify-expr core/Expression
         (-optimize [expr db]
+         ;; if there is no resource, regardless of the individual patient,
+         ;; available, just return an empty list for further optimizations
           (if (coll/empty? (d/execute-query db type-query))
             []
             expr))

modules/cql/src/blaze/elm/compiler/library.clj

@@ -97,9 +97,9 @@
   :function-defs and :parameter-default-values.
 
   There are currently no options."
-  [node library opts]
+  [context library opts]
   (let [library (normalizer/normalize-library library)
-        context (assoc opts :node node :library library)]
+        context (merge opts context {:library library})]
     (when-ok [{:keys [function-defs] :as context} (compile-function-defs context library)
               expression-defs (expression-defs context library)
               expression-defs (resolve-refs (unfiltered-expr-names expression-defs) expression-defs)

modules/cql/src/blaze/elm/compiler/library/spec.clj

@@ -5,6 +5,7 @@
    [blaze.elm.compiler.function-def :as-alias function-def]
    [blaze.elm.compiler.spec]
    [blaze.fhir.spec.spec]
+   [blaze.terminology-service.spec]
    [clojure.spec.alpha :as s]))
 
 (s/def ::expression-def/name
@@ -40,5 +41,8 @@
 (s/def ::c/library
   (s/keys :req-un [::c/expression-defs ::c/function-defs ::c/parameter-default-values]))
 
+(s/def ::c/context
+  (s/keys :req-un [:blaze.db/node :blaze/terminology-service]))
+
 (s/def ::c/options
   map?)

modules/cql/src/blaze/elm/compiler/library_spec.clj

@@ -11,7 +11,7 @@
    [cognitect.anomalies :as-alias anom]))
 
 (s/fdef library/compile-library
-  :args (s/cat :node :blaze.db/node :library :elm/library :opts ::c/options)
+  :args (s/cat :context ::c/context :library :elm/library :opts ::c/options)
   :ret (s/or :library ::c/library :anomaly ::anom/anomaly))
 
 (s/fdef library/resolve-all-refs

modules/cql/src/blaze/elm/concept.clj

@@ -33,6 +33,9 @@
   (-form [_]
     `(~'concept ~@(map core/-form codes))))
 
+(defn concept? [x]
+  (instance? Concept x))
+
 (defn concept
   "Returns a CQL concept"
   [codes]