[WIP] Implement ValueSet References

Closes: #110

Author: alexanderkiel

.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/value-set-expand/.gitignore

@@ -0,0 +1 @@
+node_modules

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

@@ -0,0 +1,20 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/../scripts/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 "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/value-set-expand/package-lock.json

@@ -0,0 +1,5 @@
+{
+  "dependencies": {
+    "@mii-termserv/de.medizininformatikinitiative.kerndatensatz.terminology.bill-of-materials": "^2024.11.7"
+  }
+}

.github/value-set-expand/package.json

@@ -0,0 +1,11 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+
+BASE="http://localhost:8080/fhir"
+
+# Upload CodeSystem resources
+find "$SCRIPT_DIR/node_modules" -name "CodeSystem-*.json" -print0 | xargs -0 -P 4 -I {} curl -H "Content-Type: application/fhir+json" -H "Prefer: return=minimal" -d @"{}" "$BASE/CodeSystem"
+
+# Upload ValueSet resources
+find "$SCRIPT_DIR/node_modules" -name "ValueSet-*.json" -print0 | xargs -0 -P 4 -I {} curl -H "Content-Type: application/fhir+json" -H "Prefer: return=minimal" -d @"{}" "$BASE/ValueSet"

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

@@ -1222,6 +1222,44 @@ 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 Node
+      uses: actions/setup-node@39370e3970a6d050c480ffad4ff0ed4d3fdee5af # v4
+      with:
+        node-version: 21
+
+    - 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: All KDS Terminology Resources
+      working-directory: .github/value-set-expand
+      run: npm install
+
+    - name: Wait for Blaze
+      run: .github/scripts/wait-for-url.sh http://localhost:8080/health
+
+    - name: Upload KDS Terminology Resources
+      run: .github/value-set-expand/upload.sh
+
+    - name: Expand KDS Terminology Resources
+      run: .github/value-set-expand/expand.sh
+
   not-enforcing-referential-integrity-test:
     needs: build
     runs-on: ubuntu-24.04
@@ -2001,6 +2039,7 @@ 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

.github/workflows/build.yml

@@ -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"}
 

deps.edn

@@ -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.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>