Merge pull request #231 from medizininformatik-initiative/release-v2.4.0

Release v2.4.0

.github/integration-test/basic-auth/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.28"
+    image: "samply/blaze:0.30"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
@@ -37,7 +37,7 @@ services:
     depends_on:
       - data-store
   proxy:
-    image: "nginx:1.27.0"
+    image: "nginx:1.27.2"
     volumes:
       - "./nginx.conf:/etc/nginx/nginx.conf"
       - "./proxy.htpasswd:/etc/auth/.htpasswd"

.github/integration-test/no-auth-cohort-enabled/docker-compose.yml

@@ -0,0 +1,40 @@
+services:
+  data-store:
+    image: "samply/blaze:0.30"
+    healthcheck:
+      test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
+      interval: "5s"
+      timeout: "5s"
+      retries: "3"
+      start_period: "60s"
+    environment:
+      BASE_URL: "http://data-store:8080"
+      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      LOG_LEVEL: "debug"
+    ports:
+      - "8082:8080"
+    volumes:
+      - "data-store-data:/app/data"
+  flare:
+    image: "flare:latest"
+    healthcheck:
+      test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/cache/stats"]
+      interval: "5s"
+      timeout: "5s"
+      retries: "3"
+      start_period: "60s"
+    environment:
+      JAVA_TOOL_OPTIONS: "-Xmx1g"
+      FLARE_FHIR_SERVER: "http://data-store:8080/fhir"
+      LOG_LEVEL: "debug"
+      FLARE_ENABLE_COHORT_ENDPOINT: true
+    ports:
+      - "8080:8080"
+    volumes:
+      - "flare-cache:/app/cache"
+      - "../synthea-test-mapping:/app/ontology"
+    depends_on:
+      - data-store
+volumes:
+  data-store-data:
+  flare-cache:

.github/integration-test/no-auth-cohort-enabled/load-data.sh

@@ -0,0 +1,5 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+
+blazectl --no-progress --server http://localhost:8082/fhir upload "$SCRIPT_DIR/../../test-data/synthea"

.github/integration-test/no-auth/docker-compose.yml

@@ -1,6 +1,6 @@
 services:
   data-store:
-    image: "samply/blaze:0.28"
+    image: "samply/blaze:0.30"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"

.github/integration-test/oauth/docker-compose.yml

@@ -29,19 +29,19 @@ services:
       generate-cert:
         condition: service_completed_successfully
   keycloak:
-    image: "keycloak/keycloak:24.0.5"
+    image: "keycloak/keycloak:25.0.6"
     command: ["start", "--import-realm"]
     healthcheck:
-      test: ["CMD-SHELL", "exec 3<>/dev/tcp/127.0.0.1/8080;echo -e \"GET /health/ready HTTP/1.1\r\nhost: localhost\r\nConnection: close\r\n\r\n\" >&3;grep \"HTTP/1.1 200 OK\" <&3"]
+      test: ["CMD-SHELL", "exec 3<>/dev/tcp/127.0.0.1/9000;echo -e \"GET /health/ready HTTP/1.1\r\nhost: localhost\r\nConnection: close\r\n\r\n\" >&3;grep \"HTTP/1.1 200 OK\" <&3"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "30s"
     networks:
       test-oauth:
     environment:
-      KC_HOSTNAME_URL: "https://secure-keycloak:8443"
-      KC_HOSTNAME_ADMIN_URL: "https://secure-keycloak:8443"
+      KC_HOSTNAME: "https://secure-keycloak:8443"
+      KC_HOSTNAME_ADMIN: "https://secure-keycloak:8443"
       KC_HTTP_RELATIVE_PATH: "/"
       KC_PROXY_HEADERS: "xforwarded"
       KC_HTTP_ENABLED: "true"
@@ -50,12 +50,12 @@ services:
     volumes:
       - "./realm-test.json:/opt/keycloak/data/import/realm-test.json"
   proxy:
-    image: "nginx:1.27.0"
+    image: "nginx:1.27.2"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "5s"
     networks:
       test-oauth:
@@ -72,12 +72,12 @@ services:
       keycloak:
         condition: service_healthy
   data-store:
-    image: "samply/blaze:0.28"
+    image: "samply/blaze:0.30"
     healthcheck:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/health"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "60s"
     networks:
       test-oauth:
@@ -106,7 +106,7 @@ services:
       test: ["CMD-SHELL", "curl --fail -s http://localhost:8080/cache/stats"]
       interval: "5s"
       timeout: "5s"
-      retries: "3"
+      retries: 3
       start_period: "60s"
     networks:
       test-oauth:

.github/scripts/execute-cohort-query-enabled.sh

@@ -0,0 +1,15 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080"
+EXPECTED_ARRAY_LENGTH=$2
+EXPECTED_ID_LENGTH=$3
+CURL_RESPONSE=$(curl -s "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"$SCRIPT_DIR/../integration-test/query-$1.json")
+
+ACTUAL_PAT_ID_ARRAY_LENGTH=$(echo "$CURL_RESPONSE" | jq '. | length')
+ACTUAL_PAT_ID_ARRAY_ID_LENGTH=$(echo "$CURL_RESPONSE" | jq '.[] | length' | uniq)
+
+test "cohort length" $ACTUAL_PAT_ID_ARRAY_LENGTH $EXPECTED_ARRAY_LENGTH
+test "cohort id length" $ACTUAL_PAT_ID_ARRAY_ID_LENGTH $EXPECTED_ID_LENGTH

.github/scripts/execute-cohort-query-not-enabled.sh

@@ -0,0 +1,10 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080"
+STATUS_CODE=$(curl -s -o /dev/null -w "%{http_code}" "$BASE/query/execute-cohort" -H "Content-Type: application/sq+json" -d @"$SCRIPT_DIR/../integration-test/query-$1.json")
+EXPECTED_STATUS_CODE=404
+
+test "cohort endpoint status code" "$STATUS_CODE" $EXPECTED_STATUS_CODE

.github/workflows/build.yml

@@ -3,20 +3,20 @@ name: Build
 on:
   push:
     branches:
-    - main
-    - develop
+      - main
+      - develop
     tags:
-    - 'v*.*.*'
+      - 'v*.*.*'
   pull_request:
     branches:
-    - main
-    - develop
+      - main
+      - develop
   schedule:
-  - cron: '0 1 * * *'
+    - cron: '0 1 * * *'
 
 jobs:
   build:
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
       - uses: actions/checkout@v4
 
@@ -57,7 +57,7 @@ jobs:
         uses: docker/setup-buildx-action@v3
 
       - name: Build and Export to Docker
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           tags: flare:latest
@@ -71,7 +71,7 @@ jobs:
 
   image-scan:
     needs: build
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Download Flare Image
@@ -94,6 +94,9 @@ jobs:
           output: trivy-results.sarif
           severity: 'CRITICAL,HIGH'
           timeout: '15m0s'
+        env:
+          TRIVY_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-db:2
+          TRIVY_JAVA_DB_REPOSITORY: public.ecr.aws/aquasecurity/trivy-java-db:1
 
       - name: Upload Trivy Scan Results to GitHub Security Tab
         uses: github/codeql-action/upload-sarif@v3
@@ -102,7 +105,7 @@ jobs:
 
   integration-test-default-config:
     needs: build
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Check out Git repository
@@ -131,7 +134,8 @@ jobs:
           - no-auth
           - basic-auth
           - oauth
-    runs-on: ubuntu-22.04
+          - no-auth-cohort-enabled
+    runs-on: ubuntu-24.04
 
     steps:
       - name: Check out Git repository
@@ -158,13 +162,21 @@ jobs:
       - name: Query for Viral sinusitis (disorder)
         run: .github/scripts/execute-query.sh 444814009 69
 
+      - name: Query for Viral sinusitis (disorder) cohort not enabled
+        if: ${{ matrix.test == 'no-auth' }}
+        run: .github/scripts/execute-cohort-query-not-enabled.sh 444814009
+
+      - name: Query for Viral sinusitis (disorder) cohort enabled
+        if: ${{ matrix.test == 'no-auth-cohort-enabled' }}
+        run: .github/scripts/execute-cohort-query-enabled.sh 444814009 69 16
+
   push-image:
     needs:
       - build
       - integration-test-default-config
       - integration-test
       - image-scan
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     if: ${{ ! startsWith(github.head_ref, 'dependabot/')}}
 
     steps:
@@ -222,7 +234,7 @@ jobs:
             type=semver,pattern={{major}}.{{minor}}
 
       - name: Build and push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         with:
           context: .
           platforms: linux/amd64,linux/arm64

.gitignore

@@ -1,4 +1,5 @@
 .mvn
+.idea/
 cache
 target
 /ontology/mapping.zip

.mvn/wrapper/maven-wrapper.properties

@@ -16,4 +16,4 @@
 # under the License.
 wrapperVersion=3.3.2
 distributionType=only-script
-distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.7/apache-maven-3.9.7-bin.zip
+distributionUrl=https://repo.maven.apache.org/maven2/org/apache/maven/apache-maven/3.9.9/apache-maven-3.9.9-bin.zip

CHANGELOG.md

@@ -1,5 +1,38 @@
 # Changelog
 
+## v2.4.0
+
+### Enhancements
+
+* Updated ontology to v3.0.0
+* Add Feature Toggle for the Cohort Endpoint ([#217](https://github.com/medizininformatik-initiative/flare/pull/217))
+* Update mapping_tree creation ([#191](https://github.com/medizininformatik-initiative/flare/issues/191))
+* Add cohort extraction endpoint ([#178](https://github.com/medizininformatik-initiative/flare/issues/178))
+* docker-compose.yml should be for flare instead of blaze ([#184](https://github.com/medizininformatik-initiative/flare/issues/184))
+
+The full changelog can be found [here](https://github.com/medizininformatik-initiative/flare/milestone/15?closed=1).
+
+## v2.4.0-alpha.3
+
+### Enhancements
+
+* Add Feature Toggle for the Cohort Endpoint ([#217](https://github.com/medizininformatik-initiative/flare/pull/217))
+* Updated ontology to v3.0.0-alpha.1
+
+## v2.4.0-alpha.2
+
+### Enhancements
+
+* Updated ontology to v3.0.0-alpha
+
+## v2.4.0-alpha.1
+
+### Enhancements
+
+* Update mapping_tree creation ([#191](https://github.com/medizininformatik-initiative/flare/issues/191))
+* Add cohort extraction endpoint ([#178](https://github.com/medizininformatik-initiative/flare/issues/178))
+* docker-compose.yml should be for flare instead of blaze ([#184](https://github.com/medizininformatik-initiative/flare/issues/184))
+
 ## v2.3.0
 
 ### Enhancements

Dockerfile

@@ -1,4 +1,4 @@
-FROM eclipse-temurin:21.0.3_9-jre
+FROM eclipse-temurin:21.0.5_11-jre
 
 RUN apt-get update && apt-get upgrade -y && \
     apt-get purge wget libbinutils libctf0 libctf-nobfd0 libncurses6 -y && \