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jgourmelenjgourmelen
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Merge hl7-eu/mapping into main
2 parents 3193aa3 + f17dfe7 commit d501be5

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+2087
-1437
lines changed

‎.github/workflows/build-images.yaml‎

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name: Build Container Images
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on:
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push:
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tags:
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- "image/v*"
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paths-ignore:
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- "charts/**"
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pull_request:
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branches: [master]
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paths-ignore:
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- "charts/**"
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env:
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IMAGES: docker.io/hapiproject/hapi
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PLATFORMS: linux/amd64,linux/arm64/v8
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jobs:
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build:
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name: Build
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runs-on: ubuntu-24.04
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steps:
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- name: Container meta for default (distroless) image
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id: docker_meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.IMAGES }}
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tags: |
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type=match,pattern=image/(.*),group=1,enable=${{github.event_name != 'pull_request'}}
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- name: Container meta for tomcat image
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id: docker_tomcat_meta
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uses: docker/metadata-action@v5
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with:
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images: ${{ env.IMAGES }}
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tags: |
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type=match,pattern=image/(.*),group=1,enable=${{github.event_name != 'pull_request'}}
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flavor: |
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suffix=-tomcat,onlatest=true
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v3
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Login to DockerHub
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uses: docker/login-action@v3
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if: github.event_name != 'pull_request'
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Cache Docker layers
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uses: actions/cache@v3
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with:
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path: /tmp/.buildx-cache
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key: ${{ runner.os }}-buildx-${{ github.sha }}
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restore-keys: |
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${{ runner.os }}-buildx-
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- name: Build and push default (distroless) image
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id: docker_build
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uses: docker/build-push-action@v5
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with:
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cache-from: type=local,src=/tmp/.buildx-cache
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cache-to: type=local,dest=/tmp/.buildx-cache
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.docker_meta.outputs.tags }}
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labels: ${{ steps.docker_meta.outputs.labels }}
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platforms: ${{ env.PLATFORMS }}
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target: default
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- name: Build and push tomcat image
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id: docker_build_tomcat
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uses: docker/build-push-action@v5
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with:
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cache-from: type=local,src=/tmp/.buildx-cache
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cache-to: type=local,dest=/tmp/.buildx-cache
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push: ${{ github.event_name != 'pull_request' }}
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tags: ${{ steps.docker_tomcat_meta.outputs.tags }}
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labels: ${{ steps.docker_tomcat_meta.outputs.labels }}
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platforms: ${{ env.PLATFORMS }}
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target: tomcat

‎.github/workflows/smoke-tests.yml‎

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distribution: zulu
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- name: Build with Maven
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env:
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MAVEN_OPTS: -Xms256m -Xmx3g -XX:+UseG1GC
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run: mvn -B package --file pom.xml -Dmaven.test.skip=true
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- name: Docker Pull HTTP client

‎README.md‎

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@@ -175,7 +175,7 @@ You can also use several profiles using coma-separated list of profiles in the v
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--e "--spring.profiles.active=qe,other"
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```
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If you want to use this with docker-compose, here is an example file using a single external profile and a postgres container for database :
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If you want to use this with docker-compose, here is an example file using a single external profile and a postgres container for database :
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```yaml
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version: "3.8"
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hapi-fhir-postgres:
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```
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You can retrieve the environment variables :
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You can retrieve the environment variables :
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```
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SPRING_CONFIG_ADDITIONAL_LOCATION: "/profiles/"
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SPRING_PROFILES_ACTIVE: "qe"
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```
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as well as the volume :
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as well as the volume :
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```
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volumes:

‎docker-compose.test.yml‎

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# docker-compose.test.yml
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# Test local des 3 conteneurs (R4, R5, mapping-service) depuis une seule image
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#
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# Usage :
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# docker compose -f docker-compose.test.yml build
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# docker compose -f docker-compose.test.yml up -d
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#
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# Endpoints :
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# - FHIR R4 : http://localhost:8080/fhir/metadata
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# - FHIR R5 : http://localhost:8081/fhir/metadata
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# - Mapping Service : http://localhost:8082/fhir/metadata
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services:
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# ──────────────────────────────────────────────
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# FHIR R4
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# ──────────────────────────────────────────────
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fhir-simulator-r4:
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build:
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context: .
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target: default
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container_name: fhir-simulator-r4
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restart: on-failure
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environment:
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HAPI_FHIR_FHIR_VERSION: "R4"
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SPRING_DATASOURCE_URL: "jdbc:postgresql://postgres-r4:5432/hapi_r4"
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SPRING_DATASOURCE_USERNAME: "admin"
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SPRING_DATASOURCE_PASSWORD: "admin"
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SPRING_DATASOURCE_DRIVERCLASSNAME: "org.postgresql.Driver"
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SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT: "ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect"
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ports:
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- "8080:8080"
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depends_on:
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postgres-r4:
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condition: service_healthy
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postgres-r4:
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image: postgres:16-alpine
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container_name: postgres-r4
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restart: always
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environment:
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POSTGRES_DB: "hapi_r4"
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POSTGRES_USER: "admin"
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POSTGRES_PASSWORD: "admin"
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healthcheck:
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test: ["CMD-SHELL", "pg_isready -U admin -d hapi_r4"]
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interval: 10s
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timeout: 5s
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start_period: 5s
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retries: 5
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volumes:
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- postgres-r4-data:/var/lib/postgresql/data
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# ──────────────────────────────────────────────
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# FHIR R5
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# ──────────────────────────────────────────────
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fhir-simulator-r5:
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build:
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context: .
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target: default
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container_name: fhir-simulator-r5
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restart: on-failure
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environment:
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HAPI_FHIR_FHIR_VERSION: "R5"
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SPRING_DATASOURCE_URL: "jdbc:postgresql://postgres-r5:5432/hapi_r5"
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SPRING_DATASOURCE_USERNAME: "admin"
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SPRING_DATASOURCE_PASSWORD: "admin"
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SPRING_DATASOURCE_DRIVERCLASSNAME: "org.postgresql.Driver"
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SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT: "ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect"
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ports:
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- "8081:8080"
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depends_on:
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postgres-r5:
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condition: service_healthy
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postgres-r5:
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image: postgres:16-alpine
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container_name: postgres-r5
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restart: always
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environment:
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POSTGRES_DB: "hapi_r5"
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POSTGRES_USER: "admin"
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POSTGRES_PASSWORD: "admin"
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healthcheck:
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test: ["CMD-SHELL", "pg_isready -U admin -d hapi_r5"]
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interval: 10s
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timeout: 5s
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start_period: 5s
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retries: 5
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volumes:
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- postgres-r5-data:/var/lib/postgresql/data
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# ──────────────────────────────────────────────
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# Mapping Service (R4 + moteur de mapping)
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# ──────────────────────────────────────────────
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mapping-service:
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build:
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context: .
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target: default
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container_name: mapping-service
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restart: on-failure
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environment:
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SPRING_PROFILES_ACTIVE: "mapping"
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SPRING_CONFIG_ADDITIONAL_LOCATION: "/profiles/"
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SPRING_DATASOURCE_URL: "jdbc:postgresql://postgres-mapping:5432/hapi_mapping"
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SPRING_DATASOURCE_USERNAME: "admin"
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SPRING_DATASOURCE_PASSWORD: "admin"
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SPRING_DATASOURCE_DRIVERCLASSNAME: "org.postgresql.Driver"
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SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT: "ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect"
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volumes:
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- ./profiles:/profiles:ro
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ports:
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- "8082:8080"
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depends_on:
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postgres-mapping:
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condition: service_healthy
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postgres-mapping:
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image: postgres:16-alpine
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container_name: postgres-mapping
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restart: always
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environment:
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POSTGRES_DB: "hapi_mapping"
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POSTGRES_USER: "admin"
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POSTGRES_PASSWORD: "admin"
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healthcheck:
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test: ["CMD-SHELL", "pg_isready -U admin -d hapi_mapping"]
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interval: 10s
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timeout: 5s
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start_period: 5s
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retries: 5
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volumes:
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- postgres-mapping-data:/var/lib/postgresql/data
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volumes:
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postgres-r4-data:
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postgres-r5-data:
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postgres-mapping-data:

‎docker-compose.yml‎

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SPRING_DATASOURCE_USERNAME: "admin"
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SPRING_DATASOURCE_PASSWORD: "admin"
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SPRING_DATASOURCE_DRIVERCLASSNAME: "org.postgresql.Driver"
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SPRING_JPA_PROPERTIES_HIBERNATE_DIALECT: ca.uhn.fhir.jpa.model.dialect.HapiFhirPostgresDialect
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SPRING_CONFIG_ADDITIONAL_LOCATION: "/profiles/"
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SPRING_PROFILES_ACTIVE: "mapping"
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volumes:

‎pom.xml‎

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<properties>
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<java.version>17</java.version>
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<hapi.fhir.jpa.server.starter.revision>1</hapi.fhir.jpa.server.starter.revision>
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<clinical-reasoning.version>4.2.0</clinical-reasoning.version>
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<clinical-reasoning.version>4.4.0</clinical-reasoning.version>
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<!-- Plugins Versions -->
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<maven.failsafe.version>3.5.4</maven.failsafe.version>
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<commons.logging.version>1.3.5</commons.logging.version>
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<spring_boot_version>3.5.9</spring_boot_version>
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<postgresql.version>42.7.9</postgresql.version>
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<logback_version>1.5.25</logback_version>
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</properties>
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<!-- one-liner to take you to the cloud with settings form the application.yaml file: -->
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<parent>
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<groupId>ca.uhn.hapi.fhir</groupId>
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<artifactId>hapi-fhir</artifactId>
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<version>8.6.1</version>
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<version>8.8.0</version>
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</parent>
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<artifactId>hapi-fhir-jpaserver-starter</artifactId>
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<dependency>
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<groupId>ch.qos.logback</groupId>
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<artifactId>logback-classic</artifactId>
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<version>1.5.19</version>
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<version>${logback_version}</version>
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</dependency>
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<dependency>
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<groupId>ch.qos.logback</groupId>
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<artifactId>logback-core</artifactId>
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<version>1.5.19</version>
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<version>${logback_version}</version>
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</dependency>
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<!-- Needed for JEE/Servlet support -->
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<dependency>
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<groupId>org.json</groupId>
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<artifactId>json</artifactId>
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<version>20231013</version>
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</dependency>
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<dependency>
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<groupId>ca.uhn.hapi</groupId>
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<artifactId>hapi-base</artifactId>
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<version>2.5.1</version>
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</dependency>
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<dependency>
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<groupId>ca.uhn.hapi</groupId>
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<artifactId>hapi-structures-v21</artifactId>
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<version>2.5.1</version>
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</dependency>
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<dependency>
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<groupId>ca.uhn.hapi</groupId>
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<artifactId>hapi-structures-v251</artifactId>
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<version>2.5.1</version>
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</dependency>
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<dependency>
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<groupId>org.json</groupId>
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<artifactId>json</artifactId>
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<dependency>
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<groupId>org.testcontainers</groupId>
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<artifactId>testcontainers-elasticsearch</artifactId>
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<version>2.0.2</version>
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>org.testcontainers</groupId>
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<artifactId>testcontainers-junit-jupiter</artifactId>
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<version>2.0.2</version>
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<scope>test</scope>
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</dependency>
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‎src/main/java/ca/uhn/fhir/jpa/starter/common/StarterJpaConfig.java‎

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package ca.uhn.fhir.jpa.starter.common;
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import ca.uhn.fhir.batch2.config.Batch2JobRegisterer;
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import ca.uhn.fhir.batch2.jobs.bulkmodify.reindex.ReindexProvider;
45
import ca.uhn.fhir.batch2.jobs.export.BulkDataExportProvider;
56
import ca.uhn.fhir.batch2.jobs.imprt.BulkDataImportProvider;
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import ca.uhn.fhir.batch2.jobs.reindex.ReindexProvider;
77
import ca.uhn.fhir.context.ConfigurationException;
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import ca.uhn.fhir.context.FhirContext;
99
import ca.uhn.fhir.context.FhirVersionEnum;
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import ca.uhn.fhir.jpa.starter.annotations.OnImplementationGuidesPresent;
5151
import ca.uhn.fhir.jpa.starter.common.validation.IRepositoryValidationInterceptorFactory;
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import ca.uhn.fhir.jpa.starter.elastic.ElasticsearchBootSvcImpl;
53+
import ca.uhn.fhir.jpa.starter.errorreport.ErrorReportingExceptionInterceptor;
5354
import ca.uhn.fhir.jpa.starter.ig.ExtendedPackageInstallationSpec;
5455
import ca.uhn.fhir.jpa.starter.ig.IImplementationGuideOperationProvider;
55-
import ca.uhn.fhir.jpa.starter.errorreport.ErrorReportingExceptionInterceptor;
5656
import ca.uhn.fhir.jpa.starter.mapping.provider.TransformProvider;
57-
import ca.uhn.fhir.jpa.starter.util.EnvironmentHelper;
5857
import ca.uhn.fhir.jpa.subscription.util.SubscriptionDebugLogInterceptor;
5958
import ca.uhn.fhir.jpa.util.ResourceCountCache;
6059
import ca.uhn.fhir.mdm.provider.MdmProviderLoader;
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460459
fhirServer.registerProvider(binaryAccessProvider.get());
461460
}
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463-
errorReportingExceptionInterceptor.ifPresent(fhirServer::registerInterceptor);
462+
errorReportingExceptionInterceptor.ifPresent(fhirServer::registerInterceptor);
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// Validation
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‎src/main/java/ca/uhn/fhir/jpa/starter/errorreport/ErrorReporter.java‎

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public interface ErrorReporter {
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void reportException(Throwable t);
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void reportMessage(String message);
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}

‎src/main/java/ca/uhn/fhir/jpa/starter/errorreport/ErrorReportingExceptionInterceptor.java‎

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errorReporter.reportException(ex);
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return true;
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}
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}
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}

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