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grahamegrievegrahamegrieve
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Merge pull request #237 from costateixeira/linux-docker
Linux installer and docker
2 parents f5ea20f + 25a6764 commit d8a9d18

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‎.github/workflows/linux-docker-build.yml

+79-87
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@@ -1,87 +1,79 @@
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on:
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# Trigger the workflow on push or pull request,
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# but only for the main branch
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push:
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branches:
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- master
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# pull_request:
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jobs:
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Build-Docker-Image:
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runs-on: ubuntu-latest
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steps:
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- name: Check out repository code
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uses: actions/checkout@v2
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# -
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# name: Login to Docker Hub
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# uses: docker/login-action@v2
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# with:
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# username: ${{ secrets.DOCKERHUB_USERNAME }}
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# password: ${{ secrets.DOCKERHUB_TOKEN }}
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- name: Cache terminology files
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uses: actions/cache@v2
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with:
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path: ~/terminology
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key: terminology-${{ github.sha }}
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restore-keys: terminology-
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- name: Setup MySQL
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run: |
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docker network create gh
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docker run \
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--network gh \
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--name mysql \
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-e MYSQL_ROOT_PASSWORD=test \
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-e MYSQL_USER=test \
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-e MYSQL_PASSWORD=test \
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-e MYSQL_DATABASE=test \
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-d mysql:8
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- name: Docker Build
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run: |
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docker build \
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--tag fhirserver \
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.
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# - name: Scan Code
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# run: |
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# export DISPLAY=0:0
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# docker run --entrypoint /work/fhirserver/utilities/codescan/codescan fhirserver /work/bootstrap
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- name: Prepare ini file
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env:
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FHIRSERVER_LOCATIONS_CLONE_PATH: /work/fhirserver
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FHIRSERVER_LOCATIONS_TEST_CASES_CLONE_PATH: /work/bootstrap/source/fhir-test-cases
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FHIRSERVER_LOCATIONS_MARKDOWN_CLONE_PATH: /work/bootstrap/source/delphi-markdown
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FHIRSERVER_LOCATIONS_SNOMED_CACHE_PATH: /terminology/fhir-server/snomed.test.cache
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FHIRSERVER_MYSQL_SERVER: mysql
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FHIRSERVER_EMAIL_SENDER: [email protected]
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FHIRSERVER_EMAIL_DESTINATION: [email protected]
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FHIRSERVER_EMAIL_PASSWORD: ${{ secrets.FHIRSERVER_EMAIL_PASSWORD }}
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FHIRSERVER_SSL_CERT_PATH: /work/fhirserver/fixtures/domain.crt
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FHIRSERVER_SSL_KEY_PATH: /work/fhirserver/fixtures/domain.key
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FHIRSERVER_SSL_CACERT_PATH: /work/fhirserver/fixtures/rootCA.crt
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FHIRSERVER_SSL_PASSWORD: password
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run: |
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cat fixtures/test-settings.ini.template | envsubst > ~/test-settings.ini
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- name: Ensure SNOMED cache is present
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run: |
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mkdir -p ~/terminology/fhir-server
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wget -q --no-clobber https://storage.googleapis.com/ig-build/snomed.test.cache -O ~/terminology/fhir-server/snomed.test.cache || true
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ls ~/terminology/fhir-server/snomed.test.cache
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- name: Run tests in docker
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run: |
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docker images --all
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docker run \
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--network gh \
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-v ~/terminology:/terminology \
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-v ~/test-settings.ini:/work/fhirserver/exec/64/test-settings.ini \
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fhirserver -tests
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# - name: Tag and push Docker image
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# run: |
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# # Extract the FHIR server version from the library/version.inc file
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# FHIR_VERSION=$(grep -oP "FHIR_CODE_FULL_VERSION = '\K[^']+" library/version.inc)
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#
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# # Tag the Docker image with the extracted version and "latest"
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# docker tag fhirserver ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:$FHIR_VERSION
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# docker tag fhirserver ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:latest
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#
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# # Push both tagged images to Docker Hub
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# docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:$FHIR_VERSION
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# docker push ${{ secrets.DOCKERHUB_USERNAME }}/fhirserver:latest
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name: Build and Push Docker Image to GHCR
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on:
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# Trigger the workflow on push or pull request for the main branch
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push:
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pull_request:
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jobs:
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Build-Docker-Image:
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runs-on: ubuntu-latest
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steps:
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# Step 1: Check out the repository code
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- name: Check out repository code
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uses: actions/checkout@v2
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# Step 2: Log in to GitHub Container Registry (GHCR)
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- name: Log in to GitHub Container Registry
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uses: docker/login-action@v2
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }} # Automatically provided by GitHub
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# Step 3: Cache terminology files (optional, to avoid re-downloading terminology files)
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- name: Cache terminology files
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uses: actions/cache@v2
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with:
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path: ~/terminology
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key: terminology-${{ github.sha }}
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restore-keys: terminology-
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# Step 4: Setup MySQL for the build
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- name: Setup MySQL
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run: |
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docker network create gh
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docker run \
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--network gh \
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--name mysql \
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-e MYSQL_ROOT_PASSWORD=test \
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-e MYSQL_USER=test \
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-e MYSQL_PASSWORD=test \
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-e MYSQL_DATABASE=test \
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-d mysql:8
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# Step 5: Build the Docker image and tag it for GitHub Container Registry (GHCR)
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- name: Docker Build
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run: |
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docker build --tag ghcr.io/${{ github.repository_owner }}/fhirserver:nightly .
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# Step 6: Prepare ini file for your FHIR Server with environment variables
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- name: Prepare ini file
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env:
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FHIRSERVER_LOCATIONS_CLONE_PATH: /work/fhirserver
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FHIRSERVER_LOCATIONS_TEST_CASES_CLONE_PATH: /work/bootstrap/source/fhir-test-cases
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FHIRSERVER_LOCATIONS_MARKDOWN_CLONE_PATH: /work/bootstrap/source/delphi-markdown
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FHIRSERVER_LOCATIONS_SNOMED_CACHE_PATH: /terminology/fhir-server/snomed.test.cache
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FHIRSERVER_MYSQL_SERVER: mysql
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FHIRSERVER_EMAIL_SENDER: [email protected]
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FHIRSERVER_EMAIL_DESTINATION: [email protected]
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FHIRSERVER_EMAIL_PASSWORD: ${{ secrets.FHIRSERVER_EMAIL_PASSWORD }}
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FHIRSERVER_SSL_CERT_PATH: /work/fhirserver/fixtures/domain.crt
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FHIRSERVER_SSL_KEY_PATH: /work/fhirserver/fixtures/domain.key
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FHIRSERVER_SSL_CACERT_PATH: /work/fhirserver/fixtures/rootCA.crt
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FHIRSERVER_SSL_PASSWORD: password
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run: |
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cat fixtures/test-settings.ini.template | envsubst > ~/test-settings.ini
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# Step 7: Ensure SNOMED cache is present
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- name: Ensure SNOMED cache is present
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run: |
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mkdir -p ~/terminology/fhir-server
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wget -q --no-clobber https://storage.googleapis.com/ig-build/snomed.test.cache -O ~/terminology/fhir-server/snomed.test.cache || true
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ls ~/terminology/fhir-server/snomed.test.cache
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# Step 8: Push the Docker image to GitHub Container Registry (GHCR)
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- name: Push Docker image to GHCR
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run: |
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docker push ghcr.io/${{ github.repository_owner }}/fhirserver:nightly

‎Dockerfile

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FROM ubuntu:22.04 as builder
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FROM ubuntu:24.04 AS builder
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt update && apt install -y tzdata wget git unixodbc-dev libgtk2.0-dev xvfb sqlite3 libsqlite3-dev build-essential curl
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RUN apt update && apt-get upgrade -y && apt install -y tzdata wget git unixodbc-dev libgtk2.0-dev xvfb sqlite3 libsqlite3-dev build-essential curl binutils && apt-get clean && rm -rf /var/lib/apt/lists/*
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# Download and build OpenSSL 1.1.1w
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WORKDIR /tmp
@@ -15,7 +15,7 @@ RUN wget https://www.openssl.org/source/openssl-1.1.1w.tar.gz \
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&& make test \
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&& make install
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RUN ls -la /usr/local/lib/
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# RUN ls -la /usr/local/lib/
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# Set the timezone
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RUN echo "UTC" > /etc/timezone
@@ -36,40 +36,114 @@ RUN /work/bootstrap/linux-toolchain.sh /work/bootstrap
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WORKDIR /work/fhirserver
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COPY . /work/fhirserver
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RUN /work/bootstrap/linux-libraries.sh /work/bootstrap
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RUN cp /usr/local/lib/*.so* /usr/lib/
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RUN /work/fhirserver/build/linux-fhirserver.sh /work/bootstrap
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RUN cp exec/pack/*.properties exec/64
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RUN /work/bootstrap/linux-libraries.sh /work/bootstrap && \
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cp /usr/local/lib/*.so* /usr/lib/ && \
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/work/fhirserver/build/linux-fhirserver.sh /work/bootstrap && \
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cp exec/pack/*.properties exec/64
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# RUN cp exec/install/* exec/64
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RUN mkdir -p /work/fhirserver/exec/install/bin && \
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mkdir -p /work/fhirserver/exec/install/x86_64 && \
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mkdir -p /work/fhirserver/exec/install/content && \
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mkdir -p /work/fhirserver/exec/install/config && \
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# mkdir -p /work/fhirserver/exec/install/config/config && \
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mkdir -p /work/fhirserver/exec/install/default_config && \
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mkdir -p /work/fhirserver/exec/install/web
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RUN cd /work/fhirserver && \
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cp /work/fhirserver/exec/64/fhirserver /work/fhirserver/exec/install/bin && \
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cp /work/fhirserver/exec/64/FHIRToolkit /work/fhirserver/exec/install/bin && \
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cp /work/fhirserver/exec/64/FHIRConsole /work/fhirserver/exec/install/bin && \
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cp /work/fhirserver/exec/pack/linux/*so* /work/fhirserver/exec/install/x86_64
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RUN cp /work/fhirserver/exec/pack/linux/start.sh /work/fhirserver/exec/install/bin/start.sh && \
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cp /work/fhirserver/exec/pack/linux/install.sh /work/fhirserver/exec/install && \
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cp /work/fhirserver/exec/pack/linux/get-openssl.sh /work/fhirserver/exec/install && \
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cp /tmp/openssl-1.1.1w/*.so* /work/fhirserver/exec/install/x86_64 && \
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cp /work/fhirserver/exec/pack/*.properties /work/fhirserver/exec/install/content && \
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cp /work/fhirserver/exec/pack/*.dat /work/fhirserver/exec/install/content && \
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cp /work/fhirserver/exec/pack/fhirserver.cfg /work/fhirserver/exec/install/config && \
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cp /work/fhirserver/exec/pack/web.ini /work/fhirserver/exec/install/config && \
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cp /work/fhirserver/exec/pack/web.ini /work/fhirserver/exec/install/default_config && \
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cp /work/fhirserver/exec/pack/fhirserver.cfg /work/fhirserver/exec/install/default_config && \
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cp /work/fhirserver/config/config.ini /work/fhirserver/exec/install/default_config/config.ini && \
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cp /work/fhirserver/config/config.json /work/fhirserver/exec/install/default_config/config.json && \
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# cp /work/fhirserver/config/config.ini /work/fhirserver/exec/install/config/config.ini && \
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# cp /work/fhirserver/config/config_bare.json /work/fhirserver/exec/install/default_config/config.json && \
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# cp /work/fhirserver/config/config.ini /work/fhirserver/exec/install/config/default_config && \
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mkdir -p /work/fhirserver/exec/install/web && \
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cp -r /work/fhirserver/server/web/* /work/fhirserver/exec/install/web && \
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cd /work/fhirserver/exec && tar -czvf ./install.tgz ./install/ && ls -la /work/fhirserver/exec
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# Set the health check
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HEALTHCHECK --interval=1m --timeout=10s --retries=5 \
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HEALTHCHECK --interval=1m --timeout=10s --retries=5 \
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CMD curl -f http://localhost:${PORT}/fhir/metadata || exit 1
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# Set the environment variables
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ENV DISPLAY :99
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ENV PORT 80
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ENV TERMINOLOGY_CACHE /terminology
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ENV DISPLAY=:99
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ENV PORT=80
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ENV TERMINOLOGY_CACHE=/terminology
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VOLUME /terminology
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ENV DEBIAN_FRONTEND=
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RUN printf '#!/bin/bash \n\
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set -e \n\
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start_xvfb() { \n\
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Xvfb :99 -screen 0 1024x768x8 -nolisten tcp & \n\
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} \n\
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stop_xvfb() { \n\
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killall Xvfb || true \n\
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} \n\
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trap stop_xvfb SIGTERM \n\
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rm -f /tmp/.X99-lock \n\
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start_xvfb \n\
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echo "[web]" > /work/fhirserver/exec/64/web.ini; \n\
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echo "http=${PORT}" >> /work/fhirserver/exec/64/web.ini; \n\
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/work/fhirserver/exec/64/fhirserver $(eval echo "$@")' > /bin/entrypoint.sh && \
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chmod +x /bin/entrypoint.sh
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ENTRYPOINT ["/bin/entrypoint.sh"]
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CMD ["-cmd", "exec", "-cfg", "/config/config.ini", "-local", "$TERMINOLOGY_CACHE"]
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# ENTRYPOINT ["/bin/entrypoint.sh"]
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# CMD ["-cmd", "exec", "-cfg", "/config/config.ini", "-local", "$TERMINOLOGY_CACHE"]
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# Runtime stage
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FROM ubuntu:24.04 AS runtime
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ENV DEBIAN_FRONTEND=noninteractive
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ENV TZ=UTC
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# Set up environment variables
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# ENV HOME=~/
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ENV DISPLAY=:99
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ENV PORT=80
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ENV TERMINOLOGY_CACHE=/var/cache/txcache
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# Install runtime dependencies
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RUN apt-get update && apt-get upgrade -y && apt-get install -y wget tzdata xvfb libgtk2.0-0 libsqlite3-dev curl && apt-get clean \
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&& rm -rf /var/lib/apt/lists/* \
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&& mkdir -p $HOME/fhirserver/config $TERMINOLOGY_CACHE /fhirserver \
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&& chmod -R 777 $TERMINOLOGY_CACHE \
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&& chmod -R 777 /fhirserver
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# Copy necessary files from the builder stage
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COPY --from=builder /work/fhirserver/exec/install.tgz /fhirserver/install.tgz
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# RUN cd /fhirserver \
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# && tar -xzvf install.tgz \
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# && cd ./install \
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# && ./install.sh > install.log 2>&1
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# Assuming /fhirserver is your working directory
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WORKDIR /fhirserver
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# Extract the contents of the tar file
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RUN tar -xzvf install.tgz
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# Change working directory to the extracted folder
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WORKDIR /fhirserver/install
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# Run the installation script for a blank, clean install
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RUN chmod a+x ./install.sh && ./install.sh
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####################################################################
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WORKDIR /root/fhirserver
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# Define entrypoint and command
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CMD ["bash", "-c", "cd ~/fhirserver/ && ./start.sh"]
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# Expose the necessary port
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EXPOSE 80

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