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update github actions workflow
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‎.Rprofile‎

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This file was deleted.

‎.github/workflows/build-test-sign-image.yaml‎

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@@ -42,13 +42,55 @@ jobs:
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Log in to Azure Container Registry
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# Log in to Azure CR with token that can pull the base image (ARACHNE_DOCKER_REGISTRY_TOKEN).
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- name: Log in to Azure CR (pull base image)
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uses: docker/login-action@v3
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with:
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registry: executionengine.azurecr.io
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username: github-actions-push
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password: ${{ secrets.ARACHNE_DOCKER_REGISTRY_TOKEN }}
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# Try to pull base image; only build if pull fails (e.g. first run or base not yet published).
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- name: Try pull base image
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id: pull_base
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run: |
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BASE_IMAGE="executionengine.azurecr.io/${{ steps.image.outputs.name }}-base:latest"
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if docker pull "$BASE_IMAGE"; then
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docker tag "$BASE_IMAGE" examplestudy-base:latest
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echo "need_build=false" >> $GITHUB_OUTPUT
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else
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echo "need_build=true" >> $GITHUB_OUTPUT
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fi
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# Build base image only when it could not be pulled.
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- name: Build base image (CI / local load)
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if: steps.pull_base.outputs.need_build == 'true'
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run: |
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docker buildx build \
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--load \
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--file ./Dockerfile.base \
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--tag examplestudy-base:latest \
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--cache-from type=gha \
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--cache-to type=gha,mode=max \
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--platform linux/amd64 \
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.
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# Re-login to Azure CR with token that can push (for release step).
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- name: Log in to Azure Container Registry (push)
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uses: docker/login-action@v3
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with:
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registry: executionengine.azurecr.io
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username: github-actions-push
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password: ${{ secrets.CONTAINER_REGISTRY_TOKEN }}
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# When we built the base locally, push it so future runs can pull it.
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- name: Push base image to Azure CR
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if: steps.pull_base.outputs.need_build == 'true'
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run: |
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BASE_REPO="executionengine.azurecr.io/${{ steps.image.outputs.name }}-base:latest"
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docker tag examplestudy-base:latest "$BASE_REPO"
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docker push "$BASE_REPO"
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# Produces tags + labels (commit SHA, semver if you use tags, etc.)
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- name: Docker metadata
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id: meta
@@ -63,17 +105,17 @@ jobs:
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org.opencontainers.image.source=${{ github.server_url }}/${{ github.repository }}
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org.opencontainers.image.revision=${{ github.sha }}
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# 1) CI build (LOAD locally) so we can run tests inside the image.
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# Attestations (sbom/provenance) require pushing, so we do that only after tests pass.
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# Build is run with --progress=plain and teed to build.log for artifact upload on failure.
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- name: Build (CI / local load)
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# 1b) Build study image (LOAD) so we can run tests inside it.
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# Attestations (sbom/provenance) require pushing, so we do that only after tests pass.
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- name: Build study image (CI / local load)
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id: build_ci
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run: |
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set -o pipefail
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docker buildx build \
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--progress=plain \
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--load \
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--file ./Dockerfile \
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--build-arg BASE_IMAGE=examplestudy-base:latest \
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--tag ${{ env.REGISTRY }}/${{ steps.image.outputs.name }}:ci-${{ github.sha }} \
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--label "org.opencontainers.image.source=${{ github.server_url }}/${{ github.repository }}" \
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--label "org.opencontainers.image.revision=${{ github.sha }}" \
@@ -118,6 +160,7 @@ jobs:
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with:
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context: .
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file: ./Dockerfile
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build-args: BASE_IMAGE=examplestudy-base:latest
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platforms: linux/amd64
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push: true
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tags: |

‎Dockerfile‎

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@@ -1,95 +1,15 @@
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# Ubuntu 22.04 (Jammy) · R 4.2 · Dependencies for ExampleStudy
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# For Snowflake ODBC use: docker build --platform linux/amd64 ...
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FROM rocker/rstudio:4.2
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# Study image: prebuilt base + repo + renv::restore().
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# Build in two steps:
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# 1) Base: docker build -f Dockerfile.base -t examplestudy-base:latest .
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# (Optionally push: docker push <registry>/examplestudy-base:latest)
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# 2) Study: docker build -t examplestudy:latest .
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# (Then sign and push per your CI, e.g. cosign sign, docker push)
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ARG BASE_IMAGE=examplestudy-base:latest
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FROM ${BASE_IMAGE}
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LABEL org.opencontainers.image.maintainer="Adam Black <a.black@darwin-eu.org>"
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# Install java and rJava
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RUN apt-get -y update && apt-get install -y \
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default-jdk \
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r-cran-rjava \
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sudo \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/ \
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&& sudo R CMD javareconf
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RUN echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2026-02-01"))' >>"${R_HOME}/etc/Rprofile.site"
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RUN install2.r --error rJava && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error DatabaseConnector && rm -rf /tmp/download_packages/ /tmp/*.rds
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ENV DATABASECONNECTOR_JAR_FOLDER="/opt/hades/jdbc_drivers"
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RUN R -e "DatabaseConnector::downloadJdbcDrivers('all');"
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RUN install2.r --error Andromeda && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error RJSONIO && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error CirceR && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error SqlRender && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error renv && rm -rf /tmp/download_packages/ /tmp/*.rds
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# Install utility R packages
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RUN apt-get -y update && apt-get install -y \
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libxml2-dev libssl-dev libcurl4-openssl-dev \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/
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RUN install2.r --error openssl httr xml2 remotes && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error duckdb && rm -rf /tmp/download_packages/ /tmp/*.rds
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# Install odbc and RPostgres drivers (unixODBC + dev headers + pkg-config for R odbc package)
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# CXX required: R was built without C++ compiler; odbc's configure invokes ${CXX} -E
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RUN apt-get -y update && apt-get install -y --install-suggests \
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unixodbc unixodbc-dev libpq-dev curl pkg-config build-essential \
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&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/ \
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&& PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib/pkgconfig \
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CXX=g++ \
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install2.r --error RPostgres duckdb odbc \
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&& rm -rf /tmp/download_packages/ /tmp/*.rds
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# Install Darwin packages (and study Imports: dplyr, ggplot2, shiny, plotly)
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RUN install2.r --error \
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omopgenerics \
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CDMConnector \
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IncidencePrevalence \
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PatientProfiles \
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TreatmentPatterns \
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DrugExposureDiagnostics \
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DrugUtilisation \
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dplyr \
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ggplot2 \
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shiny \
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plotly \
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&& rm -rf /tmp/download_packages/ /tmp/*.rds
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# GitHub token for installs (pass at build time: docker build --build-arg GITHUB_PAT=xxx)
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RUN echo "DATABASECONNECTOR_JAR_FOLDER=/opt/hades/jdbc_drivers" >> /usr/local/lib/R/etc/Renviron
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RUN echo "RENV_PATHS_CELLAR=/opt/renv_cellar" >> /usr/local/lib/R/etc/Renviron
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# SQL Server odbc
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RUN curl -fsSL https://packages.microsoft.com/keys/microsoft.asc | sudo tee /etc/apt/trusted.gpg.d/microsoft.asc > /dev/null
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RUN curl -fsSL https://packages.microsoft.com/config/ubuntu/22.04/prod.list | sudo tee /etc/apt/sources.list.d/mssql-release.list
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RUN apt-get clean && apt-get update && ACCEPT_EULA=Y apt-get install -y msodbcsql17
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# Snowflake odbc
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RUN curl -fsSL --output snowflake-odbc-3.1.1.x86_64.deb https://sfc-repo.snowflakecomputing.com/odbc/linux/3.1.1/snowflake-odbc-3.1.1.x86_64.deb
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RUN sudo dpkg -i snowflake-odbc-3.1.1.x86_64.deb
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RUN install2.r --error here log4r testthat renv \
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&& rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN echo "EUNOMIA_DATA_FOLDER=/opt/eunomia_data" >> /usr/local/lib/R/etc/Renviron
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RUN R -e 'CDMConnector::downloadEunomiaData()'
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# Install vim
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RUN apt-get -y update && apt-get install -y vim && apt-get clean && rm -rf /var/lib/apt/lists/
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# Fix Snowflake odbc lib path
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RUN sed -i 's/libodbcinst.so.1/libodbcinst.so.2/g' /usr/lib/snowflake/odbc/lib/simba.snowflake.ini
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RUN mkdir /results
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# Copy package source into image (for running study and CI tests)
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COPY . /code
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WORKDIR /code
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COPY . /code
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# Install R package dependencies from renv.lock
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RUN R -e "renv::restore()"

‎Dockerfile.base‎

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Original file line numberDiff line numberDiff line change
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# Base image for ExampleStudy: R 4.2, Java, DB drivers, Darwin R packages, ODBC, etc.
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# Build and tag before building the study image, e.g.:
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# docker build -f Dockerfile.base -t examplestudy-base:latest .
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# For Snowflake ODBC use: docker build -f Dockerfile.base --platform linux/amd64 -t examplestudy-base:latest .
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FROM rocker/rstudio:4.2
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LABEL org.opencontainers.image.maintainer="Adam Black <a.black@darwin-eu.org>"
7+
8+
# Install java and rJava
9+
RUN apt-get -y update && apt-get install -y \
10+
default-jdk \
11+
r-cran-rjava \
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sudo \
13+
&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/ \
15+
&& sudo R CMD javareconf
16+
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RUN echo 'options(repos = c(CRAN = "https://packagemanager.posit.co/cran/__linux__/jammy/2026-02-01"))' >>"${R_HOME}/etc/Rprofile.site"
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RUN install2.r --error rJava && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error DatabaseConnector && rm -rf /tmp/download_packages/ /tmp/*.rds
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ENV DATABASECONNECTOR_JAR_FOLDER="/opt/hades/jdbc_drivers"
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RUN R -e "DatabaseConnector::downloadJdbcDrivers('all');"
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RUN install2.r --error Andromeda && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error RJSONIO && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error CirceR && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error SqlRender && rm -rf /tmp/download_packages/ /tmp/*.rds
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RUN install2.r --error renv && rm -rf /tmp/download_packages/ /tmp/*.rds
28+
29+
# Install utility R packages
30+
RUN apt-get -y update && apt-get install -y \
31+
libxml2-dev libssl-dev libcurl4-openssl-dev \
32+
&& apt-get clean \
33+
&& rm -rf /var/lib/apt/lists/
34+
35+
RUN install2.r --error openssl httr xml2 remotes && rm -rf /tmp/download_packages/ /tmp/*.rds
36+
RUN install2.r --error duckdb && rm -rf /tmp/download_packages/ /tmp/*.rds
37+
38+
# Install odbc and RPostgres drivers (unixODBC + dev headers + pkg-config for R odbc package)
39+
# CXX required: R was built without C++ compiler; odbc's configure invokes ${CXX} -E
40+
RUN apt-get -y update && apt-get install -y --install-suggests \
41+
unixodbc unixodbc-dev libpq-dev curl pkg-config build-essential \
42+
&& apt-get clean \
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&& rm -rf /var/lib/apt/lists/ \
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&& PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig:/usr/lib/pkgconfig \
45+
CXX=g++ \
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install2.r --error RPostgres duckdb odbc \
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&& rm -rf /tmp/download_packages/ /tmp/*.rds
48+
49+
# Install Darwin packages (and study Imports: dplyr, ggplot2, shiny, plotly)
50+
RUN install2.r --error \
51+
omopgenerics \
52+
CDMConnector \
53+
IncidencePrevalence \
54+
PatientProfiles \
55+
TreatmentPatterns \
56+
DrugExposureDiagnostics \
57+
DrugUtilisation \
58+
dplyr \
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ggplot2 \
60+
shiny \
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plotly \
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&& rm -rf /tmp/download_packages/ /tmp/*.rds
63+
64+
# GitHub token for installs (pass at build time: docker build --build-arg GITHUB_PAT=xxx)
65+
RUN echo "DATABASECONNECTOR_JAR_FOLDER=/opt/hades/jdbc_drivers" >> /usr/local/lib/R/etc/Renviron
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RUN echo "RENV_PATHS_CELLAR=/opt/renv_cellar" >> /usr/local/lib/R/etc/Renviron
67+
68+
# SQL Server odbc
69+
RUN curl -fsSL https://packages.microsoft.com/keys/microsoft.asc | sudo tee /etc/apt/trusted.gpg.d/microsoft.asc > /dev/null
70+
RUN curl -fsSL https://packages.microsoft.com/config/ubuntu/22.04/prod.list | sudo tee /etc/apt/sources.list.d/mssql-release.list
71+
RUN apt-get clean && apt-get update && ACCEPT_EULA=Y apt-get install -y msodbcsql17
72+
73+
# Snowflake odbc
74+
RUN curl -fsSL --output snowflake-odbc-3.1.1.x86_64.deb https://sfc-repo.snowflakecomputing.com/odbc/linux/3.1.1/snowflake-odbc-3.1.1.x86_64.deb
75+
RUN sudo dpkg -i snowflake-odbc-3.1.1.x86_64.deb
76+
77+
RUN install2.r --error here log4r testthat renv \
78+
&& rm -rf /tmp/download_packages/ /tmp/*.rds
79+
80+
RUN echo "EUNOMIA_DATA_FOLDER=/opt/eunomia_data" >> /usr/local/lib/R/etc/Renviron
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RUN R -e 'CDMConnector::downloadEunomiaData()'
82+
83+
# Install vim
84+
RUN apt-get -y update && apt-get install -y vim && apt-get clean && rm -rf /var/lib/apt/lists/
85+
86+
# Fix Snowflake odbc lib path
87+
RUN sed -i 's/libodbcinst.so.1/libodbcinst.so.2/g' /usr/lib/snowflake/odbc/lib/simba.snowflake.ini
88+
89+
RUN mkdir /results
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CMD ["bash"]

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