From 43dd193379feaceebb9df165d4132c865d632ef7 Mon Sep 17 00:00:00 2001
From: ymarcon <yannick.marcon@epfl.ch>
Date: Mon, 6 Jan 2025 13:46:25 +0100
Subject: [PATCH] feat: docker file and R bin

---
 .github/workflows/publish-app-container.yml | 55 +++++++++++++++++++++
 Dockerfile                                  | 26 ++++++++++
 Makefile                                    |  5 ++
 R/app.R                                     |  6 +++
 R/install.R                                 | 23 +++++++++
 README.md                                   |  5 ++
 6 files changed, 120 insertions(+)
 create mode 100644 .github/workflows/publish-app-container.yml
 create mode 100644 Dockerfile
 create mode 100644 Makefile
 create mode 100644 R/app.R
 create mode 100644 R/install.R
 create mode 100644 README.md

diff --git a/.github/workflows/publish-app-container.yml b/.github/workflows/publish-app-container.yml
new file mode 100644
index 0000000..b2c664d
--- /dev/null
+++ b/.github/workflows/publish-app-container.yml
@@ -0,0 +1,55 @@
+name: Docker Shiny App
+
+on:
+  push:
+    # Publish `main` as Docker `latest` image.
+    branches:
+      - main
+
+    # Publish `v1.2.3` tags as releases.
+    tags:
+      - v*
+
+env:
+  IMAGE_NAME: airspec-app
+
+jobs:
+  # Push image to GitHub Packages.
+  # See also https://docs.docker.com/docker-hub/builds/
+  push:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'push'
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+        with:
+          lfs: true
+
+      - name: Build image
+        run: docker build backend --tag $IMAGE_NAME
+
+      - name: Log into registry
+        run: echo "${{ secrets.GITHUB_TOKEN }}" | docker login docker.pkg.github.com -u ${{ github.actor }} --password-stdin
+
+      - name: Push image
+        run: |
+          IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
+
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "main" ] && VERSION=latest
+
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION
\ No newline at end of file
diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 0000000..2427aeb
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,26 @@
+# Use the R Shiny base image
+FROM rocker/shiny:latest
+
+# Install R packages
+COPY R/install.R /srv
+RUN Rscript /srv/install.R
+
+# Copy your app into the container
+COPY R/app.R /srv/shiny-server/
+
+# Create a new user
+RUN useradd -m -u 1000 shiny_user \
+    && chown -R shiny_user:shiny_user /srv/shiny-server
+
+# Set proper permissions
+RUN chown -R shiny_user:shiny_user /usr/local/lib/R/site-library/AIRSpec/ShinyApp/
+
+# Switch to non-root user
+USER shiny_user
+    
+# Make the app available at port 3838
+EXPOSE 3838
+
+# Run the app
+#CMD ["/usr/bin/shiny-server"]
+CMD ["Rscript", "/srv/shiny-server/app.R"]
\ No newline at end of file
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000..d152ff7
--- /dev/null
+++ b/Makefile
@@ -0,0 +1,5 @@
+build:
+	docker build --pull --no-cache=false -t airspec-app .
+
+run:
+	docker run -p 3838:3838 airspec-app
\ No newline at end of file
diff --git a/R/app.R b/R/app.R
new file mode 100644
index 0000000..18634f5
--- /dev/null
+++ b/R/app.R
@@ -0,0 +1,6 @@
+library(shiny)
+library(methods)
+library(AIRSpec)
+
+AIRSPECDir <- "/usr/local/lib/R/site-library/AIRSpec/ShinyApp/"
+runApp(appDir = AIRSPECDir, host = "0.0.0.0", port = 3838)
\ No newline at end of file
diff --git a/R/install.R b/R/install.R
new file mode 100644
index 0000000..9f30d22
--- /dev/null
+++ b/R/install.R
@@ -0,0 +1,23 @@
+#pkglist <- c("AIRSpec", "Rfunctools", "APRLspec", "APRLmpf", "APRLmvr", "APRLssb")
+# pkglist <- c("AIRSpec", "APRLspec", "APRLmpf", "APRLmvr", "APRLssb")
+# 
+# for (pkg in pkglist) {
+#   print(paste("Installing package:", pkg, "..."))
+#   remotes::install_gitlab(sprintf('aprl/%s', pkg), dependencies = TRUE)
+# }
+
+extras <- c("RSQLite", "RJSONIO", "tidyverse", "shinythemes", "purrr", "shiny", "pls", "grDevices", "envDocument", "reshape2", "pryr", "Hmisc", "quantreg", "abind", "remotes")
+for (p in extras) {
+  install.packages(p)
+}
+
+url <- "https://www.dropbox.com/scl/fo/zcvv8xhvjg1wgad6gwep2/ABJGNldXXWS1z_w0_IuNHxk?rlkey=ch45dvbwcmohu6csa3eqxonn0&e=2&dl=1"
+destzip <- file.path(tempdir(), "AIRSpec_packages.zip")
+download.file(url, destzip)
+destfolder <- file.path(tempdir(), "AIRSpec_packages")
+unzip(destzip, exdir = destfolder)
+
+pkglist <- c("AIRSpec", "Rfunctools", "APRLspec", "APRLmpf", "APRLmvr", "APRLssb")
+for (pkg in pkglist) {
+  remotes::install_local(file.path(destfolder, pkg), dependencies = TRUE, force = TRUE)
+}
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..1b286be
--- /dev/null
+++ b/README.md
@@ -0,0 +1,5 @@
+# AIRSpec
+
+R Shiny app exposing Tools for Aerosol InfraRed Spectroscopy.
+
+See [https://airspec.epfl.ch](https://airspec.epfl.ch).
\ No newline at end of file