From 5083d15b28f6b9ebd2f17ab04b48ac523a61a6cb Mon Sep 17 00:00:00 2001
From: Tom Palmer <remlapmot@hotmail.com>
Date: Tue, 3 Sep 2024 15:54:17 +0100
Subject: [PATCH] Add rstudio-server to r image as rstudio image

---
 .gitignore               | 10 ++++++++++
 Dockerfile               | 42 ++++++++++++++++++++++++++++++++++++++++
 README.md                | 20 +++++++++++++++++++
 docker-compose.yaml      | 10 +++++++++-
 justfile                 | 16 +++++++++++++++
 rstudio-dependencies.txt |  5 +++++
 rstudio-entrypoint.sh    | 33 +++++++++++++++++++++++++++++++
 rstudio-rprofile.R       |  5 +++++
 test-rstudio.sh          | 39 +++++++++++++++++++++++++++++++++++++
 9 files changed, 179 insertions(+), 1 deletion(-)
 create mode 100644 rstudio-dependencies.txt
 create mode 100755 rstudio-entrypoint.sh
 create mode 100644 rstudio-rprofile.R
 create mode 100755 test-rstudio.sh

diff --git a/.gitignore b/.gitignore
index 540c779..e0352eb 100644
--- a/.gitignore
+++ b/.gitignore
@@ -2,3 +2,13 @@
 renv.lock.bak
 renv/
 .tests.R
+
+# rstudio-server directories
+*.config
+*.local
+
+# R files
+.Rhistory
+
+# metadata directory, ignored in research-template, ignore for rstudio test
+metadata/
diff --git a/Dockerfile b/Dockerfile
index 2106170..9750ba1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -94,3 +94,45 @@ WORKDIR /workspace
 COPY --from=builder /renv /renv
 # this will ensure the renv is activated by default
 RUN echo 'source("/renv/renv/activate.R")' >> /etc/R/Rprofile.site
+
+#################################################
+#
+# Add rstudio-server to r image - creating rstudio image
+ARG RSTUDIO_BASE_URL="default-arg-to-silence-docker"
+ARG RSTUDIO_DEB="default-arg-to-silence-docker"
+FROM r as rstudio
+
+# Install rstudio-server (and a few dependencies)
+COPY rstudio-dependencies.txt /root/rstudio-dependencies.txt
+RUN --mount=type=cache,target=/var/cache/apt /root/docker-apt-install.sh /root/rstudio-dependencies.txt &&\
+    test -f /var/cache/apt/"${RSTUDIO_DEB}" ||\
+    /usr/lib/apt/apt-helper download-file "${RSTUDIO_BASE_URL}${RSTUDIO_DEB}" /var/cache/apt/"${RSTUDIO_DEB}" &&\
+    apt-get install --no-install-recommends -y /var/cache/apt/"${RSTUDIO_DEB}"
+
+# Configuration
+## Start by setting up rstudio user using approach in opensafely-core/research-template-docker
+RUN useradd rstudio &&\
+    # Disable rstudio-server authentication
+    echo "auth-none=1" >> /etc/rstudio/rserver.conf &&\
+    # Run the server under the single user account
+    echo "server-user=rstudio" >> /etc/rstudio/rserver.conf &&\
+    echo "USER=rstudio" >> /etc/environment &&\
+    # Give the rstudio user sudo (aka root) permissions
+    usermod -aG sudo rstudio &&\
+    echo '%sudo ALL=(ALL) NOPASSWD:ALL' >> /etc/sudoers &&\
+    # Add a home directory for the rstudio user
+    mkdir /home/rstudio &&\
+    chown -R rstudio:rstudio /home/rstudio/ &&\
+    # Use renv R packages
+    # Remember that the second renv library directory /renv/sandbox/R-4.0/x86_64-pc-linux-gnu/9a444a72
+    # contains 14 symlinks to 14 of the 15 packages in ${R_HOME}/library which is /usr/lib/R/library/
+    # so that is already setup
+    echo "R_LIBS_SITE=/renv/lib/R-4.0/x86_64-pc-linux-gnu" >> /usr/lib/R/etc/Renviron.site &&\
+    # open RStudio in /workspace
+    echo "session-default-working-dir=/workspace" >> /etc/rstudio/rsession.conf
+
+COPY rstudio-entrypoint.sh /usr/local/bin/rstudio-entrypoint.sh
+COPY rstudio-rprofile.R /home/rstudio/rstudio-rprofile.R
+
+ENV USER rstudio
+ENTRYPOINT ["/usr/local/bin/rstudio-entrypoint.sh"]
diff --git a/README.md b/README.md
index 2c3ef96..eced32c 100644
--- a/README.md
+++ b/README.md
@@ -102,3 +102,23 @@ Find a previous version at `https://cran.r-project.org/src/contrib/Archive/{PACK
 ```sh
 just add-package PACKAGE@VERSION
 ```
+
+## Building, testing, and publishing the rstudio image
+
+The rstudio image is based on the r image including rstudio-server. To build run
+
+```sh
+just build-rstudio
+```
+
+To test that rstudio-server appears at `http://localhost:8787` run
+
+```sh
+just test-rstudio
+```
+
+And then push the new rstudio image to the GitHub container registry with
+
+```sh
+just publish-rstudio
+```
diff --git a/docker-compose.yaml b/docker-compose.yaml
index ada0ab0..681107c 100644
--- a/docker-compose.yaml
+++ b/docker-compose.yaml
@@ -23,4 +23,12 @@ services:
       target: add-package
       args:
        - PACKAGE
-
+  rstudio:
+    extends: r
+    image: rstudio
+    build:
+      target: rstudio
+      args:
+        # supplied by just
+        - RSTUDIO_BASE_URL
+        - RSTUDIO_DEB
diff --git a/justfile b/justfile
index 99a0bbb..2dea518 100644
--- a/justfile
+++ b/justfile
@@ -22,11 +22,23 @@ build:
 add-package package:
     bash ./add-package.sh {{ package }}
 
+# r image containing rstudio-server
+build-rstudio:
+    #!/usr/bin/env bash
+    set -euo pipefail
+
+    # Set RStudio Server .deb filename
+    export RSTUDIO_BASE_URL=https://download2.rstudio.org/server/focal/amd64/
+    export RSTUDIO_DEB=rstudio-server-2024.09.0-375-amd64.deb
+    docker-compose build --pull rstudio
 
 # test the locally built image
 test image="r": build
     bash ./test.sh "{{ image }}"
 
+# test rstudio-server launches
+test-rstudio:
+    bash ./test-rstudio.sh
 
 # lint source code
 lint:
@@ -36,3 +48,7 @@ lint:
 publish:
     docker tag r ghcr.io/opensafely-core/r:latest
     docker push ghcr.io/opensafely-core/r:latest
+
+publish-rstudio:
+    docker tag rstudio ghcr.io/opensafely-core/rstudio:latest
+    docker push ghcr.io/opensafely-core/rstudio:latest
diff --git a/rstudio-dependencies.txt b/rstudio-dependencies.txt
new file mode 100644
index 0000000..2054785
--- /dev/null
+++ b/rstudio-dependencies.txt
@@ -0,0 +1,5 @@
+git
+libclang-dev
+lsb-release
+psmisc
+sudo
diff --git a/rstudio-entrypoint.sh b/rstudio-entrypoint.sh
new file mode 100755
index 0000000..fe79957
--- /dev/null
+++ b/rstudio-entrypoint.sh
@@ -0,0 +1,33 @@
+#!/bin/bash
+
+# On Linux set rstudio user id to same as id of host if rstudio user id not already the same
+if [ "$HOSTPLATFORM" = "linux" -a "$(id -u rstudio)" != "$HOSTUID" ]; then
+  usermod -u $HOSTUID rstudio
+fi
+
+# Check for 1 .Rproj file
+if [ $(find /workspace -type f -name "*.Rproj" | wc -w) -eq 1 ]; then
+
+  # Copy in Git user.name and user.email from copied local-gitconfig from additionally mounted volume
+  if test -f /home/rstudio/local-gitconfig; then
+    grep -e "\[user\]" -e "name = *" -e "email = *" /home/rstudio/local-gitconfig >> /home/rstudio/.gitconfig
+  fi
+
+  # Avoid Git error: fatal detected dubious ownership of repository if using Git in container
+  # Without this the Git pane fails to open when RStudio project opened
+  echo -e "[safe]\n\tdirectory = \"*\"" >> /home/rstudio/.gitconfig
+
+  # Open RStudio project on opening RStudio Server session using an rstudio hook in .Rprofile
+  cat /home/rstudio/rstudio-rprofile.R >> /home/rstudio/.Rprofile
+fi
+
+# Set file line endings as crlf if docker run from Windows
+if [ "$HOSTPLATFORM" = "win32" ]; then
+  echo -e "{\n\t\"line_ending_conversion\": \"windows\"\n}" >> /etc/rstudio/rstudio-prefs.json
+fi
+
+# Start RStudio Server session in foreground
+# Hence don't use `rstudio-server start` which runs in background
+# and attempt to capture std out and err to a metadata log file
+mkdir -p /workspace/metadata
+exec /usr/lib/rstudio-server/bin/rserver --server-daemonize 0 >/workspace/metadata/rstudio.log 2>&1
diff --git a/rstudio-rprofile.R b/rstudio-rprofile.R
new file mode 100644
index 0000000..d7a5097
--- /dev/null
+++ b/rstudio-rprofile.R
@@ -0,0 +1,5 @@
+setHook("rstudio.sessionInit", function(newSession) {
+  if (newSession && is.null(rstudioapi::getActiveProject())) {
+    rstudioapi::openProject(paste0("/workspace/", list.files(pattern = "Rproj")))
+  }
+}, action = "append")
diff --git a/test-rstudio.sh b/test-rstudio.sh
new file mode 100755
index 0000000..51cdadd
--- /dev/null
+++ b/test-rstudio.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+set -eu
+
+# Detect operating system for `docker run` call
+OSTYPEFIRSTFIVE=$(echo "$OSTYPE" | cut -c1-5)
+if [[ "$OSTYPEFIRSTFIVE" == "linux" ]]; then
+  PLATFORM="linux"
+else
+  PLATFORM="somethingelse"
+fi
+
+trap "docker stop test_rstudio > /dev/null 2>&1 || true" EXIT
+
+docker run \
+    --rm \
+    --init \
+    --label=opensafely \
+    --interactive \
+    --user=0:0 --volume="/${PWD}://workspace" \
+    --platform=linux/amd64 \
+    -p=8787:8787 \
+    --name=test_rstudio \
+    --hostname=test_rstudio \
+    --volume="/${HOME}/.gitconfig:/home/rstudio/local-gitconfig" \
+    --env=HOSTPLATFORM=${PLATFORM} \
+    --env=HOSTUID=$(id -u) \
+    --detach \
+    rstudio > /dev/null 2>&1
+
+sleep 5
+
+status_code=$(curl --write-out %{http_code} --silent --output /dev/null -L --retry 3 --max-time 10 http://localhost:8787)
+if [[ "$status_code" -ne 200 ]] ; then
+  echo "200 response not received from http://localhost:8787"
+  exit 1
+else
+  echo "200 response successfully received from http://localhost:8787"
+  exit 0
+fi