AoU Compliant RStudio App

.github/workflows/test-pr.yaml

@@ -33,6 +33,12 @@ jobs:
               user: rstudio
               workbench_tools: true
               postgres_client: true
+            r-analysis-aou:
+              user: rstudio
+              workbench_tools: true
+              postgres_client: true
+              filters:
+                - 'src/aou-common/**'
             vscode:
               user: abc
               workbench_tools: true
@@ -143,7 +149,7 @@ jobs:
     needs: [detect-changes]
     runs-on: ubuntu-latest
     continue-on-error: true
-    if : ${{ needs.detect-changes.outputs.templates != '[]' }}
+    if : ${{ needs.detect-changes.outputs.apps != '[]' }}
     strategy:
       matrix:
         app: ${{ fromJSON(needs.detect-changes.outputs.apps) }}

src/r-analysis-aou/.devcontainer.json

@@ -0,0 +1,42 @@
+{
+  "name": "R Analysis Environment for AoU",
+  "dockerComposeFile": "docker-compose.yaml",
+  "service": "app",
+  "shutdownAction": "none",
+  "workspaceFolder": "/workspace",
+  "postCreateCommand": [
+    "./startupscript/post-startup.sh",
+    "rstudio",
+    "/home/rstudio",
+    "${templateOption:cloud}",
+    "${templateOption:login}"
+  ],
+  // re-mount bucket files on container start up
+  "postStartCommand": [
+    "./startupscript/remount-on-restart.sh",
+    "rstudio",
+    "/home/rstudio",
+    "${templateOption:cloud}",
+    "${templateOption:login}"
+  ],
+  "features": {
+    "ghcr.io/devcontainers/features/java@sha256:df67d6ff6e9cdd858207ae9e92a99ddb88384b789f79eecd6f873216e951d286": {
+      "version": "17"
+    },
+    "ghcr.io/rocker-org/devcontainer-features/r-packages@sha256:1a4ec64c4d2060e78e9c812bd3b3622c7e008465d566a2781c0e2b17a82592e5": {
+      "packages": "shiny,shinydashboard",
+      "installSystemRequirements": true
+    },
+    "ghcr.io/devcontainers/features/aws-cli@sha256:bbc9fd513c22e331953126c75ad7b2ed1f9044f1cd5890b7073b634810459b18": {},
+    "ghcr.io/dhoeric/features/google-cloud-cli@sha256:fa5d894718825c5ad8009ac8f2c9f0cea3d1661eb108a9d465cba9f3fc48965f": {},
+    "./.devcontainer/features/workbench-tools": {
+      "cloud": "${templateOption:cloud}",
+      "username": "rstudio",
+      "userHomeDir": "/home/rstudio"
+    },
+    "./.devcontainer/features/postgres-client": {
+      "version": "16"
+    }
+  },
+  "remoteUser": "root"
+}

src/r-analysis-aou/Dockerfile

@@ -0,0 +1,17 @@
+FROM ghcr.io/rocker-org/devcontainer/tidyverse:4.5
+
+ARG USER=rstudio
+ARG HOME=/home/$USER
+
+COPY static /usr/lib/rstudio-server/www/aou-static
+RUN sed -i 's|</head>|<script src="/aou-static/aou-policy-interceptor.js"></script><link rel="stylesheet" href="/aou-static/aou-policy-styles.css"></head>|' /usr/lib/rstudio-server/www/index.htm
+
+# Remove sudo access
+RUN rm /etc/sudoers.d/${USER}
+
+COPY --from=load-envs --chown=$USER \
+    /dist/load-env /dist/load-env.sh $HOME
+
+RUN echo "source $HOME/load-env.sh" >> $HOME/.bashrc
+
+# TODO(PHP-87353): Add remotefuse back. See https://github.com/verily-src/workbench-app-devcontainers/pull/227

src/r-analysis-aou/README.md

@@ -0,0 +1,17 @@
+
+# R Analysis Environment for AoU (r-analysis-aou)
+
+A Template to run R Analysis Environment on Workbench for AoU
+
+## Options
+
+| Options Id | Description | Type | Default Value |
+|-----|-----|-----|-----|
+| cloud | VM cloud environment | string | gcp |
+| login | Whether to log in to workbench CLI | string | false |
+
+
+
+---
+
+_Note: This file was auto-generated from the [devcontainer-template.json](https://github.com/verily-src/workbench-app-devcontainers/blob/main/src/r-analysis/devcontainer-template.json).  Add additional notes to a `NOTES.md`._

src/r-analysis-aou/devcontainer-template.json

@@ -0,0 +1,23 @@
+{
+  "id": "r-analysis-aou",
+  "version": "0.0.2",
+  "name": "R Analysis Environment for AoU",
+  "description": "A Template to run the R Analysis Environment on workbench for AoU",
+  "documentationURL": "https://github.com/verily-src/workbench-app-devcontainers/tree/master/src/r-analysis-aou",
+  "licenseURL": "https://github.com/verily-src/workbench-app-devcontainers/blob/master/LICENSE",
+  "options": {
+    "cloud": {
+      "type": "string",
+      "description": "VM cloud environment",
+      "proposals": ["gcp", "aws"],
+      "default": "gcp"
+    },
+    "login": {
+      "type": "string",
+      "description": "Whether to log in to workbench CLI",
+      "proposals": ["true", "false"],
+      "default": "false"
+    }
+  },
+  "platforms": ["Any"]
+}

src/r-analysis-aou/docker-compose.yaml

@@ -0,0 +1,39 @@
+include:
+  - ../aou-common/aou-common-compose.yaml
+services:
+  app:
+    container_name: "application-server"
+    build:
+      context: .
+      additional_contexts:
+        load-envs: service:aou-common-load-envs
+    restart: always
+    ports: 
+      - "8787:8787"
+    volumes:
+      - .:/workspace:cached
+      - work:/home/rstudio:cached
+    tmpfs:
+      - /home/rstudio/workspace:uid=1000,gid=1000
+    environment:
+      "DISABLE_AUTH": "true"
+    networks:
+      - app-network
+    cap_add:
+      - SYS_ADMIN
+    devices:
+      - /dev/fuse
+    security_opt:
+      - apparmor:unconfined
+  wondershaper:
+    container_name: "wondershaper"
+    image: "us-west2-docker.pkg.dev/shared-pub-buckets-94mvrf/workbench-artifacts/app-wondershaper@sha256:1aee5cd4032d4888f382e3b11c0b775479ccaf55d97943f64049f90cfba05fac"
+    restart: always
+    network_mode: "host"
+    cap_add:
+      - NET_ADMIN
+networks:
+  app-network:
+    external: true
+volumes:
+  work: