OasisLMF · sambles · Nov 10, 2023 · Nov 9, 2023 · Nov 9, 2023 · Nov 10, 2023
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,5 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+compose/OasisPiWind
diff --git a/README.md b/README.md
@@ -3,27 +3,32 @@
 [![OasisUI Build](https://github.com/OasisLMF/OasisUI/actions/workflows/build.yml/badge.svg?branch=master&event=push)](https://github.com/OasisLMF/OasisUI/actions/workflows/build.yml)
 
 # Oasis UI
+
 Web-based application client for managing exposure data and operating modelling workflows.There are three components:
-  * Shiny UI application (This repository)
-  * Python Django server providing services for interacting with exposure and output data
-  * PostgreSQL server database
+
+* Shiny UI application (This repository)
+* Python Django server providing services for interacting with exposure and output data
+* PostgreSQL server database
 
 ## Usage and documentation
+
 For a detailed guide on using the OasisUI see
+
 * [Oasis_UI_Guide.pdf](documentation/Oasis_UI_Guide.pdf?raw=true)
 * [Oasis UI - Youtube Walkthrough](https://www.youtube.com/watch?v=tHRetuhpQzA)
 
 ## Deploying
 
 To try out the OasisUI run the docker installation script `./install.sh` from [OasisEvaluation](https://github.com/OasisLMF/OasisEvaluation).
 For tutorials on running the Oasis Stack locally see: (The full stack is required for the UI to work)
+
 * [Windows 10 - Installation Guide](https://www.youtube.com/watch?v=SxRt5E-Y5Sw)
 * [Linux - Installation Guide](https://www.youtube.com/watch?v=OFLTpGGEM10)
 
-
 ## Testing and development
 
 The script `./run_rstudio.sh` deploys and runs a development version of OasisUI, it runs using an [RStudio Server](https://documentation.dnanexus.com/getting-started/developer-tutorials/web-app-let-tutorials/running-rstudio-server).
+
 1. run the script open the url [http://localhost:8787/](http://localhost:8787/) in a browser.
 2. Load the project file
 ![Load Project](.img/dev_load_project.png?raw=true "Load RStudio Project")
@@ -33,6 +38,28 @@ The script `./run_rstudio.sh` deploys and runs a development version of OasisUI,
 4. In the R console enter `> oasisui::runOasisui()`, this will run the OasisUI in a new window
 ![Run App](.img/dev_run_oasisui.png?raw=true "Run Application")
 
+## Running with Docker compose
+
+1. build the R Studio container
+
+```bash
+    ./rstudio build
+```
+
+2. bring up the stack
+
+```bash
+    ./rstudio start
+```
+
+open the url [http://localhost:8787/](http://localhost:8787/) in a browser.
+
+3. bring down the stack
+
+```bash
+    ./rstudio stop
+```
+
 ## License
-The code in this project is licensed under BSD 3-clause license.
 
+The code in this project is licensed under BSD 3-clause license.
diff --git a/compose/oasis-platform-ui-dev.yml b/compose/oasis-platform-ui-dev.yml
@@ -0,0 +1,141 @@
+version: "3.8"
+volumes:
+  server-db-OasisData:
+  celery-db-OasisData:
+  filestore-OasisData:
+services:
+  server:
+    restart: always
+    image: ${SERVER_IMG:-coreoasis/api_server}:${VERS_API:-latest}
+    ports:
+      - 8000:8000
+    links:
+      - server-db
+      - celery-db
+      - rabbit
+    environment:
+      - OASIS_ADMIN_USER=admin
+      - OASIS_ADMIN_PASS=password
+      - OASIS_DEBUG=1
+      - OASIS_RABBIT_HOST=rabbit
+      - OASIS_RABBIT_PORT=5672
+      - OASIS_RABBIT_USER=rabbit
+      - OASIS_RABBIT_PASS=rabbit
+      - OASIS_SERVER_DB_HOST=server-db
+      - OASIS_SERVER_DB_PASS=oasis
+      - OASIS_SERVER_DB_USER=oasis
+      - OASIS_SERVER_DB_NAME=oasis
+      - OASIS_SERVER_DB_PORT=5432
+      - OASIS_SERVER_DB_ENGINE=django.db.backends.postgresql_psycopg2
+      - OASIS_CELERY_DB_ENGINE=db+postgresql+psycopg2
+      - OASIS_CELERY_DB_HOST=celery-db
+      - OASIS_CELERY_DB_PASS=password
+      - OASIS_CELERY_DB_USER=celery
+      - OASIS_CELERY_DB_NAME=celery
+      - OASIS_CELERY_DB_PORT=5432
+      - STARTUP_RUN_MIGRATIONS=true
+    volumes:
+      - filestore-OasisData:/shared-fs:rw
+  worker-monitor:
+    restart: always
+    image: ${SERVER_IMG:-coreoasis/api_server}:${VERS_API:-latest}
+    command:
+      [
+        wait-for-server,
+        "server:8000",
+        celery,
+        -A,
+        src.server.oasisapi,
+        worker,
+        --loglevel=INFO,
+      ]
+    links:
+      - server-db
+      - celery-db
+      - rabbit
+    environment:
+      - OASIS_DEBUG=1
+      - OASIS_RABBIT_HOST=rabbit
+      - OASIS_RABBIT_PORT=5672
+      - OASIS_RABBIT_USER=rabbit
+      - OASIS_RABBIT_PASS=rabbit
+      - OASIS_SERVER_DB_HOST=server-db
+      - OASIS_SERVER_DB_PASS=oasis
+      - OASIS_SERVER_DB_USER=oasis
+      - OASIS_SERVER_DB_NAME=oasis
+      - OASIS_SERVER_DB_PORT=5432
+      - OASIS_SERVER_DB_ENGINE=django.db.backends.postgresql_psycopg2
+      - OASIS_CELERY_DB_ENGINE=db+postgresql+psycopg2
+      - OASIS_CELERY_DB_HOST=celery-db
+      - OASIS_CELERY_DB_PASS=password
+      - OASIS_CELERY_DB_USER=celery
+      - OASIS_CELERY_DB_NAME=celery
+      - OASIS_CELERY_DB_PORT=5432
+    volumes:
+      - filestore-OasisData:/shared-fs:rw
+  worker:
+    restart: always
+    image: ${WORKER_IMG:-coreoasis/model_worker}:${VERS_WORKER:-latest}
+    links:
+      - celery-db
+      - rabbit:myrabbit
+    environment:
+      - OASIS_MODEL_SUPPLIER_ID=OasisLMF
+      - OASIS_MODEL_ID=PiWind
+      - OASIS_MODEL_VERSION_ID=1
+      - OASIS_RABBIT_HOST=rabbit
+      - OASIS_RABBIT_PORT=5672
+      - OASIS_RABBIT_USER=rabbit
+      - OASIS_RABBIT_PASS=rabbit
+      - OASIS_SERVER_DB_ENGINE=django.db.backends.postgresql_psycopg2
+      - OASIS_CELERY_DB_ENGINE=db+postgresql+psycopg2
+      - OASIS_CELERY_DB_HOST=celery-db
+      - OASIS_CELERY_DB_PASS=password
+      - OASIS_CELERY_DB_USER=celery
+      - OASIS_CELERY_DB_NAME=celery
+      - OASIS_CELERY_DB_PORT=5432
+      - OASIS_MODEL_DATA_DIRECTORY=/home/worker/model
+    volumes:
+      - ./OasisPiWind/:/home/worker/model
+      - filestore-OasisData:/shared-fs:rw
+  server-db:
+    restart: always
+    image: postgres
+    environment:
+      - POSTGRES_DB=oasis
+      - POSTGRES_USER=oasis
+      - POSTGRES_PASSWORD=oasis
+    volumes:
+      - server-db-OasisData:/var/lib/postgresql/data:rw
+  celery-db:
+    restart: always
+    image: postgres
+    environment:
+      - POSTGRES_DB=celery
+      - POSTGRES_USER=celery
+      - POSTGRES_PASSWORD=password
+    volumes:
+      - celery-db-OasisData:/var/lib/postgresql/data:rw
+  rabbit:
+    restart: always
+    image: rabbitmq:3.8.14-management
+    environment:
+      - RABBITMQ_DEFAULT_USER=rabbit
+      - RABBITMQ_DEFAULT_PASS=rabbit
+    ports:
+      - 5672:5672
+      - 15672:15672
+  rstudio:
+    image: oasisui_dev:latest
+    restart: always
+    environment:
+      - DISABLE_AUTH=true
+      - USERID=${UID:-1000}
+      - DISPLAY=${DISPLAY:-:0}
+    volumes:
+      - ${SHARED_DIR}:/home/rstudio/oasisui
+      - /tmp/.X11-unix:/tmp/.X11-unix:ro
+    ports:
+      - 8787:8787
+    networks:
+      - default
diff --git a/docker/Dockerfile.oasisui_development b/docker/Dockerfile.oasisui_development
@@ -29,7 +29,7 @@ RUN R -e 'devtools::install(pkg = "./BFE_RShiny/oasisui", dependencies = TRUE)'
 # Create .Rprofile and set default values
 RUN echo 'message("Run app with:   oasisui::runOasisui()")' >> /home/rstudio/.Rprofile
 
-ENV API_IP="127.0.0.1"
+ENV API_IP="server"
 ENV API_PORT="8000"
 ENV API_VERSION="v1"
 ENV API_SHARE_FILEPATH="./downloads"

diff --git a/rstudio b/rstudio
@@ -0,0 +1,83 @@
+#!/bin/bash
+
+SHARED_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+R_PROJECT_FILE="$SHARED_DIR/oasisui_dev.Rproj"
+R_CONTAINER_NAME='rstudio_oasisui'
+DOCKERFILE_PATH="$SHARED_DIR/docker/Dockerfile.oasisui_development"
+IMAGE_NAME="oasisui_dev:latest"
+COMPOSE_FILE="$SHARED_DIR/compose/oasis-platform-ui-dev.yml"
+
+export SHARED_DIR
+export UID=${UID:-1000}
+export DISPLAY=${DISPLAY:-:0}
+
+function build() {
+echo "Creating a new R project file with default configurations..."
+{
+  echo "Version: 1.0"
+  echo "RestoreWorkspace: Default"
+  echo "SaveWorkspace: Default"
+  echo "AlwaysSaveHistory: Default"
+  echo "EnableCodeIndexing: Yes"
+  echo "UseSpacesForTab: Yes"
+  echo "NumSpacesForTab: 2"
+  echo "Encoding: UTF-8"
+  echo "RnwWeave: Sweave"
+  echo "LaTeX: pdfLaTeX"
+  echo "BuildType: Package"
+  echo "PackageUseDevtools: Yes"
+  echo "PackagePath: BFE_RShiny/oasisui"
+  echo "PackageInstallArgs: --no-multiarch --with-keep.source"
+} > "$R_PROJECT_FILE"
+
+  if [ -s "$R_PROJECT_FILE" ]; then
+    echo "R project file created successfully with content."
+  else
+    echo "R project file is empty or could not be created."
+    return 1 # Exit the function with an error status
+  fi
+
+  echo "Building UI Docker image..."
+  docker build -f "$DOCKERFILE_PATH" -t "$IMAGE_NAME" .
+}
+
+
+
+
+
+function stop() {
+  echo "Stopping and removing containers..."
+  docker-compose -f "$COMPOSE_FILE" down
+}
+
+function start() {
+  echo "Starting services..."
+  docker-compose -f "$COMPOSE_FILE" up -d
+  echo "connect using: http://localhost:8787/"
+}
+
+# Check and create the R project file if it doesn't exist.
+if [ ! -f "$R_PROJECT_FILE" ]; then
+  cat >> "$R_PROJECT_FILE" <<EOL
+# ... your existing R project configuration ...
+EOL
+fi
+
+# Parse command line argument.
+case "$1" in
+  build)
+    build
+    ;;
+  stop)
+    stop
+    ;;
+  start)
+    start
+    ;;
+  *)
+    echo "Usage: $0 {build|stop|start}"
+    exit 1
+    ;;
+esac
+
+echo "Done."