Ft create deployment script

.env.production

@@ -0,0 +1,4 @@
+# .env.production
+
+REACT_APP_API_URL=https://cellmigration.isas.de/api
+REACT_APP_UPLOAD_FOLDER=https://cellmigration.isas.de/uploads

README.md

@@ -1,70 +1,92 @@
-# Getting Started with Create React App
+# 3D Volume Viewer Application
 
-This project was bootstrapped with [Create React App](https://github.com/facebook/create-react-app).
+This application is a 3D volume viewer designed to visualize medical imaging data of mouse body parts. The frontend is built with React and communicates with a Node.js backend that serves the volume files. Users can select different body parts and view the corresponding 3D volume files.
 
-## Available Scripts
+## Table of Contents
 
-In the project directory, you can run:
+1. [Features](#features)
+2. [Installation](#installation)
+3. [Usage](#usage)
+4. [File Structure](#file-structure)
+5. [API Endpoints](#api-endpoints)
+6. [Technologies Used](#technologies-used)
+7. [Contributing](#contributing)
+8. [License](#license)
 
-### `npm start`
+## Features
 
-Runs the app in the development mode.\
-Open [http://localhost:3000](http://localhost:3000) to view it in your browser.
+- Visualize 3D volume data in various formats (OME-TIFF, OME-ZARR, TIFF).
+- Control rendering modes (Path Trace, Ray March).
+- Adjust visualization parameters such as density, exposure, and gamma.
+- Manipulate lighting settings and camera modes.
+- Playback functionality for time-series data.
+- Dynamic channel controls to adjust color and material properties.
+- Set clipping regions and view bounding boxes.
+- Flip volume along different axes.
+- Screenshot capturing functionality.
+- RESTful API for serving volume files.
 
-The page will reload when you make changes.\
-You may also see any lint errors in the console.
+## Installation
 
-### `npm test`
+### Prerequisites
 
-Launches the test runner in the interactive watch mode.\
-See the section about [running tests](https://facebook.github.io/create-react-app/docs/running-tests) for more information.
+- Node.js (v12 or later)
+- npm (v6 or later)
 
-### `npm run build`
+### Backend Setup
 
-Builds the app for production to the `build` folder.\
-It correctly bundles React in production mode and optimizes the build for the best performance.
+1. Clone the repository:
+    ```bash
+    git clone https://github.com/yourusername/3d-volume-viewer.git
+    cd 3d-volume-viewer
+    ```
 
-The build is minified and the filenames include the hashes.\
-Your app is ready to be deployed!
+2. Navigate to the backend directory:
+    ```bash
+    cd server
+    ```
 
-See the section about [deployment](https://facebook.github.io/create-react-app/docs/deployment) for more information.
+3. Install dependencies:
+    ```bash
+    npm install
+    ```
 
-### `npm run eject`
+4. Start the server:
+    ```bash
+    npm start
+    ```
 
-**Note: this is a one-way operation. Once you `eject`, you can't go back!**
+### Frontend Setup
 
-If you aren't satisfied with the build tool and configuration choices, you can `eject` at any time. This command will remove the single build dependency from your project.
+1. Navigate to the frontend directory:
+    ```bash
+    cd ../client
+    ```
 
-Instead, it will copy all the configuration files and the transitive dependencies (webpack, Babel, ESLint, etc) right into your project so you have full control over them. All of the commands except `eject` will still work, but they will point to the copied scripts so you can tweak them. At this point you're on your own.
+2. Install dependencies:
+    ```bash
+    npm install
+    ```
 
-You don't have to ever use `eject`. The curated feature set is suitable for small and middle deployments, and you shouldn't feel obligated to use this feature. However we understand that this tool wouldn't be useful if you couldn't customize it when you are ready for it.
+3. Start the development server:
+    ```bash
+    npm start
+    ```
 
-## Learn More
+4. Open your browser and navigate to `http://localhost:3000`.
 
-You can learn more in the [Create React App documentation](https://facebook.github.io/create-react-app/docs/getting-started).
+## Usage
 
-To learn React, check out the [React documentation](https://reactjs.org/).
+### Upload Files
 
-### Code Splitting
+1. Place your volume files in the appropriate directories under `server/uploads`. Each directory represents a different body part (e.g., `liver`, `brain`).
 
-This section has moved here: [https://facebook.github.io/create-react-app/docs/code-splitting](https://facebook.github.io/create-react-app/docs/code-splitting)
+### View and Manipulate Volumes
 
-### Analyzing the Bundle Size
+1. Use the file selector in the frontend to choose a body part and a specific volume file.
+2. Adjust rendering and visualization settings using the provided controls.
+3. Use playback controls to navigate through time-series data.
+4. Capture screenshots using the screenshot button.
 
-This section has moved here: [https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size](https://facebook.github.io/create-react-app/docs/analyzing-the-bundle-size)
+## File Structure
 
-### Making a Progressive Web App
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app](https://facebook.github.io/create-react-app/docs/making-a-progressive-web-app)
-
-### Advanced Configuration
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/advanced-configuration](https://facebook.github.io/create-react-app/docs/advanced-configuration)
-
-### Deployment
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/deployment](https://facebook.github.io/create-react-app/docs/deployment)
-
-### `npm run build` fails to minify
-
-This section has moved here: [https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify](https://facebook.github.io/create-react-app/docs/troubleshooting#npm-run-build-fails-to-minify)

deploy.sh

@@ -0,0 +1,96 @@
+#!/bin/bash
+
+# Exit the script if any command fails
+set -e
+
+# Configuration variables
+PROJECT_DIR="."  # Frontend root remains in 3D-Cell-Viewer
+FRONTEND_DIR="$PROJECT_DIR"
+WEB_SERVER_ROOT="/var/www/vhosts/lsfm.isas.de"
+
+# Generate a new release branch name with timestamp
+RELEASE_BRANCH="release-$(date +'%Y%m%d%H%M%S')"
+
+echo "Creating a new release branch: $RELEASE_BRANCH"
+
+# Get the current branch name
+CURRENT_BRANCH=$(git branch --show-current)
+
+# Checkout to the 'ft-create-deployment-script' branch if not already on it
+if [ "$CURRENT_BRANCH" != "ft-create-deployment-script" ]; then
+  echo "Switching to 'ft-create-deployment-script' branch..."
+  git checkout ft-create-deployment-script
+else
+  echo "Already on 'ft-create-deployment-script' branch."
+fi
+
+# Pull the latest changes from the remote repository
+echo "Pulling the latest changes from 'ft-create-deployment-script' branch..."
+git pull origin ft-create-deployment-script
+
+# Create a new release branch from the current branch
+git checkout -b "$RELEASE_BRANCH"
+
+# Optionally, push the new release branch to the remote repository (uncomment if needed)
+# git push origin "$RELEASE_BRANCH"
+
+# Set environment variables for the API and file storage server
+export REACT_APP_API_URL="https://cellmigration.isas.de/api"
+export REACT_APP_UPLOAD_FOLDER="https://cellmigration.isas.de/uploads"
+
+# Create .htaccess file in the public directory
+echo "Creating .htaccess file..."
+cat > "$FRONTEND_DIR/public/.htaccess" << 'EOL'
+# Enable rewrite engine
+RewriteEngine On
+
+# If the requested resource exists as a file or directory, serve it directly
+RewriteCond %{REQUEST_FILENAME} !-f
+RewriteCond %{REQUEST_FILENAME} !-d
+
+# Otherwise, redirect all requests to index.html
+RewriteRule ^ index.html [QSA,L]
+
+# Set security headers
+Header set X-Content-Type-Options "nosniff"
+Header set X-Frame-Options "SAMEORIGIN"
+Header set X-XSS-Protection "1; mode=block"
+Header set Referrer-Policy "strict-origin-when-cross-origin"
+
+EOL
+
+# Proceed with the frontend deployment
+echo "Starting frontend-only deployment..."
+
+# Move to the frontend directory and install dependencies
+echo "Installing npm dependencies..."
+cd "$FRONTEND_DIR"
+npm install
+
+# Building the React Application
+echo "Building and minifying the React app for production..."
+NODE_ENV=production npm run build
+
+# Check if the web server root directory exists, if not, create it
+if [ ! -d "$WEB_SERVER_ROOT" ]; then
+  echo "Directory $WEB_SERVER_ROOT does not exist. Creating it now..."
+  sudo mkdir -p "$WEB_SERVER_ROOT"
+  sudo chown -R www-data:www-data "$WEB_SERVER_ROOT"
+  sudo chmod -R 755 "$WEB_SERVER_ROOT"
+  echo "Directory $WEB_SERVER_ROOT created successfully."
+fi
+
+# Deploy the built React app
+echo "Copying the React build files to the web server root..."
+sudo rm -rf "$WEB_SERVER_ROOT"/*
+sudo cp -r "$FRONTEND_DIR/build/"* "$WEB_SERVER_ROOT"
+
+# Copy .htaccess file
+echo "Copying .htaccess file..."
+sudo cp "$FRONTEND_DIR/public/.htaccess" "$WEB_SERVER_ROOT/.htaccess"
+
+# Set correct ownership and permissions
+echo "Changing ownership of the web server root directory to www-data user..."
+sudo chown -R www-data:www-data "$WEB_SERVER_ROOT"
+
+echo "Frontend deployment completed successfully."