Add deploy.sh script for EC2 deployment

Added deploy.sh script that automatically pull git, build, test, and
deploy Comptox AI web on EC2.
Intended to be used inside EC2 instance and added here as backup.

deploy.sh

@@ -0,0 +1,391 @@
+#!/bin/bash
+
+# Comptox AI Deployment Script (Updated 10/05/2023)
+
+# Overview: This script automates the deployment of Comptox AI on an EC2
+# instance. It can also be executed locally for testing purposes. Below are the
+# key tasks performed by this script.
+
+# The script currently supports only Linux and macOS.
+
+# Key Deployment Tasks:
+
+# 1. **Update from GitHub:**
+#    - Fetches the latest master version of Comptox AI from GitHub, ensuring
+#      your deployment is always up-to-date.
+
+# 2. **Python Environment Setup:**
+#    - Activates the Micromamba environment to manage Python dependencies and
+#      avoid conflicts.
+
+# 3. **Python Package Installation:**
+#    - Upgrades pip and setuptools to their latest versions.
+#    - Installs Python packages required for Comptox AI, including packages
+#      necessary for building documentation.
+
+# 4. **Sphinx Documentation:**
+#    - Cleans any previous documentation builds.
+#    - Generates Sphinx documentation, ensuring the successful creation of HTML
+#      documentation.
+#    - Verifies the presence of required documentation files.
+
+# 5. **JavaScript Package Installation:**
+#    - Installs JavaScript packages using npm, verifying the installation in
+#      case others install Comptox AI.
+
+# 6. **React App Integration:**
+#    - Cleans any existing React app builds.
+#    - Builds the React app and merges it with Sphinx documentation, creating a
+#      cohesive final deployment.
+
+# 7. **Nginx Server Update:**
+#    - Copies and pastes the updated documentation and React app build to the
+#      Nginx server root.
+#    - Reloads the Nginx server to reflect the latest changes made in the
+#      deployment.
+
+# 8. **API Installation:**
+#    - Installs necessary packages for the API.
+#    - Stops the API service with a brief delay and then restarts it.
+
+# === Dependencies ===
+
+# This script relies on the following dependencies:
+# - Micromamba: A package manager for managing Python environments.
+# - npm: A package manager for JavaScript packages.
+# - pm2: A process manager for running Node.js applications.
+
+# Ensure you have these dependencies installed before running this script.
+
+# To install Micromamba:
+# - Follow the installation instructions at:
+#   https://micromamba.snakepit.net/docs/tutorials/installation
+
+# To install npm:
+# - npm is typically bundled with Node.js. You can download Node.js from:
+#   https://nodejs.org/en/download/
+
+# To install pm2:
+# - You can install pm2 using npm: npm install pm2 -g
+
+# === Define Directories ===
+# It is essential to configure the directory paths at the beginning of this
+# script to match your environment before execution.
+home_dir="/home/ec2-user"
+comptox_ai_dir="${home_dir}/comptox_ai"
+app_dir="${comptox_ai_dir}/web/packages/app"
+api_dir="${comptox_ai_dir}/web/packages/api"
+docs_dir="${comptox_ai_dir}/docs"
+docs_build_dir="${docs_dir}/build/html"
+
+# Define the web root directory, which is used as the root for Nginx in EC2 and
+# for local testing.
+web_root_dir="/usr/share/nginx/html" # For EC2
+# web_root_dir="${home_dir}/merged_build" # For local testing
+
+# Check if the required directories exist
+required_dirs=("${home_dir}" "${comptox_ai_dir}" "${app_dir}" "${api_dir}" "${docs_dir}" "${docs_build_dir}" "${web_root_dir}")
+
+for dir in "${required_dirs[@]}"; do
+  if [ ! -d "${dir}" ]; then
+    check_error 1 "Directory ${dir} does not exist."
+  fi
+done
+
+# Check if the script has permissions to access the directories
+if [ ! -r "${home_dir}" ] || [ ! -w "${home_dir}" ]; then
+  check_error 1 "Script does not have read and write permissions for ${home_dir}."
+fi
+
+if [ ! -r "${comptox_ai_dir}" ] || [ ! -w "${comptox_ai_dir}" ]; then
+  check_error 1 "Script does not have read and write permissions for ${comptox_ai_dir}."
+fi
+
+# === Define Functions ===
+
+# Function to log errors or steps
+log_message() {
+  local message="${1}"
+  local log_file="${2:-${deploy_run_log}}" # Use deploy_run_log as default log file if not provided
+  local timestamp
+  timestamp="$(date +'%Y_%m_%d_%H_%M_%S')"
+  local log_message="${timestamp} - ${message}"
+
+  # Log message to console
+  echo "${log_message}"
+
+  # Log message to the specified log file
+  echo "${log_message}" >>"${log_file}"
+}
+
+# Function to check for errors and exit if an error occurs
+check_error() {
+  local exit_code="${1}"
+  local error_message="${2}"
+  if [ "${exit_code}" -ne 0 ]; then
+    log_message "ERROR: ${error_message}. Exit code: ${exit_code}"
+    exit 1
+  fi
+}
+
+# === Set Environment Variables ===
+
+# Function to detect the service manager and execute commands accordingly
+detect_and_execute_service_manager() {
+  local os_type
+  os_type=$(uname)
+
+  if [[ "${os_type}" == "Darwin" ]]; then
+    # macOS uses launchctl
+    SERVICE_MANAGER="launchctl"
+  elif [[ "${os_type}" == "Linux" ]]; then
+    # Linux uses systemctl
+    SERVICE_MANAGER="systemctl"
+  else
+    # Handle unsupported OS
+    check_error 1 "Unsupported operating system: ${os_type}"
+  fi
+
+  # Execute the provided command
+  if [[ "${SERVICE_MANAGER}" == "systemctl" ]]; then
+    sudo systemctl "$@"
+  elif [[ "${SERVICE_MANAGER}" == "launchctl" ]]; then
+    sudo launchctl "$@"
+  else
+    # Handle unsupported service manager
+    check_error 1 "Unsupported service manager: ${SERVICE_MANAGER}"
+  fi
+}
+
+# Set the Python virtual environment name to be used for Comptox AI
+python_venv="comptox_ai_v1.1.3_py3.8"
+
+# Define GitHub repository URL
+github_repo_url="https://github.com/RomanoLab/comptox_ai.git"
+
+# Timezone set to EST
+export TZ="America/New_York"
+
+# Define timestamp format
+timestamp_format='%Y_%m_%d_%H_%M_%S'
+
+# Generate a timestamp for the log file name and save it to timestamp.sh
+current_time=$(date +"${timestamp_format}")
+echo "#!/bin/bash" >timestamp.sh # timestamp.sh is to be used as a reference for creating the log file name of this specific deployment run.
+echo "# Timestamp of when deploy script was run" >>timestamp.sh
+echo "current_time=\"${current_time}\"" >>timestamp.sh
+
+# Source the timestamp.sh file to set the current timestamp
+source "${home_dir}/timestamp.sh"
+
+# Define log directory
+log_dir="${home_dir}/deploy_logs"
+# Define error log file path
+deploy_run_log="${log_dir}/deploy_run_log_${current_time}.txt"
+# Define log file path
+npm_install_log="${log_dir}/npm_install_times_${current_time}.log"
+
+# Create the log directory if it doesn't exist
+mkdir -p "${log_dir}"
+check_error "${?}" "Failed to create the log directory ${log_dir}"
+
+# Function to log npm package installation times
+log_npm_install_time() {
+  local package="${1}"
+  local duration="${2}"
+  echo "### ${package} ###" >>"${npm_install_log}"
+  echo "Completed in ${duration} ms" >>"${npm_install_log}"
+}
+
+# === Main Code Execution Starts Here ===
+
+cd "${comptox_ai_dir}" || exit
+
+# === Step 1: Update from GitHub ===
+log_message "Step 1: Update from GitHub started"
+
+# Git pull
+if ! git pull "${github_repo_url}"; then
+  check_error 1 "Git pull failed"
+fi
+
+log_message "Step 1: Update from GitHub completed without error"
+
+# === Step 2: Python Environment Setup ===
+log_message "Step 2: Python Environment Setup started"
+
+# Initialize the shell for Micromamba
+eval "$(micromamba shell hook --shell bash)"
+# Activate the Python environment
+micromamba activate "${python_venv}"
+check_error "${?}" "Failed to initialize the shell for Micromamba"
+
+log_message "Step 2: Python Environment Setup completed without error"
+
+# === Step 3: Python Package Installation ===
+log_message "Step 3: Python Package Installation started"
+
+# Install project dependencies using pip
+pip install --upgrade pip setuptools
+pip install . ".[docs]"
+check_error "${?}" "Failed to install project dependencies using pip"
+
+log_message "Step 3: Python Package Installation completed without error"
+
+# === Step 4: Sphinx Documentation ===
+log_message "Step 4: Sphinx Documentation started"
+
+# Clean the previous doc build
+cd "${docs_dir}" || exit # pwd: /home/ec2-user/comptox_ai/docs
+rm -rf ./build
+
+# Build Sphinx doc
+make html
+check_error "${?}" "Failed to build Sphinx documentation"
+
+# Check if docs are properly built by checking necessary files
+required_files=("index.html" "browse.html")
+missing_files=()
+
+for file in "${required_files[@]}"; do
+  if [[ ! -f "${docs_build_dir}/${file}" ]]; then
+    missing_files+=("${file}")
+  fi
+done
+
+if [[ ${#missing_files[@]} -gt 0 ]]; then
+  check_error 1 "These files are missing in '${docs_build_dir}': ${missing_files[*]}"
+fi
+
+log_message "Step 4: Sphinx Documentation completed without error"
+
+# === Step 5: JavaScript Package Installation ===
+log_message "Step 5: JavaScript Package Installation started"
+
+# Install npm packages for the app dir
+cd "${app_dir}" || exit               # pwd: /home/ec2-user/comptox_ai/web/packages/app
+npm ci --verbose >"${deploy_run_log}" # Redirect verbose output to the log file
+check_error "${?}" "npm ci for the app directory failed"
+
+# Clean the previous React build
+rm -rf ./build
+
+if touch "${npm_install_log}"; then
+  echo "Log file created: ${npm_install_log}"
+else
+  check_error 1 "Log file could not be created or already exists."
+fi
+
+# Show the contents of package.json for app directory
+echo "Contents of app/package.json:"
+cat "${app_dir}/package.json"
+
+# Show the result of npm ci for the app directory
+echo "npm ci exit code for app: ${?}"
+
+log_message "Step 5: JavaScript Package Installation completed without error"
+
+# === Step 6: React App Integration ===
+log_message "Step 6: React App Integration started"
+
+# Build the React app
+npm run build
+
+# Check if the required React app build files exist
+cd "${comptox_ai_dir}" || exit # pwd: /home/ec2-user/comptox_ai/
+if [ ! -f "${app_dir}/build/static/js/main.js" ] || [ ! -f "${app_dir}/build/static/css/main.css" ]; then
+  check_error 1 "Required files (main.js or main.css) are missing in '${app_dir}/build/static'"
+fi
+
+log_message "Step 6: React App Integration completed without error"
+
+# === Step 7: Nginx Server Update ===
+log_message "Step 7: Nginx Server Update started"
+
+# Copy JavaScript and CSS files from React app build to Sphinx documentation
+cp "${app_dir}/build/static/js/"* "${docs_dir}/build/html/_static/js"
+cp "${app_dir}/build/static/css/"* "${docs_dir}/build/html/_static/css"
+check_error "${?}" "Failed to copy and paste the doc build files"
+
+# Copy and paste the Sphinx documentation HTML files to the web root directory
+cd / || exit # Navigate to the root directory (set web_root_dir accordingly)
+cp -r "${docs_dir}/build/html/"* "${web_root_dir}"
+
+# Check if copy and paste was done successfully
+cd "${comptox_ai_dir}" || exit # pwd: /home/ec2-user/comptox_ai
+
+if cmp --silent "${app_dir}/build/static/js/main.js" "${docs_dir}/build/html/_static/js/main.js" &&
+  cmp --silent "${app_dir}/build/static/css/main.css" "${docs_dir}/build/html/_static/css/main.css"; then
+  echo "Files were copied successfully."
+else
+  check_error 1 "Files were not copied successfully."
+fi
+
+# Reload Nginx and check if the webpage is working as intended
+if [[ "${SERVICE_MANAGER}" == "systemctl" ]]; then
+  # Use systemctl on Linux
+  if sudo nginx -t; then
+    sudo systemctl reload nginx
+  else
+    check_error 1 "Nginx configuration test failed. Reloading Nginx aborted."
+  fi
+else
+  # Use launchctl on macOS
+  if sudo nginx -t; then
+    sudo nginx -s reload
+  else
+    check_error 1 "Nginx configuration test failed. Reloading Nginx aborted."
+  fi
+fi
+
+# Check if the Nginx service is running (for both macOS and Linux)
+if [[ "${SERVICE_MANAGER}" == "launchctl" ]]; then
+  # For macOS using launchctl
+  if launchctl list | grep -q "nginx"; then
+    echo "Nginx is running."
+  else
+    check_error 1 "Nginx failed to run."
+  fi
+elif [[ "${SERVICE_MANAGER}" == "systemctl" ]]; then
+  # For Linux using systemctl
+  if sudo systemctl is-active --quiet nginx; then
+    echo "Nginx is running."
+  else
+    check_error 1 "Nginx failed to run."
+  fi
+fi
+
+log_message "Step 7: Nginx Server Update completed without error"
+
+# === Step 8: API Installation ===
+log_message "Step 8: API Installation started"
+
+# Install packages needed for the API
+cd "${api_dir}" || exit # pwd: /home/ec2-user/comptox_ai/web/packages/api
+
+# Show the contents of package.json for the API dir
+echo "Contents of api/package.json:"
+cat "${api_dir}/package.json"
+
+# Run npm ci for the API dir
+cd "${api_dir}" || exit
+npm ci
+check_error "${?}" "npm ci for the API directory failed"
+
+# Show the result of npm ci for the API dir
+echo "npm ci exit code for API: ${?}"
+
+# Stop API with a delay and start it again
+if pm2 list | grep -q "api-app"; then
+  pm2 stop api-app
+  sleep 5 # Add a 5-second delay before starting it again
+  check_error "${?}" "Failed to stop api-app"
+  pm2 start app.js --name=api-app
+  check_error "${?}" "Failed to start api-app"
+else
+  pm2 start app.js --name=api-app
+  check_error "${?}" "Failed to start api-app"
+fi
+
+pm2 list
+log_message "Step 8: API Installation completed without error"