run.sh

#!/usr/bin/env bash
#
# OmicsBase single-command POC setup.
#
# Prerequisite: Docker (with the Compose plugin). Nothing else.
#   git clone <repo> omicsbase && cd omicsbase
#   ./run.sh           # configure, pull, start, print URLs
#   ./run.sh down      # stop (data is kept in ./data)
#
set -euo pipefail

COMPOSE_FILE="docker-compose.poc.yml"
DATA_DIR="data"
ENV_FILE=".env"
FRONTEND_URL="http://localhost:3000"
API_URL="http://localhost:8000"

say()  { printf '\033[1;36m%s\033[0m\n' "$*"; }
warn() { printf '\033[1;33m%s\033[0m\n' "$*"; }
die()  { printf '\033[1;31m%s\033[0m\n' "$*" >&2; exit 1; }

if [ "${1:-}" = "down" ]; then
  say "Stopping OmicsBase..."
  docker compose -f "$COMPOSE_FILE" down
  say "Stopped. Your data is preserved in ./$DATA_DIR."
  exit 0
fi

if [ "${1:-}" != "" ]; then
  die "Unknown argument '$1'. Usage: ./run.sh   |   ./run.sh down"
fi

# --- 1. Prerequisites -------------------------------------------------------
if [ "$(id -u)" = "0" ]; then
  die "Do not run this script as root."
fi
if ! command -v docker >/dev/null 2>&1; then
  die "Docker is not installed.
  Linux:   sudo apt install docker.io docker-compose-v2   (or Docker Engine per your distro)
  macOS:   install Docker Desktop from https://www.docker.com/products/docker-desktop/
  Windows: install Docker Desktop, then run this script inside WSL2."
fi
if ! docker compose version >/dev/null 2>&1; then
  die "Docker is installed but the Compose plugin is missing.
  Linux:   sudo apt install docker-compose-v2   (or 'docker compose' from your distro)
  Other:   Docker Desktop includes Compose."
fi
if ! docker info >/dev/null 2>&1; then
  die "Docker is installed but not accessible from this shell.
  If your user is not in the docker group yet:   sudo usermod -aG docker \$USER
  then log out and back in. Alternatively run:  sg docker -c './run.sh'"
fi

# --- 2. Data directories (owned by the current user, no sudo) ---------------
mkdir -p "$DATA_DIR/projects" "$DATA_DIR/knowledge"
if [ ! -f "$DATA_DIR/knowledge/bioc_books.yaml" ] && [ -f "backend/knowledge/bioc_books.yaml" ]; then
  cp -r backend/knowledge/. "$DATA_DIR/knowledge/"
  say "Seeded knowledge catalog into ./$DATA_DIR/knowledge."
fi

# --- 3. Configuration -------------------------------------------------------
if [ ! -f "$ENV_FILE" ]; then
  say "First run: let's configure your LLM provider."
  printf 'LLM provider [anthropic|openai|gemini|groq|openrouter|ollama] (default: anthropic): '
  read -r PROVIDER
  PROVIDER="${PROVIDER:-anthropic}"
  case "$PROVIDER" in
    ollama)
      API_KEY="not-needed"
      ;;
    *)
      if [ -n "${ANTHROPIC_API_KEY:-}" ] || [ -n "${OPENAI_API_KEY:-}" ] || [ -n "${GEMINI_API_KEY:-}" ] || [ -n "${GROQ_API_KEY:-}" ] || [ -n "${OPENROUTER_API_KEY:-}" ]; then
        warn "An LLM API key is already exported in this shell; reusing it."
      fi
      printf 'Paste your %s API key (input is hidden): ' "$PROVIDER"
      read -rs API_KEY
      printf '\n'
      if [ -z "$API_KEY" ]; then
        die "No API key provided. OmicsBase needs an LLM API key to run."
      fi
      ;;
  esac
  case "$PROVIDER" in
    anthropic) KEY_LINE="ANTHROPIC_API_KEY=$API_KEY" ;;
    openai)    KEY_LINE="OPENAI_API_KEY=$API_KEY" ;;
    gemini)    KEY_LINE="GEMINI_API_KEY=$API_KEY" ;;
    groq)      KEY_LINE="GROQ_API_KEY=$API_KEY" ;;
    openrouter) KEY_LINE="OPENROUTER_API_KEY=$API_KEY" ;;
    ollama)    KEY_LINE="OLLAMA_API_KEY=$API_KEY" ;;
    *)         die "Unsupported provider '$PROVIDER'." ;;
  esac
  cat > "$ENV_FILE" <<EOF
# Generated by ./run.sh
LLM_PROVIDER=$PROVIDER
$KEY_LINE
DATABASE_URL=postgresql://omicsbase:omicsbase@localhost:5433/omicsbase
REDIS_URL=redis://localhost:6379/0
TASK_BACKEND=celery
PROJECTS_DIR=./projects
DEV_MODE=true
USE_DOCKER_SANDBOX=false
EOF
  say "Configuration written to $ENV_FILE."
else
  say "Using existing $ENV_FILE (remove it to reconfigure)."
fi

# --- 4. Pull and start ------------------------------------------------------
say "Pulling OmicsBase images (first run may take a few minutes)..."
docker compose -f "$COMPOSE_FILE" pull
say "Starting OmicsBase..."
docker compose -f "$COMPOSE_FILE" up -d --wait || {
  warn "Some services did not become healthy. Showing logs:"
  docker compose -f "$COMPOSE_FILE" logs --tail=40 backend frontend
  die "Startup failed. Run './run.sh down' and try again, or open an issue with the logs above."
}

say ""
say "OmicsBase is running!"
say "  Frontend:  $FRONTEND_URL"
say "  API docs:  $API_URL/docs"
say ""
say "Try: New note -> attach a CSV -> ask the agent about your data."
warn "Keep this machine running while you work; stop anytime with: ./run.sh down"