start_OHMind_full.sh

#!/usr/bin/env bash

# Full OHMind Launcher - Starts MCP servers and CLI
# This script starts all MCP servers and then launches the CLI.
#
# Usage:
#   chmod +x start_OHMind_full.sh
#   ./start_OHMind_full.sh                    # Run as TUI
#   ./start_OHMind_full.sh --debug            # Enable CLI debug mode
#   ./start_OHMind_full.sh deploy             # Serve as web app on default port 8000
#   ./start_OHMind_full.sh deploy --port 9000 # Serve on custom port
#   ./start_OHMind_full.sh deploy --host 0.0.0.0 --port 8080  # Custom host and port
#
# Environment variables you can override:
#   PYTHON       - python executable to use

set -euo pipefail

ROOT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
LOG_DIR="${ROOT_DIR}/OHMind_logs"
mkdir -p "${LOG_DIR}"

export PYTHON_BIN="${PYTHON:-/home/polyai/anaconda3/envs/OHMind_copy/bin/python}"
export MCP_CHEM_PORT="${MCP_CHEM_PORT:-8101}"
export MCP_HEMDESIGN_PORT="${MCP_HEMDESIGN_PORT:-8102}"
export MCP_ORCA_PORT="${MCP_ORCA_PORT:-8103}"
export MCP_MULTIWFN_PORT="${MCP_MULTIWFN_PORT:-8104}"
export MCP_GROMACS_PORT="${MCP_GROMACS_PORT:-8105}"

# Load environment variables
GLOBAL_ENV_FILE="${ROOT_DIR}/.env"
if [ -f "$GLOBAL_ENV_FILE" ]; then
  echo "[OHMind] Loading environment from ${GLOBAL_ENV_FILE}"
  set -a
  . "$GLOBAL_ENV_FILE"
  set +a
fi

ENV_FILE="${ROOT_DIR}/OHMind_ui/.env"
if [ -f "$ENV_FILE" ]; then
  echo "[OHMind] Loading environment from ${ENV_FILE}"
  set -a
  . "$ENV_FILE"
  set +a
fi

export PYTHONPATH="${PYTHONPATH:-${ROOT_DIR}}"
export OHMind_workspace="${OHMind_workspace:-/media/polyai/8T/MyResearch/CationDesign/OHMind_workspace}"
export HEM_SAVE_PATH="${OHMind_workspace}"
export QM_WORK_DIR="${OHMind_workspace}"
export MD_WORK_DIR="${OHMind_workspace}"
export MULTIWFN_WORK_DIR="${OHMind_workspace}"
export CHEM_WORK_DIR="${OHMind_workspace}"
export OHMind_ORCA="${OHMind_ORCA:-/home/polyai/ORCA610/orca-6.1.0-f.0_linux_x86-64/bin/orca}"
export OHMind_MPI="${OHMind_MPI:-/usr/local/bin}"
export MULTIWFN_PATH="${MULTIWFN_PATH:-/home/polyai/Multiwfn38/Multiwfn}"

mkdir -p "${OHMind_workspace}"

cd "${ROOT_DIR}"

echo "[OHMind] ================================================"
echo "[OHMind] Starting OHMind Full System (MCP + CLI)"
echo "[OHMind] ================================================"

# Track PIDs for cleanup
PIDS=()

cleanup() {
    echo ""
    echo "[OHMind] Cleaning up..."
    for pid in "${PIDS[@]}"; do
        if kill -0 "$pid" 2>/dev/null; then
            echo "[OHMind] Stopping process $pid"
            kill "$pid" 2>/dev/null || true
        fi
    done
    echo "[OHMind] Cleanup complete"
}

trap cleanup EXIT INT TERM

# Start MCP servers
start_mcp_if_needed() {
    local port=$1
    local name=$2
    local module=$3
    local logname=$4
    
    if lsof -i ":${port}" >/dev/null 2>&1; then
        echo "[OHMind] ✓ ${name} already running on port ${port}"
    else
        echo "[OHMind] Starting ${name} on port ${port}..."
        "${PYTHON_BIN}" -m "${module}" --transport streamable-http --host 0.0.0.0 --port "${port}" > "${LOG_DIR}/${logname}.log" 2>&1 &
        PIDS+=($!)
        sleep 2  # Give each server time to start
        
        # Verify it started
        if lsof -i ":${port}" >/dev/null 2>&1; then
            echo "[OHMind] ✓ ${name} started successfully"
        else
            echo "[OHMind] ✗ ${name} failed to start - check ${LOG_DIR}/${logname}.log"
        fi
    fi
}

echo ""
echo "[OHMind] Starting MCP servers..."

start_mcp_if_needed "${MCP_CHEM_PORT}" "Chem MCP" "OHMind_agent.MCP.Chem.server" "chem_mcp"
start_mcp_if_needed "${MCP_HEMDESIGN_PORT}" "HEMDesign MCP" "OHMind_agent.MCP.HEMDesign.server" "hem_mcp"
start_mcp_if_needed "${MCP_ORCA_PORT}" "ORCA MCP" "OHMind_agent.MCP.ORCA.server" "orca_mcp"
start_mcp_if_needed "${MCP_MULTIWFN_PORT}" "Multiwfn MCP" "OHMind_agent.MCP.Multiwfn.server" "multiwfn_mcp"
start_mcp_if_needed "${MCP_GROMACS_PORT}" "GROMACS MCP" "OHMind_agent.MCP.GROMACS.server" "gromacs_mcp"

# Wait for all servers to be fully initialized
echo ""
echo "[OHMind] Waiting for MCP servers to fully initialize..."
sleep 5

echo ""

# Check if 'deploy' is in the arguments
if [[ " $* " =~ " deploy " ]]; then
    echo "[OHMind] Starting Web Server (deploy mode)..."
    echo ""
else
    echo "[OHMind] Starting CLI..."
    echo ""
fi

# Run CLI (this will block until exit)
# Use the new Textual-based app instead of the old rich-based cli
# Pass all arguments to support both TUI and deploy modes
"${PYTHON_BIN}" -m OHMind_cli "$@"