run.sh

#!/bin/bash
set -e

# ============================================================
# NATURA-EVIDENCE — Single-Command Launcher
# Starts: Backend (FastAPI) + Celery Worker + Frontend (React)
# Kills stale processes on ports 8000, 5173, and old Celery workers
# ============================================================

PROJECT_DIR="$(cd "$(dirname "$0")" && pwd)"
BACKEND_DIR="$PROJECT_DIR/natura-evidence-api"
FRONTEND_DIR="$PROJECT_DIR/natura-evidence-ui"
PIDS=()

# ---- Colors ----
RED='\033[0;31m'
GREEN='\033[0;32m'
YELLOW='\033[1;33m'
CYAN='\033[0;36m'
NC='\033[0m'

cleanup() {
    echo ""
    echo -e "${YELLOW}Shutting down NATURA-EVIDENCE...${NC}"
    for pid in "${PIDS[@]}"; do
        kill "$pid" 2>/dev/null || true
    done
    # Kill anything remaining on our ports
    for port in 8000 5173; do
        fuser -k "$port/tcp" 2>/dev/null || true
    done
    # Kill all celery workers for this project
    pkill -f "app.tasks.celery_app" 2>/dev/null || true
    wait 2>/dev/null
    echo -e "${GREEN}All services stopped. Ports 8000 and 5173 freed.${NC}"
}
trap cleanup EXIT INT TERM

echo -e "${CYAN}"
echo "============================================"
echo "   NATURA-EVIDENCE Platform Launcher"
echo "============================================"
echo -e "${NC}"

# ---- Step 0: Kill ALL stale processes on our ports ----
echo -e "${YELLOW}[0/7]${NC} Cleaning up stale processes..."
fuser -k 8000/tcp 2>/dev/null || true
fuser -k 5173/tcp 2>/dev/null || true
pkill -f "app.tasks.celery_app" 2>/dev/null || true
sleep 1
echo -e "  ${GREEN}✓${NC} Ports 8000, 5173 cleared. Old Celery workers killed."

# ---- Reset stuck pipeline states in Redis ----
echo -e "  ${YELLOW}⏳${NC} Resetting stuck pipeline states in Redis..."
cd "$BACKEND_DIR"
source .venv/bin/activate 2>/dev/null
python3 -c "
import redis, os
url = os.environ.get('REDIS_URL', 'redis://localhost:6380/0')
r = redis.from_url(url, decode_responses=True)
# Find all pipeline hashes and reset stuck states
for key in r.keys('pipeline:*:steps'):
    pid = key.split(':')[1]
    steps = r.hgetall(key)
    stuck = [s for s, st in steps.items() if st in ('running', 'queued')]
    if stuck:
        r.delete(key)
        r.delete(f'pipeline:{pid}')
        r.delete(f'pipeline:{pid}:logs')
        r.delete(f'pipeline:{pid}:stage_runtimes')
        r.delete(f'pipeline:{pid}:warnings')
        
        import shutil
        import glob
        for path in glob.glob(f'data/*/{pid}'):
            shutil.rmtree(path, ignore_errors=True)
            
        print(f'  Erased stuck pipeline {pid[:8]} completely...')
# Also clear any orphaned task results
for key in r.keys('celery-task-meta-*'):
    r.delete(key)
print('  Done.')
" 2>/dev/null || echo -e "  ${YELLOW}⚠${NC} Could not reset Redis (will happen on first API call)"

# ---- Start Docker Infrastructure ----
echo -e "${YELLOW}[1/7]${NC} Starting Docker infrastructure (Postgres + Redis)..."

if ! command -v docker >/dev/null 2>&1; then
    echo -e "  ${RED}✗${NC} Docker not found. Database and cache will not be available."
else
    if docker ps --format '{{.Names}}' 2>/dev/null | grep -q '^natura_evidence_db$'; then
        echo -e "  ${GREEN}✓${NC} PostgreSQL already running on port 5433"
    else
        docker rm natura_evidence_db 2>/dev/null || true
        docker run -d --name natura_evidence_db \
            -e POSTGRES_USER=natura \
            -e POSTGRES_PASSWORD=natura_password \
            -e POSTGRES_DB=natura_evidence \
            -p 5433:5432 \
            postgres:15-alpine > /dev/null 2>&1
        echo -e "  ${GREEN}✓${NC} PostgreSQL started on port 5433"
    fi

    if docker ps --format '{{.Names}}' 2>/dev/null | grep -q '^natura_evidence_redis$'; then
        echo -e "  ${GREEN}✓${NC} Redis already running on port 6380"
    else
        docker rm natura_evidence_redis 2>/dev/null || true
        docker run -d --name natura_evidence_redis \
            -p 6380:6379 \
            redis:7-alpine redis-server --save 60 1 > /dev/null 2>&1
        echo -e "  ${GREEN}✓${NC} Redis started on port 6380"
    fi
fi

echo -e "  ${YELLOW}⏳${NC} Waiting for containers to initialize..."
sleep 3

# ---- Check Redis ----
echo -e "${YELLOW}[2/7]${NC} Checking Redis..."
if redis-cli -p 6380 ping > /dev/null 2>&1; then
    echo -e "  ${GREEN}✓${NC} Redis is running on port 6380"
else
    echo -e "  ${RED}✗${NC} Redis not responding. Check docker logs."
    exit 1
fi

# ---- Check Python venv ----
echo -e "${YELLOW}[3/7]${NC} Checking Python environment..."
if [ ! -d "$BACKEND_DIR/.venv" ]; then
    echo -e "  ${YELLOW}⚠${NC} Creating Python virtual environment..."
    cd "$BACKEND_DIR"
    python3 -m venv .venv
    source .venv/bin/activate
    echo -e "  ${YELLOW}⚠${NC} Installing dependencies..."
    pip install -r requirements.txt > /dev/null 2>&1
    echo -e "  ${GREEN}✓${NC} Dependencies installed"
else
    source "$BACKEND_DIR/.venv/bin/activate"
    echo -e "  ${GREEN}✓${NC} Python venv ready"
fi

# ---- Check AutoDock Vina ----
echo -e "${YELLOW}[4/7]${NC} Checking AutoDock Vina..."
if python -c "from vina import Vina" 2>/dev/null; then
    echo -e "  ${GREEN}✓${NC} AutoDock Vina available (full docking)"
else
    echo -e "  ${YELLOW}⚠${NC} AutoDock Vina not installed — using RDKit conformer energy fallback"
fi

# ---- Check Node modules ----
echo -e "${YELLOW}[5/7]${NC} Checking Node.js environment..."
if [ ! -d "$FRONTEND_DIR/node_modules" ]; then
    echo -e "  ${YELLOW}⚠${NC} Installing frontend dependencies..."
    cd "$FRONTEND_DIR"
    npm install > /dev/null 2>&1
    echo -e "  ${GREEN}✓${NC} Frontend dependencies installed"
else
    echo -e "  ${GREEN}✓${NC} Node modules ready"
fi

# ---- Start Backend ----
echo -e "${YELLOW}[6/7]${NC} Starting Backend API (port 8000)..."
cd "$BACKEND_DIR"
source .venv/bin/activate
uvicorn app.main:app --host 0.0.0.0 --port 8000 > /tmp/natura-backend.log 2>&1 &
BACKEND_PID=$!
PIDS+=($BACKEND_PID)
sleep 4

if kill -0 $BACKEND_PID 2>/dev/null; then
    echo -e "  ${GREEN}✓${NC} Backend running on http://localhost:8000"
else
    echo -e "  ${RED}✗${NC} Backend failed. Check /tmp/natura-backend.log"
    tail -10 /tmp/natura-backend.log
    exit 1
fi

# ---- Start Celery Worker (with ALL queues including 'default') ----
echo -e "${YELLOW}[7/7]${NC} Starting Celery Worker..."
if redis-cli -p 6380 ping > /dev/null 2>&1; then
    cd "$BACKEND_DIR"
    source .venv/bin/activate
    # Use ALL queues that task_routes define + default as safety net
    # --pool=solo avoids asyncio event loop issues in Celery fork-pool workers
    celery -A app.tasks.celery_app worker \
        -Q default,compound,target,protein,disease,pathway,network,docking,admet,literature,clinical,ai,dossier \
        --pool=solo \
        --loglevel=info \
        --concurrency=1 \
        > /tmp/natura-celery.log 2>&1 &
    CELERY_PID=$!
    PIDS+=($CELERY_PID)
    sleep 3
    if kill -0 $CELERY_PID 2>/dev/null; then
        echo -e "  ${GREEN}✓${NC} Celery worker running (pool=solo, all queues)"
    else
        echo -e "  ${RED}✗${NC} Celery worker failed. Check /tmp/natura-celery.log"
        tail -10 /tmp/natura-celery.log
    fi
else
    echo -e "  ${YELLOW}⚠${NC} Skipping Celery (Redis not available)"
fi

# ---- Start Frontend ----
echo ""
echo -e "${CYAN}Starting Frontend (port 5173)...${NC}"
cd "$FRONTEND_DIR"
npm run dev > /tmp/natura-frontend.log 2>&1 &
FRONTEND_PID=$!
PIDS+=($FRONTEND_PID)
sleep 3

if kill -0 $FRONTEND_PID 2>/dev/null; then
    echo -e "  ${GREEN}✓${NC} Frontend running on http://localhost:5173"
else
    echo -e "  ${RED}✗${NC} Frontend failed. Check /tmp/natura-frontend.log"
fi

# ---- Summary ----
echo ""
echo -e "${GREEN}============================================"
echo "   NATURA-EVIDENCE is running!"
echo -e "============================================${NC}"
echo ""
echo -e "  ${CYAN}Frontend:${NC}  http://localhost:5173"
echo -e "  ${CYAN}API Docs:${NC}  http://localhost:8000/docs"
echo -e "  ${CYAN}API:${NC}       http://localhost:8000"
echo ""
echo -e "  ${YELLOW}Logs:${NC}"
echo "    Backend:   /tmp/natura-backend.log"
echo "    Celery:    /tmp/natura-celery.log"
echo "    Frontend:  /tmp/natura-frontend.log"
echo ""
echo -e "  Press ${RED}Ctrl+C${NC} to stop all services"
echo ""

# ---- Keep running ----
wait