Daily Operations

# Start all services in the background
madsci start -d

# Verify everything is running
madsci status

# Or start in the foreground (logs streamed to terminal)
madsci start

# Start all managers in-process with in-memory backends
madsci start --mode=local

# Data is ephemeral and will not persist across restarts

# Use docker compose directly for more control
docker compose up -d

# Verify everything is running
docker compose ps

# Check health of all MADSci services
madsci status

1. Infrastructure    MongoDB, PostgreSQL, Redis, MinIO
       ↓
2. Managers          Event, Experiment, Resource, Data, Location, Workcell
       ↓
3. Lab Manager       Squid (central dashboard)
       ↓
4. Nodes             Instrument nodes (liquidhandler, robotarm, etc.)

# Start a specific manager
madsci start manager event

# Start a specific node
madsci start node ./path/to/node.py

# Start in the background with PID tracking
madsci start manager event -d

# Start only infrastructure
docker compose up -d mongodb redis postgres minio

# Start a specific manager via Docker
docker compose up -d event_manager

# Start a specific node via Docker
docker compose up -d liquidhandler_1

# Start managers without nodes
docker compose up -d lab_manager event_manager experiment_manager \
  resource_manager data_manager location_manager workcell_manager

# Start a manager directly
python -m madsci.event_manager

# Start a node directly
python example_modules/liquidhandler.py

# Start with custom settings
EVENT_SERVER_PORT=8001 EVENT_MONGO_DB_URL=mongodb://localhost:27017 \
  python -m madsci.event_manager

# Stop all services (preserves data volumes)
madsci stop

# Stop a specific background manager
madsci stop manager event

# Stop a specific background node
madsci stop node <name>

# Stop and remove images
madsci stop --remove

# Stop and remove volumes (data loss — requires confirmation)
madsci stop --volumes

# Stop all services via docker compose directly
docker compose down

# Stop a specific service
docker compose stop liquidhandler_1

# Stop and remove everything including data volumes (DESTRUCTIVE)
docker compose down -v

# Force stop all containers
docker compose kill

# Force stop a specific container
docker kill <container_name>

# Quick status check of all services
madsci status

# Watch status continuously (updates every 5 seconds)
madsci status --watch

# JSON output for scripting
madsci status --json

# Check specific service health
curl http://localhost:8000/health  # Lab Manager
curl http://localhost:8001/health  # Event Manager
curl http://localhost:8005/health  # Workcell Manager

# Check a specific node
curl http://localhost:2000/health

# Get node info
curl http://localhost:2000/info

# Get node state
curl http://localhost:2000/state

# Run comprehensive diagnostics
madsci doctor

# Check specific categories
madsci doctor --check python
madsci doctor --check docker
madsci doctor --check ports

# View recent logs
madsci logs --tail 50

# Follow logs in real time
madsci logs --follow

# Filter by log level
madsci logs --level ERROR
madsci logs --level WARNING

# Filter by pattern
madsci logs --grep "workflow"
madsci logs --grep "liquidhandler"

# Logs from a specific time period
madsci logs --since 1h
madsci logs --since 30m

# All service logs
docker compose logs -f

# Specific service logs
docker compose logs -f workcell_manager

# Last 100 lines
docker compose logs --tail 100 event_manager

# Logs since a timestamp
docker compose logs --since 2026-02-09T10:00:00 workcell_manager

madsci tui

from madsci.client import WorkcellClient

wc = WorkcellClient(workcell_server_url="http://localhost:8005/")

# List active workflows
active = wc.get_active_workflows()
for wf_id, wf in active.items():
    print(f"{wf_id}: step {wf.status.current_step_index}, "
          f"started {wf.submitted_time}")

# Check the workflow queue
queue = wc.get_workflow_queue()
print(f"{len(queue)} workflows queued")

from madsci.client import WorkcellClient

wc = WorkcellClient(workcell_server_url="http://localhost:8005/")
wc.cancel_workflow("workflow_id_here")

# Pause a running workflow
wc.pause_workflow("workflow_id_here")

# Resume a paused workflow
wc.resume_workflow("workflow_id_here")

from madsci.client import WorkcellClient

wc = WorkcellClient(workcell_server_url="http://localhost:8005/")
nodes = wc.get_nodes()
for name, node in nodes.items():
    print(f"{name}: {node.status}")

# Restart via Docker
docker compose restart liquidhandler_1

# Or stop and start
docker compose stop liquidhandler_1
docker compose start liquidhandler_1

# Lock a node
curl -X POST http://localhost:2000/admin/lock

# Unlock a node
curl -X POST http://localhost:2000/admin/unlock