paperclipai doctor

Overview

The doctor command runs comprehensive diagnostic checks on your Paperclip installation. It validates configuration, tests connections, verifies file permissions, and can automatically repair common issues.

Syntax

paperclipai doctor [options]

Options

`--config <path>`

Path to config file to check. Default: ~/.paperclip/instances/default/config.json

paperclipai doctor --config /etc/paperclip/config.json

`--data-dir <path>`

Paperclip data directory root.

paperclipai doctor --data-dir /custom/data

`--repair`

Attempt to repair issues automatically.

paperclipai doctor --repair

`--fix`

Alias for --repair.

paperclipai doctor --fix

`--yes` / `-y`

Skip repair confirmation prompts. Auto-confirm all repairs.

paperclipai doctor --repair --yes

Health Checks

Doctor runs these checks in order:

1. Config File

Validates configuration file exists and is readable. Pass:

✓ Config file: Valid config at /home/user/.paperclip/instances/default/config.json

Fail:

✗ Config file: Config file not found
  Run paperclipai onboard to create initial configuration

Can repair: No (must run onboard)

2. Deployment/Auth Mode

Verifies deployment mode and auth configuration are consistent. Valid combinations:

local_trusted + any exposure
authenticated + private or public

Pass:

✓ Deployment/auth mode: local_trusted mode (no authentication required)

Warn:

! Deployment/auth mode: authenticated mode with public exposure — ensure proper security
  Consider private exposure with allowedHostnames in production

Can repair: No (configuration choice)

3. Agent JWT Secret

Checks for PAPERCLIP_AGENT_JWT_SECRET in environment or .env.local file. Pass:

✓ Agent JWT secret: PAPERCLIP_AGENT_JWT_SECRET configured

Fail:

✗ Agent JWT secret: PAPERCLIP_AGENT_JWT_SECRET not found
  Generate with: paperclipai onboard or set manually

Can repair: Yes - Generates new secret and writes to .env.local

4. Secrets Adapter

Validates secrets configuration and key file. Pass:

✓ Secrets adapter: Local encrypted secrets configured

Fail:

✗ Secrets adapter: Secrets key file missing at /home/user/.paperclip/instances/default/secrets/master.key
  Will be created on first run

Can repair: Yes - Creates key file and directory

5. Storage Adapter

Verifies storage configuration and paths. Pass (local_disk):

✓ Storage adapter: Local disk storage configured at /home/user/.paperclip/instances/default/data/storage

Pass (s3):

✓ Storage adapter: S3 storage configured (bucket: my-bucket, region: us-east-1)

Fail:

✗ Storage adapter: Storage directory does not exist
  Directory will be created: /home/user/.paperclip/instances/default/data/storage

Can repair: Yes - Creates storage directory

6. Database

Tests database connectivity and configuration. Pass (embedded-postgres):

✓ Database: Embedded Postgres will start on port 54329

Pass (postgres):

✓ Database: Connected to postgres://***@host:5432/paperclip

Fail:

✗ Database: Connection failed - ECONNREFUSED
  Check connection string and database availability

Can repair: Yes - Can create database directory for embedded mode

7. LLM Provider

Validates LLM configuration if present. Pass:

✓ LLM provider: Claude configured (API key present)

Warn:

! LLM provider: Not configured (agents will fail without LLM access)
  Configure with: paperclipai configure --section llm

Fail:

✗ LLM provider: API key configured but invalid
  Update key with: paperclipai configure --section llm

Can repair: No (requires valid API key)

8. Log Directory

Verifies log directory exists and is writable. Pass:

✓ Log directory: /home/user/.paperclip/instances/default/logs

Fail:

✗ Log directory: Directory missing or not writable
  Will create: /home/user/.paperclip/instances/default/logs

Can repair: Yes - Creates log directory

9. Server Port

Checks if configured port is available. Pass:

✓ Server port: Port 3100 is available

Warn:

! Server port: Port 3100 is in use
  Change port with: paperclipai configure --section server

Can repair: No (requires manual port change)

Output Format

Status Icons

✓ (green) - Check passed
! (yellow) - Warning (non-blocking)
✗ (red) - Check failed (may block startup)

Check Result

Each check shows:

<icon> <check name>: <status message>
  <repair hint if applicable>

Summary

At the end:

┌  Summary
│  8 passed, 1 warnings, 0 failed
│
└  All critical checks passed with some warnings.

Outcomes:

All passed: All checks passed! (green)
Warnings only: All critical checks passed with some warnings. (yellow)
Failures: Some checks failed. Fix the issues above and re-run doctor. (red)

Auto-Repair

Interactive Repair

With --repair (no --yes):

paperclipai doctor --repair

You’ll be prompted for each repairable issue:

✗ Agent JWT secret: PAPERCLIP_AGENT_JWT_SECRET not found
  Generate with: paperclipai onboard or set manually
│
◆  Repair "Agent JWT secret"?
│  ● Yes
│  ○ No
│
✔  Repaired: Agent JWT secret

Non-Interactive Repair

With --repair --yes:

paperclipai doctor --repair --yes

All repairs are applied automatically without prompts:

✗ Agent JWT secret: PAPERCLIP_AGENT_JWT_SECRET not found
✔  Repaired: Agent JWT secret
✗ Log directory: Directory missing
✔  Repaired: Log directory

Repair Actions

Doctor can automatically:

Generate JWT secret - Creates new secret in .env.local
Create secrets key - Generates master encryption key
Create directories - Makes missing log, storage, or database directories
Fix permissions - Ensures directories are writable (if possible)

Examples

Basic health check

paperclipai doctor

Runs all checks, reports issues, no repairs.

Check and repair

paperclipai doctor --repair

Prompts before each repair action.

Fully automated repair

paperclipai doctor --repair --yes

Fixes everything automatically, no prompts.

Check specific config

paperclipai doctor --config /etc/paperclip/prod.json

Checks production configuration.

Pre-deployment check

# Non-interactive, fail if issues found
paperclipai doctor --repair --yes
if [ $? -ne 0 ]; then
  echo "Health check failed"
  exit 1
fi

Exit Codes

Doctor returns:

0 - All checks passed (or only warnings)
1 - One or more checks failed

Integration with Other Commands

Used by `run`

The run command automatically calls doctor:

paperclipai run
# Internally runs: paperclipai doctor --repair --yes

After `onboard`

Recommended to verify setup:

paperclipai onboard
paperclipai doctor

Before `configure`

Check current state:

paperclipai doctor
paperclipai configure --section database
paperclipai doctor  # Verify changes

Troubleshooting

All checks fail with “Config file not found”

Solution: Run onboard first:

paperclipai onboard
paperclipai doctor

Database check fails

For embedded-postgres:

# Ensure data directory exists
paperclipai doctor --repair --yes

# Or manually create
mkdir -p ~/.paperclip/instances/default/db

For external postgres:

# Test connection manually
psql "$(paperclipai env | grep DATABASE_URL | cut -d= -f2-)"

# Update if needed
paperclipai configure --section database

Port check warns “in use”

Find what’s using the port:

lsof -i :3100

Kill the process:

kill <PID>

Or change port:

paperclipai configure --section server

LLM provider check fails

Update API key:

paperclipai configure --section llm

Test manually:

# For Claude
curl -X POST https://api.anthropic.com/v1/messages \
  -H "x-api-key: YOUR_KEY" \
  -H "anthropic-version: 2023-06-01" \
  -H "content-type: application/json" \
  -d '{"model":"claude-sonnet-4-5-20250929","max_tokens":1,"messages":[{"role":"user","content":"hi"}]}'

# For OpenAI
curl https://api.openai.com/v1/models \
  -H "Authorization: Bearer YOUR_KEY"

Secrets key file check fails

Auto-create:

paperclipai doctor --repair --yes

Manual creation:

mkdir -p ~/.paperclip/instances/default/secrets
openssl rand -hex 32 > ~/.paperclip/instances/default/secrets/master.key
chmod 600 ~/.paperclip/instances/default/secrets/master.key

Storage directory check fails

Auto-create:

paperclipai doctor --repair --yes

Manual creation:

mkdir -p ~/.paperclip/instances/default/data/storage

Permission errors during repair

Run with proper permissions:

sudo paperclipai doctor --repair --yes

Or fix ownership:

sudo chown -R $USER:$USER ~/.paperclip
paperclipai doctor --repair --yes

CI/CD Integration

Pre-deployment Health Check

#!/bin/bash
set -e

# Ensure config exists
if [ ! -f /etc/paperclip/config.json ]; then
  echo "Config file missing"
  exit 1
fi

# Run health checks with auto-repair
paperclipai doctor --config /etc/paperclip/config.json --repair --yes

if [ $? -ne 0 ]; then
  echo "Health checks failed"
  exit 1
fi

echo "Health checks passed"

GitHub Actions

name: Health Check
on: [push]
jobs:
  doctor:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-node@v3
        with:
          node-version: '20'
      - run: npm install -g paperclipai
      - run: paperclipai doctor --config ./config.json --repair --yes

Docker Health Check

FROM node:20-alpine
RUN npm install -g paperclipai

COPY config.json /app/config.json
WORKDIR /app

HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
  CMD paperclipai doctor --config /app/config.json || exit 1

CMD ["paperclipai", "run", "--config", "/app/config.json"]

Best Practices

Regular Health Checks

Run doctor periodically:

# Daily cron job
0 2 * * * /usr/bin/paperclipai doctor --config /etc/paperclip/config.json >> /var/log/paperclip-health.log 2>&1

After Configuration Changes

Always verify after changes:

paperclipai configure --section database
paperclipai doctor --repair
paperclipai run

Before Production Deploy

Validate staging environment:

paperclipai doctor --config staging.json --repair --yes
# Review output
# If passed, deploy to production

Monitor Exit Code

In scripts:

if paperclipai doctor --repair --yes; then
  paperclipai run
else
  echo "Fix issues before starting"
  exit 1
fi

Next Steps

Fix configuration

Update configuration sections

Start server

Run Paperclip after repairs

Re-run setup

Go through onboarding again

Commands

Documentation Index

​Overview

​Syntax

​Options

​--config <path>

​--data-dir <path>

​--repair

​--fix

​--yes / -y

​Health Checks

​1. Config File

​2. Deployment/Auth Mode

​3. Agent JWT Secret

​4. Secrets Adapter

​5. Storage Adapter

​6. Database

​7. LLM Provider

​8. Log Directory

​9. Server Port

​Output Format

​Status Icons

​Check Result

​Summary

​Auto-Repair

​Interactive Repair

​Non-Interactive Repair

​Repair Actions

​Examples

​Basic health check

​Check and repair

​Fully automated repair

​Check specific config

​Pre-deployment check

​Exit Codes

​Integration with Other Commands

​Used by run

​After onboard

​Before configure

​Troubleshooting

​All checks fail with “Config file not found”

​Database check fails

​Port check warns “in use”

​LLM provider check fails

​Secrets key file check fails

​Storage directory check fails

​Permission errors during repair

​CI/CD Integration

​Pre-deployment Health Check

​GitHub Actions

​Docker Health Check

​Best Practices

​Regular Health Checks

​After Configuration Changes

​Before Production Deploy

​Monitor Exit Code

​Next Steps

Fix configuration

Start server

Re-run setup

Overview

Syntax

Options

`--config <path>`

`--data-dir <path>`

`--repair`

`--fix`

`--yes` / `-y`

Health Checks

1. Config File

2. Deployment/Auth Mode

3. Agent JWT Secret

4. Secrets Adapter

5. Storage Adapter

6. Database

7. LLM Provider

8. Log Directory

9. Server Port

Output Format

Status Icons

Check Result

Summary

Auto-Repair

Interactive Repair

Non-Interactive Repair

Repair Actions

Examples

Basic health check

Check and repair

Fully automated repair

Check specific config

Pre-deployment check

Exit Codes

Integration with Other Commands

Used by `run`

After `onboard`

Before `configure`

Troubleshooting

All checks fail with “Config file not found”

Database check fails

Port check warns “in use”

LLM provider check fails

Secrets key file check fails

Storage directory check fails

Permission errors during repair

CI/CD Integration

Pre-deployment Health Check

GitHub Actions

Docker Health Check

Best Practices

Regular Health Checks

After Configuration Changes

Before Production Deploy

Monitor Exit Code

Next Steps