Elnora CLI

Command-line interface for the Elnora bioprotocol optimization platform.

What is Elnora?

Elnora is an AI-powered platform that helps researchers generate, optimize, and manage bioprotocols for wet-lab experiments. This CLI lets you interact with Elnora from your terminal or integrate it into scripts and automation pipelines.

Quick Start

Install

# Install with uv (recommended)
uv tool install elnora

# Or with pip
pip install elnora

Authenticate

elnora auth login

This prompts for your API key (get one from platform.elnora.ai > Settings > API Keys), verifies it, and saves it to ~/.elnora/profiles.toml.

Alternatively, set an environment variable:

export ELNORA_API_KEY=your_api_key

Multi-Org Setup

If you belong to multiple organizations, save a separate API key per org as a named profile:

elnora auth login --profile university
elnora auth login --profile work

# Use a specific profile
elnora --profile university projects list

# List all profiles
elnora auth profiles

Verify

elnora auth status

Usage

Projects

# List projects
elnora projects list

# Get a specific project
elnora projects get <PROJECT_ID>

# Create a project
elnora projects create --name "My Protocol Library"

Tasks

# List all tasks
elnora tasks list

# List tasks in a project
elnora tasks list --project <PROJECT_ID>

# Create a task
elnora tasks create --project <PROJECT_ID> --title "Generate HEK 293 protocol"

# Send a message to a task
elnora tasks send <TASK_ID> --message "Optimize for 6-well plates"

# Get task messages
elnora tasks messages <TASK_ID>

# Update a task
elnora tasks update <TASK_ID> --status completed

# Archive a task
elnora tasks archive <TASK_ID>

Files

# List files in a project
elnora files list --project <PROJECT_ID>

# Get file metadata
elnora files get <FILE_ID>

# Get file content
elnora files content <FILE_ID>

# Get file version history
elnora files versions <FILE_ID>

Search

# Search tasks
elnora search tasks --query "HEK 293"

# Search files
elnora search files --query "transfection protocol"

Health Check

# Check if the Elnora platform is reachable
elnora health

Global Options

Option	Description
--profile	Named profile to use (default: default)
--compact	Token-efficient minimal JSON output
--output json|csv	Output format (default: json)
--fields	Comma-separated fields to include in output
--version	Show version
--help	Show help

Examples

# Compact JSON for piping
elnora --compact projects list

# CSV output
elnora --output csv tasks list

# Select specific fields
elnora --fields "id,name,createdAt" projects list

# Combine options
elnora --output csv --fields "id,title,status" tasks list --project <ID>

Shell Completions

# Bash
elnora completion bash >> ~/.bashrc

# Zsh
elnora completion zsh >> ~/.zshrc

# Fish
elnora completion fish > ~/.config/fish/completions/elnora.fish

Output Format

All commands output structured JSON to stdout on success and structured JSON errors to stderr on failure.

Success (exit 0):

{
  "items": [...],
  "totalCount": 42,
  "page": 1,
  "pageSize": 25
}

Error (typed exit codes):

{
  "error": "Invalid project_id: 'abc'. Expected UUID format.",
  "code": "VALIDATION_ERROR",
  "suggestion": "Run: elnora projects list"
}

Exit Code	Meaning
0	Success
1	General / unexpected error
2	Validation error (bad input)
3	Authentication error
4	Not found
5	Rate limited
6	Server error

This makes the CLI easy to integrate with jq, scripts, and AI agents.

Authentication

The CLI resolves API keys in this order:

1. ELNORA_API_KEY environment variable
2. ELNORA_MCP_API_KEY environment variable (alias)
3. .env file in the nearest project root (directory containing pyproject.toml, package.json, .git, etc.)
4. ~/.elnora/profiles.toml — active profile (selected by --profile flag or ELNORA_PROFILE env var, default: default)
5. ~/.elnora/config.toml (legacy fallback)

Existing config.toml credentials are automatically migrated to profiles.toml on first use.

Security best practices:

• Never commit API keys to version control
• Use elnora auth login (saves to ~/.elnora/profiles.toml with 600 permissions)
• Or use environment variables / a gitignored .env file
• Rotate keys periodically via the Elnora dashboard
• Run elnora auth logout to remove saved credentials

Development

# Clone the repo
git clone https://github.com/Elnora-AI/elnora-cli.git
cd elnora-cli

# Install in development mode
uv sync

# Run the CLI
uv run elnora --help

# Run tests
uv run pytest

Troubleshooting

Error	Cause	Solution
AUTH_FAILED	Missing or invalid API key	Run elnora auth login or set ELNORA_API_KEY env var
VALIDATION_ERROR	Invalid UUID format	Check the ID — use elnora <resource> list to find valid IDs
NOT_FOUND	Resource doesn't exist	Verify the ID with elnora <resource> list
RATE_LIMITED	Too many requests	Wait a moment and retry
NETWORK_ERROR	Can't reach Elnora API	Check your internet connection
SERVER_ERROR	Elnora API issue	Try again later; contact support@elnora.ai if persistent

Claude Code Plugin

This package includes a Claude Code plugin with built-in skills that teach Claude how to use every CLI command. Skills are bundled with the package — no separate installation needed.

When Claude Code detects the Elnora CLI, it automatically gets access to command syntax, pagination patterns, error handling, and agent-optimized recipes.

Example

Tell Claude: "Create a new Elnora project called PCR Library and generate a BRCA1 protocol"

Claude will run the right sequence of CLI commands automatically.

Related

• Elnora MCP Server — Connect AI agents to Elnora via the Model Context Protocol
• Elnora Platform — Web application

Security

We take security seriously. If you discover a vulnerability, please report it responsibly — see our security policy.

Changelog

See CHANGELOG.md for version history.

Contributing

See CONTRIBUTING.md for contribution guidelines.

License

This project is licensed under the Apache License 2.0.

Support

• Bug reports and feature requests: GitHub Issues
• Account and billing questions: support@elnora.ai
• Security vulnerabilities: security@elnora.ai