labarchive-integration

LabArchives Integration

Overview

LabArchives is an electronic lab notebook platform for research documentation and data management. Access notebooks, manage entries and attachments, generate reports, and integrate with third-party tools programmatically via REST API.

When to Use This Skill

This skill should be used when:

Core Capabilities

1. Authentication and Configuration

Set up API access credentials and regional endpoints for LabArchives API integration.

Prerequisites:

Configuration setup:

Use the scripts/setup_config.py script to create a configuration file:

python3 scripts/setup_config.py

This creates a config.yaml file with the following structure:

api_url: https://api.labarchives.com/api  # or regional endpoint
access_key_id: YOUR_ACCESS_KEY_ID
access_password: YOUR_ACCESS_PASSWORD

Regional API endpoints:

For detailed authentication instructions and troubleshooting, refer to references/authentication_guide.md.

2. User Information Retrieval

Obtain user ID (UID) and access information required for subsequent API operations.

Workflow:

Example using Python wrapper:

from labarchivespy.client import Client

# Initialize client
client = Client(api_url, access_key_id, access_password)

# Get user access info
login_params = {'login_or_email': user_email, 'password': auth_token}
response = client.make_call('users', 'user_access_info', params=login_params)

# Extract UID from response
import xml.etree.ElementTree as ET
uid = ET.fromstring(response.content)[0].text

# Get detailed user info
params = {'uid': uid}
user_info = client.make_call('users', 'user_info_via_id', params=params)

3. Notebook Operations

Manage notebook access, backup, and metadata retrieval.

Key operations:

Notebook backup example:

Use the scripts/notebook_operations.py script:

# Backup with attachments (default, creates 7z archive)
python3 scripts/notebook_operations.py backup --uid USER_ID --nbid NOTEBOOK_ID

# Backup without attachments, JSON format
python3 scripts/notebook_operations.py backup --uid USER_ID --nbid NOTEBOOK_ID --json --no-attachments

API endpoint format:

https://<api_url>/notebooks/notebook_backup?uid=<UID>&nbid=<NOTEBOOK_ID>&json=true&no_attachments=false

For comprehensive API method documentation, refer to references/api_reference.md.

4. Entry and Attachment Management

Create, modify, and manage notebook entries and file attachments.

Entry operations:

Attachment workflow:

Use the scripts/entry_operations.py script:

# Upload attachment to an entry
python3 scripts/entry_operations.py upload --uid USER_ID --nbid NOTEBOOK_ID --entry-id ENTRY_ID --file /path/to/file.pdf

# Create a new entry with text content
python3 scripts/entry_operations.py create --uid USER_ID --nbid NOTEBOOK_ID --title "Experiment Results" --content "Results from today's experiment..."

Supported file types:

5. Site Reports and Analytics

Generate institutional reports on notebook usage, activity, and compliance (Enterprise feature).

Available reports:

Report generation:

# Generate detailed usage report
response = client.make_call('site_reports', 'detailed_usage_report',
                           params={'start_date': '2025-01-01', 'end_date': '2025-10-20'})

6. Third-Party Integrations

LabArchives integrates with numerous scientific software platforms. This skill provides guidance on leveraging these integrations programmatically.

Supported integrations:

OAuth authentication:
LabArchives now uses OAuth for all new integrations. Legacy integrations may use API key authentication.

For detailed integration setup instructions and use cases, refer to references/integrations.md.

Common Workflows

Complete notebook backup workflow

# Complete backup script
python3 scripts/notebook_operations.py backup-all --email user@example.edu --password AUTH_TOKEN

Automated data upload workflow

Integration workflow example (Jupyter → LabArchives)

Python Package Installation

Install the labarchives-py wrapper for simplified API access:

git clone https://github.com/mcmero/labarchives-py
cd labarchives-py
uv pip install .

Alternatively, use direct HTTP requests via Python's requests library for custom implementations.

Best Practices

Troubleshooting

Common issues:

For additional support, contact LabArchives at support@labarchives.com.

Resources

This skill includes bundled resources to support LabArchives API integration:

scripts/

references/