labarchive-integration

Files (10)

• SKILL.md
• api_reference.md · references/
• authentication_guide.md · references/
• integrations.md · references/
• entry_operations.cpython-313.pyc · scripts/__pycache__/
• notebook_operations.cpython-313.pyc · scripts/__pycache__/
• setup_config.cpython-313.pyc · scripts/__pycache__/
• entry_operations.py · scripts/
• notebook_operations.py · scripts/
• setup_config.py · scripts/

SKILL.md (first lines)

# 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:
- Working with LabArchives REST API for notebook automation
- Backing up notebooks programmatically
- Creating or managing notebook entries and attachments
- Generating site reports and analytics
- Integrating LabArchives with third-party tools (Protocols.io, Jupyter, REDCap)
- Automating data upload to electronic lab notebooks
- Managing user access and permissions programmatically

## Core Capabilities

### 1. Authentication and Configuration

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

**Prerequisites:**
- Enterprise LabArchives license with API access enabled
- API access key ID and password from LabArchives administrator
- User authentication credentials (email and external applications password)

**Configuration setup:**

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

```bash
python3 scripts/setup_config.py
```

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

```yaml
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:**
- US/International: `https://api.labarchives.com/api`
- Australia: `https://auapi.labarchives.com/api`
- UK: `https://ukapi.labarchives.com/api`

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:**

1. Call the `users/user_access_info` API method with login credentials
2. Parse the XML/JSON response to extract the user ID (UID)
3. Use the UID to retrieve detailed user information via `users/user_info_via_id`

**Example using Python wrapper:**

```python
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:**

- **List notebooks:** Retrieve all notebooks accessible to a user
- **Backup notebooks:** Download complete notebook data with optional attachment inclusion
- **Get notebook IDs:** Retrieve institution-defined notebook identifiers for integration with grants/project management systems
- **Get notebook members:** List all users with access to a specific notebook
- **Get notebook settings:** Retrieve configuration and permissions for notebooks

**Notebook backup example:**

Use the `scripts/notebook_operations.py` script:

```bash
# 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:**
- Create new entries in notebooks

From lamm-mit/scienceclaw, Apache-2.0.

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