@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78

package/bin/skills/labarchive-integration/references/api_reference.md

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+# LabArchives API Reference
+
+## API Structure
+
+All LabArchives API calls follow this URL pattern:
+
+```
+https://<base_url>/api/<api_class>/<api_method>?<authentication_parameters>&<method_parameters>
+```
+
+## Regional API Endpoints
+
+| Region | Base URL |
+|--------|----------|
+| US/International | `https://api.labarchives.com/api` |
+| Australia | `https://auapi.labarchives.com/api` |
+| UK | `https://ukapi.labarchives.com/api` |
+
+## Authentication
+
+All API calls require authentication parameters:
+
+- `access_key_id`: Provided by LabArchives administrator
+- `access_password`: Provided by LabArchives administrator
+- Additional user-specific credentials may be required for certain operations
+
+## API Classes and Methods
+
+### Users API Class
+
+#### `users/user_access_info`
+
+Retrieve user ID and notebook access information.
+
+**Parameters:**
+- `login_or_email` (required): User's email address or login username
+- `password` (required): User's external applications password (not regular login password)
+
+**Returns:** XML or JSON response containing:
+- User ID (uid)
+- List of accessible notebooks with IDs (nbid)
+- Account status and permissions
+
+**Example:**
+```python
+params = {
+    'login_or_email': 'researcher@university.edu',
+    'password': 'external_app_password'
+}
+response = client.make_call('users', 'user_access_info', params=params)
+```
+
+#### `users/user_info_via_id`
+
+Retrieve detailed user information by user ID.
+
+**Parameters:**
+- `uid` (required): User ID obtained from user_access_info
+
+**Returns:** User profile information including:
+- Name and email
+- Account creation date
+- Institution affiliation
+- Role and permissions
+- Storage quota and usage
+
+**Example:**
+```python
+params = {'uid': '12345'}
+response = client.make_call('users', 'user_info_via_id', params=params)
+```
+
+### Notebooks API Class
+
+#### `notebooks/notebook_backup`
+
+Download complete notebook data including entries, attachments, and metadata.
+
+**Parameters:**
+- `uid` (required): User ID
+- `nbid` (required): Notebook ID
+- `json` (optional, default: false): Return data in JSON format instead of XML
+- `no_attachments` (optional, default: false): Exclude attachments from backup
+
+**Returns:**
+- When `no_attachments=false`: 7z compressed archive containing all notebook data
+- When `no_attachments=true`: XML or JSON structured data with entry content
+
+**File format:**
+The returned archive includes:
+- Entry text content in HTML format
+- File attachments in original formats
+- Metadata XML files with timestamps, authors, and version history
+- Comment threads and annotations
+
+**Example:**
+```python
+# Full backup with attachments
+params = {
+    'uid': '12345',
+    'nbid': '67890',
+    'json': 'false',
+    'no_attachments': 'false'
+}
+response = client.make_call('notebooks', 'notebook_backup', params=params)
+
+# Write to file
+with open('notebook_backup.7z', 'wb') as f:
+    f.write(response.content)
+```
+
+```python
+# Metadata only backup (JSON format, no attachments)
+params = {
+    'uid': '12345',
+    'nbid': '67890',
+    'json': 'true',
+    'no_attachments': 'true'
+}
+response = client.make_call('notebooks', 'notebook_backup', params=params)
+import json
+notebook_data = json.loads(response.content)
+```
+
+#### `notebooks/list_notebooks`
+
+Retrieve all notebooks accessible to a user (method name may vary by API version).
+
+**Parameters:**
+- `uid` (required): User ID
+
+**Returns:** List of notebooks with:
+- Notebook ID (nbid)
+- Notebook name
+- Creation and modification dates
+- Access level (owner, editor, viewer)
+- Member count
+
+### Entries API Class
+
+#### `entries/create_entry`
+
+Create a new entry in a notebook.
+
+**Parameters:**
+- `uid` (required): User ID
+- `nbid` (required): Notebook ID
+- `title` (required): Entry title
+- `content` (optional): HTML-formatted entry content
+- `date` (optional): Entry date (defaults to current date)
+
+**Returns:** Entry ID and creation confirmation
+
+**Example:**
+```python
+params = {
+    'uid': '12345',
+    'nbid': '67890',
+    'title': 'Experiment 2025-10-20',
+    'content': '<p>Conducted PCR amplification of target gene...</p>',
+    'date': '2025-10-20'
+}
+response = client.make_call('entries', 'create_entry', params=params)
+```
+
+#### `entries/create_comment`
+
+Add a comment to an existing entry.
+
+**Parameters:**
+- `uid` (required): User ID
+- `nbid` (required): Notebook ID
+- `entry_id` (required): Target entry ID
+- `comment` (required): Comment text (HTML supported)
+
+**Returns:** Comment ID and timestamp
+
+#### `entries/create_part`
+
+Add a component/part to an entry (e.g., text section, table, image).
+
+**Parameters:**
+- `uid` (required): User ID
+- `nbid` (required): Notebook ID
+- `entry_id` (required): Target entry ID
+- `part_type` (required): Type of part (text, table, image, etc.)
+- `content` (required): Part content in appropriate format
+
+**Returns:** Part ID and creation confirmation
+
+#### `entries/upload_attachment`
+
+Upload a file attachment to an entry.
+
+**Parameters:**
+- `uid` (required): User ID
+- `nbid` (required): Notebook ID
+- `entry_id` (required): Target entry ID
+- `file` (required): File data (multipart/form-data)
+- `filename` (required): Original filename
+
+**Returns:** Attachment ID and upload confirmation
+
+**Example using requests library:**
+```python
+import requests
+
+url = f'{api_url}/entries/upload_attachment'
+files = {'file': open('/path/to/data.csv', 'rb')}
+params = {
+    'uid': '12345',
+    'nbid': '67890',
+    'entry_id': '11111',
+    'filename': 'data.csv',
+    'access_key_id': access_key_id,
+    'access_password': access_password
+}
+response = requests.post(url, files=files, data=params)
+```
+
+### Site Reports API Class
+
+Enterprise-only features for institutional reporting and analytics.
+
+#### `site_reports/detailed_usage_report`
+
+Generate comprehensive usage statistics for the institution.
+
+**Parameters:**
+- `start_date` (required): Report start date (YYYY-MM-DD)
+- `end_date` (required): Report end date (YYYY-MM-DD)
+- `format` (optional): Output format (csv, json, xml)
+
+**Returns:** Usage metrics including:
+- User login frequency
+- Entry creation counts
+- Storage utilization
+- Collaboration statistics
+- Time-based activity patterns
+
+#### `site_reports/detailed_notebook_report`
+
+Generate detailed report on all notebooks in the institution.
+
+**Parameters:**
+- `include_settings` (optional, default: false): Include notebook settings
+- `include_members` (optional, default: false): Include member lists
+
+**Returns:** Notebook inventory with:
+- Notebook names and IDs
+- Owner information
+- Creation and last modified dates
+- Member count and access levels
+- Storage size
+- Settings (if requested)
+
+#### `site_reports/pdf_offline_generation_report`
+
+Track PDF exports for compliance and auditing purposes.
+
+**Parameters:**
+- `start_date` (required): Report start date
+- `end_date` (required): Report end date
+
+**Returns:** Export activity log with:
+- User who generated PDF
+- Notebook and entry exported
+- Export timestamp
+- IP address
+
+### Utilities API Class
+
+#### `utilities/institutional_login_urls`
+
+Retrieve institutional login URLs for SSO integration.
+
+**Parameters:** None required (uses access key authentication)
+
+**Returns:** List of institutional login endpoints
+
+## Response Formats
+
+### XML Response Example
+
+```xml
+<?xml version="1.0" encoding="UTF-8"?>
+<response>
+    <uid>12345</uid>
+    <email>researcher@university.edu</email>
+    <notebooks>
+        <notebook>
+            <nbid>67890</nbid>
+            <name>Lab Notebook 2025</name>
+            <role>owner</role>
+        </notebook>
+    </notebooks>
+</response>
+```
+
+### JSON Response Example
+
+```json
+{
+    "uid": "12345",
+    "email": "researcher@university.edu",
+    "notebooks": [
+        {
+            "nbid": "67890",
+            "name": "Lab Notebook 2025",
+            "role": "owner"
+        }
+    ]
+}
+```
+
+## Error Codes
+
+| Code | Message | Meaning | Solution |
+|------|---------|---------|----------|
+| 401 | Unauthorized | Invalid credentials | Verify access_key_id and access_password |
+| 403 | Forbidden | Insufficient permissions | Check user role and notebook access |
+| 404 | Not Found | Resource doesn't exist | Verify uid, nbid, or entry_id are correct |
+| 429 | Too Many Requests | Rate limit exceeded | Implement exponential backoff |
+| 500 | Internal Server Error | Server-side issue | Retry request or contact support |
+
+## Rate Limiting
+
+LabArchives implements rate limiting to ensure service stability:
+
+- **Recommended:** Maximum 60 requests per minute per API key
+- **Burst allowance:** Short bursts up to 100 requests may be tolerated
+- **Best practice:** Implement 1-2 second delays between requests for batch operations
+
+## API Versioning
+
+LabArchives API is backward compatible. New methods are added without breaking existing implementations. Monitor LabArchives announcements for new capabilities.
+
+## Support and Documentation
+
+For API access requests, technical questions, or feature requests:
+- Email: support@labarchives.com
+- Include your institution name and specific use case for faster assistance

package/bin/skills/labarchive-integration/references/authentication_guide.md

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+# LabArchives Authentication Guide
+
+## Prerequisites
+
+### 1. Enterprise License
+
+API access requires an Enterprise LabArchives license. Contact your LabArchives administrator or sales@labarchives.com to:
+- Verify your institution has Enterprise access
+- Request API access enablement for your account
+- Obtain institutional API credentials
+
+### 2. API Credentials
+
+You need two sets of credentials:
+
+#### Institutional API Credentials (from LabArchives administrator)
+- **Access Key ID**: Institution-level identifier
+- **Access Password**: Institution-level secret
+
+#### User Authentication Credentials (self-configured)
+- **Email**: Your LabArchives account email (e.g., researcher@university.edu)
+- **External Applications Password**: Set in your LabArchives account settings
+
+## Setting Up External Applications Password
+
+The external applications password is different from your regular LabArchives login password. It provides API access without exposing your primary credentials.
+
+**Steps to create external applications password:**
+
+1. Log into your LabArchives account at mynotebook.labarchives.com (or your institutional URL)
+2. Navigate to **Account Settings** (click your name in top-right corner)
+3. Select **Security & Privacy** tab
+4. Find **External Applications** section
+5. Click **Generate New Password** or **Reset Password**
+6. Copy and securely store this password (you won't see it again)
+7. Use this password for all API authentication
+
+**Security note:** Treat this password like an API token. If compromised, regenerate it immediately from account settings.
+
+## Configuration File Setup
+
+Create a `config.yaml` file to store your credentials securely:
+
+```yaml
+# Regional API endpoint
+api_url: https://api.labarchives.com/api
+
+# Institutional credentials (from administrator)
+access_key_id: YOUR_ACCESS_KEY_ID_HERE
+access_password: YOUR_ACCESS_PASSWORD_HERE
+
+# User credentials (for user-specific operations)
+user_email: researcher@university.edu
+user_external_password: YOUR_EXTERNAL_APP_PASSWORD_HERE
+```
+
+**Alternative: Environment variables**
+
+For enhanced security, use environment variables instead of config file:
+
+```bash
+export LABARCHIVES_API_URL="https://api.labarchives.com/api"
+export LABARCHIVES_ACCESS_KEY_ID="your_key_id"
+export LABARCHIVES_ACCESS_PASSWORD="your_access_password"
+export LABARCHIVES_USER_EMAIL="researcher@university.edu"
+export LABARCHIVES_USER_PASSWORD="your_external_app_password"
+```
+
+## Regional Endpoints
+
+Select the correct regional API endpoint for your institution:
+
+| Region | Endpoint | Use if your LabArchives URL is |
+|--------|----------|--------------------------------|
+| US/International | `https://api.labarchives.com/api` | `mynotebook.labarchives.com` |
+| Australia | `https://auapi.labarchives.com/api` | `aunotebook.labarchives.com` |
+| UK | `https://ukapi.labarchives.com/api` | `uknotebook.labarchives.com` |
+
+Using the wrong regional endpoint will result in authentication failures even with correct credentials.
+
+## Authentication Flow
+
+### Option 1: Using labarchives-py Python Wrapper
+
+```python
+from labarchivespy.client import Client
+import yaml
+
+# Load configuration
+with open('config.yaml', 'r') as f:
+    config = yaml.safe_load(f)
+
+# Initialize client with institutional credentials
+client = Client(
+    config['api_url'],
+    config['access_key_id'],
+    config['access_password']
+)
+
+# Authenticate as specific user to get UID
+login_params = {
+    'login_or_email': config['user_email'],
+    'password': config['user_external_password']
+}
+response = client.make_call('users', 'user_access_info', params=login_params)
+
+# Parse response to extract UID
+import xml.etree.ElementTree as ET
+uid = ET.fromstring(response.content)[0].text
+print(f"Authenticated as user ID: {uid}")
+```
+
+### Option 2: Direct HTTP Requests with Python requests
+
+```python
+import requests
+import yaml
+
+# Load configuration
+with open('config.yaml', 'r') as f:
+    config = yaml.safe_load(f)
+
+# Construct API call
+url = f"{config['api_url']}/users/user_access_info"
+params = {
+    'access_key_id': config['access_key_id'],
+    'access_password': config['access_password'],
+    'login_or_email': config['user_email'],
+    'password': config['user_external_password']
+}
+
+# Make authenticated request
+response = requests.get(url, params=params)
+
+if response.status_code == 200:
+    print("Authentication successful!")
+    print(response.content.decode('utf-8'))
+else:
+    print(f"Authentication failed: {response.status_code}")
+    print(response.content.decode('utf-8'))
+```
+
+### Option 3: Using R
+
+```r
+library(httr)
+library(xml2)
+
+# Configuration
+api_url <- "https://api.labarchives.com/api"
+access_key_id <- "YOUR_ACCESS_KEY_ID"
+access_password <- "YOUR_ACCESS_PASSWORD"
+user_email <- "researcher@university.edu"
+user_external_password <- "YOUR_EXTERNAL_APP_PASSWORD"
+
+# Make authenticated request
+response <- GET(
+    paste0(api_url, "/users/user_access_info"),
+    query = list(
+        access_key_id = access_key_id,
+        access_password = access_password,
+        login_or_email = user_email,
+        password = user_external_password
+    )
+)
+
+# Parse response
+if (status_code(response) == 200) {
+    content <- content(response, as = "text", encoding = "UTF-8")
+    xml_data <- read_xml(content)
+    uid <- xml_text(xml_find_first(xml_data, "//uid"))
+    print(paste("Authenticated as user ID:", uid))
+} else {
+    print(paste("Authentication failed:", status_code(response)))
+}
+```
+
+## OAuth Authentication (New Integrations)
+
+LabArchives now uses OAuth 2.0 for new third-party integrations. Legacy API key authentication (described above) continues to work for direct API access.
+
+**OAuth flow (for app developers):**
+
+1. Register your application with LabArchives
+2. Obtain client ID and client secret
+3. Implement OAuth 2.0 authorization code flow
+4. Exchange authorization code for access token
+5. Use access token for API requests
+
+Contact LabArchives developer support for OAuth integration documentation.
+
+## Troubleshooting Authentication Issues
+
+### 401 Unauthorized Error
+
+**Possible causes and solutions:**
+
+1. **Incorrect access_key_id or access_password**
+   - Verify credentials with your LabArchives administrator
+   - Check for typos or extra whitespace in config file
+
+2. **Wrong external applications password**
+   - Confirm you're using the external applications password, not your regular login password
+   - Regenerate external applications password in account settings
+
+3. **API access not enabled**
+   - Contact your LabArchives administrator to enable API access for your account
+   - Verify your institution has Enterprise license
+
+4. **Wrong regional endpoint**
+   - Confirm your api_url matches your institution's LabArchives instance
+   - Check if you're using .com, .auapi, or .ukapi domain
+
+### 403 Forbidden Error
+
+**Possible causes and solutions:**
+
+1. **Insufficient permissions**
+   - Verify your account role has necessary permissions
+   - Check if you have access to the specific notebook (nbid)
+
+2. **Account suspended or expired**
+   - Contact your LabArchives administrator to check account status
+
+### Network and Connection Issues
+
+**Firewall/proxy configuration:**
+
+If your institution uses a firewall or proxy:
+
+```python
+import requests
+
+# Configure proxy
+proxies = {
+    'http': 'http://proxy.university.edu:8080',
+    'https': 'http://proxy.university.edu:8080'
+}
+
+# Make request with proxy
+response = requests.get(url, params=params, proxies=proxies)
+```
+
+**SSL certificate verification:**
+
+For self-signed certificates (not recommended for production):
+
+```python
+# Disable SSL verification (use only for testing)
+response = requests.get(url, params=params, verify=False)
+```
+
+## Security Best Practices
+
+1. **Never commit credentials to version control**
+   - Add `config.yaml` to `.gitignore`
+   - Use environment variables or secret management systems
+
+2. **Rotate credentials regularly**
+   - Change external applications password every 90 days
+   - Regenerate API keys annually
+
+3. **Use least privilege principle**
+   - Request only necessary API permissions
+   - Create separate API credentials for different applications
+
+4. **Monitor API usage**
+   - Regularly review API access logs
+   - Set up alerts for unusual activity
+
+5. **Secure storage**
+   - Encrypt configuration files at rest
+   - Use system keychain or secret management tools (e.g., AWS Secrets Manager, Azure Key Vault)
+
+## Testing Authentication
+
+Use this script to verify your authentication setup:
+
+```python
+#!/usr/bin/env python3
+"""Test LabArchives API authentication"""
+
+from labarchivespy.client import Client
+import yaml
+import sys
+
+def test_authentication():
+    try:
+        # Load config
+        with open('config.yaml', 'r') as f:
+            config = yaml.safe_load(f)
+
+        print("Configuration loaded successfully")
+        print(f"API URL: {config['api_url']}")
+
+        # Initialize client
+        client = Client(
+            config['api_url'],
+            config['access_key_id'],
+            config['access_password']
+        )
+        print("Client initialized")
+
+        # Test authentication
+        login_params = {
+            'login_or_email': config['user_email'],
+            'password': config['user_external_password']
+        }
+        response = client.make_call('users', 'user_access_info', params=login_params)
+
+        if response.status_code == 200:
+            print("✅ Authentication successful!")
+
+            # Extract UID
+            import xml.etree.ElementTree as ET
+            uid = ET.fromstring(response.content)[0].text
+            print(f"User ID: {uid}")
+
+            # Get user info
+            user_response = client.make_call('users', 'user_info_via_id', params={'uid': uid})
+            print("✅ User information retrieved successfully")
+
+            return True
+        else:
+            print(f"❌ Authentication failed: {response.status_code}")
+            print(response.content.decode('utf-8'))
+            return False
+
+    except Exception as e:
+        print(f"❌ Error: {str(e)}")
+        import traceback
+        traceback.print_exc()
+        return False
+
+if __name__ == '__main__':
+    success = test_authentication()
+    sys.exit(0 if success else 1)
+```
+
+Run this script to confirm everything is configured correctly:
+
+```bash
+python3 test_auth.py
+```
+
+## Getting Help
+
+If authentication continues to fail after troubleshooting:
+
+1. Contact your institutional LabArchives administrator
+2. Email LabArchives support: support@labarchives.com
+3. Include:
+   - Your institution name
+   - Your LabArchives account email
+   - Error messages and response codes
+   - Regional endpoint you're using
+   - Programming language and library versions