labarchive-integration — Автоматизация взаимодействия с LabArchives

--- name: labarchive-integration description: Electronic lab notebook API integration. Access notebooks, manage entries/attachments, backup notebooks, integrate with Protocols.io/Jupyter/REDCap, for programmatic ELN workflows. license: Unknown metadata: skill-author: K-Dense Inc. --- # 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 - Add comments to existing entries - Create entry parts/components - Upload file attachments to entries **Attachment workflow:** Use the `scripts/entry_operations.py` script: ```bash # 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:** - Documents (PDF, DOCX, TXT) - Images (PNG, JPG, TIFF) - Data files (CSV, XLSX, HDF5) - Scientific formats (CIF, MOL, PDB) - Archives (ZIP, 7Z) ### 5. Site Reports and Analytics Generate institutional reports on notebook usage, activity, and compliance (Enterprise feature). **Available reports:** - Detailed Usage Report: User activity metrics and engagement statistics - Detailed Notebook Report: Notebook metadata, member lists, and settings - PDF/Offline Notebook Generation Report: Export tracking for compliance - Notebook Members Report: Access control and collaboration analytics - Notebook Settings Report: Configuration and permission auditing **Report generation:** ```python # 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:** - **Protocols.io:** Export protocols directly to LabArchives notebooks - **GraphPad Prism:** Export analyses and figures (Version 8+) - **SnapGene:** Direct molecular biology workflow integration - **Geneious:** Bioinformatics analysis export - **Jupyter:** Embed Jupyter notebooks as entries - **REDCap:** Clinical data capture integration - **Qeios:** Research publishing platform - **SciSpace:** Literature management **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 1. Authenticate and obtain user ID 2. List all accessible notebooks 3. Iterate through notebooks and backup each one 4. Store backups with timestamp metadata ```bash # Complete backup script python3 scripts/notebook_operations.py backup-all --email user@example.edu --password AUTH_TOKEN ``` ### Automated data upload workflow 1. Authenticate with LabArchives API 2. Identify target notebook and entry 3. Upload experimental data files 4. Add metadata comments to entries 5. Generate activity report ### Integration workflow example (Jupyter → LabArchives) 1. Export Jupyter notebook to HTML or PDF 2. Use entry_operations.py to upload to LabArchives 3. Add comment with execution timestamp and environment info 4. Tag entry for easy retrieval ## Python Package Installation Install the `labarchives-py` wrapper for simplified API access: ```bash 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 1. **Rate limiting:** Implement appropriate delays between API calls to avoid throttling 2. **Error handling:** Always wrap API calls in try-except blocks with appropriate logging 3. **Authentication security:** Store credentials in environment variables or secure config files (never in code) 4. **Backup verification:** After notebook backup, verify file integrity and completeness 5. **Incremental operations:** For large notebooks, use pagination and batch processing 6. **Regional endpoints:** Use the correct regional API endpoint for optimal performance ## Troubleshooting **Common issues:** - **401 Unauthorized:** Verify access key ID and password are correct; check API access is enabled for your account - **404 Not Found:** Confirm notebook ID (nbid) exists and user has access permissions - **403 Forbidden:** Check user permissions for the requested operation - **Empty response:** Ensure required parameters (uid, nbid) are provided correctly - **Attachment upload failures:** Verify file size limits and format compatibility For additional support, contact LabArchives at support@labarchives.com. ## Resources This skill includes bundled resources to support LabArchives API integration: ### scripts/ - `setup_config.py`: Interactive configuration file generator for API credentials - `notebook_operations.py`: Utilities for listing, backing up, and managing notebooks - `entry_operations.py`: Tools for creating entries and uploading attachments ### references/ - `api_reference.md`: Comprehensive API endpoint documentation with parameters and examples - `authentication_guide.md`: Detailed authentication setup and configuration instructions - `integrations.md`: Third-party integration setup guides and use cases