labarchive-integration

LabArchives Integration - ELN API Integration Plan

Skills Overview

LabArchives Integration provides a complete solution to access LabArchives Electronic Lab Notebooks (ELNs) via REST API and a Python SDK. It supports notebook automation for backups, bulk upload of experimental data, and integration with third-party research tools—helping research teams implement programmatic workflows for laboratory data management.

Use Cases

1. Automated Laboratory Data Backups

Back up complete LabArchives notebook data on a regular or on-demand basis, including text records, attachment files, and user permission information. Supports JSON format export and 7z compressed backup packages to ensure secure storage of research data and to meet compliance requirements.

2. Integration of Research Workflows

Seamlessly connect LabArchives with everyday research tools: automatically upload Jupyter Notebook analysis results, synchronize REDCap clinical data, export protocols from Protocols.io, and integrate GraphPad Prism charts. Use the API to automate the full workflow of “experiment—analysis—record.”

3. Multi-User and Permission Management

Use the API to query notebook member lists, access permissions, and configuration settings. Suitable for enterprise-level needs such as centralized management of multiple project notebooks by lab administrators, generation of user activity reports, and audit/compliance checks.

Core Features

1. Authentication Configuration and User Information Management

Provide enterprise-grade API authentication configuration (supports regional endpoints for the United States, Australia, and the United Kingdom). Use setup_config.py to quickly set up access keys. Use the users/user_access_info and users/user_info_via_id interfaces to obtain user IDs and detailed information, providing identity credentials for subsequent API calls.

2. Notebook Operations and Backups

Use the notebook_operations.py script to perform notebook list queries, full backups (optionally including or excluding attachments), notebook ID retrieval, and member management. Backups support JSON format for programmatic processing, or 7z format for long-term archiving—ideal for scheduled automated backup strategies.

3. Entry and Attachment Management

Use entry_operations.py to create new entries with text content, add comments to existing entries, and upload various research files (PDFs, images, data files, chemical structure formats, etc.). Supports bulk uploads, suitable for automated experiment result recording and archival of raw data.

4. Third-Party Platform Integration

Supports OAuth authentication integration with major research tools: Protocols.io protocol export, Jupyter Notebook embedding, REDCap clinical data synchronization, Geneious bioinformatics analysis result import, and more. Programmatic interfaces connect the research data pipeline and eliminate manual data entry bottlenecks.

5. Site Reports and Analytics

Enterprise users can generate detailed usage reports (user activity metrics, notebook metadata, collaboration analysis among members, permission audits, export tracking, etc.) for lab management decision-making, resource allocation, and compliance checks.

Common Questions

How do I obtain LabArchives API access?

You need an enterprise LabArchives license and the API access feature must be enabled. Contact the LabArchives administrator to obtain the access key ID and password, then use scripts/setup_config.py to generate a configuration file. For personal accounts, create an “external application password” in account settings for user authentication.

What file formats does the LabArchives API support for upload?

Supports common research file formats, including document types (PDF, DOCX, TXT), image types (PNG, JPG, TIFF), data types (CSV, XLSX, HDF5), scientific formats (CIF, MOL, PDB), and compressed archives (ZIP, 7Z). Attachment uploads are implemented via the upload command in entry_operations.py.

Can LabArchives integrate with Jupyter Notebook?

Yes. The integration workflow is: export the Jupyter Notebook to HTML or PDF, upload it to a specified LabArchives entry using entry_operations.py, then add comments that include execution timestamps and environment information, and apply tags to facilitate later search. This automatically links analysis results with experiment records.

Does the LabArchives API have call frequency limits?

Rate limits are implemented to prevent abuse. It’s recommended to add appropriate delays during batch operations (e.g., 1–2 seconds between calls) and use an exponential backoff strategy to handle 429 errors. For large notebook backups, use pagination and batch processing to avoid timeouts.

How can I manage user permissions via the API?

Use the notebooks/notebook_members interface to query the notebook member list and access permission levels, and use notebooks/notebook_settings to retrieve configuration information. Permission changes usually require using the LabArchives web interface or contacting an administrator. The API is primarily used to read permission information to generate audit reports.

What should I do if LabArchives API authentication fails (401 error)?

First, verify that the access key ID and password are correct, and confirm whether the account has API access enabled. Make sure you are using the correct regional endpoint (United States/Australia/United Kingdom). If using external application password authentication, ensure the password has not expired and the account status is normal. Refer to references/authentication_guide.md for detailed troubleshooting steps.