How omic/jailbreak works
This is an EMR extraction and research-data preparation tool. A user supplies provider credentials; the CLI reads them and dispatches to a provider bot, which retrieves portal records, parses them, transforms them toward OMOP, and loads them for research. The sampled runtime implements UW Medicine extraction and vital-sign parsing; the README describes broader anonymization, normalization, and publishing goals, while the Kaiser implementation is a separate proof of concept. The OMOP transformation and Redshift upload are incomplete in the sampled code.
Main entry points: uw.js UW portal bot · master.js Bot workflow · index.js CLI dispatcher · util.js Credential reader
Components 19
CLI and orchestration
- Provider credentials
- CLI dispatcher
src/index.js - Local config
src/config.js - Bot workflow
src/bot/master.js - Credential reader
src/util.js
UW extraction
- UW portal bot
src/bot/uw.js - Downloaded records
src/bot/uw.js - ZIP extraction
src/bot/uw.js - C-CDA records
src/bot/uw.js
Data preparation
- Vitals parser
src/bot/uw.js - Identity aliasing
src/bot/master.js - OMOP transformation
src/bot/master.js - Database loader
src/bot/uw.js
Providers and research
- UW Medicine portal
- Research database
- Kaiser downloader PoC
PoC/wa_kaiser_PoC/kaiser_wa.py - Kaiser portal
Other components
- Data donor
- Researchers
Connections 19
- Data donor → Provider credentials: provides
- Provider credentials → Credential reader: stored for
- CLI dispatcher → Local config: loads
- CLI dispatcher → Credential reader: reads
- CLI dispatcher → UW portal bot: dispatches
- UW portal bot → Bot workflow: extends
- Bot workflow → UW portal bot: calls extract
- UW portal bot → UW Medicine portal: logs in; requests export
- UW Medicine portal → Downloaded records: provides download
- UW portal bot → ZIP extraction: uncompresses
- ZIP extraction → C-CDA records: extracts files
- UW portal bot → Vitals parser: parses records
- Vitals parser → Identity aliasing: returns parsed data
- Bot workflow → OMOP transformation: calls tx
- OMOP transformation → Database loader: returns queries
- Bot workflow → Database loader: calls load
- Database loader → Research database: planned upload
- Research database → Researchers: research access
- Kaiser downloader PoC → Kaiser portal: logs in; requests download