i2b2 to PCORnet Common Data Model Transformation - requires i2b2 PCORnet ontology
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README.md

i2p-transform

The Greater Plains Collaborative (GPC) and the Accessible Research Commons for Health (ARCH) are PCORI CDRNs that i2b2 as a core technology. The i2b2 PCORnet Common Data Model Ontology is a representation of the PCORnet Common Data Model (CDM) which allows not only i2b2 style ad-hoc query of clinical data but also this i2p-transform of data from an i2b2 datamart into a PCORNet CDM datamart.

Copyright and License

Copyright (c) 2014-2017 Univeristy of Kansas Medical Center License: MIT

Portions copyright The Brigham and Women’s Hospital, Inc. License: i2b2 Software License

Usage

To build flowsheet transformation views, once installation and configuration (below) is done, invoke the FlowsheetViews task following luigi conventions:

luigi --module i2p_tasks MedAdmin

In more detail:

PYTHONPATH=. LUIGI_CONFIG_PATH=my-client.cfg luigi \
  --local-scheduler \
  --module i2p_tasks MedAdmin

Troubleshooting is discussed in CONTRIBUTING.

Installation, Dependencies

See requirements.txt.

luigid (optional)

@@TODO elaborate on this once we establish production conventions.

docker run --name luigid -p8082:8082 -v/STATE:/luigi/state -v/CONFIG:/etc/luigi -t stockport/luigid

Configuration

See client.cfg.

Design and Development

For design info and project coding style, see CONTRIBUTING.

References