Carrot-Transform Quick Start Guide

Installation

Carrot-Transform is now available on PyPI, so you can install it with:

pip install carrot-transform

If you are working with the source code, refer to the Development Notes

Running Carrot-Transform

To execute Carrot-Transform, run:

carrot-transform [command] [options]

For example, you can get the version number with:

carrot-transform -v

There are many mandatory and optional arguments for carrot transform. In the quick start, we will demonstrate the mandatory arguments on a test case (taken from carrot-CDM) included in the repository. Enter the following (as one command):

Basic Example

To process a test dataset included in the repository, run:

carrot-transform run mapstream \
  --input-dir @carrot/examples/test/inputs \
  --rules-file @carrot/examples/test/rules/rules_14June2021.json \
  --person-file @carrot/examples/test/inputs/Demographics.csv \
  --output-dir carrottransform/examples/test/test_output \
  --omop-ddl-file @carrot/config/OMOPCDM_postgresql_5.3_ddl.sql \
  --omop-config-file @carrot/config/omop.json

The ‘@carrot’ is an alias to the folder containing the carrot-transform module, which can be used with either installation method. When using your own files, use your file path, and omit this.

This will generate a set of output files in this directory:

carrottransform/examples/test/test_output

If it doesn’t exist, this directory should be created for you.

Arguments

Required Arguments

OMOP Configuration (Choose One Approach)

Optional Arguments