Configuration

This application can be configured by altering the appsettings.json file.

The tool uses DuckDB for storage, so the ConnectionString uses DuckDB’s DuckDB.NET connection string format.

An example configuration

{
    "ConnectionString": "DataSource=/data/omop.db;memory_limit=4GB",
    "VocabularyDirectory": "/vocabulary",
    "BatchSize": 200000
}

Property	Remarks
ConnectionString	DuckDB.NET connection string specifying the DuckDB file that holds the OMOP data. A .db file is created at this location by the init command.
VocabularyDirectory	Path to the directory containing the unpacked Athena vocabulary CSVs. Used by the init command. Defaults to /vocabulary.
BatchSize	The maximum number of rows that can be inserted by any operation. Increasing this value can increase the speed of the transform operation.

Any of these settings can also be provided on the Docker command line as -e environment variables (for example -e ConnectionString=...), which overrides the value in appsettings.json.