The v1 loader expects an already existing i2b2 database (in .csv format) that will be converted in a way that is compliant with the MedCo data model. This involves encrypting and deterministically tagging some of the data.
NAME:
medco-loader v1 - Convert existing i2b2 data model
USAGE:
medco-loader v1 [command options] [arguments...]
OPTIONS:
--group value, -g value UnLynx group definition file
--entryPointIdx value, --entry value Index (relative to the group definition file) of the collective authority server to load the data
--sensitive value, --sen value File containing a list of sensitive concepts
--dbHost value, --dbH value Database hostname
--dbPort value, --dbP value Database port (default: 0)
--dbName value, --dbN value Database name
--dbUser value, --dbU value Database user
--dbPassword value, --dbPw value Database password
--files value, -f value Configuration toml with the path of the all the necessary i2b2 files
--empty, -e Empty patient and visit dimension tables (y/n)
Test that the loading was successful
To check that it is working you can query for:
-> Diagnoses -> Neoplasm -> Benign neoplasm -> Benign neoplasm of breast