README.md

Oxford OMOP script generator

This tool interrogates clinical data and attempts to detect the order in which the data files should be loaded and transformed.

It supports the following data types

• CDS
• COSD
• SACT
• RTDS

It generates two powershell script files, which can be used to undertake the ETL process.

• stage-and-transform.ps1 is used to stage then transform the data.
• stage-only.ps1 can be used to just only stage the data. This option leaves the data in the staging tables.

The tool can be configured by the appsetting.json file.

Setting	Explanation
PathToCdsDirectory	Directory of CDS data
PathToCosdDirectory	Directory of COSD data
PathToSactDirectory	Root directory of SACT data
PathToRtdsDirectory	Root directory of RTDS data
OmopToolPath	Path to OMOP importing tool to call
OutputPath	Output directory for generated scripts

{
    "PathToCdsDirectory": "D:\\OMOP_Mapping\\EMIS\\CDS_v6.2",
    "PathToCosdDirectory": "D:\\Cancer_Reporting\\COSD",
    "PathToSactDirectory": "D:\\Cancer_Reporting\\SACT\\SACT V.3",
    "PathToRtdsDirectory": "D:\\Cancer_Reporting\\RTDS",
    "OmopToolPath": "publish\\publish\\omop.exe",
    "OutputPath": "../../"
}

Usage

.\oxford-import-script-generator.exe