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Convert a legacy CSV results data model specification to a YAML definition

Source: R/convert_csv.R
convertCsvToYaml.Rd

Reads a CSV file describing a module's results data model and writes a definition.yaml compatible with the HADES module schema to outputDir/moduleName/version/definition.yaml.

Usage

convertCsvToYaml(
  csvFile,
  outputDir,
  moduleName,
  prefix,
  version = "v1.0.0",
  addPrefix = NULL
)

Arguments

csvFile

Path to the input CSV file.

outputDir

Root output directory. The definition is written to outputDir/moduleName/version/definition.yaml.

moduleName

Name of the module (e.g.\ "CohortMethod").

prefix

Table name prefix including trailing underscore (e.g.\ "cm_").

version

Target module version string (default "v1.0.0").

addPrefix

Whether to prepend prefix to table names that do not already carry it. NULL (default) auto-detects based on the table names found in the CSV.

Value

Invisibly returns the path to the written YAML file.

Details

The CSV must contain at least columns for table name, column/field name, and data type. Optional columns for description, primary key flag, and deprecation flag are used when present. Column names are matched case-insensitively against common variants (e.g.\ table_name, column_name, data_type, description, primary_key).