LORIS to ReproSchema Conversion

The reproschema loris2reproschema command converts a LORIS data dictionary in CSV format to the ReproSchema format.

Usage

reproschema loris2reproschema [OPTIONS] CSV_FILE CONFIG_FILE

Arguments

• CSV_FILE: Path to the LORIS data dictionary CSV file. (Required)
• CONFIG_FILE: Path to the YAML configuration file. (Required)

Options

• --output-path PATH: Path to the output directory. Defaults to the current directory.
• --encoding TEXT: Encoding to use for reading the CSV file (e.g., utf-8, latin-1).
• --analyze: Only analyze the CSV file structure and exit without conversion.
• --verbose: Enable verbose logging.
• --help: Show the help message and exit.

Configuration File

The conversion process is controlled by a YAML configuration file. This file specifies how to map the columns in your LORIS CSV to ReproSchema fields, and provides metadata for the protocol.

Here is an example of a configuration file:

# Protocol information
protocol_name: "HBCD_LORIS"
protocol_display_name: "HEALthy Brain and Child Development Study"
protocol_description: "Protocol for the HBCD study using LORIS data dictionary"
loris_version: "1.0.0"

# Column mappings from LORIS CSV to ReproSchema
column_mappings:
  activity_name: "full_instrument_name"
  item_name: "name"
  question: "question"
  field_type: "field_type"
  response_option_labels: "option_labels"
  response_option_values: "option_values"

Example

To convert a LORIS CSV file named HBCD_LORIS.csv using a configuration file hbcd-loris.yml, you would run:

reproschema loris2reproschema HBCD_LORIS.csv hbcd-loris.yml --output-path my-protocol

This will create a new directory named my-protocol/HBCD_LORIS containing the ReproSchema representation of your protocol.