Reproschema Python library and Command Line Interface (CLI)

Installation

reproschema requires Python 3.10+.

pip install reproschema

Developer installation

After you create a fork, you can clone and install repo in developer mode:

git clone https://github.com/<your github>/reproschema-py.git
cd reproschema-py
pip install -e .[dev]

Style

This repo uses pre-commit to check styling.

• Install pre-commit with pip: pip install pre-commit
• In order to use it with the repository, you have to run run pre-commit install in the root directory the first time you use it.

When pre-commit is used you may have to run git commit twice, since pre-commit may make additional changes to your code for styling and will not commit these changes by default.

CLI usage

This package installs reproschema Command Line Interface (CLI).

$ reproschema --help

$  A client to support interactions with ReproSchema

  To see help for a specific command, run

  reproschema COMMAND --help     e.g. reproschema validate --help

Options:
  --version
  -l, --log-level [DEBUG|INFO|WARNING|ERROR|CRITICAL]
                                  Log level name  [default: INFO]
  --help                          Show this message and exit.

Commands:
  convert             Converts a path to a different format, jsonld,...
  create
  migrate             Updates to a new reproschema version
  redcap2reproschema  Converts REDCap CSV files to Reproschema format.
  reproschema2redcap  Converts reproschema protocol to REDCap CSV format.
  serve
  validate            Validates if the path has a valid reproschema format

reproschema2redcap

CLI Usage

You can use this feature directly from the command line. To convert ReproSchema protocol to REDCap CSV format, use the following command

reproschema reproschema2redcap <input_dir_path> <output_csv_filename>

• <input_dir_path>: The path to the root folder of a protocol. For example, to convert the reproschema-demo-protocol provided by ReproNim, you can use the following commands:

  git clone https://github.com/ReproNim/reproschema-demo-protocol.git
  cd reproschema-demo-protocol
  pwd
  

  In this case, the output from pwd (which shows your current directory path) should be your <input_dir_path>.
• <output_csv_filename>: The name of the output CSV file where the converted data will be saved.

Python Function Usage

You can also use the reproschema2redcap function from the reproschema-py package in your Python code.

from reproschema import reproschema2redcap

input_dir_path = "path-to/reproschema-demo-protocol"
output_csv_filename = "output.csv"

reproschema2redcap(input_dir_path, output_csv_filename)

redcap2reproschema

The redcap2reproschema function is designed to process a given REDCap CSV file and YAML configuration to generate the output in the reproschema format.

Prerequisites

Before the conversion, ensure you have the following:

YAML Configuration File:

• Download templates/redcap2rs.yaml and fill it out with your protocol details.

YAML File Configuration

In the templates/redcap2rs.yaml file, provide the following information:

• protocol_name: This is a unique identifier for your protocol. Use underscores for spaces and avoid special characters.
• protocol_display_name: The name that will appear in the application.
• protocol_description: A brief description of your protocol.

Example:

protocol_name: "My_Protocol"
protocol_display_name: "Assessment Protocol"
protocol_description: "This protocol is for assessing cognitive skills."

CLI Usage

The `redcap2reproschema`` function has been integrated into a CLI tool, use the following command:

reproschema redcap2reproschema path/to/your_redcap_data_dic.csv path/to/your_redcap2rs.yaml

Optionally you can provide a path to the output directory (defaults is the current directory) by adding option: --output-path PATH

Python Function Usage

You can also use the redcap2reproschema function from the reproschema-py package in your Python code.

from reproschema import redcap2reproschema

csv_path = "path-to/your_redcap_data_dic.csv"
yaml_path = "path-to/your_redcap2rs.yaml"
output_path = "path-to/directory_you_want_to_save_output"

reproschema2redcap(csv_file, yaml_file, output_path)

Notes

1. The script requires an active internet connection to access the GitHub repository.