Reproschema Python library and Command Line Interface (CLI)

Installation

reproschema requires Python 3.10+.

pip install reproschema

Developer installation

Fork this repo to your own GitHub account, then clone and install your forked repo in the developer mode:

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

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
  reproschema2fhir       Generates FHIR questionnaire resources from reproschema activities
  output2redcap  Generates redcap csv given the audio and survey data from reproschema ui

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: A unique identifier for your protocol. Use underscores for spaces and avoid special characters.
• protocol_display_name: Name that will appear in the application.
• protocol_description: A brief description of your protocol.
• redcap_version: Version of your redcap file (you can customize it).

Example:

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

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 (default is the current directory) by adding the 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"

redcap2reproschema(csv_file, yaml_file, output_path)

output2redcap

The output2redcap function is designed to process the output from reproschema-ui into a REDCap CSV file as seen here.

CLI Usage

The output2redcap function has been integrated into a CLI tool, use the following command:

reproschema output2redcap ./path/to/your_reproschema-ui_files ./path/to/directory_you_want_to_save_output

reproschema2fhir

The reproschema2fhir function is designed to convert reproschema activities and items into a FHIR Questionnaire resource as seen here.

CLI Usage

The reproschema2fhir function has been integrated into a CLI tool, use the following command:

reproschema reproschema2fhir ./path/to/your_reproschema_activities ./path/to/directory_you_want_to_save_output

Notes

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