reproschema requires Python 3.10+.

pip install reproschema 

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 . 

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.

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 

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.

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)

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

Before the conversion, ensure you have the following:

YAML Configuration File:

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

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"

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

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)

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