reproschema requires Python 3.7+.

pip install reproschema 

Install repo in developer mode:

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

It is also useful to install pre-commit, which takes care of styling when committing code. 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:

pre-commit install 

This package installs reproschema a CLI.

$ reproschema Usage: reproschema [OPTIONS] COMMAND [ARGS]... 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 create redcap2reproschema Convert REDCap CSV files to Reproschema format. reproschema2redcap Convert reproschema protocol to REDCap CSV format. serve validate 

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: 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."

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

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" reproschema2redcap(input_dir_path, output_csv_filename)

After configuring the YAML file:

1. Run the Python script with the paths to your CSV file and the YAML file as arguments.
2. Command Format: python script_name.py path/to/your_redcap_data_dic.csv path/to/your_redcap2rs.yaml

1. The script requires an active internet connection to access the GitHub repository.
2. Make sure you use git add, git commit, git push properly afterwards to maintain a good version control for your converted data.