https://github.com/repronim/reproschema-py
https://github.com/repronim/reproschema-py
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/repronim/reproschema-py
- Owner: ReproNim
- License: apache-2.0
- Created: 2020-06-21T19:28:29.000Z (almost 6 years ago)
- Default Branch: main
- Last Pushed: 2025-03-20T04:08:15.000Z (about 1 year ago)
- Last Synced: 2025-03-27T02:21:28.111Z (about 1 year ago)
- Language: Python
- Size: 386 KB
- Stars: 2
- Watchers: 9
- Forks: 9
- Open Issues: 17
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# 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//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
```
- ``: 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:
```bash
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 ``.
- ``: 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.
```python
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](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:
```yaml
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:
```bash
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.
```python
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](reproschema/example/redcap).
### CLI Usage
The `output2redcap` function has been integrated into a CLI tool, use the following command:
```bash
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](reproschema/example/fhir).
### CLI Usage
The `reproschema2fhir` function has been integrated into a CLI tool, use the following command:
```bash
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.