Gradio Uploader

Project Purpose

This repository provides a simple interface for sending experimental data to a FastAPI backend and optionally registering the results in MinIO and SciCat. The gradio_uploader.py script creates a small Gradio UI where a user can fill in metadata and select files to upload. The backend defined in flask_backend.py accepts the upload and writes the files to disk. Utilities in minio_scicat_ingestion.py show how the same files can be pushed to MinIO object storage and recorded in SciCat.

Installation

1. Clone the repository and change into the folder.
2. Install the required dependencies:

   pip install -r requirements.txt

Python 3.10+ is recommended.

Running the Application

Start the backend first. From the repository root run:

uvicorn flask_backend:app --reload

By default, this serves the API on http://127.0.0.1:8000.

In a separate terminal launch the Gradio interface:

python gradio_uploader.py

The UI will open in the browser and submit uploads to the FastAPI endpoint.

Environment Configuration

Several values used throughout the ingestion scripts are currently hard coded. They should be provided as environment variables instead:

Variable	Description
MINIO_SERVER	Hostname for the MinIO server (e.g. localhost).
MINIO_ACCESS_KEY	Access key for MinIO.
MINIO_SECRET_KEY	Secret key for MinIO.
MINIO_BUCKET	Bucket that will store uploaded data.
SCICAT_URL	Base API URL of SciCat (e.g. http://localhost:3000/api/v3).
SCICAT_USERNAME	SciCat username used to register datasets.
SCICAT_PASSWORD	SciCat password used to register datasets.
DATA_PATH	Directory where uploaded data files are written.
THUMBNAIL_PATH	Directory for saving uploaded thumbnails.

Set these variables in your shell or in a .env file before running any scripts. This removes the need to edit the source to change paths or credentials.