OpenBIS Upload Helper

The openBIS Upload Helper is a tool to parse files and extract their relevant metadata into objects and vocabularies in openBIS.

This tool works using the package bam-masterdata to grep the object types definitions. Each parser is loaded via entry points from individual GitHub repositories (see e.g., masterdata-parser-example).

Usage

If you want to use this tool for your own openBIS instance, we recommend:

1. Fork the bam-masterdata repository.
2. Fork this openbis-upload-helper repository.
3. Adapt both forks to your specific openBIS instance.
4. Create your own GitHub repositories for your parsers.
5. Deploy the app at your convenience.

Development

If you want to develop locally this package, clone the project and enter in the workspace folder:

git clone https://github.com/BAMresearch/openbis-upload-helper.git
cd openbis-upload-helper

Create a virtual environment (you can use Python>3.10) in your workspace:

python3 -m venv .venv
source .venv/bin/activate

Run the following commands to pip install the dependencies:

pip install --upgrade pip
pip install uv
uv pip install -e '.[dev,parsers]'

Note: The parsers are loaded as entry points via the optional dependencies in the pyproject.toml of this repository.

Run the app

You can locally deploy the app for development by running:

python openbis_upload_helper/manage.py runserver

This will run the Django app server:

Performing system checks...

System check identified no issues (0 silenced).
June 05, 2025 - 06:24:20
Django version 5.2.1, using settings 'uploader.settings'
Starting development server at http://127.0.0.1:8000/
Quit the server with CONTROL-C.

Simply click on the localhost address, http://127.0.0.1:8000/, to launch the app locally.