This repository is for taking data as BIDS and uploading it to an NDA collection.

The full documentation lives here: ndabids.readthedocs.io

# Clone the repository with submodules
git clone --recursive https://github.com/nimh-dsst/nda-bids-upload.git
cd nda-bids-upload

# Install with uv (recommended)
uv pip install -e .

# Or with pip
pip install -e .

For detailed installation instructions, see INSTALL.md.

1. Create a lookup.csv file to map BIDS subject/sessions to NDA GUID's

   # Run the script directly
   python -m utilities.lookup <source_dir> <destination_dir>
   
   # Or use the installed command
   nda-lookup <source_dir> <destination_dir>

   If you have your GUID's ready and want to enter them immediately you can append the --edit-now flag to the above command:

   nda-lookup <source_dir> <destination_dir> --edit-now

   

2. Create file mapper json's and NDA Yaml files:

   # Run the script directly
   python -m utilities.mapping <source_dir> <destination_dir>
   
   # Or use the installed command
   nda-mapping <source_dir> <destination_dir>

   This produces mapper JSONs and YAMLs per BIDS datatype (e.g. anat, pet) and also image03_sourcedata.bids.toplevel (top-level BIDS files only: README, dataset_description.json, participants.tsv, etc.) for NDA image03 upload.

3. Use file mapper and nda manifests tool to create packages for uploading to NDA:

   # Prepare data for NDA upload
   python prepare.py -s <source_dir> -d <destination_dir>
   
   # Or use the installed command
   nda-prepare -s <source_dir> -d <destination_dir>

This package includes:

• NDAR/manifest-data: Git submodule providing the nda_manifests.py script
• bendhouseart/file-mapper: Git dependency for file mapping operations
• Standard Python packages: mkdocs-material, PyYAML, pandas

All dependencies are managed via pyproject.toml for easy installation with uv or pip.