metahq-build download¶

Download raw data from external sources.

Downloads must be run before processing the corresponding source.

Usage:

metahq-build download [OPTIONS] COMMAND [ARGS]...

Options:

  --help  Show this message and exit.

gemma¶

Download raw annotations from the Gemma database.

Fetches study annotations from the Gemma REST API in batches and saves them to a single JSON file. This file is required before running 'metahq-build process gemma'.

Examples:

# Download with defaults
metahq-build download gemma

# Download to a custom path
metahq-build download gemma --output /data/gemma.json

Usage:

metahq-build download gemma [OPTIONS]

Options:

  -o, --output PATH          Override output file path (default:
                             data/unprocessed/gemma.json)
  -q, --query TEXT           Gemma API query string  [default: sort=-id]
  -m, --max-studies INTEGER  Maximum number of studies to download. Used to
                             tell the GemmaFetcher when to stop fetching.
                             [default: 60000]
  --help                     Show this message and exit.