biohub-data-cli 0.4.0

Biohub data CLI

data-cli

Command-line tool for downloading datasets published by CZ Biohub. Resolves a collection ID to its constituent datasets and downloads files from S3 and HTTP, with progress bars, size estimates, and dry-run accounting.

Installation

To install the OPS data CLI, run:

pip install biohub-data-cli

Quick start

See what a collection contains without downloading:

ops-data download collection <collection-id> --dry-run

Download a collection to the current directory:

ops-data download collection <collection-id>

Download multiple collections to a specific directory, skipping the prompt:

ops-data download collection <id-a> <id-b> -o ./data -y

Files land under <outdir>/<collection-slug>/<dataset-slug>/.

Commands

ops-data download collection IDS...

Download one or more collections by ID.

Option	Description
-o, --outdir PATH	Output directory. Defaults to ..
-y, --yes	Skip the size-estimate confirmation prompt.
--dry-run	Print per-dataset size statistics without downloading. Mutually exclusive with -y.

Dry run resolves every S3 URI (listing prefixes, heading objects) to report exact byte totals per dataset. HTTP URLs are not sized during dry run and surface as a warning in the summary.

Confirmation prompt shows the aggregate size estimate before any bytes move. Pass -y to skip it in scripts.

Failures are collected and reported at the end. The process exits non-zero if any download failed, but other downloads continue — one bad URL won't abort the run.

Development

This project uses uv for dependency management.

Install dependencies (including dev extras):

uv sync

Run tests:

uv run pytest

Run tests with coverage report:

uv run pytest --cov=biohub_data_cli --cov-report=term-missing

Run the CLI from a checkout:

uv run ops-data --help

Integration tests

Tests marked integration hit real S3 buckets / HTTP servers and are deselected by default. Run them explicitly:

uv run pytest -m integration

Code of Conduct

This project adheres to the Contributor Covenant code of conduct. By participating, you are expected to uphold this code. Please report unacceptable behavior to [e-mail].

Reporting Security Issues

If you believe you have found a security issue, please responsibly disclose by contacting us at [e-mail].