dnastack-client

The command line interface and client library for DNAstack services and GA4GH-compatible service, implemented in Python

• This is a fork from the old repository.
• Copyright 2024 DNAstack Corp.
• All usages are permitted under Apache 2 License.

Development Setup

Prerequisites

This project uses uv for Python dependency management. Install uv using one of these methods:

# Using the official installer (recommended)
curl -LsSf https://astral.sh/uv/install.sh | sh

# Using Homebrew (macOS)
brew install uv

# Using pipx
pipx install uv

For more installation options, see the uv documentation.

Setup

1. Clone the repository and set up the development environment:

git clone omairvalence:DNAstack/dnastack-client.git
cd dnastack-client
make setup  # Creates virtual environment and installs all dependencies

2. Run commands using uv (no activation needed):

make test-unit      # Run unit tests
make test-e2e       # Run E2E tests (requires .env file)
make test-all       # Run both unit and E2E tests
make lint           # Run linting checks
uv run dnastack --help  # Run CLI commands

Tips

Run the client in development mode using uv:

uv run dnastack --help
uv run dnastack auth login
uv run dnastack collections list
uv run dnastack explorer questions list
uv run omics --help

IntelliJ/PyCharm run configuration:

• Run the "Omics CLI" configuration in IntelliJ/PyCharm.
• This configuration runs the CLI using python -m dnastack to avoid module shadowing issues

FAQ

Q: Why do I get a ModuleNotFoundError: No module named 'http.client' error when I run the omics_cli.__main__ function through IntelliJ/PyCharm?

A: The default run configuration in IntelliJ/PyCharm tries to run the CLI script as a standalone file. This causes Python to add dnastack/ to sys.path. Since there is an http/ directory inside dnastack/, it shadows Python's built-in http module. As a result, imports like import http.client will fail with a ModuleNotFoundError.

To avoid this, use the python -m dnastack command or the provided "Omics CLI" run configuration in IntelliJ/PyCharm.

Q: Why do I get a ModuleNotFoundError: No module named 'http.client' error when I run a test through IntelliJ/PyCharm?

A: Same as above

To avoid this set a default test configuration:

1. Click the Run Configuration dropdown (next to the green play button)
2. Select Edit Configurations...
3. Go to "Edit configuration templates..."
4. Select Pythons tests → pytest
5. Set the Working directory to the project root: /Users/alaska/git/work/dnastack/dnastack-client
6. Remove options "Add content roots to PYTHONPATH" and "Add source roots to PYTHONPATH"
7. Save the run configuration template