evidence-normalizer 0.0.3a3

VICC normalization routine for evidence

Evidence Normalization

Service for normalizing evidence

Developer instructions

The following sections include instructions specifically for developers.

Installation

Pipenv

For a development install, we recommend using Pipenv. See the pipenv docs for direction on installing pipenv in your compute environment.

Once installed, from the project root dir, just run:

pipenv shell
pipenv lock && pipenv sync

Pip

If you wish to install developer dependencies for evidence.dev:

pip install evidence-normalizer[dev]

If you do not need the extra dependencies:

pip install evidence-normalizer

Backend Services

Evidence Normalization relies on Variation Normalization for normalizing Cancer Hotspots data. You will need to setup backend services and set the appropriate environment variables. See the README for more information.

Starting the Evidence Normalization Service Locally

To start the service, run the following:

uvicorn evidence.main:app --reload

Next, view the OpenAPI docs on your local machine: http://127.0.0.1:8000/evidence

Init coding style tests

Code style is managed by flake8 and checked prior to commit.

We use pre-commit to run conformance tests.

This ensures:

• Check code style
• Check for added large files
• Detect AWS Credentials
• Detect Private Key

Before first commit run:

pre-commit install

Running unit tests

Running unit tests is as easy as pytest.

pipenv run pytest