VICC normalization routine for evidence
Project description
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
Project details
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