VICC normalization routine for genes
Project description
Gene Normalization
Services and guidelines for normalizing gene terms
Developer instructions
Following are sections include instructions specifically for developers.
Installation
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 sync
Data files
For now, data files supporting the normalizers need to be obtained independently. See issue #7 for progress on updaters.
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
Starting the gene normalization service
From the project root, run the following:
uvicorn main:app --reload
Next, view the OpenAPI docs on your local machine:
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