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VICC normalization routine for therapies

Project description

Therapy Normalization

Services and guidelines for normalizing drug (and non-drug therapy) terms

Developer instructions

The following 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

Deploying DynamoDB Locally

We use Amazon DynamoDB for our database. To deploy locally, follow these instructions.

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

Updating the therapy normalization database

Before you use the CLI to update the database, run the following in a separate terminal to start DynamoDB on port 8000:

java -Djava.library.path=./DynamoDBLocal_lib -jar DynamoDBLocal.jar -sharedDb

To change the port, simply add -port value.

Setting Environment Variables

RxNorm requires a UMLS license, which you can register for one here. You must set the RxNORM_API_KEY environment variable to your API key. This can be found in the UTS 'My Profile' area after singing in.

export RXNORM_API_KEY={rxnorm_api_key}

Update source(s)

The sources we currently use are: ChEMBL, NCIt, DrugBank, RxNorm, ChemIDplus, and Wikidata.

To update one source, simply set --normalizer to the source you wish to update.

From the project root, run the following to update the ChEMBL source:

python3 -m therapy.cli --normalizer="chembl"

To update multiple sources, you can use the normalizer flag with the source names separated by spaces.

Update all sources

To update all sources, use the --update_all flag.

From the project root, run the following to update all sources:

python3 -m therapy.cli --update_all

Create Merged Concept Groups

The normalize endpoint relies on merged concept groups.

To create merged concept groups, use the --update_merged flag with the --update_all flag.

python3 -m therapy.cli --update_all --update_merged

Specifying the database URL endpoint

The default URL endpoint is http://localhost:8000. There are two different ways to specify the database URL endpoint.

The first way is to set the --db_url flag to the URL endpoint.

python3 -m therapy.cli --update_all --db_url="http://localhost:8001"

The second way is to set the THERAPY_NORM_DB_URL to the URL endpoint.

export THERAPY_NORM_DB_URL="http://localhost:8001"
python3 -m therapy.cli --update_all

Starting the therapy normalization service

From the project root, run the following:

 uvicorn therapy.main:app --reload

Next, view the OpenAPI docs on your local machine:

http://127.0.0.1:8000/therapy

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