parser

Parser - Parse phenotype codelists, keyword lists or Phenoflow-based steplists

Prerequisites

1. Docker (machine).
2. Python 3.

Install and Run

1. Create a node virtual environment (within a python virtual environment), and activate it:

python -m venv .venv
. .venv/bin/activate
pip install nodeenv
nodeenv .nenv
. .nenv/bin/activate

2. Install dependencies:

cat requirements.txt | xargs npm install -g

3. Run server:

npm start

Deployment

1. Deployment is via Docker. If using remote machine, ensure it is activated:

docker context use [machine-name]

2. From the root directory, build container:

docker-compose build

3. Run container:

docker-compose up -d

Tests

Development

• Run all tests:

npm test

• Run specific test(s), e.g.:

NODE_ENV=test npx mocha -g "basic" --exit

Deployment

• From the root directory run:

docker-compose -f docker-compose.test.yml build;
docker-compose -f docker-compose.test.yml up;

Tests can also be used to import phenotypes from different data sources.

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

kclhi

License

This project is licensed under the MIT License - see the LICENSE.md file for details.