bento-sts 0.1.21

Bento Simple Terminology Server

bento-sts

Simple Terminology Service for Bento MDB.

The STS provides a web-based UI and a RESTful API for browsing and accessing graph data models and associated controlled vocabulary. See https://cbiit.github.io/bento-meta/ for an overview of the backend Metamodel Database (MDB).

Install

pip install bento-sts

Run

In the run directory, provide a .env file, with your appropriate values for the environment variables given the the example file bento-sts.env.eg.

For testing:

flask --app "bento_sts.sts:create_app()" run

For production, consider using gunicorn. ./src contains two gunicorn config file examples, for development and production.

gunicorn -c gunicorn.conf.dev.py

will start STS on a gunicorn server at http://localhost:8000.

Dev Install

To work on bento-sts, make sure you have Poetry:

pip install poetry

Then use it from the python working directory to install dependencies into a virtualenv:

cd bento-sts/python
poetry install

Dev Model Database for Testing

The easiest way to provide a backend graph database for a local STS is to use Docker. The following will get a workable model database running for STS development:

docker pull maj1/test-mdb
docker run -d -p7687:7687 --env NEO4J_AUTH=none --name test-mdb maj1/test-mdb

Then set the following in your src/.env file:

NEO4J_MDB_URI=bolt://localhost:7867
NEO4J_MDB_USER=neo4j
NEO4J_MDB_PASS=neo4j
STS_LOGFILE=./sts.log

Run Local STS

Once the database is running and configured, start the local STS as follows:

cd bento-sts/python/src
poetry run flask --app "bento_sts.sts:create_app()" run

You should be able to see the frontend on your machine at http://localhost:5000.

API Docs

The API is documented in an OpenAPI (Swagger) schema.

Docker is probably the easiest way to run a local Swagger server. This will bring up a Swagger server at port 6000:

# from the repo root, run...
docker run -p 6000:8080 -e SWAGGER_JSON=/work/swagger.json -v ${PWD}/swagger:/work docker.swagger.io/swaggerapi/swagger-ui

(see https://swagger.io/docs/open-source-tools/swagger-ui/usage/installation/)