Feature: Add a run script for building an ontologies_api server

Context

This repository at first started as a way to easily do an ontoportal development environment using Docker for the API. Since then in each of our projects we developed, Dockerfiles, docker-compose, and dip files, making it possible to run an environment development for each directly in the working repository.

So maintaining a separate repository for docker development makes no more sense. This PR is the first push to transform this repository from OntoPortal docker development environment to OntoPortal docker appliance

Requirements

[x] Have a script to run an Ontoportal API server, using as source Bioportal or Agroportal images or any other if existent.
[ ] Have a script to run an Ontoportal UI server, using as a source Bioportal, Agroportal images, or any other if existent.
[ ] Have a script to run an Ontoportal appliance server, using as a source Bioportal, Agroportal images, or any other if existent

How it works

See Help using run --help

➜  ontoportal_docker git:(main) run --help
Usage: run -k API_KEY -u API_URL -s STARTER_ONTOLOGY
    -k, --api-key API_KEY            Your Ontoportal API key
    -u, --api-url API_URL            Ontoportal API URL (default: https://data.bioontology.org)
    -r DOCKER_HUB_REPOSITORY,        Ontoportal API image repository (default: bioportal)
        --docker-hub-repository
    -t, --image-tag DOCKER_IMAGE_TAG Ontoportal API image version (default: latest)
    -s [STARTER_ONTOLOGY],           Starter ontology code (default: STY)
        --starter-ontology
    -h, --help                       Show this message

Run an API using Bioportal code

run -k <api_key> -r bioportal

Run an API using Agroportal code

run -k <api_key> -r agroportal -t stage

Changes

Extend to env file to add images sources option (8a99e0d535d8e82eb0f365f62d438fcf33b6fcf3)
Add a run script to execute the necessary commands to run a API server (8a99e0d535d8e82eb0f365f62d438fcf33b6fcf3)

ontoportal / ontoportal_docker