CanDIG / service-registry

Service Registry

Stack

• Connexion for implementing the API
• SQLAlchemy, using Sqlite3 for ORM
• Dredd and Dredd-Hooks-Python for API testing
• Python 3.7+
• Pytest, tox
• Travis CI

Installation

The server software can be installed in a virtual environment:

pip install -r requirements.txt
pip install -r requirements_dev.txt
python3 setup.py develop

For automated testing you can install Dredd. Assuming you already have Node and npm installed:

npm install -g dredd

Running

The server can be run with:

python3 -m service_registry

There are several command line arguments you can pass in when running the server:

--database Path to the database. Default path is ./data/services.sqlite.

--host Hostname for where this application is running. Default hostname is localhost.

--port Port on which this application is running. Default port is 3000.

--logfile Path to the log file. Default path is ./log/services.log.

--loglevel Verbosity of the logging. Must be one of {'DEBUG', 'INFO', 'WARN', 'ERROR', 'CRITICAL'}. Default level is INFO.

--remove-active When this argument is given, the active field is not shown in responses. By default, the active field is shown in responses.

After starting up the server, sending a request to host:port (localhost:3000 by default) should give you the following response:

{
  "detail": "The requested URL was not found on the server. If you entered the URL manually please check your spelling and try again.",
  "status": 404,
  "title": "Not Found",
  "type": "about:blank"
}

There are a few endpoints:

/services Returns a list consisting of each service's information.

/services/types Returns a list of all the service types.

/services/{serviceID} Returns service information for the service with ID serviceID.

/service-info Returns service information for this application.

Before you can get a useful response from the first three endpoints, you need to add the services you want the application to look at:

python3 -m add_service "ELIXIR Beacon FI" "https://staging-elixirbeacon.rahtiapp.fi"

There are a few command line arguments to be aware of when adding a service:

--database Path to the database to add the service to. Default path is ./data/services.sqlite.

name Name of the service being added. The first string in the command is the name of the service.

url URL of the service being added. The second string in the command is the URL of the service.

Without adding any services, sending a request to /services will return the following response:

[]

Adding a service:

python3 -m add_service "ELIXIR Beacon FI" "https://staging-elixirbeacon.rahtiapp.fi"

Now, sending a request to /services will return a response similar to:

[
  {
    "active": true,
    "contactUrl": "https://www.csc.fi/contact-info",
    "createdAt": "2018-07-25T00:00:00Z",
    "description": "Beacon API Web Server based on the GA4GH Beacon API",
    "documentationUrl": "https://beacon-python.readthedocs.io/en/latest/",
    "environment": "dev",
    "id": "431c9524-4e0e-4dbc-86b2-328d69c14931",
    "name": "ELIXIR Beacon FI",
    "organization": {
      "name": "CSC - IT Center for Science",
      "url": "https://www.csc.fi/"
    },
    "type": {
      "artifact": "beacon",
      "group": "org.ga4gh",
      "version": "1.1.0"
    },
    "updatedAt": "2020-06-30T11:44:09Z",
    "url": "https://staging-elixirbeacon.rahtiapp.fi",
    "version": "1.7.0"
  }
]

For testing, the Dredd config is currently set up to launch the service itself, so no server needs to be running:

cd tests
dredd --hookfiles=dreddhooks.py