ontology-loader 0.1.5

ontology_loader

ontology_loader

Suite of tools to configure and load an ontology from the OboFoundary into the data object for OntologyClass as specified by NMDC schema.

Development Environment

Pre-requisites

• =Python 3.9

• Poetry
• Docker
• MongoDB
• NMDC materialized schema
• ENV variable for MONGO_PASSWORD (or pass it in via the cli/runner itself directly)

% docker pull mongo
% docker run -d --name mongodb-container -p 27018:27017 mongo

Basic mongosh commands

% docker ps
% docker exec -it [mongodb-container-id] bash
% mongosh mongodb://admin:root@mongo:27017/nmdc?authSource=admin
% show dbs
% use nmdc
% db.ontology_class_set.find().pretty()
% db.ontology_relation_set.find().pretty()

Command line

% poetry install
% poetry run ontology_loader --help
% poetry run ontology_loader --source-ontology "envo"
% poetry run ontology_loader --source-ontology "go"

Running the tests

% make test

Running the linter

% make lint

python example usage

pip install nmdc-ontology-loader

from  nmdc_ontology_loader.ontology_loader import OntologyLoader
import tempfile

def test_load_ontology():
    """Test the load_ontology method."""
    ontology_loader = OntologyLoader(
        source_ontology="envo",
        output_directory=tempfile.gettempdir(),
        generate_reports=True,
    )
    ontology_loader.load_ontology()
    assert ontology_loader.ontology_class_set
    assert ontology_loader.ontology_relation_set
    assert ontology_loader.ontology_class_set.count() > 0
    assert ontology_loader.ontology_relation_set.count() > 0

Reset collections in dev

% docker exec -it mongodb-container bash
% mongosh mongodb://admin:root@mongo:27017/nmdc?authSource=admin
% db.ontology_class_set.drop()
% db.ontology_relation_set.drop()