Deploying a Custom Biomappings Instance

While it’s preferred that curations using the Biomappings workflow are contributed back to the upstream repository, custom instances can be deployed, e.g., within a company that wants to curate mappings to its own internal controlled vocabulary.

You can get started by creating a file called biomappings_custom.py. You can name this file whatever you want, just make sure to update the names in the various parts of the tutorial:

# biomappings_custom.py

from pathlib import Path

from biomappings.testing import PathIntegrityTestCase
from biomappings.wsgi import get_app

HERE = Path(__file__).parent.resolve()

PREDICTIONS = HERE.joinpath("predictions.tsv")
POSITIVES = HERE.joinpath("positive.tsv")
NEGATIVES = HERE.joinpath("negative.tsv")
UNSURE = HERE.joinpath("unsure.tsv")


class TestCustom(PathIntegrityTestCase):
    """A custom test case for integrity."""

    predictions_path = PREDICTIONS
    positives_path = POSITIVES
    negatives_path = NEGATIVES
    unsure_path = UNSURE


def ensure_example_predictions():
    """Ensure that there are some predictions for use."""
    if PREDICTIONS.is_file():
        return
    from random import Random
    from biomappings.resources import load_predictions, write_predictions

    mappings = load_predictions()
    Random(0).shuffle(mappings)
    write_predictions(mappings[:100], path=PREDICTIONS)


def main():
    """Run a custom Biomappings curation service."""
    ensure_example_predictions()

    app = get_app(
        predictions_path=PREDICTIONS,
        positives_path=POSITIVES,
        negatives_path=NEGATIVES,
        unsure_path=UNSURE,
    )
    app.run()


if __name__ == "__main__":
    main()

Running the Curation Interface

The curation app can be run by installing Biomappings and invoking the script directly:

python -m pip install biomappings[web]
python python biomappings_custom.py

Running Tests

Biomappings implements a generic testing suite inside biomappings.testing.PathIntegrityTestCase, which itself is based on unittest.TestCase and is paremetrized by the paths to the curation files.

This means that this file can also be run by any test runnier that can discover test cases such as unittest itself, pytest, or others. Therefore you can run the tests with:

python -m pip install biomappings[tests]
python -m pytest biomappings_custom.py