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A marshmallow schema for the National Wastewater Surveillance System

Project description

💧 nwss-data-standard

A marshmallow schema for the National Wastewater Surveillance System.

Usage

Installation

# Install from PyPI
pip install nwss

# Install local copy
git clone https://github.com/datamade/nwss-data-standard.git && cd nwss-data-standard
pip install .

See Data dictionary version compatibility for historical versions of the schema.

Data dictionary version compatibility

The CDC uses semantic versioning to track changes to the expected format for DCIPHER uploads. This table maps versions of the nwss Python package to versions of the data dictionary.

Package version CDC version
1.0.0 2.0.2
1.0.1 2.0.3

You can retrieve the CDC version from the nwss module for use in your scripts:

>>> import nwss
>>> print(nwss.CDC_VERSION)
'2.0.2'

Demo

On the web

Head to https://datamade.github.io/nwss-data-standard/ to validate a file against the standard!

In Python

from marshmallow import ValidationError
from nwss.schemas import WaterSampleSchema

sample_data = [
    # array of dictionaries
]

schema = WaterSampleSchema(many=True)

try:
    schema.load(sample_data)
except ValidationError as e:
    print(e.messages)
else:
    print('Data is valid!')

Development

Patches and pull requests

Your patches are welcome. Here's our suggested workflow:

  • Fork the project.
  • Create a new branch, then make your feature addition or bug fix.
  • Send us a pull request with a description of your work.

Python Schema

Install the app locally.

git clone https://github.com/datamade/nwss-data-standard.git && cd nwss-data-standard
pip install -e .[dev]

Make your changes, then run the tests.

pytest

JSON Schema

nwss comes with a Python implementation of the NWSS schema, as well as a convenience script to translate it to a JSON schema:

python3 -m nwss.dump_to_jsonschema > schema.json

Much of the JSON schema is determined by the marshmallow schema, however some conditional validation is written into the convenience script. You may need to update the script to make your desired change.

Demo

Run a local server and auto-bundle your scripts:

npm run develop

Navigate to the app: http://localhost:8000/docs/

Errors and bugs

If something is not behaving intuitively, it is a bug and should be reported. Report it here by creating an issue: https://github.com/datamade/nwss-data-standard/issues

Help us fix the problem as quickly as possible by following Mozilla's guidelines for reporting bugs.

Copyright and attribution

Copyright (c) 2021 DataMade. Released under the MIT License.

Project details


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