Py-de-id

A python microservice to deidentify fhir resources - made with CherryPy

• GET /health — returns status 200 (healthy) or 503 (unhealthy).
• POST /deidentify/:id — The deidentifier Payload:

{
    transaction_id: "The caller's transaction id",
    fhir_source: "The source url for Patient/:id/$everything",
    source_token: "The source bearer token",
    fhir_target: "The target url - where the clone is to be sent",
    target_token: "The target bearer token",
    id: "The id of the patient to be cloned",
    deid: true | false,
}

If deid is false then the clone is not modified during the operation. Otherwise the $everything Bundle is modified according to the instructions in the configuration

deidentification rules configuration

Deidentification is accomplished globally (i.e. on every resource) and on a per-resource basis using simple configuration.

Configuration recognizes the following actions:

• erase - completely remove a field from the input Bundle
• replace - replace a field with a literal value or values
• randomize - randomize the input value based upon parameters (e.g. replace the birthDate with a random date from -15 to +15 days of the original)
• merge - use list comprehension to selectively modify the input field

See config.yaml for examples

Build Instructions

1. Install build tools

pip install build

2. Build the wheel

python -m build

The .whl file will be created in the dist/ directory.

Run the Application

1. Install dependencies

pip install -r requirements.txt

2. Run the app

python py_de_id/pydeid.py

The app will be available at http://127.0.0.1:5000/.

Testing Endpoints

• GET /health

curl -i http://127.0.0.1:5000/health

• POST /deidentify/123-xyz

curl -X POST http://127.0.0.1:5000/deidentify/123-zyz \
 -H "Content-Type: application/json" \
 -d '{"source_url":"http://consumer:8103/fhir/R4","source_token":"example-token","target_url":"http://customer:8103/fhir/R4","target_token":"example-token","patient_id":"123-xyz","deid":true}'

Running Tests

To run the tests, first ensure you have pytest installed:

pip install pytest

Then run:

pytest