fhir-kindling 0.4.0

Generates synthetic FHIR resources.

:fire: FHIR Kindling

CRUD library for fhir servers, with resource validation and parsing powered by the pydantic models created by fhir.resources. More details in the Documentation.

Features

• Create, Read, Update, Delete using a server's REST API
• Bundle creation, validation and data management on a FHIR server via the REST API
• Supports Hapi, Blaze and IBM FHIR servers

Installation

Install the package using pip:

pip install fhir_kindling --user

Usage

Connecting to a FHIR server

from fhir_kindling import FhirServer

# Connect with basic auth 
basic_auth_server = FhirServer("https://fhir.server/fhir", username="admin", password="admin")
# Connect with static token
token_server = FhirServer("https://fhir.server/fhir", token="your_token")

# Connect using oauth2/oidc
oidc_server = FhirServer("https://fhir.server/fhir", client_id="client_id", client_secret="secret", 
                         oidc_provider_url="url")

# Print the server's capability statement
print(basic_auth_server.capabilities)

Query resources from the server

from fhir_kindling import FhirServer
from fhir.resources.patient import Patient


# Connect using oauth2/oidc
oidc_server = FhirServer("https://fhir.server/fhir", client_id="client_id", client_secret="secret",
                         oidc_provider_url="url")

# query all patients on the server
query = oidc_server.query(Patient, output_format="json").all()
print(query.response)

# Query resources based on name of resource
query = oidc_server.query("Patient", output_format="json").all()
print(query.response)

CLI

With the virtual environment activated you can use the CLI directly in the terminal

CLI - Uploading a bundle to a server

fhir_kindling upload <path-to-bundle.json> --url <base-url-fhir-api> -u <username> -p <password> --token <token>

CLI - Querying a server

For an overview of the options of the CLI query command

fhir_kindling query --help

Examples

To query all instances of a resource use the -r option. This command queries all Patients from the server and stores the results as csv into the query_results.json file.

fhir_kindling query -r Patient --url <base-url-fhir-api> -u <username> -p <password> --token <token> -f "query_results.csv" -o csv

This example uses the -q option to execute a predefined url query string against the server and also stores the output as csv in a file called query_results.csv

fhir_kindling query -q "/MolecularSequence?patient.organization.name=DEMO_HIV&_format=json" --url <base-url-fhir-api> -u <username> -p <password> --token <token> -f "query_results.csv" -o csv

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

Change Log

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[0.3.0] - 2021-10-30

Response classes, reference parsing and basic xml support

Added

XML output format and resolving xml pagination. Response objects containig resources and references

Changed

Outsourced resolving of response pagination into response classes

Fixed

[0.2.0] - 2021-09-18

FHIR server and query API

Added

Classes for fhir servers and queries. Oauth2/OIDC support.

Changed

Moved location of cli

Fixed

[0.1.0] - 2021-08-24

Initial cli

Added

Changed

Fixed

Hashing order guarantees the right index of the query.json file in the hash