Clover's fork of smart-on-fhir/client-py

This is a fork of fhirclient==3.2.0 which is being added to and maintained by Clover. In the immediate, it is supporting integration with CMS' Blue Button API.

This repo has no master branch, instead has a clover branch that all feature branches can be merged into.

With each merge to clover, please also bump the clover version in fhirclient/client.py by 1. For example: '3.2.0-clover-1' -> '3.2.0-clover-2'.

More importantly: once you've merged into clover, also create a tag with that same version number (e.g. '3.2.0-clover-2'). The tag is what we will reference in requirements files.

SMART FHIR Client

This is fhirclient, a flexible Python client for FHIR servers supporting the SMART on FHIR protocol. The client is compatible with Python 2.7.10 and Python 3.

Client versioning is not identical to FHIR versioning. The master branch is usually on the latest version of the client as shown below, possibly on bugfix releases thereof. The develop branch should be on recent freezes, and the feature/latest-ci branch is periodically updated to the latest FHIR continuous integration builds.

Version	FHIR
3.0.0	3.0.0	(STU-3)
x.x	1.8.0	(STU-3 Ballot, Jan 2017)
x.x	1.6.0	(STU-3 Ballot, Sep 2016)
1.0.3	1.0.2	(DSTU 2)
1.0	1.0.1	(DSTU 2)
0.5	0.5.0.5149	(DSTU 2 Ballot, May 2015)
0.0.4	0.0.82.2943	(DSTU 1)
0.0.3	0.0.82.2943	(DSTU 1)
0.0.2	0.0.82.2943	(DSTU 1)

Installation

pip install fhirclient

Documentation

Technical documentation is available at docs.smarthealthit.org/client-py/.

Client Use

To connect to a SMART on FHIR server (or any open FHIR server), you can use the FHIRClient class. It will initialize and handle a FHIRServer instance, your actual handle to the FHIR server you'd like to access.

Read Data from Server

To read a given patient from an open FHIR server, you can use:

from fhirclient import client
settings = {
    'app_id': 'my_web_app',
    'api_base': 'https://fhir-open-api-dstu2.smarthealthit.org'
}
smart = client.FHIRClient(settings=settings)

import fhirclient.models.patient as p
patient = p.Patient.read('hca-pat-1', smart.server)
patient.birthDate.isostring
# '1963-06-12'
smart.human_name(patient.name[0])
# 'Christy Ebert'

If this is a protected server, you will first have to send your user to the authorize endpoint to log in. Just call smart.authorize_url to obtain the correct URL. You can use smart.prepare(), which will return False if the server is protected and you need to authorize. The smart.ready property has the same purpose, it will however not retrieve the server's CapabilityStatement resource and hence is only useful as a quick check whether the server instance is ready.

smart = client.FHIRClient(settings=settings)
smart.ready
# prints `False`
smart.prepare()
# prints `True` after fetching CapabilityStatement
smart.ready
# prints `True`
smart.prepare()
# prints `True` immediately
smart.authorize_url
# is `None`

You can work with the FHIRServer class directly, without using FHIRClient, but this is not recommended:

smart = server.FHIRServer(None, 'https://fhir-open-api-dstu2.smarthealthit.org')
import fhirclient.models.patient as p
patient = p.Patient.read('hca-pat-1', smart)
patient.name[0].given
# ['Christy']

Search Records on Server

You can also search for resources matching a particular set of criteria:

smart = client.FHIRClient(settings=settings)
import fhirclient.models.procedure as p
search = p.Procedure.where(struct={'subject': 'hca-pat-1', 'status': 'completed'})
procedures = search.perform_resources(smart.server)
for procedure in procedures:
    procedure.as_json()
    # {'status': u'completed', 'code': {'text': u'Lumpectomy w/ SN', ...

# to get the raw Bundle instead of resources only, you can use:
bundle = search.perform(smart.server)

Data Model Use

The client contains data model classes, built using fhir-parser, that handle (de)serialization and allow to work with FHIR data in a Pythonic way. Starting with version 1.0.5, data model validity are enforced to a certain degree.

Initialize Data Model

import fhirclient.models.patient as p
import fhirclient.models.humanname as hn
patient = p.Patient({'id': 'patient-1'})
patient.id
# prints `patient-1`

name = hn.HumanName()
name.given = ['Peter']
name.family = 'Parker'
patient.name = [name]
patient.as_json()
# prints patient's JSON representation, now with id and name

name.given = 'Peter'
patient.as_json()
# throws FHIRValidationError:
# {root}:
#   name:
#     given:
#       Expecting property "given" on <class 'fhirclient.models.humanname.HumanName'> to be list, but is <class 'str'>

Initialize from JSON file

import json
import fhirclient.models.patient as p
with open('path/to/patient.json', 'r') as h:
    pjs = json.load(h)
patient = p.Patient(pjs)
patient.name[0].given
# prints patient's given name array in the first `name` property

Flask App

Take a look at flask_app.py to see how you can use the client in a simple (Flask) app. This app starts a webserver, listening on localhost:8000, and prompts you to login to our sandbox server and select a patient. It then goes on to retrieve the selected patient's demographics and med prescriptions and lists them in a simple HTML page.

The Flask demo app has separate requirements. Clone the client-py repository, then best create a virtual environment and install the needed packages like so:

git clone https://github.com/smart-on-fhir/client-py.git
cd client-py
virtualenv -p python3 env
. env/bin/activate
pip install -r requirements_flask_app.txt
python flask_app.py

Building Distribution

pip install -r requirements.txt
python setup.py sdist
python setup.py bdist_wheel

Incrementing the lib version

bumpversion patch
bumpversion minor
bumpversion major

Docs Generation

Docs are generated with Doxygen and doxypypy. You can install doxypypy via pip: pip install doxypypy. Then you can just run Doxygen, configuration is stored in the Doxyfile.

Running Doxygen will put the generated documentation into docs, the HTML files into docs/html. Those files make up the content of the gh-pages branch. I usually perform a second checkout of the gh-pages branch and copy the html files over, with:

doxygen
rsync -a docs/html/ ../client-py-web/

PyPi Publishing (notes for SMART team)

Using setuptools (Note: Alternatively, you can use twine https://pypi.python.org/pypi/twine/):

Make sure that you have the PyPi account credentials in your account

copy server.smarthealthit.org:/home/fhir/.pypirc to ~/.pypirc

Test the build

python setup.py sdist
python setup.py bdist_wheel

Upload the packages to PyPi

python setup.py sdist upload -r pypi
python setup.py bdist_wheel upload -r pypi