Smart-on-FHIR Python Client with Bundles

Question

So I have a FHIR patient bundle json from the "$everything" operation: https://www.hl7.org/fhir/operation-patient-everything.html

I am now interested in using the Smart on FHIR Python Client Models to make working with the json file a lot easier. An example given is the following:

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

Would it be possible to do instantiate something with just a generic bundle object class to be able access different resources inside the bundle?

Hi, do you have a complete example on importing data into python from FHIR?, is so can you share. I would like to learn how I can get the FHIR data into R — user5249203, Apr 26 '19 at 17:15

Pascal · Accepted Answer · 2016-08-28T09:21:15.920

Yes, you can instantiate a Bundle like you can instantiate any other model, either manually from JSON or by a read from the server. Every search returns a Bundle as well. Then you can just iterate over the bundle's entries and work with them, like put them in an array:

resources = []
if bundle.entry is not None:
    for entry in bundle.entry:
        resources.append(entry.resource)

p.s. It should be possible to execute any $operation with the client, returning the Bundle you mention, but I have to check if we've exposed that or if it has not been committed.

Command line example:

import fhirclient.models.bundle as b
import json
with open('fhir-parser/downloads/bundle-example.json', 'r') as h:
    js = json.load(h)
bundle = b.Bundle(js)
bundle.entry
[<fhirclient.models.bundle.BundleEntry object at 0x10f40ae48>, 
 <fhirclient.models.bundle.BundleEntry object at 0x10f40ac88>]
for entry in bundle.entry:
    print(entry.resource)

// prints
<fhirclient.models.medicationorder.MedicationOrder object at 0x10f407390>
<fhirclient.models.medication.Medication object at 0x10f407e48>

@ Pascal Thanks for the additional details! I think I gather what you are suggesting. In my circumstance, I have written all my complete patient FHIR bundles (from $everything) into individual json files in a directory, since the server in question does not utilize Smart on FHIR. So I was hoping to manually use the Smart Models on these arbitrary bundles as opposed to iterate through so many fields. It does not appear that "import fhirclient.models.object.bundle as b" allows me to do the same as the patient example I posted. — Pylander, Aug 25 '16 at 18:07
Hy @Pylander. This should definitely work, I've added complete code that I just executed from the command line, reading the file `Bundle-example.json` available from the FHIR website. Is that what you're trying to achieve? — Pascal, Aug 28 '16 at 09:22

Smart-on-FHIR Python Client with Bundles

1 Answers1