Metadata-Version: 2.1
Name: fhir-biobank
Version: 0.1.1
Summary: Python library working with FHIR standard in scope of BBMRI.de biobanks requirements
Home-page: https://fhir-biobank.readthedocs.io/
Author: Simon Konar
Author-email: simon.konar@gmail.com
License: MIT
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3.7
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
Requires-Dist: fhirclient
Requires-Dist: pytest

# FHIR Library

This Python library is simplifying work with FHIR library focused on BBMRI.de biobanks.
This library works with Patient, Specimen, and Condition resources, along with
extensions needed for these resources as defined by [simplifier.net/bbrmi.de](https://simplifier.net/bbmri.de)

## Installation
pip install fhir-biobank

## Usage
This library allows you to easily create FHIR resources along with all the data in a single constructor.
Use case of creating a simple Patient resource:
```python
from fhir_biobank import PatientResource

internal_id = "0"
patient_identifier = "4816522"
patient_gender = "female"
patient_birthdate = date(2000, 12, 11)
patient = PatientResource(internal_id, patient_identifier, patient_gender, patient_birthdate)
```

Standard action is to convert FHIR resource to a JSON representation.
Use case of converting Patient resource to a JSON representation:

```python
json_representation = patient.patientJSON()
```

JSON representation of the Patient resource initialized above looks like this:
```json
{
  "id": "0",
  "meta": { "profile": [ "https://fhir.bbmri.de/StructureDefinition/Patient" ] },
  "birthDate": "2000-12-11",
  "deceasedBoolean": "False",
  "gender": "female",
  "identifier": [
    {
      "type": {
        "coding": [
          {
            "code": "ACSN",
            "system": "http://terminology.hl7.org/CodeSystem/v2-0203",
            "userSelected": "True"
          }
        ]
      },
      "use": "usual",
      "value": "4816522"
    }
  ],
  "multipleBirthBoolean": "False",
  "resourceType": "Patient"
}
```
In order to upload resource to a server, creating Bundle resource containing all of the resources that you want to upload is necessary.
Bundle contains list of Entry resources, where each Entry resource represents specific resource(for example Patient resource).
Here is a example how to create Bundle resource containing the Patient resource made earlier:

```python
from fhir_biobank.bundle import Bundle, Entry

fullURL_patient_resource = "https://example.com/patient/0"
shortURL_patient_resource = "patient/0"
entry = Entry(patient, fullURL_patient_resource, shortURL_patient_resource)
entries = [entry]
bundle_id = "424242"
bundle = Bundle(bundle_id, entries)
```



