A Handy set of utilities with convenience methods to make working with FHIR easier and saner (such as common display of HumanName, Address, etc resource types where many parent types include lists of these requiring frequent display.
One of the good/bad things about FHIR resources is they are designed to accommodate a huge array of data formats that healthcare users around the globe use. This means that the flexibility of data formats is also extremely flexible and accomodating that flexibility can be frustrating when doing simple tasks such as displaying a patient's name, since a large number of fields are both optional and can be single elements or lists. This does of course take into account your specific use case, but provides a pretty good general use case output.
This is a python library so is oriented towards a python developer working with FHIR in a healthcare context where you need to display FHIR data in a human readable format (rather than the typical demo of dumping the JSON, even if pretty-printed to the screen).
Including the fhir_text_utils class will make parsing Fhir data elements easier when outputting for display. Note each of the methods takes an optional parameter to make the output either plain text or HTML formatted.
The LinuxForHealth {library name} development environment relies on the following software packages:
- git for project version control
- Python 3.8 or higher for runtime/coding support
- fhir.resources
pip install --upgrade pip setuptools
git clone https://github.com/LinuxForHealth/{library name}
cd {library name}
python3 -m venv venv && source venv/bin/activate && pip install --upgrade pip setuptools
pip install -e .[dev]
pytestIn python applications that deal with FHIR resources, you can import the fhir_text_utils.py module and inside you will find a collection of useful utility methods for frequently performed FHIR tasks (such as printing a patient's address or HumanName)
The 2 most commonly used methods will be:
turning FHIR HumanName) lists into strings:
```
patient_name: str = humanname_as_string(test_patient.name, False)
# it can also return a HTML formatted version with the second parameter to true (by default it is plain-text)
# note: you will typically wrap that in a <div></div> or some other structure
patient_name_html: str = humanname_as_string(test_patient.name, True)
```
and turning FHIR Address information into a usual looking address:
```
from fhir_text_utils import FhirTextUtils
from fhir.resources.patient import Patient
from fhir.resources.practicioner import Practicioner
patient: Patient = myFhirServer.fetch(patient_id)
practicioner: Practicioner = myFhirServer.fetch(practicioner_id)
practicioner_address: str = address_as_string(practicioner.address, False)
#like the HumanName it can be either HTML or plain-text based on the second parameter
print(practicioner_address)
>>>postal home:
202 Clinton St.
Woburn, MA 01807
# pseudocode for the fhir server here. To see this happen via a local file look at the test_lib.py unit test
print('patient: '+FhirTextUtils.humanname_as_string(patient.name))
>>> patient: Washington Jr., Dr. Fred Lawrence
```
humanname_as_string(humannames: List[HumanName], usehtml: bool = False, last_first_order: bool = True)
this will turn a HumanName list from a resource (e.g. Patient.name) into a readable name. It supports HTML formatting (off by default) and last-first or natural order naming (last-first default) Example:
```
Patient Name (last-first): Hart III, Dr. Julia (last-first)
Patient Name (natural order): Dr. Julia Hart III (natural)
```
this will return an Address List from a resource (e.g. Patient.address) into a readble address string. It supports HTML formatting (off by default) Example:
```
postal home:
202 Clinton St.
Woburn, MA 01807
```
this will return a Telecom List from a resource (e.g. Practitioner.address) into a human readable list of contact information. Example:
```
phone:
work phone : (505) 555 1212
phone:
mobile phone : (418) 555 5613
url:
home url : http://wwww.juliahart.com/about/
phone:
old phone : (702) 555 8834
```
this is a simple routine that takes any FHIR resource and returns a Reference to it. For those unfamiliar with FHIR references you can think of FHIR references as equivalent to Foreign Keys in a relational Database, except unlike relational databases these are generic so the type is included in the value: Type/id Example:
```
Patient/a9831a75-3ff9-458c-9dbb-081ea3d71684
```
Unit Tests are contained in test_lib.py inside of the tests folder which utilizes pytest to test using a static Patient FHIR Resource contained in patient.json. Since the address is a longer multi-line string we use a test file to compare to via the assertion
LinuxForHealth {library name} adheres to the Black Code Style and Convention
The following command executes the black formatter with default options
```
user@mbp {library name} % source venv/bin/activate
(venv) user@mbp {library name} % black ./src
```
Use the --help flag to view all available options for the black code formatter
```
(venv) user@mbp {library name} % black --help
```
LinuxForHealth {library name} is aligned, to a degree, with the PEP-517 standard. setup.cfg stores build metadata/configuration.
pyproject.toml contains the build toolchain specification and black formatter configurations.
The commands below creates a source and wheel distribution within a clean build environment.
```
python3 -m venv build-venv && source build-venv/bin/activate && pip install --upgrade pip setuptools build wheel twine
python3 -m build --no-isolation
```