Skip to content

python

Directory actions

More options

Directory actions

More options

Latest commit

 

History

History
 
 

python

Folders and files

NameName
Last commit message
Last commit date

parent directory

..
fpml
fpml
 
 
tests
tests
 
 
.gitignore
.gitignore
 
 
README.md
README.md
 
 
poetry.lock
poetry.lock
 
 
pyproject.toml
pyproject.toml
 
 

README.md

fpml (FHIRPathMappingLanguage)

The FHIRPath Mapping Language (FPML) is a data DSL designed to convert data from QuestionnaireResponse (and not only) to any FHIR Resource.

For more details visit the FHIRPathMappingLanguage specification.

Installation

You can install the package from PyPI using the following command:

pip install fpml

API Reference

resolve_template

The resolve_template function processes a given template with a specified FHIR resource, optionally applying a context and additional processing options.

from fpml import resolve_template

result = resolve_template(
    resource,
    template,
    context=None,
    fp_options=None,
    strict=False
)

Arguments:

  • resource (Resource): The input FHIR resource to process.
  • template (Any): The template describing the transformation.
  • context (Optional[Context], optional): Additional context data. Defaults to None.
  • fp_options (Optional[FPOptions], optional): Options for controlling FHIRPath evaluation. Defaults to None.
  • strict (bool, optional): Whether to enforce strict mode. Defaults to False. See more details on strict mode.

Returns:

  • Any: The processed output based on the template.

Raises:

  • FPMLValidationError: If validation of the template or resource fails.

Usage

For the following QuestionnaireResponse resource:

resource = {
    "resourceType": "QuestionnaireResponse",
    "status": "completed",
    "item": [
        {
            "linkId": "name",
            "answer": [
                {
                    "valueString": "Name"
                }
            ]
        }
    ]
}

Here's an example demonstrating how to use the resolve_template function:

from fpml import resolve_template


template = {
    "resourceType": "Patient",
    "name": [
        {
            "text": "{{ item.where(linkId='name').answer.valueString }}"
        }
    ]
}

context = {}

result = resolve_template(resource, template, context)
print(result)

Output:

{'resourceType': 'Patient', 'name': [{'text': 'Name'}]}

Using FHIR data-model

from fpml import resolve_template
from fhirpathpy.models import models


template = {
    "resourceType": "Patient",
    "name": [
        {
            "text": "{{ item.where(linkId='name').answer.value }}"  # <-- according R4 model
        }
    ]
}

context = {}

fp_options = {
    "model": models["r4"]
}

result = resolve_template(resource, template, context, fp_options)
print(result)

Output:

{'resourceType': 'Patient', 'name': [{'text': 'Name'}]}

Using user-defined functions

from fpml import resolve_template


template = {
    "resourceType": "Patient",
    "name": [
        {
            "text": "{{ item.where(linkId='name').answer.valueString.strip() }}"  # <-- Custom function
        }
    ]
}

context = {}

user_invocation_table = {
    "strip": {
        "fn": lambda inputs: [i.strip() for i in inputs],
        "arity": {0: []},
    }
}

fp_options = {
    "userInvocationTable": user_invocation_table
}

result = resolve_template(resource, template, context, fp_options)
print(result)

Output:

{'resourceType': 'Patient', 'name': [{'text': 'Name'}]}

Caching compiled expressions

Parsing FHIRPath expressions is expensive, so expressions can be compiled once and reused via ExpressionCache passed through fp_options. The cache size is the number of compiled expressions kept in memory, zero disables caching.

Entries are keyed by the expression only, while compilation binds the model and the user-defined functions, so keep one long-living cache per fp_options. A cache is safe to share between threads.

from fhirpathpy.models import models

from fpml import ExpressionCache, resolve_template


# 1024 long expressions take up to 100mb
fp_options = {
    "model": models["r4"],
    "cache": ExpressionCache(max_size=1024),
}

for resource in resources:
    resolve_template(resource, template, context, fp_options)

Handling validation errors

from fpml import FPMLValidationError, resolve_template


template = {
    "resourceType": "Patient",
    "name": [
        {
            "text": "{{ item.where( }}"  # <-- Invalid expression
        }
    ]
}

context = {}

try:
    resolve_template(resource, template, context)
except FPMLValidationError as e:
    print(f"Validation error: {e.error_message}")
    print(f"Error path: `{e.error_path}`")

Output:

"Validation error: Cannot evaluate 'item.where(': where wrong arity: got 0"
"Error path: `name.0.text`"

Using strict mode

In strict mode only context variables can be used (starting with percent sigh). Any access of the resource property will raise a validation error.

from fpml import resolve_template


template = {
    "resourceType": "Patient",
    "name": [
        {
            "text": "{{ item.where(linkId='name').answer.valueString }}"  # <-- Accessing resource attribute
        }
    ]
}

context = {} 


resolve_template(resource, template, context, strict=True)

Raises an error:

FPMLValidationError: Cannot evaluate 'item.where(linkId='name').answer.valueString': "Forbidden access to resource property 'item' in strict mode. Use context instead.". Path 'name.0.text'

Meanwhile using context:

from fpml import resolve_template


template = {
    "resourceType": "Patient",
    "name": [
        {
            "text": "{{ %QuestionnaireResponse.item.where(linkId='name').answer.valueString }}"  # <-- Accessing context variable
        }
    ]
}

context = {"QuestionnaireResponse": resource}  # <-- Context 

result = resolve_template(resource, template, context, strict=True)
print(result)

Output:

{'resourceType': 'Patient', 'name': [{'text': 'Name'}]}

Development

Local environment and testing

cd ./python
poetry install

To run tests:

poetry run pytest

Pre-commit hook

In ./python directory:

Run in the shell

autohooks activate

And edit ../.git/hooks/pre-commit replacing the first line with

#!/usr/bin/env -S poetry --project=./python run python

License

This project is licensed under the MIT License.