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FHIR Helpers

FHIR utilities for HealthChain.

CodedEntry

Bases: BaseModel

Flattened coded identity of a clinical resource.

JSON-serializable via model_dump() so it can be returned directly from agent tools. code/display/system come from the first coding; codings carries all of them.

EntryCoding

Bases: BaseModel

A single coding (code/display/system) from a CodeableConcept.

FHIRValidationError

Bases: Exception

Raised when FHIR validation fails. Carries the full ValidationReport.

FHIRVersion

Bases: str, Enum

Supported FHIR versions.

R5 is the default version in fhir.resources library. R4B and STU3 are available via subpackages (e.g., fhir.resources.R4B).

ValidationIssue

Bases: BaseModel

A single validation issue, mirroring FHIR OperationOutcome.issue fields.

https://www.hl7.org/fhir/operationoutcome.html

ValidationReport

Bases: BaseModel

Result of validating a FHIR resource.

JSON-serializable via model_dump() so it can be returned directly from agent tools. Convert to a FHIR OperationOutcome resource with to_operation_outcome().

to_operation_outcome()

Convert the report to a FHIR OperationOutcome resource.

RETURNS DESCRIPTION
Resource

An OperationOutcome of the report's FHIR version, with one issue
Resource

per validation issue (or a single 'informational' issue if valid).

add_coding_to_codeable_concept(codeable_concept, code, system, display=None)

Add a coding to an existing CodeableConcept.

Useful for adding standardized codes (e.g., SNOMED CT) to resources that already have codes from other systems (e.g., ICD-10).

PARAMETER DESCRIPTION
codeable_concept

The CodeableConcept to add coding to

TYPE: CodeableConcept

code

The code value from the code system

TYPE: str

system

The code system URI

TYPE: str

display

Optional display text for the code

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
CodeableConcept

The updated CodeableConcept with the new coding added

TYPE: CodeableConcept

Example

Add SNOMED CT code to a condition that has ICD-10

condition_code = condition.code condition_code = add_coding_to_codeable_concept( ... condition_code, ... code="44054006", ... system="http://snomed.info/sct", ... display="Type 2 diabetes mellitus" ... )

add_provenance_metadata(resource, source, tag_code=None, tag_display=None)

Add provenance metadata to a FHIR resource.

Adds source system identifier, timestamp, and optional processing tags to track data lineage and transformations for audit trails.

PARAMETER DESCRIPTION
resource

The FHIR resource to annotate

TYPE: Any

source

Name of the source system (e.g., "epic", "cerner")

TYPE: str

tag_code

Optional tag code for processing operations (e.g., "aggregated", "deduplicated")

TYPE: Optional[str] DEFAULT: None

tag_display

Optional display text for the tag

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
Resource

The resource with added provenance metadata

TYPE: Any

Example

condition = create_condition(subject="Patient/123", code="E11.9") condition = add_provenance_metadata(condition, "epic", "aggregated", "Aggregated from source")

add_resource(bundle, resource, full_url=None)

Add a resource to a bundle.

PARAMETER DESCRIPTION
bundle

The bundle to add to

TYPE: Bundle

resource

The resource to add, e.g. Condition, MedicationStatement, AllergyIntolerance

TYPE: Resource

full_url

Optional full URL for the resource

TYPE: Optional[str] DEFAULT: None

calculate_age_from_birthdate(birth_date)

Calculate age in years from a birth date string.

PARAMETER DESCRIPTION
birth_date

Birth date in ISO format (YYYY-MM-DD or full ISO datetime)

TYPE: str

RETURNS DESCRIPTION
Optional[int]

Age in years, or None if birth date is invalid

calculate_age_from_event_date(birth_date, event_date)

Calculate age in years from birth date and event date (MIMIC-IV style).

Uses the formula: age = year(eventDate) - year(birthDate) This matches MIMIC-IV on FHIR de-identified age calculation.

PARAMETER DESCRIPTION
birth_date

Birth date in ISO format (YYYY-MM-DD or full ISO datetime)

TYPE: str

event_date

Event date in ISO format (YYYY-MM-DD or full ISO datetime)

TYPE: str

RETURNS DESCRIPTION
Optional[int]

Age in years based on year difference, or None if dates are invalid
Example

calculate_age_from_event_date("1990-06-15", "2020-03-10") 30

convert_prefetch_to_fhir_objects(prefetch_dict)

Convert a dictionary of FHIR resource dicts to FHIR Resource objects.

Takes a prefetch dictionary where values may be either dict representations of FHIR resources or already instantiated FHIR Resource objects, and ensures all values are FHIR Resource objects.

PARAMETER DESCRIPTION
prefetch_dict

Dictionary mapping keys to FHIR resource dicts or objects

TYPE: Dict[str, Any]

RETURNS DESCRIPTION
Dict[str, Resource]

Dict[str, Resource]: Dictionary with same keys but all values as FHIR Resource objects
Example

prefetch = { ... "patient": {"resourceType": "Patient", "id": "123"}, ... "condition": Condition(id="456", ...) ... } fhir_objects = convert_prefetch_to_fhir_objects(prefetch) isinstance(fhir_objects["patient"], Patient) # True isinstance(fhir_objects["condition"], Condition) # True

convert_resource(resource, target_version)

Convert a FHIR resource to a different version.

Converts by serializing the resource to a dictionary and deserializing with the target version's resource class. This approach works for resources with compatible field structures.

Note

Field mappings between FHIR versions may not be 1:1. Some fields may be added, removed, or renamed between versions. This function performs a best-effort conversion and may raise validation errors if the resource data is incompatible with the target version.

PARAMETER DESCRIPTION
resource

The FHIR resource to convert

TYPE: Any

target_version

The target FHIR version

TYPE: Union[FHIRVersion, str]

RETURNS DESCRIPTION
Any

A new resource instance of the target version
RAISES DESCRIPTION
ValueError

If the resource type cannot be determined or imported
ValidationError

If the resource data is incompatible with target version
Example

from fhir.resources.patient import Patient patient_r5 = Patient(id="123", gender="male") patient_r4b = convert_resource(patient_r5, "R4B") print(patient_r4b.class.module) fhir.resources.R4B.patient

count_resources(bundle)

Count resources by type in a bundle.

PARAMETER DESCRIPTION
bundle

The FHIR Bundle to analyze

TYPE: Bundle

RETURNS DESCRIPTION
dict[str, int]

Dictionary mapping resource type names to their counts.
Example

{"Condition": 2, "MedicationStatement": 1, "Patient": 1}

TYPE: dict[str, int]

Example

bundle = create_bundle() add_resource(bundle, create_condition(...)) add_resource(bundle, create_condition(...)) add_resource(bundle, create_medication_statement(...)) counts = count_resources(bundle) print(counts)

create_allergy_intolerance(patient, code=None, display=None, system='http://snomed.info/sct', *, generate_id=True, warn=True)

Create a minimal active FHIR AllergyIntolerance. If you need to create a more complex allergy intolerance, use the FHIR AllergyIntolerance resource directly. https://build.fhir.org/allergyintolerance.html

PARAMETER DESCRIPTION
patient

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

code

The allergen code

TYPE: Optional[str] DEFAULT: None

display

The display name for the allergen

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
AllergyIntolerance

A FHIR AllergyIntolerance resource with an auto-generated ID prefixed with 'hc-'

TYPE: AllergyIntolerance

create_bundle(bundle_type='collection')

Create an empty FHIR Bundle. https://www.hl7.org/fhir/bundle.html

PARAMETER DESCRIPTION
bundle_type

The type of bundle (default: collection) Valid types: document, message, transaction, transaction-response, batch, batch-response, history, searchset, collection

TYPE: str DEFAULT: 'collection'

create_condition(subject, clinical_status='active', code=None, display=None, system='http://snomed.info/sct', onset=None, *, generate_id=True, warn=True)

Create a minimal active FHIR Condition. If you need to create a more complex condition, use the FHIR Condition resource directly. https://build.fhir.org/condition.html

PARAMETER DESCRIPTION
subject

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

clinical_status

REQUIRED. Clinical status (default: active)

TYPE: str DEFAULT: 'active'

code

The condition code

TYPE: Optional[str] DEFAULT: None

display

The display name for the condition

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

onset

When the condition began, as an ISO 8601 date/datetime string, set as onsetDateTime (e.g. "2024-01-15" or "2024-01-15T09:00:00Z")

TYPE: Optional[str] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Condition

A FHIR Condition resource with an auto-generated ID prefixed with 'hc-'

TYPE: Condition

create_document_reference(data=None, url=None, content_type=None, status='current', description='DocumentReference created by HealthChain', attachment_title='Attachment created by HealthChain', *, generate_id=True, warn=True)

Create a minimal FHIR DocumentReference. If you need to create a more complex document reference, use the FHIR DocumentReference resource directly. https://build.fhir.org/documentreference.html

PARAMETER DESCRIPTION
data

The data content of the document attachment

TYPE: Optional[Any] DEFAULT: None

url

URL where the document can be accessed

TYPE: Optional[str] DEFAULT: None

content_type

MIME type of the document (e.g. "application/pdf", "text/xml", "image/png")

TYPE: Optional[str] DEFAULT: None

status

REQUIRED. Status of the document reference (default: current)

TYPE: str DEFAULT: 'current'

description

Description of the document reference

TYPE: Optional[str] DEFAULT: 'DocumentReference created by HealthChain'

attachment_title

Title for the document attachment

TYPE: Optional[str] DEFAULT: 'Attachment created by HealthChain'

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
DocumentReference

A FHIR DocumentReference resource with an auto-generated ID prefixed with 'hc-'

TYPE: DocumentReference

create_document_reference_content(attachment_data=None, url=None, content_type='text/plain', language='en-US', title=None, **kwargs)

Create a FHIR DocumentReferenceContent object.

Creates a DocumentReferenceContent structure that can be added to a DocumentReference. Either attachment_data or url must be provided. If attachment_data is provided, it will be base64 encoded automatically.

PARAMETER DESCRIPTION
attachment_data

The content data (text that will be base64 encoded)

TYPE: Optional[str] DEFAULT: None

url

URL where the content can be accessed

TYPE: Optional[str] DEFAULT: None

content_type

MIME type (e.g., 'text/plain', 'text/html', 'application/pdf') (default: text/plain)

TYPE: str DEFAULT: 'text/plain'

language

Language code (default: en-US)

TYPE: Optional[str] DEFAULT: 'en-US'

title

Optional title for the content (default: "Attachment created by HealthChain")

TYPE: Optional[str] DEFAULT: None

**kwargs

Additional DocumentReferenceContent fields (e.g., format, profile)

DEFAULT: {}

RETURNS DESCRIPTION
Dict[str, Any]

Dict[str, Any]: A FHIR DocumentReferenceContent dictionary with attachment and optional language
Example

Create content with inline data

content = create_document_reference_content( ... attachment_data="Patient presents with fever...", ... content_type="text/plain", ... title="Clinical Note" ... )

Create content with URL reference

content = create_document_reference_content( ... url="https://example.com/document.pdf", ... content_type="application/pdf", ... title="Lab Report" ... )

Add content to a DocumentReference

doc_ref = DocumentReference( ... id="doc-1", ... status="current", ... content=[content] ... )

create_dosage(text=None, route_code=None, route_display=None, route_system='http://snomed.info/sct', dose_value=None, dose_unit=None, frequency=None, period=None, period_unit=None, as_needed=None)

Create a minimal FHIR Dosage element.

Builds a minimum viable Dosage suitable for attaching to a MedicationStatement or MedicationRequest. Only the fields you provide are populated. For anything more complex, construct the FHIR Dosage directly. https://build.fhir.org/dosage.html

PARAMETER DESCRIPTION
text

Free-text dosage instructions (e.g. "1 tablet twice daily")

TYPE: Optional[str] DEFAULT: None

route_code

The route of administration code (e.g. SNOMED CT code for "oral")

TYPE: Optional[str] DEFAULT: None

route_display

The display name for the route code

TYPE: Optional[str] DEFAULT: None

route_system

The code system for the route (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

dose_value

The numeric dose amount, set as doseAndRate.doseQuantity.value

TYPE: Optional[float] DEFAULT: None

dose_unit

The unit for the dose amount (e.g. "mg", "tablet")

TYPE: Optional[str] DEFAULT: None

frequency

How many times per period the dose is taken (Timing.repeat.frequency)

TYPE: Optional[int] DEFAULT: None

period

The length of the period (Timing.repeat.period)

TYPE: Optional[float] DEFAULT: None

period_unit

The unit of the period (e.g. "d" for day, "h" for hour)

TYPE: Optional[str] DEFAULT: None

as_needed

Whether the medication is taken as needed (asNeededBoolean)

TYPE: Optional[bool] DEFAULT: None

RETURNS DESCRIPTION
Dosage

A FHIR Dosage element populated with the provided fields

TYPE: Dosage

create_medication_statement(subject, status='unknown', code=None, display=None, system='http://snomed.info/sct', dosage=None, *, generate_id=True, warn=True)

Create a minimal FHIR MedicationStatement. If you need to create a more complex medication statement, use the FHIR MedicationStatement resource directly. https://build.fhir.org/medicationstatement.html

PARAMETER DESCRIPTION
subject

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

status

REQUIRED. Status of the medication. Default "unknown" (an R4B-valid code that makes no clinical assertion). Allowed R4B values: active, completed, entered-in-error, intended, stopped, on-hold, unknown, not-taken

TYPE: Optional[str] DEFAULT: 'unknown'

code

The medication code

TYPE: Optional[str] DEFAULT: None

display

The display name for the medication

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

dosage

Dosage instructions. A plain string is wrapped as a single free-text Dosage; a single Dosage is wrapped in a one-element list; a list of Dosage elements is used as-is. See create_dosage().

TYPE: Optional[Union[str, Dosage, List[Dosage]]] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
MedicationStatement

A FHIR MedicationStatement resource with an auto-generated ID prefixed with 'hc-'

TYPE: MedicationStatement

create_patient(gender=None, birth_date=None, identifier=None, identifier_system='http://hospital.example.org', *, generate_id=True, warn=True)

Create a minimal FHIR Patient resource with basic gender and birthdate If you need to create a more complex patient, use the FHIR Patient resource directly https://hl7.org/fhir/patient.html (No required fields).

PARAMETER DESCRIPTION
gender

Administrative gender (male, female, other, unknown)

TYPE: Optional[str] DEFAULT: None

birth_date

Birth date in YYYY-MM-DD format

TYPE: Optional[str] DEFAULT: None

identifier

Optional identifier value for the patient (e.g., MRN)

TYPE: Optional[str] DEFAULT: None

identifier_system

The system for the identifier (default: "http://hospital.example.org")

TYPE: Optional[str] DEFAULT: 'http://hospital.example.org'

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Patient

A FHIR Patient resource with an auto-generated ID prefixed with 'hc-'

TYPE: Patient

create_resource_from_dict(resource_dict, resource_type, raise_on_error=False)

Create a FHIR resource instance from a dictionary

PARAMETER DESCRIPTION
resource_dict

Dictionary representation of the resource

TYPE: Dict

resource_type

Type of FHIR resource to create

TYPE: str

raise_on_error

If True, raise FHIRValidationError with a full ValidationReport instead of returning None on failure

TYPE: bool DEFAULT: False

RETURNS DESCRIPTION
Optional[Resource]

Optional[Resource]: FHIR resource instance or None if creation failed
RAISES DESCRIPTION
FHIRValidationError

If raise_on_error is True and validation fails

create_risk_assessment_from_prediction(subject, prediction, status='final', method=None, basis=None, comment=None, occurrence_datetime=None, *, generate_id=True, warn=True)

Create a FHIR RiskAssessment from ML model prediction output. If you need to create a more complex risk assessment, use the FHIR RiskAssessment resource directly. https://hl7.org/fhir/riskassessment.html

PARAMETER DESCRIPTION
subject

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

prediction

Dictionary containing prediction details with keys: - outcome: CodeableConcept or dict with code, display, system for the predicted outcome - probability: float between 0 and 1 representing the risk probability - qualitative_risk: Optional str indicating risk level (e.g., "high", "moderate", "low")

TYPE: Dict[str, Any]

status

REQUIRED. The status of the assessment (default: "final")

TYPE: str DEFAULT: 'final'

method

Optional CodeableConcept describing the assessment method/model used

TYPE: Optional[CodeableConcept] DEFAULT: None

basis

Optional list of References to observations or other resources used as input

TYPE: Optional[List[Reference]] DEFAULT: None

comment

Optional text comment about the assessment

TYPE: Optional[str] DEFAULT: None

occurrence_datetime

When the assessment was made (ISO format). Omitted when not provided — the helper never invents a timestamp

TYPE: Optional[str] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
RiskAssessment

A FHIR RiskAssessment resource with an auto-generated ID prefixed with 'hc-'

TYPE: RiskAssessment

Example

prediction = { ... "outcome": {"code": "A41.9", "display": "Sepsis", "system": "http://hl7.org/fhir/sid/icd-10"}, ... "probability": 0.85, ... "qualitative_risk": "high" ... } risk = create_risk_assessment("Patient/123", prediction)

create_single_attachment(content_type=None, data=None, url=None, title='Attachment created by HealthChain')

Create a minimal FHIR Attachment.

Creates a FHIR Attachment resource with basic fields. Either data or url should be provided. If data is provided, it will be base64 encoded.

PARAMETER DESCRIPTION
content_type

The MIME type of the content

TYPE: Optional[str] DEFAULT: None

data

The actual data content to be base64 encoded

TYPE: Optional[str] DEFAULT: None

url

The URL where the data can be found

TYPE: Optional[str] DEFAULT: None

title

A title for the attachment (default: "Attachment created by HealthChain")

TYPE: Optional[str] DEFAULT: 'Attachment created by HealthChain'

RETURNS DESCRIPTION
Attachment

A FHIR Attachment resource with basic metadata and content

TYPE: Any

create_single_codeable_concept(code, display=None, system='http://snomed.info/sct')

Create a minimal FHIR CodeableConcept with a single coding.

PARAMETER DESCRIPTION
code

REQUIRED. The code value from the code system

TYPE: str

display

The display name for the code

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

RETURNS DESCRIPTION
CodeableConcept

A FHIR CodeableConcept resource with a single coding

TYPE: Any

create_single_reaction(code, display=None, system='http://snomed.info/sct', severity=None)

Create a minimal FHIR Reaction with a single coding.

Creates a FHIR Reaction object with a single manifestation coding. The manifestation describes the clinical reaction that was observed. The severity indicates how severe the reaction was.

PARAMETER DESCRIPTION
code

REQUIRED. The code value from the code system representing the reaction manifestation

TYPE: str

display

The display name for the manifestation code

TYPE: Optional[str] DEFAULT: None

system

The code system for the manifestation code (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

severity

The severity of the reaction (mild, moderate, severe)

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
List[Dict[str, Any]]

A list containing a single FHIR Reaction dictionary with manifestation and severity fields

create_value_quantity_observation(code, value, unit, status='final', subject=None, system='http://loinc.org', display=None, effective_datetime=None, *, generate_id=True, warn=True)

Create a minimal FHIR Observation for vital signs or laboratory values. If you need to create a more complex observation, use the FHIR Observation resource directly. https://hl7.org/fhir/observation.html

PARAMETER DESCRIPTION
status

REQUIRED. The status of the observation (default: "final")

TYPE: str DEFAULT: 'final'

code

REQUIRED. The observation code (e.g., LOINC code for the measurement)

TYPE: str

value

The numeric value of the observation

TYPE: float

unit

The unit of measure (e.g., "beats/min", "mg/dL")

TYPE: str

system

The code system for the observation code (default: LOINC)

TYPE: str DEFAULT: 'http://loinc.org'

display

The display name for the observation code

TYPE: Optional[str] DEFAULT: None

effective_datetime

When the observation was made (ISO format). Omitted when not provided — the helper never invents a timestamp, so only record a time the caller can actually assert

TYPE: Optional[str] DEFAULT: None

subject

Reference to the patient (e.g. "Patient/123")

TYPE: Optional[str] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Observation

A FHIR Observation resource with an auto-generated ID prefixed with 'hc-'

TYPE: Observation

encode_gender(gender)

Encode gender as integer for ML models.

Standard encoding: Male=1, Female=0, Other/Unknown=None

PARAMETER DESCRIPTION
gender

Gender string (case-insensitive)

TYPE: str

RETURNS DESCRIPTION
Optional[int]

Encoded gender (1 for male, 0 for female, None for other/unknown)

extract_resources(bundle, resource_type)

Remove resources of a given type from a bundle and return them.

Useful for extracting and separating specific resource types (e.g., OperationOutcome) from a FHIR Bundle, modifying the bundle in place.

PARAMETER DESCRIPTION
bundle

The FHIR Bundle to process (modified in place)

TYPE: Bundle

resource_type

The FHIR resource class or string name to extract (e.g., OperationOutcome or "OperationOutcome")

TYPE: Union[str, Type[Resource]]

RETURNS DESCRIPTION
List[Resource]

List[Resource]: All resources of the specified type that were in the bundle

fhir_version_context(version)

Context manager for temporarily changing the default FHIR version.

PARAMETER DESCRIPTION
version

The FHIR version to use within the context

TYPE: Union[FHIRVersion, str]

YIELDS DESCRIPTION
FHIRVersion

The resolved FHIRVersion being used
Example

with fhir_version_context("R4B") as v: ... patient = get_fhir_resource("Patient") # R4B Patient ... print(f"Using {v}")

After context, default is restored

get_coded_entries(bundle, resource_type, status=None)

Read the flattened coded identity of resources in a bundle.

The read-side counterpart to the create_* helpers: instead of walking nested CodeableConcepts by hand, get code/display/system/status and entry metadata as flat records. Medication resources are handled specially: medicationCodeableConcept is read directly, and medicationReference is resolved to its target (bundled or contained) Medication.

Resources with no coded identity at all (no codings and no concept text) are skipped.

PARAMETER DESCRIPTION
bundle

The bundle to read

TYPE: Bundle

resource_type

A resource type name or list of names (e.g. "Condition" or ["MedicationStatement", "MedicationRequest"])

TYPE: Union[str, List[str]]

status

Only return entries with this status. For Condition and AllergyIntolerance this matches the clinicalStatus code

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
List[CodedEntry]

List of CodedEntry records, in bundle order per requested type
Example

bundle = load_bundle("synthea_patient.json") for entry in get_coded_entries(bundle, "Condition", status="active"): ... print(entry.code, entry.display, entry.authored_on) meds = get_coded_entries(bundle, ["MedicationStatement", "MedicationRequest"])

get_default_version()

Get the current default FHIR version.

RETURNS DESCRIPTION
FHIRVersion

The current default FHIRVersion (R4B if not explicitly set)

get_fhir_resource(resource_name, version=None)

Dynamically import a FHIR resource class based on version.

PARAMETER DESCRIPTION
resource_name

Name of the FHIR resource (e.g., "Patient", "Condition")

TYPE: str

version

FHIR version (None for default, or FHIRVersion enum/string)

TYPE: Optional[Union[FHIRVersion, str]] DEFAULT: None

RETURNS DESCRIPTION
Type[Any]

The FHIR resource class for the specified version
RAISES DESCRIPTION
ValueError

If version is invalid or resource cannot be imported
Example

Patient_R5 = get_fhir_resource("Patient") Patient_R4B = get_fhir_resource("Patient", "R4B") Patient_STU3 = get_fhir_resource("Patient", FHIRVersion.STU3)

get_medications(bundle, status=None)

Read all medications in a bundle as flat coded entries.

Sugar over get_coded_entries spanning MedicationStatement and MedicationRequest, with medicationReference resolved within the bundle.

PARAMETER DESCRIPTION
bundle

The bundle to read

TYPE: Bundle

status

Only return medications with this status (e.g. "active")

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
List[CodedEntry]

List of CodedEntry records for all medications found
Example

for med in get_medications(bundle, status="active"): ... print(med.code, med.display, med.system)

get_resource_type(resource_type)

Get the resource type class from string or type.

PARAMETER DESCRIPTION
resource_type

String name of the resource type (e.g. "Condition") or the type itself

TYPE: Union[str, Type[Resource]]

RETURNS DESCRIPTION
Type[Resource]

The R4B resource type class
RAISES DESCRIPTION
ValueError

If the resource type is not supported or cannot be imported

get_resource_version(resource)

Detect the FHIR version of a resource based on its module path.

PARAMETER DESCRIPTION
resource

A FHIR resource instance

TYPE: Any

RETURNS DESCRIPTION
Optional[FHIRVersion]

The FHIRVersion if detectable, None otherwise
Example

from fhir.resources.R4B.patient import Patient patient = Patient(id="123") version = get_resource_version(patient) print(version) FHIRVersion.R4B

get_resources(bundle, resource_type)

Get all resources of a specific type from a bundle.

PARAMETER DESCRIPTION
bundle

The bundle to search

TYPE: Bundle

resource_type

String name of the resource type (e.g. "Condition") or the type itself

TYPE: Union[str, Type[Resource]]

RETURNS DESCRIPTION
List[Resource]

List of resources of the specified type
Example

bundle = create_bundle()

Using string identifier

conditions = get_resources(bundle, "Condition") medications = get_resources(bundle, "MedicationStatement") allergies = get_resources(bundle, "AllergyIntolerance")

Or using type directly

from fhir.resources.condition import Condition conditions = get_resources(bundle, Condition)

load_bundle(source, version=None)

Load and validate a FHIR Bundle, raising on any validation error.

Validates the bundle structure and every entry resource, aggregating all issues into a single report rather than failing on the first error. Issue expressions locate the offending entry, e.g. Bundle.entry[2].resource.subject. See the module docstring for exactly what is and is not checked.

PARAMETER DESCRIPTION
source

A file path, a JSON string, or a dict representation of a Bundle

TYPE: Union[str, Path, Dict[str, Any]]

version

FHIR version to validate against (default: session default)

TYPE: Optional[Union[FHIRVersion, str]] DEFAULT: None

RETURNS DESCRIPTION
Bundle

The validated Bundle instance

TYPE: Resource

RAISES DESCRIPTION
FHIRValidationError

If parsing or validation fails; carries the full ValidationReport in .report
FileNotFoundError

If a file path is given but does not exist
Example

bundle = load_bundle("synthea_patient.json") try: ... bundle = load_bundle({"resourceType": "Bundle", "entry": [...]}) ... except FHIRValidationError as e: ... print(e.report.model_dump())

merge_bundles(bundles, bundle_type='collection', deduplicate=False, dedupe_key='id')

Merge multiple FHIR bundles into a single bundle.

Combines entries from multiple bundles while preserving resource metadata. Useful for aggregating search results from multiple FHIR sources.

PARAMETER DESCRIPTION
bundles

List of bundles to merge

TYPE: List[Bundle]

bundle_type

Type for the merged bundle (default: "collection")

TYPE: str DEFAULT: 'collection'

deduplicate

If True, remove duplicate resources based on dedupe_key

TYPE: bool DEFAULT: False

dedupe_key

Resource attribute to use for deduplication (default: "id")

TYPE: str DEFAULT: 'id'

RETURNS DESCRIPTION
Bundle

A new bundle containing all entries from input bundles
Example

Merge search results from multiple sources

epic_bundle = gateway.search(Condition, {"patient": "123"}, "epic") cerner_bundle = gateway.search(Condition, {"patient": "123"}, "cerner") merged = merge_bundles([epic_bundle, cerner_bundle], deduplicate=True)

Use in Document workflow

doc = Document(data=merged) doc.fhir.bundle # Contains all conditions from both sources

prefetch_to_bundle(prefetch)

Flatten CDS Hooks prefetch into a collection Bundle dict.

Converts the keyed prefetch format (used in CDS Hooks) into a flat collection bundle for downstream processing.

PARAMETER DESCRIPTION
prefetch

CDS Hooks prefetch dict with format: {"patient": {...}, "observations": {"entry": [...]}, ...}

TYPE: Dict[str, Any]

RETURNS DESCRIPTION
Dict[str, Any]

Bundle dict with type "collection" and flattened entries
Example

prefetch = request.prefetch bundle = prefetch_to_bundle(prefetch)

read_content_attachment(document_reference, include_data=True)

Read the attachments in a human readable format from a FHIR DocumentReference content field.

PARAMETER DESCRIPTION
document_reference

The FHIR DocumentReference resource

TYPE: DocumentReference

include_data

Whether to include the data of the attachments. If true, the data will be also be decoded (default: True)

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Optional[List[Dict[str, Any]]]

Optional[List[Dict[str, Any]]]: List of dictionaries containing attachment data and metadata, or None if no attachments are found: [ { "data": str, "metadata": Dict[str, Any] } ]

resolve_reference(bundle, reference, parent=None)

Resolve a FHIR Reference to its target resource within a bundle.

Read-side counterpart to add_resource: given a reference string or an R4B Reference element, find the resource it points to. Resolution is attempted in this order:

  1. Contained: references starting with # are resolved against parent.contained by resource id.
  2. Exact fullUrl match against entry.fullUrl (covers absolute URLs and urn:uuid:... references).
  3. Type/id relative references: match an entry whose resource type name and id match, or an absolute fullUrl ending in /Type/id.
  4. urn:uuid:{id} fallback: when no fullUrl matched, match a resource whose id equals the uuid part.

Never raises on unresolvable or malformed references; returns None instead. The lookup is built lazily per call (no caching or state).

PARAMETER DESCRIPTION
bundle

The bundle to search

TYPE: Bundle

reference

A reference string (e.g. "Patient/123", "urn:uuid:...", "#contained-id") or an R4B Reference element

TYPE: Union[str, Reference]

parent

The resource that owns the reference, required only to resolve contained ("#id") references against its contained list

TYPE: Optional[Resource] DEFAULT: None

RETURNS DESCRIPTION
Optional[Resource]

The first matching resource, or None if the reference cannot be resolved
Example

bundle = load_bundle("synthea_patient.json") med_request = get_resources(bundle, "MedicationRequest")[0] medication = resolve_reference(bundle, med_request.medicationReference) patient = resolve_reference(bundle, "Patient/patient-1")

set_condition_category(condition, category)

Set the category of a FHIR Condition to either 'problem-list-item' or 'encounter-diagnosis'.

PARAMETER DESCRIPTION
condition

The FHIR Condition resource to modify

TYPE: Condition

category

The category to set. Must be 'problem-list-item' or 'encounter-diagnosis'.

TYPE: str

RETURNS DESCRIPTION
Condition

The modified FHIR Condition resource with the specified category set

TYPE: Condition

RAISES DESCRIPTION
ValueError

If the category is not one of the allowed values.

set_resources(bundle, resources, resource_type, replace=True)

Set resources of a specific type in the bundle.

PARAMETER DESCRIPTION
bundle

The bundle to modify

TYPE: Bundle

resources

The new resources to add

TYPE: List[Resource]

resource_type

String name of the resource type (e.g. "Condition") or the type itself

TYPE: Union[str, Type[Resource]]

replace

If True, remove existing resources of this type before adding new ones. If False, append new resources to existing ones. Defaults to True.

TYPE: bool DEFAULT: True

Example

bundle = create_bundle()

Append to existing resources (default behavior)

set_resources(bundle, [condition1, condition2], "Condition") set_resources(bundle, [medication1], "MedicationStatement")

Replace existing resources

set_resources(bundle, [condition3], "Condition", replace=True)

Or using type directly

from fhir.resources.condition import Condition set_resources(bundle, [condition1, condition2], Condition)

validate_resource(resource, resource_type=None, version=None)

Validate a FHIR resource and return a report. Never raises.

Runs structural validation (types, required fields, unknown fields) and checks primitive code fields against their required bindings. Binding issues are only reported once structural validation passes. See the module docstring for exactly what is and is not checked.

PARAMETER DESCRIPTION
resource

A dict representation or an instantiated FHIR resource

TYPE: Union[Dict[str, Any], Resource]

resource_type

Resource type name (e.g. "Condition"). Optional if the dict has a "resourceType" key or the input is already a resource

TYPE: Optional[str] DEFAULT: None

version

FHIR version to validate against (default: session default). Ignored for instantiated resources, which carry their own version

TYPE: Optional[Union[FHIRVersion, str]] DEFAULT: None

RETURNS DESCRIPTION
ValidationReport

valid is True when no error/fatal issues exist

TYPE: ValidationReport

Example

report = validate_resource({"resourceType": "Condition"}) report.valid False report.issues[0].expression 'Condition.subject'

bundlehelpers

Helper functions for working with FHIR Bundles. Patterns: - create_(): create a new FHIR bundle - add_(): add a resource to a bundle - get_(): get resources from a bundle - set_(): set resources in a bundle - merge_(): merge multiple bundles into a single bundle - extract_(): extract resources from a bundle

add_resource(bundle, resource, full_url=None)

Add a resource to a bundle.

PARAMETER DESCRIPTION
bundle

The bundle to add to

TYPE: Bundle

resource

The resource to add, e.g. Condition, MedicationStatement, AllergyIntolerance

TYPE: Resource

full_url

Optional full URL for the resource

TYPE: Optional[str] DEFAULT: None

count_resources(bundle)

Count resources by type in a bundle.

PARAMETER DESCRIPTION
bundle

The FHIR Bundle to analyze

TYPE: Bundle

RETURNS DESCRIPTION
dict[str, int]

Dictionary mapping resource type names to their counts.
Example

{"Condition": 2, "MedicationStatement": 1, "Patient": 1}

TYPE: dict[str, int]

Example

bundle = create_bundle() add_resource(bundle, create_condition(...)) add_resource(bundle, create_condition(...)) add_resource(bundle, create_medication_statement(...)) counts = count_resources(bundle) print(counts)

create_bundle(bundle_type='collection')

Create an empty FHIR Bundle. https://www.hl7.org/fhir/bundle.html

PARAMETER DESCRIPTION
bundle_type

The type of bundle (default: collection) Valid types: document, message, transaction, transaction-response, batch, batch-response, history, searchset, collection

TYPE: str DEFAULT: 'collection'

extract_resources(bundle, resource_type)

Remove resources of a given type from a bundle and return them.

Useful for extracting and separating specific resource types (e.g., OperationOutcome) from a FHIR Bundle, modifying the bundle in place.

PARAMETER DESCRIPTION
bundle

The FHIR Bundle to process (modified in place)

TYPE: Bundle

resource_type

The FHIR resource class or string name to extract (e.g., OperationOutcome or "OperationOutcome")

TYPE: Union[str, Type[Resource]]

RETURNS DESCRIPTION
List[Resource]

List[Resource]: All resources of the specified type that were in the bundle

get_resource_type(resource_type)

Get the resource type class from string or type.

PARAMETER DESCRIPTION
resource_type

String name of the resource type (e.g. "Condition") or the type itself

TYPE: Union[str, Type[Resource]]

RETURNS DESCRIPTION
Type[Resource]

The R4B resource type class
RAISES DESCRIPTION
ValueError

If the resource type is not supported or cannot be imported

get_resources(bundle, resource_type)

Get all resources of a specific type from a bundle.

PARAMETER DESCRIPTION
bundle

The bundle to search

TYPE: Bundle

resource_type

String name of the resource type (e.g. "Condition") or the type itself

TYPE: Union[str, Type[Resource]]

RETURNS DESCRIPTION
List[Resource]

List of resources of the specified type
Example

bundle = create_bundle()

Using string identifier

conditions = get_resources(bundle, "Condition") medications = get_resources(bundle, "MedicationStatement") allergies = get_resources(bundle, "AllergyIntolerance")

Or using type directly

from fhir.resources.condition import Condition conditions = get_resources(bundle, Condition)

merge_bundles(bundles, bundle_type='collection', deduplicate=False, dedupe_key='id')

Merge multiple FHIR bundles into a single bundle.

Combines entries from multiple bundles while preserving resource metadata. Useful for aggregating search results from multiple FHIR sources.

PARAMETER DESCRIPTION
bundles

List of bundles to merge

TYPE: List[Bundle]

bundle_type

Type for the merged bundle (default: "collection")

TYPE: str DEFAULT: 'collection'

deduplicate

If True, remove duplicate resources based on dedupe_key

TYPE: bool DEFAULT: False

dedupe_key

Resource attribute to use for deduplication (default: "id")

TYPE: str DEFAULT: 'id'

RETURNS DESCRIPTION
Bundle

A new bundle containing all entries from input bundles
Example

Merge search results from multiple sources

epic_bundle = gateway.search(Condition, {"patient": "123"}, "epic") cerner_bundle = gateway.search(Condition, {"patient": "123"}, "cerner") merged = merge_bundles([epic_bundle, cerner_bundle], deduplicate=True)

Use in Document workflow

doc = Document(data=merged) doc.fhir.bundle # Contains all conditions from both sources

resolve_reference(bundle, reference, parent=None)

Resolve a FHIR Reference to its target resource within a bundle.

Read-side counterpart to add_resource: given a reference string or an R4B Reference element, find the resource it points to. Resolution is attempted in this order:

  1. Contained: references starting with # are resolved against parent.contained by resource id.
  2. Exact fullUrl match against entry.fullUrl (covers absolute URLs and urn:uuid:... references).
  3. Type/id relative references: match an entry whose resource type name and id match, or an absolute fullUrl ending in /Type/id.
  4. urn:uuid:{id} fallback: when no fullUrl matched, match a resource whose id equals the uuid part.

Never raises on unresolvable or malformed references; returns None instead. The lookup is built lazily per call (no caching or state).

PARAMETER DESCRIPTION
bundle

The bundle to search

TYPE: Bundle

reference

A reference string (e.g. "Patient/123", "urn:uuid:...", "#contained-id") or an R4B Reference element

TYPE: Union[str, Reference]

parent

The resource that owns the reference, required only to resolve contained ("#id") references against its contained list

TYPE: Optional[Resource] DEFAULT: None

RETURNS DESCRIPTION
Optional[Resource]

The first matching resource, or None if the reference cannot be resolved
Example

bundle = load_bundle("synthea_patient.json") med_request = get_resources(bundle, "MedicationRequest")[0] medication = resolve_reference(bundle, med_request.medicationReference) patient = resolve_reference(bundle, "Patient/patient-1")

set_resources(bundle, resources, resource_type, replace=True)

Set resources of a specific type in the bundle.

PARAMETER DESCRIPTION
bundle

The bundle to modify

TYPE: Bundle

resources

The new resources to add

TYPE: List[Resource]

resource_type

String name of the resource type (e.g. "Condition") or the type itself

TYPE: Union[str, Type[Resource]]

replace

If True, remove existing resources of this type before adding new ones. If False, append new resources to existing ones. Defaults to True.

TYPE: bool DEFAULT: True

Example

bundle = create_bundle()

Append to existing resources (default behavior)

set_resources(bundle, [condition1, condition2], "Condition") set_resources(bundle, [medication1], "MedicationStatement")

Replace existing resources

set_resources(bundle, [condition3], "Condition", replace=True)

Or using type directly

from fhir.resources.condition import Condition set_resources(bundle, [condition1, condition2], Condition)

elementhelpers

FHIR element creation functions.

This module provides convenience functions for creating FHIR elements that are used as building blocks within FHIR resources (e.g., CodeableConcept, Attachment, Coding).

create_dosage(text=None, route_code=None, route_display=None, route_system='http://snomed.info/sct', dose_value=None, dose_unit=None, frequency=None, period=None, period_unit=None, as_needed=None)

Create a minimal FHIR Dosage element.

Builds a minimum viable Dosage suitable for attaching to a MedicationStatement or MedicationRequest. Only the fields you provide are populated. For anything more complex, construct the FHIR Dosage directly. https://build.fhir.org/dosage.html

PARAMETER DESCRIPTION
text

Free-text dosage instructions (e.g. "1 tablet twice daily")

TYPE: Optional[str] DEFAULT: None

route_code

The route of administration code (e.g. SNOMED CT code for "oral")

TYPE: Optional[str] DEFAULT: None

route_display

The display name for the route code

TYPE: Optional[str] DEFAULT: None

route_system

The code system for the route (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

dose_value

The numeric dose amount, set as doseAndRate.doseQuantity.value

TYPE: Optional[float] DEFAULT: None

dose_unit

The unit for the dose amount (e.g. "mg", "tablet")

TYPE: Optional[str] DEFAULT: None

frequency

How many times per period the dose is taken (Timing.repeat.frequency)

TYPE: Optional[int] DEFAULT: None

period

The length of the period (Timing.repeat.period)

TYPE: Optional[float] DEFAULT: None

period_unit

The unit of the period (e.g. "d" for day, "h" for hour)

TYPE: Optional[str] DEFAULT: None

as_needed

Whether the medication is taken as needed (asNeededBoolean)

TYPE: Optional[bool] DEFAULT: None

RETURNS DESCRIPTION
Dosage

A FHIR Dosage element populated with the provided fields

TYPE: Dosage

create_single_attachment(content_type=None, data=None, url=None, title='Attachment created by HealthChain')

Create a minimal FHIR Attachment.

Creates a FHIR Attachment resource with basic fields. Either data or url should be provided. If data is provided, it will be base64 encoded.

PARAMETER DESCRIPTION
content_type

The MIME type of the content

TYPE: Optional[str] DEFAULT: None

data

The actual data content to be base64 encoded

TYPE: Optional[str] DEFAULT: None

url

The URL where the data can be found

TYPE: Optional[str] DEFAULT: None

title

A title for the attachment (default: "Attachment created by HealthChain")

TYPE: Optional[str] DEFAULT: 'Attachment created by HealthChain'

RETURNS DESCRIPTION
Attachment

A FHIR Attachment resource with basic metadata and content

TYPE: Any

create_single_codeable_concept(code, display=None, system='http://snomed.info/sct')

Create a minimal FHIR CodeableConcept with a single coding.

PARAMETER DESCRIPTION
code

REQUIRED. The code value from the code system

TYPE: str

display

The display name for the code

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

RETURNS DESCRIPTION
CodeableConcept

A FHIR CodeableConcept resource with a single coding

TYPE: Any

create_single_reaction(code, display=None, system='http://snomed.info/sct', severity=None)

Create a minimal FHIR Reaction with a single coding.

Creates a FHIR Reaction object with a single manifestation coding. The manifestation describes the clinical reaction that was observed. The severity indicates how severe the reaction was.

PARAMETER DESCRIPTION
code

REQUIRED. The code value from the code system representing the reaction manifestation

TYPE: str

display

The display name for the manifestation code

TYPE: Optional[str] DEFAULT: None

system

The code system for the manifestation code (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

severity

The severity of the reaction (mild, moderate, severe)

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
List[Dict[str, Any]]

A list containing a single FHIR Reaction dictionary with manifestation and severity fields

r4b

Version-aware re-exports for FHIR R4B resources.

Import FHIR R4B resource classes from here instead of fhir.resources directly:

from healthchain.fhir.r4b import Condition, Patient, Appointment

This ensures version consistency with HealthChain's FHIR version management.

readers

FHIR conversion and reading functions.

This module provides functions for converting between different FHIR representations and reading data from FHIR resources.

CodedEntry

Bases: BaseModel

Flattened coded identity of a clinical resource.

JSON-serializable via model_dump() so it can be returned directly from agent tools. code/display/system come from the first coding; codings carries all of them.

EntryCoding

Bases: BaseModel

A single coding (code/display/system) from a CodeableConcept.

convert_prefetch_to_fhir_objects(prefetch_dict)

Convert a dictionary of FHIR resource dicts to FHIR Resource objects.

Takes a prefetch dictionary where values may be either dict representations of FHIR resources or already instantiated FHIR Resource objects, and ensures all values are FHIR Resource objects.

PARAMETER DESCRIPTION
prefetch_dict

Dictionary mapping keys to FHIR resource dicts or objects

TYPE: Dict[str, Any]

RETURNS DESCRIPTION
Dict[str, Resource]

Dict[str, Resource]: Dictionary with same keys but all values as FHIR Resource objects
Example

prefetch = { ... "patient": {"resourceType": "Patient", "id": "123"}, ... "condition": Condition(id="456", ...) ... } fhir_objects = convert_prefetch_to_fhir_objects(prefetch) isinstance(fhir_objects["patient"], Patient) # True isinstance(fhir_objects["condition"], Condition) # True

create_resource_from_dict(resource_dict, resource_type, raise_on_error=False)

Create a FHIR resource instance from a dictionary

PARAMETER DESCRIPTION
resource_dict

Dictionary representation of the resource

TYPE: Dict

resource_type

Type of FHIR resource to create

TYPE: str

raise_on_error

If True, raise FHIRValidationError with a full ValidationReport instead of returning None on failure

TYPE: bool DEFAULT: False

RETURNS DESCRIPTION
Optional[Resource]

Optional[Resource]: FHIR resource instance or None if creation failed
RAISES DESCRIPTION
FHIRValidationError

If raise_on_error is True and validation fails

get_coded_entries(bundle, resource_type, status=None)

Read the flattened coded identity of resources in a bundle.

The read-side counterpart to the create_* helpers: instead of walking nested CodeableConcepts by hand, get code/display/system/status and entry metadata as flat records. Medication resources are handled specially: medicationCodeableConcept is read directly, and medicationReference is resolved to its target (bundled or contained) Medication.

Resources with no coded identity at all (no codings and no concept text) are skipped.

PARAMETER DESCRIPTION
bundle

The bundle to read

TYPE: Bundle

resource_type

A resource type name or list of names (e.g. "Condition" or ["MedicationStatement", "MedicationRequest"])

TYPE: Union[str, List[str]]

status

Only return entries with this status. For Condition and AllergyIntolerance this matches the clinicalStatus code

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
List[CodedEntry]

List of CodedEntry records, in bundle order per requested type
Example

bundle = load_bundle("synthea_patient.json") for entry in get_coded_entries(bundle, "Condition", status="active"): ... print(entry.code, entry.display, entry.authored_on) meds = get_coded_entries(bundle, ["MedicationStatement", "MedicationRequest"])

get_medications(bundle, status=None)

Read all medications in a bundle as flat coded entries.

Sugar over get_coded_entries spanning MedicationStatement and MedicationRequest, with medicationReference resolved within the bundle.

PARAMETER DESCRIPTION
bundle

The bundle to read

TYPE: Bundle

status

Only return medications with this status (e.g. "active")

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
List[CodedEntry]

List of CodedEntry records for all medications found
Example

for med in get_medications(bundle, status="active"): ... print(med.code, med.display, med.system)

prefetch_to_bundle(prefetch)

Flatten CDS Hooks prefetch into a collection Bundle dict.

Converts the keyed prefetch format (used in CDS Hooks) into a flat collection bundle for downstream processing.

PARAMETER DESCRIPTION
prefetch

CDS Hooks prefetch dict with format: {"patient": {...}, "observations": {"entry": [...]}, ...}

TYPE: Dict[str, Any]

RETURNS DESCRIPTION
Dict[str, Any]

Bundle dict with type "collection" and flattened entries
Example

prefetch = request.prefetch bundle = prefetch_to_bundle(prefetch)

read_content_attachment(document_reference, include_data=True)

Read the attachments in a human readable format from a FHIR DocumentReference content field.

PARAMETER DESCRIPTION
document_reference

The FHIR DocumentReference resource

TYPE: DocumentReference

include_data

Whether to include the data of the attachments. If true, the data will be also be decoded (default: True)

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Optional[List[Dict[str, Any]]]

Optional[List[Dict[str, Any]]]: List of dictionaries containing attachment data and metadata, or None if no attachments are found: [ { "data": str, "metadata": Dict[str, Any] } ]

resourcehelpers

FHIR resource creation and modification functions.

This module provides convenience functions for creating and modifying FHIR resources.

Patterns: - create_(): create a new FHIR resource with sensible defaults - set_(): set specific fields of resources with soft validation - add_*(): add data to resources safely

Parameters marked REQUIRED are required by FHIR specification.

add_coding_to_codeable_concept(codeable_concept, code, system, display=None)

Add a coding to an existing CodeableConcept.

Useful for adding standardized codes (e.g., SNOMED CT) to resources that already have codes from other systems (e.g., ICD-10).

PARAMETER DESCRIPTION
codeable_concept

The CodeableConcept to add coding to

TYPE: CodeableConcept

code

The code value from the code system

TYPE: str

system

The code system URI

TYPE: str

display

Optional display text for the code

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
CodeableConcept

The updated CodeableConcept with the new coding added

TYPE: CodeableConcept

Example

Add SNOMED CT code to a condition that has ICD-10

condition_code = condition.code condition_code = add_coding_to_codeable_concept( ... condition_code, ... code="44054006", ... system="http://snomed.info/sct", ... display="Type 2 diabetes mellitus" ... )

add_provenance_metadata(resource, source, tag_code=None, tag_display=None)

Add provenance metadata to a FHIR resource.

Adds source system identifier, timestamp, and optional processing tags to track data lineage and transformations for audit trails.

PARAMETER DESCRIPTION
resource

The FHIR resource to annotate

TYPE: Any

source

Name of the source system (e.g., "epic", "cerner")

TYPE: str

tag_code

Optional tag code for processing operations (e.g., "aggregated", "deduplicated")

TYPE: Optional[str] DEFAULT: None

tag_display

Optional display text for the tag

TYPE: Optional[str] DEFAULT: None

RETURNS DESCRIPTION
Resource

The resource with added provenance metadata

TYPE: Any

Example

condition = create_condition(subject="Patient/123", code="E11.9") condition = add_provenance_metadata(condition, "epic", "aggregated", "Aggregated from source")

create_allergy_intolerance(patient, code=None, display=None, system='http://snomed.info/sct', *, generate_id=True, warn=True)

Create a minimal active FHIR AllergyIntolerance. If you need to create a more complex allergy intolerance, use the FHIR AllergyIntolerance resource directly. https://build.fhir.org/allergyintolerance.html

PARAMETER DESCRIPTION
patient

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

code

The allergen code

TYPE: Optional[str] DEFAULT: None

display

The display name for the allergen

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
AllergyIntolerance

A FHIR AllergyIntolerance resource with an auto-generated ID prefixed with 'hc-'

TYPE: AllergyIntolerance

create_condition(subject, clinical_status='active', code=None, display=None, system='http://snomed.info/sct', onset=None, *, generate_id=True, warn=True)

Create a minimal active FHIR Condition. If you need to create a more complex condition, use the FHIR Condition resource directly. https://build.fhir.org/condition.html

PARAMETER DESCRIPTION
subject

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

clinical_status

REQUIRED. Clinical status (default: active)

TYPE: str DEFAULT: 'active'

code

The condition code

TYPE: Optional[str] DEFAULT: None

display

The display name for the condition

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

onset

When the condition began, as an ISO 8601 date/datetime string, set as onsetDateTime (e.g. "2024-01-15" or "2024-01-15T09:00:00Z")

TYPE: Optional[str] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Condition

A FHIR Condition resource with an auto-generated ID prefixed with 'hc-'

TYPE: Condition

create_document_reference(data=None, url=None, content_type=None, status='current', description='DocumentReference created by HealthChain', attachment_title='Attachment created by HealthChain', *, generate_id=True, warn=True)

Create a minimal FHIR DocumentReference. If you need to create a more complex document reference, use the FHIR DocumentReference resource directly. https://build.fhir.org/documentreference.html

PARAMETER DESCRIPTION
data

The data content of the document attachment

TYPE: Optional[Any] DEFAULT: None

url

URL where the document can be accessed

TYPE: Optional[str] DEFAULT: None

content_type

MIME type of the document (e.g. "application/pdf", "text/xml", "image/png")

TYPE: Optional[str] DEFAULT: None

status

REQUIRED. Status of the document reference (default: current)

TYPE: str DEFAULT: 'current'

description

Description of the document reference

TYPE: Optional[str] DEFAULT: 'DocumentReference created by HealthChain'

attachment_title

Title for the document attachment

TYPE: Optional[str] DEFAULT: 'Attachment created by HealthChain'

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
DocumentReference

A FHIR DocumentReference resource with an auto-generated ID prefixed with 'hc-'

TYPE: DocumentReference

create_document_reference_content(attachment_data=None, url=None, content_type='text/plain', language='en-US', title=None, **kwargs)

Create a FHIR DocumentReferenceContent object.

Creates a DocumentReferenceContent structure that can be added to a DocumentReference. Either attachment_data or url must be provided. If attachment_data is provided, it will be base64 encoded automatically.

PARAMETER DESCRIPTION
attachment_data

The content data (text that will be base64 encoded)

TYPE: Optional[str] DEFAULT: None

url

URL where the content can be accessed

TYPE: Optional[str] DEFAULT: None

content_type

MIME type (e.g., 'text/plain', 'text/html', 'application/pdf') (default: text/plain)

TYPE: str DEFAULT: 'text/plain'

language

Language code (default: en-US)

TYPE: Optional[str] DEFAULT: 'en-US'

title

Optional title for the content (default: "Attachment created by HealthChain")

TYPE: Optional[str] DEFAULT: None

**kwargs

Additional DocumentReferenceContent fields (e.g., format, profile)

DEFAULT: {}

RETURNS DESCRIPTION
Dict[str, Any]

Dict[str, Any]: A FHIR DocumentReferenceContent dictionary with attachment and optional language
Example

Create content with inline data

content = create_document_reference_content( ... attachment_data="Patient presents with fever...", ... content_type="text/plain", ... title="Clinical Note" ... )

Create content with URL reference

content = create_document_reference_content( ... url="https://example.com/document.pdf", ... content_type="application/pdf", ... title="Lab Report" ... )

Add content to a DocumentReference

doc_ref = DocumentReference( ... id="doc-1", ... status="current", ... content=[content] ... )

create_medication_statement(subject, status='unknown', code=None, display=None, system='http://snomed.info/sct', dosage=None, *, generate_id=True, warn=True)

Create a minimal FHIR MedicationStatement. If you need to create a more complex medication statement, use the FHIR MedicationStatement resource directly. https://build.fhir.org/medicationstatement.html

PARAMETER DESCRIPTION
subject

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

status

REQUIRED. Status of the medication. Default "unknown" (an R4B-valid code that makes no clinical assertion). Allowed R4B values: active, completed, entered-in-error, intended, stopped, on-hold, unknown, not-taken

TYPE: Optional[str] DEFAULT: 'unknown'

code

The medication code

TYPE: Optional[str] DEFAULT: None

display

The display name for the medication

TYPE: Optional[str] DEFAULT: None

system

The code system (default: SNOMED CT)

TYPE: Optional[str] DEFAULT: 'http://snomed.info/sct'

dosage

Dosage instructions. A plain string is wrapped as a single free-text Dosage; a single Dosage is wrapped in a one-element list; a list of Dosage elements is used as-is. See create_dosage().

TYPE: Optional[Union[str, Dosage, List[Dosage]]] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
MedicationStatement

A FHIR MedicationStatement resource with an auto-generated ID prefixed with 'hc-'

TYPE: MedicationStatement

create_patient(gender=None, birth_date=None, identifier=None, identifier_system='http://hospital.example.org', *, generate_id=True, warn=True)

Create a minimal FHIR Patient resource with basic gender and birthdate If you need to create a more complex patient, use the FHIR Patient resource directly https://hl7.org/fhir/patient.html (No required fields).

PARAMETER DESCRIPTION
gender

Administrative gender (male, female, other, unknown)

TYPE: Optional[str] DEFAULT: None

birth_date

Birth date in YYYY-MM-DD format

TYPE: Optional[str] DEFAULT: None

identifier

Optional identifier value for the patient (e.g., MRN)

TYPE: Optional[str] DEFAULT: None

identifier_system

The system for the identifier (default: "http://hospital.example.org")

TYPE: Optional[str] DEFAULT: 'http://hospital.example.org'

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Patient

A FHIR Patient resource with an auto-generated ID prefixed with 'hc-'

TYPE: Patient

create_risk_assessment_from_prediction(subject, prediction, status='final', method=None, basis=None, comment=None, occurrence_datetime=None, *, generate_id=True, warn=True)

Create a FHIR RiskAssessment from ML model prediction output. If you need to create a more complex risk assessment, use the FHIR RiskAssessment resource directly. https://hl7.org/fhir/riskassessment.html

PARAMETER DESCRIPTION
subject

REQUIRED. Reference to the patient (e.g. "Patient/123")

TYPE: str

prediction

Dictionary containing prediction details with keys: - outcome: CodeableConcept or dict with code, display, system for the predicted outcome - probability: float between 0 and 1 representing the risk probability - qualitative_risk: Optional str indicating risk level (e.g., "high", "moderate", "low")

TYPE: Dict[str, Any]

status

REQUIRED. The status of the assessment (default: "final")

TYPE: str DEFAULT: 'final'

method

Optional CodeableConcept describing the assessment method/model used

TYPE: Optional[CodeableConcept] DEFAULT: None

basis

Optional list of References to observations or other resources used as input

TYPE: Optional[List[Reference]] DEFAULT: None

comment

Optional text comment about the assessment

TYPE: Optional[str] DEFAULT: None

occurrence_datetime

When the assessment was made (ISO format). Omitted when not provided — the helper never invents a timestamp

TYPE: Optional[str] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
RiskAssessment

A FHIR RiskAssessment resource with an auto-generated ID prefixed with 'hc-'

TYPE: RiskAssessment

Example

prediction = { ... "outcome": {"code": "A41.9", "display": "Sepsis", "system": "http://hl7.org/fhir/sid/icd-10"}, ... "probability": 0.85, ... "qualitative_risk": "high" ... } risk = create_risk_assessment("Patient/123", prediction)

create_value_quantity_observation(code, value, unit, status='final', subject=None, system='http://loinc.org', display=None, effective_datetime=None, *, generate_id=True, warn=True)

Create a minimal FHIR Observation for vital signs or laboratory values. If you need to create a more complex observation, use the FHIR Observation resource directly. https://hl7.org/fhir/observation.html

PARAMETER DESCRIPTION
status

REQUIRED. The status of the observation (default: "final")

TYPE: str DEFAULT: 'final'

code

REQUIRED. The observation code (e.g., LOINC code for the measurement)

TYPE: str

value

The numeric value of the observation

TYPE: float

unit

The unit of measure (e.g., "beats/min", "mg/dL")

TYPE: str

system

The code system for the observation code (default: LOINC)

TYPE: str DEFAULT: 'http://loinc.org'

display

The display name for the observation code

TYPE: Optional[str] DEFAULT: None

effective_datetime

When the observation was made (ISO format). Omitted when not provided — the helper never invents a timestamp, so only record a time the caller can actually assert

TYPE: Optional[str] DEFAULT: None

subject

Reference to the patient (e.g. "Patient/123")

TYPE: Optional[str] DEFAULT: None

generate_id

Stamp an auto-generated 'hc-' id. Pass False for deterministic output (snapshot tests, evals)

TYPE: bool DEFAULT: True

warn

Log a warning for spec-invalid codes. Pass False if you validate explicitly with validate_resource()

TYPE: bool DEFAULT: True

RETURNS DESCRIPTION
Observation

A FHIR Observation resource with an auto-generated ID prefixed with 'hc-'

TYPE: Observation

set_condition_category(condition, category)

Set the category of a FHIR Condition to either 'problem-list-item' or 'encounter-diagnosis'.

PARAMETER DESCRIPTION
condition

The FHIR Condition resource to modify

TYPE: Condition

category

The category to set. Must be 'problem-list-item' or 'encounter-diagnosis'.

TYPE: str

RETURNS DESCRIPTION
Condition

The modified FHIR Condition resource with the specified category set

TYPE: Condition

RAISES DESCRIPTION
ValueError

If the category is not one of the allowed values.

utilities

FHIR utility functions.

This module provides utility functions for common operations like ID generation, age calculation, and gender encoding.

calculate_age_from_birthdate(birth_date)

Calculate age in years from a birth date string.

PARAMETER DESCRIPTION
birth_date

Birth date in ISO format (YYYY-MM-DD or full ISO datetime)

TYPE: str

RETURNS DESCRIPTION
Optional[int]

Age in years, or None if birth date is invalid

calculate_age_from_event_date(birth_date, event_date)

Calculate age in years from birth date and event date (MIMIC-IV style).

Uses the formula: age = year(eventDate) - year(birthDate) This matches MIMIC-IV on FHIR de-identified age calculation.

PARAMETER DESCRIPTION
birth_date

Birth date in ISO format (YYYY-MM-DD or full ISO datetime)

TYPE: str

event_date

Event date in ISO format (YYYY-MM-DD or full ISO datetime)

TYPE: str

RETURNS DESCRIPTION
Optional[int]

Age in years based on year difference, or None if dates are invalid
Example

calculate_age_from_event_date("1990-06-15", "2020-03-10") 30

encode_gender(gender)

Encode gender as integer for ML models.

Standard encoding: Male=1, Female=0, Other/Unknown=None

PARAMETER DESCRIPTION
gender

Gender string (case-insensitive)

TYPE: str

RETURNS DESCRIPTION
Optional[int]

Encoded gender (1 for male, 0 for female, None for other/unknown)

validation

FHIR resource validation.

This module provides an explicit validation surface for FHIR resources: a report-returning validate_resource suitable for agent tool loops, a raising load_bundle for loading bundles from files or dicts, and the ValidationReport/FHIRValidationError types they share.

What IS checked: - Structure: field types, required fields, and unknown fields, as enforced by the underlying fhir.resources Pydantic models. - Required bindings on primitive code fields: values are checked against the value set shipped with the model metadata (e.g. MedicationStatement.status).

What is NOT checked: - Bindings on CodeableConcept/Coding fields (no ValueSet expansion is bundled). - FHIRPath invariants/constraints (e.g. "co-33: only one onset[x]"). - Profile conformance (e.g. US Core, UK Core). - Reference integrity (whether referenced resources exist).

For full conformance validation, use a FHIR server's $validate operation against the relevant profiles.

FHIRValidationError

Bases: Exception

Raised when FHIR validation fails. Carries the full ValidationReport.

ValidationIssue

Bases: BaseModel

A single validation issue, mirroring FHIR OperationOutcome.issue fields.

https://www.hl7.org/fhir/operationoutcome.html

ValidationReport

Bases: BaseModel

Result of validating a FHIR resource.

JSON-serializable via model_dump() so it can be returned directly from agent tools. Convert to a FHIR OperationOutcome resource with to_operation_outcome().

to_operation_outcome()

Convert the report to a FHIR OperationOutcome resource.

RETURNS DESCRIPTION
Resource

An OperationOutcome of the report's FHIR version, with one issue
Resource

per validation issue (or a single 'informational' issue if valid).

load_bundle(source, version=None)

Load and validate a FHIR Bundle, raising on any validation error.

Validates the bundle structure and every entry resource, aggregating all issues into a single report rather than failing on the first error. Issue expressions locate the offending entry, e.g. Bundle.entry[2].resource.subject. See the module docstring for exactly what is and is not checked.

PARAMETER DESCRIPTION
source

A file path, a JSON string, or a dict representation of a Bundle

TYPE: Union[str, Path, Dict[str, Any]]

version

FHIR version to validate against (default: session default)

TYPE: Optional[Union[FHIRVersion, str]] DEFAULT: None

RETURNS DESCRIPTION
Bundle

The validated Bundle instance

TYPE: Resource

RAISES DESCRIPTION
FHIRValidationError

If parsing or validation fails; carries the full ValidationReport in .report
FileNotFoundError

If a file path is given but does not exist
Example

bundle = load_bundle("synthea_patient.json") try: ... bundle = load_bundle({"resourceType": "Bundle", "entry": [...]}) ... except FHIRValidationError as e: ... print(e.report.model_dump())

validate_resource(resource, resource_type=None, version=None)

Validate a FHIR resource and return a report. Never raises.

Runs structural validation (types, required fields, unknown fields) and checks primitive code fields against their required bindings. Binding issues are only reported once structural validation passes. See the module docstring for exactly what is and is not checked.

PARAMETER DESCRIPTION
resource

A dict representation or an instantiated FHIR resource

TYPE: Union[Dict[str, Any], Resource]

resource_type

Resource type name (e.g. "Condition"). Optional if the dict has a "resourceType" key or the input is already a resource

TYPE: Optional[str] DEFAULT: None

version

FHIR version to validate against (default: session default). Ignored for instantiated resources, which carry their own version

TYPE: Optional[Union[FHIRVersion, str]] DEFAULT: None

RETURNS DESCRIPTION
ValidationReport

valid is True when no error/fatal issues exist

TYPE: ValidationReport

Example

report = validate_resource({"resourceType": "Condition"}) report.valid False report.issues[0].expression 'Condition.subject'

version

FHIR version management for multi-version support.

This module provides utilities for working with different FHIR versions (STU3, R4B, R5). It enables dynamic resource loading, version context management, and basic resource conversion.

Usage

from healthchain.fhir.version import get_fhir_resource, FHIRVersion

Get a resource class for a specific version

Patient_R4B = get_fhir_resource("Patient", "R4B") Patient_R5 = get_fhir_resource("Patient", FHIRVersion.R5)

Set the default version for the session

set_default_version("R4B")

Use context manager for temporary version changes

with fhir_version_context("STU3"): patient = get_fhir_resource("Patient") # Returns STU3 Patient

Convert resources between versions

patient_r5 = Patient(id="123", gender="male") patient_r4b = convert_resource(patient_r5, "R4B")

FHIRVersion

Bases: str, Enum

Supported FHIR versions.

R5 is the default version in fhir.resources library. R4B and STU3 are available via subpackages (e.g., fhir.resources.R4B).

convert_resource(resource, target_version)

Convert a FHIR resource to a different version.

Converts by serializing the resource to a dictionary and deserializing with the target version's resource class. This approach works for resources with compatible field structures.

Note

Field mappings between FHIR versions may not be 1:1. Some fields may be added, removed, or renamed between versions. This function performs a best-effort conversion and may raise validation errors if the resource data is incompatible with the target version.

PARAMETER DESCRIPTION
resource

The FHIR resource to convert

TYPE: Any

target_version

The target FHIR version

TYPE: Union[FHIRVersion, str]

RETURNS DESCRIPTION
Any

A new resource instance of the target version
RAISES DESCRIPTION
ValueError

If the resource type cannot be determined or imported
ValidationError

If the resource data is incompatible with target version
Example

from fhir.resources.patient import Patient patient_r5 = Patient(id="123", gender="male") patient_r4b = convert_resource(patient_r5, "R4B") print(patient_r4b.class.module) fhir.resources.R4B.patient

fhir_version_context(version)

Context manager for temporarily changing the default FHIR version.

PARAMETER DESCRIPTION
version

The FHIR version to use within the context

TYPE: Union[FHIRVersion, str]

YIELDS DESCRIPTION
FHIRVersion

The resolved FHIRVersion being used
Example

with fhir_version_context("R4B") as v: ... patient = get_fhir_resource("Patient") # R4B Patient ... print(f"Using {v}")

After context, default is restored

get_default_version()

Get the current default FHIR version.

RETURNS DESCRIPTION
FHIRVersion

The current default FHIRVersion (R4B if not explicitly set)

get_fhir_resource(resource_name, version=None)

Dynamically import a FHIR resource class based on version.

PARAMETER DESCRIPTION
resource_name

Name of the FHIR resource (e.g., "Patient", "Condition")

TYPE: str

version

FHIR version (None for default, or FHIRVersion enum/string)

TYPE: Optional[Union[FHIRVersion, str]] DEFAULT: None

RETURNS DESCRIPTION
Type[Any]

The FHIR resource class for the specified version
RAISES DESCRIPTION
ValueError

If version is invalid or resource cannot be imported
Example

Patient_R5 = get_fhir_resource("Patient") Patient_R4B = get_fhir_resource("Patient", "R4B") Patient_STU3 = get_fhir_resource("Patient", FHIRVersion.STU3)

get_resource_version(resource)

Detect the FHIR version of a resource based on its module path.

PARAMETER DESCRIPTION
resource

A FHIR resource instance

TYPE: Any

RETURNS DESCRIPTION
Optional[FHIRVersion]

The FHIRVersion if detectable, None otherwise
Example

from fhir.resources.R4B.patient import Patient patient = Patient(id="123") version = get_resource_version(patient) print(version) FHIRVersion.R4B

reset_default_version()

Reset the default FHIR version to R4B.

set_default_version(version)

Set the global default FHIR version.

PARAMETER DESCRIPTION
version

The FHIR version to use as default

TYPE: Union[FHIRVersion, str]

Example

set_default_version("R4B") patient = get_fhir_resource("Patient") # Returns R4B Patient