Bits & Flames
bitsandflames/fyron

FHIR Reference

FHIR REST, SQL, authentication, resource builders, mapping, and defensive extraction helpers.

For workflow context, see FHIR module guide.

Functions And Classes

fyron.fhir.auth.Auth

Simplified authentication wrapper for Fyron sessions.

Import path: fyron.fhir.auth.Auth

python
Auth(self, auth_url: Optional[str] = None, auth_type: str = 'token', refresh_url: Optional[str] = None, username: Optional[str] = None, auth_method: str = 'env', token_auth_method: Optional[str] = None, token: Optional[str] = None, max_login_attempts: int = 3, token_refresh_delta: Optional[Union[int, timedelta]] = None, session: Optional[requests.Session] = None)

Parameters

ParameterRequiredTypeDefaultDescription
auth_urlnoOptional[str]NoneSee signature.
auth_typenostr'token'See signature.
refresh_urlnoOptional[str]NoneSee signature.
usernamenoOptional[str]NoneSee signature.
auth_methodnostr'env'See signature.
token_auth_methodnoOptional[str]NoneSee signature.
tokennoOptional[str]NoneSee signature.
max_login_attemptsnoint3See signature.
token_refresh_deltanoOptional[Union[int, timedelta]]NoneSee signature.
sessionnoOptional[requests.Session]NoneSee signature.

Returns

Class constructor.

See also: FHIR module guide.

Public Methods

fyron.fhir.auth.Auth.token_env

Create token-based auth using credentials from environment variables.

Import path: fyron.fhir.auth.Auth.token_env

python
Auth.token_env(cls, *, auth_url: str, refresh_url: Optional[str] = None, token_auth_method: str = 'basic', token: Optional[str] = None, max_login_attempts: int = 3, token_refresh_delta: Optional[Union[int, timedelta]] = None, session: Optional[requests.Session] = None) -> 'Auth'

Parameters

ParameterRequiredTypeDefaultDescription
auth_urlyesstrSee signature.
refresh_urlnoOptional[str]NoneSee signature.
token_auth_methodnostr'basic'See signature.
tokennoOptional[str]NoneSee signature.
max_login_attemptsnoint3See signature.
token_refresh_deltanoOptional[Union[int, timedelta]]NoneSee signature.
sessionnoOptional[requests.Session]NoneSee signature.

Returns

'Auth'

See also: FHIR module guide.

fyron.fhir.auth.Auth.close

Close the underlying session.

Import path: fyron.fhir.auth.Auth.close

python
Auth.close(self) -> None

Parameters

No parameters documented.

Returns

None

See also: FHIR module guide.

fyron.fhir.auth.TokenAuth

Very small token auth helper.

Import path: fyron.fhir.auth.TokenAuth

python
TokenAuth(self, username: str, password: str, auth_url: str, refresh_url: Optional[str] = None, token: Optional[str] = None, token_refresh_delta: Optional[Union[int, timedelta]] = None, max_login_attempts: int = 3, session: Optional[requests.Session] = None, token_field: str = 'access_token', auth_method: str = 'basic')

Parameters

ParameterRequiredTypeDefaultDescription
usernameyesstrSee signature.
passwordyesstrSee signature.
auth_urlyesstrSee signature.
refresh_urlnoOptional[str]NoneSee signature.
tokennoOptional[str]NoneSee signature.
token_refresh_deltanoOptional[Union[int, timedelta]]NoneSee signature.
max_login_attemptsnoint3See signature.
sessionnoOptional[requests.Session]NoneSee signature.
token_fieldnostr'access_token'See signature.
auth_methodnostr'basic'See signature.

Returns

Class constructor.

See also: FHIR module guide.

Public Methods

fyron.fhir.auth.TokenAuth.is_refresh_required

Return True if token should be refreshed.

Import path: fyron.fhir.auth.TokenAuth.is_refresh_required

python
TokenAuth.is_refresh_required(self) -> bool

Parameters

No parameters documented.

Returns

bool

See also: FHIR module guide.

fyron.fhir.auth.now_utc

Return current UTC datetime.

Import path: fyron.fhir.auth.now_utc

python
now_utc() -> datetime

Parameters

No parameters documented.

Returns

datetime

See also: FHIR module guide.

fyron.fhir.builder.attachment

Build a FHIR Attachment.

Import path: fyron.fhir.builder.attachment

python
attachment(url: str | None = None, *, content_type: str | None = None, title: str | None = None, data: str | None = None, creation: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
urlnostr or NoneNoneSee signature.
content_typenostr or NoneNoneSee signature.
titlenostr or NoneNoneSee signature.
datanostr or NoneNoneSee signature.
creationnostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_bundle

Build a collection or transaction FHIR Bundle.

Import path: fyron.fhir.builder.build_bundle

python
build_bundle(resources: Sequence[dict[str, Any]], *, bundle_type: str, bundle_id: str | None = None, transaction_method: str = 'POST', if_none_exist: str | dict[str, str] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourcesyesSequence[dict[str, Any]]See signature.
bundle_typeyesstrSee signature.
bundle_idnostr or NoneNoneSee signature.
transaction_methodnostr'POST'See signature.
if_none_existnostr or dict[str, str] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_condition

Build a FHIR Condition with optional evidence links.

Import path: fyron.fhir.builder.build_condition

python
build_condition(*, subject: str | dict[str, Any], code: dict[str, Any] | str, condition_id: str | None = None, clinical_status: dict[str, Any] | str | None = None, verification_status: dict[str, Any] | str | None = None, onset: str | None = None, recorded_date: str | None = None, evidence: Sequence[str | dict[str, Any]] | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
codeyesdict[str, Any] or strSee signature.
condition_idnostr or NoneNoneSee signature.
clinical_statusnodict[str, Any] or str or NoneNoneSee signature.
verification_statusnodict[str, Any] or str or NoneNoneSee signature.
onsetnostr or NoneNoneSee signature.
recorded_datenostr or NoneNoneSee signature.
evidencenoSequence[str or dict[str, Any]] or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_diagnostic_report

Build a FHIR DiagnosticReport that groups observations or summaries.

Import path: fyron.fhir.builder.build_diagnostic_report

python
build_diagnostic_report(*, subject: str | dict[str, Any], code: dict[str, Any] | str, results: Sequence[str | dict[str, Any]] | None = None, report_id: str | None = None, status: str = 'final', effective: str | None = None, issued: str | None = None, imaging_study: Sequence[str | dict[str, Any]] | None = None, conclusion: str | None = None, presented_form: Sequence[dict[str, Any]] | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
codeyesdict[str, Any] or strSee signature.
resultsnoSequence[str or dict[str, Any]] or NoneNoneSee signature.
report_idnostr or NoneNoneSee signature.
statusnostr'final'See signature.
effectivenostr or NoneNoneSee signature.
issuednostr or NoneNoneSee signature.
imaging_studynoSequence[str or dict[str, Any]] or NoneNoneSee signature.
conclusionnostr or NoneNoneSee signature.
presented_formnoSequence[dict[str, Any]] or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_document_reference

Build a FHIR DocumentReference for source reports or generated summaries.

Import path: fyron.fhir.builder.build_document_reference

python
build_document_reference(*, subject: str | dict[str, Any], url: str | None = None, title: str | None = None, content_type: str | None = None, document_id: str | None = None, status: str = 'current', doc_status: str | None = None, type_code: dict[str, Any] | str | None = None, date: str | None = None, description: str | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
urlnostr or NoneNoneSee signature.
titlenostr or NoneNoneSee signature.
content_typenostr or NoneNoneSee signature.
document_idnostr or NoneNoneSee signature.
statusnostr'current'See signature.
doc_statusnostr or NoneNoneSee signature.
type_codenodict[str, Any] or str or NoneNoneSee signature.
datenostr or NoneNoneSee signature.
descriptionnostr or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_encounter

Build a minimal FHIR Encounter resource.

Import path: fyron.fhir.builder.build_encounter

python
build_encounter(*, subject: str | dict[str, Any], status: str = 'finished', encounter_class: dict[str, Any] | str | None = None, encounter_id: str | None = None, period_start: str | None = None, period_end: str | None = None, reason_code: dict[str, Any] | str | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
statusnostr'finished'See signature.
encounter_classnodict[str, Any] or str or NoneNoneSee signature.
encounter_idnostr or NoneNoneSee signature.
period_startnostr or NoneNoneSee signature.
period_endnostr or NoneNoneSee signature.
reason_codenodict[str, Any] or str or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_endpoint

Build a FHIR Endpoint resource for a model or FHIR API endpoint.

Import path: fyron.fhir.builder.build_endpoint

python
build_endpoint(*, address: str, endpoint_id: str | None = None, name: str | None = None, status: str = 'active', connection_type_code: str = 'hl7-fhir-rest', profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
addressyesstrSee signature.
endpoint_idnostr or NoneNoneSee signature.
namenostr or NoneNoneSee signature.
statusnostr'active'See signature.
connection_type_codenostr'hl7-fhir-rest'See signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_imaging_measurement_bundle

Build a FHIR bundle for imaging-derived quantitative measurements.

Import path: fyron.fhir.builder.build_imaging_measurement_bundle

python
build_imaging_measurement_bundle(*, subject: str | dict[str, Any], study_instance_uid: str, measurements: Sequence[dict[str, Any]], series_instance_uid: str | None = None, series_description: str | None = None, model_name: str | None = None, model_endpoint_url: str | None = None, id_prefix: str | None = None, bundle_type: str, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
study_instance_uidyesstrSee signature.
measurementsyesSequence[dict[str, Any]]See signature.
series_instance_uidnostr or NoneNoneSee signature.
series_descriptionnostr or NoneNoneSee signature.
model_namenostr or NoneNoneSee signature.
model_endpoint_urlnostr or NoneNoneSee signature.
id_prefixnostr or NoneNoneSee signature.
bundle_typeyesstrSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_imaging_study_reference

Build a minimal FHIR ImagingStudy resource with optional series context.

Import path: fyron.fhir.builder.build_imaging_study_reference

python
build_imaging_study_reference(*, subject: str | dict[str, Any], study_instance_uid: str, imaging_study_id: str | None = None, series_instance_uid: str | None = None, series_description: str | None = None, modality_code: str | None = None, started: str | None = None, profile: str | Sequence[str] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
study_instance_uidyesstrSee signature.
imaging_study_idnostr or NoneNoneSee signature.
series_instance_uidnostr or NoneNoneSee signature.
series_descriptionnostr or NoneNoneSee signature.
modality_codenostr or NoneNoneSee signature.
startednostr or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_llm_extraction_bundle

Build a FHIR bundle for LLM-extracted report evidence.

Import path: fyron.fhir.builder.build_llm_extraction_bundle

python
build_llm_extraction_bundle(*, subject: str | dict[str, Any], source_report_url: str, observations: Sequence[dict[str, Any]] | None = None, conditions: Sequence[dict[str, Any]] | None = None, summary_text: str | None = None, model_name: str, model_endpoint_url: str | None = None, model_version: str | None = None, prompt_version: str | None = None, id_prefix: str | None = None, bundle_type: str, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
source_report_urlyesstrSee signature.
observationsnoSequence[dict[str, Any]] or NoneNoneSee signature.
conditionsnoSequence[dict[str, Any]] or NoneNoneSee signature.
summary_textnostr or NoneNoneSee signature.
model_nameyesstrSee signature.
model_endpoint_urlnostr or NoneNoneSee signature.
model_versionnostr or NoneNoneSee signature.
prompt_versionnostr or NoneNoneSee signature.
id_prefixnostr or NoneNoneSee signature.
bundle_typeyesstrSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_medication_statement

Build a minimal FHIR MedicationStatement resource.

Import path: fyron.fhir.builder.build_medication_statement

python
build_medication_statement(*, subject: str | dict[str, Any], medication: dict[str, Any] | str, medication_statement_id: str | None = None, status: str = 'active', effective: str | None = None, date_asserted: str | None = None, reason_code: dict[str, Any] | str | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
medicationyesdict[str, Any] or strSee signature.
medication_statement_idnostr or NoneNoneSee signature.
statusnostr'active'See signature.
effectivenostr or NoneNoneSee signature.
date_assertednostr or NoneNoneSee signature.
reason_codenodict[str, Any] or str or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_model_device

Build a FHIR Device resource for an AI/model system.

Import path: fyron.fhir.builder.build_model_device

python
build_model_device(*, model_name: str, model_version: str | None = None, device_id: str | None = None, manufacturer: str = 'Bits & Flames', endpoint: str | dict[str, Any] | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
model_nameyesstrSee signature.
model_versionnostr or NoneNoneSee signature.
device_idnostr or NoneNoneSee signature.
manufacturernostr'Bits & Flames'See signature.
endpointnostr or dict[str, Any] or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_observation

Build a FHIR Observation for extracted or measured values.

Import path: fyron.fhir.builder.build_observation

python
build_observation(*, subject: str | dict[str, Any], code: dict[str, Any] | str, value: Any | None = None, status: str = 'final', observation_id: str | None = None, effective: str | None = None, issued: str | None = None, category: dict[str, Any] | Sequence[dict[str, Any]] | None = None, unit: str | None = None, value_type: str = 'quantity', derived_from: Sequence[str | dict[str, Any]] | None = None, method: dict[str, Any] | str | None = None, body_site: dict[str, Any] | str | None = None, imaging_series_uid: str | None = None, components: Sequence[dict[str, Any]] | None = None, data_absent_reason: dict[str, Any] | str | None = None, performer: Sequence[str | dict[str, Any]] | None = None, encounter: str | dict[str, Any] | None = None, interpretation: dict[str, Any] | str | Sequence[dict[str, Any] | str] | None = None, note: str | Sequence[str] | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
codeyesdict[str, Any] or strSee signature.
valuenoAny or NoneNoneSee signature.
statusnostr'final'See signature.
observation_idnostr or NoneNoneSee signature.
effectivenostr or NoneNoneSee signature.
issuednostr or NoneNoneSee signature.
categorynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
unitnostr or NoneNoneSee signature.
value_typenostr'quantity'See signature.
derived_fromnoSequence[str or dict[str, Any]] or NoneNoneSee signature.
methodnodict[str, Any] or str or NoneNoneSee signature.
body_sitenodict[str, Any] or str or NoneNoneSee signature.
imaging_series_uidnostr or NoneNoneSee signature.
componentsnoSequence[dict[str, Any]] or NoneNoneSee signature.
data_absent_reasonnodict[str, Any] or str or NoneNoneSee signature.
performernoSequence[str or dict[str, Any]] or NoneNoneSee signature.
encounternostr or dict[str, Any] or NoneNoneSee signature.
interpretationnodict[str, Any] or str or Sequence[dict[str, Any] or str] or NoneNoneSee signature.
notenostr or Sequence[str] or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_observation_component

Build a FHIR Observation.component item.

Import path: fyron.fhir.builder.build_observation_component

python
build_observation_component(*, code: dict[str, Any] | str, value: Any | None = None, unit: str | None = None, value_type: str = 'quantity', data_absent_reason: dict[str, Any] | str | None = None, interpretation: dict[str, Any] | str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
codeyesdict[str, Any] or strSee signature.
valuenoAny or NoneNoneSee signature.
unitnostr or NoneNoneSee signature.
value_typenostr'quantity'See signature.
data_absent_reasonnodict[str, Any] or str or NoneNoneSee signature.
interpretationnodict[str, Any] or str or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_procedure

Build a minimal FHIR Procedure resource.

Import path: fyron.fhir.builder.build_procedure

python
build_procedure(*, subject: str | dict[str, Any], code: dict[str, Any] | str, procedure_id: str | None = None, status: str = 'completed', performed: str | None = None, encounter: str | dict[str, Any] | None = None, reason_code: dict[str, Any] | str | None = None, body_site: dict[str, Any] | str | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
codeyesdict[str, Any] or strSee signature.
procedure_idnostr or NoneNoneSee signature.
statusnostr'completed'See signature.
performednostr or NoneNoneSee signature.
encounternostr or dict[str, Any] or NoneNoneSee signature.
reason_codenodict[str, Any] or str or NoneNoneSee signature.
body_sitenodict[str, Any] or str or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_provenance

Build a FHIR Provenance resource linking generated outputs to evidence.

Import path: fyron.fhir.builder.build_provenance

python
build_provenance(*, targets: Sequence[str | dict[str, Any]], agent: str | dict[str, Any] | None = None, entity: Sequence[str | dict[str, Any]] | None = None, provenance_id: str | None = None, recorded: str | None = None, activity: dict[str, Any] | str | None = None, prompt_version: str | None = None, profile: str | Sequence[str] | None = None, meta_source: str | None = None, tag: dict[str, Any] | Sequence[dict[str, Any]] | None = None, security: dict[str, Any] | Sequence[dict[str, Any]] | None = None, extension: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
targetsyesSequence[str or dict[str, Any]]See signature.
agentnostr or dict[str, Any] or NoneNoneSee signature.
entitynoSequence[str or dict[str, Any]] or NoneNoneSee signature.
provenance_idnostr or NoneNoneSee signature.
recordednostr or NoneNoneSee signature.
activitynodict[str, Any] or str or NoneNoneSee signature.
prompt_versionnostr or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
meta_sourcenostr or NoneNoneSee signature.
tagnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
securitynodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
extensionnodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_service_request

Build a minimal FHIR ServiceRequest resource.

Import path: fyron.fhir.builder.build_service_request

python
build_service_request(*, subject: str | dict[str, Any], code: dict[str, Any] | str, service_request_id: str | None = None, status: str = 'active', intent: str = 'order', authored_on: str | None = None, requester: str | dict[str, Any] | None = None, reason_code: dict[str, Any] | str | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
codeyesdict[str, Any] or strSee signature.
service_request_idnostr or NoneNoneSee signature.
statusnostr'active'See signature.
intentnostr'order'See signature.
authored_onnostr or NoneNoneSee signature.
requesternostr or dict[str, Any] or NoneNoneSee signature.
reason_codenodict[str, Any] or str or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.build_specimen

Build a minimal FHIR Specimen resource.

Import path: fyron.fhir.builder.build_specimen

python
build_specimen(*, subject: str | dict[str, Any], specimen_type: dict[str, Any] | str | None = None, specimen_id: str | None = None, status: str = 'available', received_time: str | None = None, collection_time: str | None = None, profile: str | Sequence[str] | None = None, identifier: dict[str, Any] | Sequence[dict[str, Any]] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
subjectyesstr or dict[str, Any]See signature.
specimen_typenodict[str, Any] or str or NoneNoneSee signature.
specimen_idnostr or NoneNoneSee signature.
statusnostr'available'See signature.
received_timenostr or NoneNoneSee signature.
collection_timenostr or NoneNoneSee signature.
profilenostr or Sequence[str] or NoneNoneSee signature.
identifiernodict[str, Any] or Sequence[dict[str, Any]] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.codeable_concept

Build a FHIR CodeableConcept.

Import path: fyron.fhir.builder.codeable_concept

python
codeable_concept(code: str | None = None, *, system: str | None = None, display: str | None = None, text: str | None = None, codings: Sequence[dict[str, Any]] | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
codenostr or NoneNoneSee signature.
systemnostr or NoneNoneSee signature.
displaynostr or NoneNoneSee signature.
textnostr or NoneNoneSee signature.
codingsnoSequence[dict[str, Any]] or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.coding

Build a FHIR Coding.

Import path: fyron.fhir.builder.coding

python
coding(code: str, system: str | None = None, display: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
codeyesstrSee signature.
systemnostr or NoneNoneSee signature.
displaynostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.dicom_code

Build a DICOM ontology Coding.

Import path: fyron.fhir.builder.dicom_code

python
dicom_code(code: str, display: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
codeyesstrSee signature.
displaynostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.icd10

Build an ICD-10 Coding.

Import path: fyron.fhir.builder.icd10

python
icd10(code: str, display: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
codeyesstrSee signature.
displaynostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.identifier

Build a FHIR Identifier.

Import path: fyron.fhir.builder.identifier

python
identifier(value: str, system: str | None = None, use: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
valueyesstrSee signature.
systemnostr or NoneNoneSee signature.
usenostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.loinc

Build a LOINC Coding.

Import path: fyron.fhir.builder.loinc

python
loinc(code: str, display: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
codeyesstrSee signature.
displaynostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.quantity

Build a FHIR Quantity.

Import path: fyron.fhir.builder.quantity

python
quantity(value: int | float, unit: str | None = None, *, system: str = 'http://unitsofmeasure.org', code: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
valueyesint or floatSee signature.
unitnostr or NoneNoneSee signature.
systemnostr'http://unitsofmeasure.org'See signature.
codenostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.read_fhir_json

Read a FHIR JSON payload from disk.

Import path: fyron.fhir.builder.read_fhir_json

python
read_fhir_json(path: StrPath) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
pathyesStrPathSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.reference

Build a FHIR Reference.

Import path: fyron.fhir.builder.reference

python
reference(target: str | dict[str, Any], display: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
targetyesstr or dict[str, Any]See signature.
displaynostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.snomed

Build a SNOMED CT Coding.

Import path: fyron.fhir.builder.snomed

python
snomed(code: str, display: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
codeyesstrSee signature.
displaynostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.summarize_fhir_bundle

Return bundle counts, request methods, and local-reference status.

Import path: fyron.fhir.builder.summarize_fhir_bundle

python
summarize_fhir_bundle(bundle: dict[str, Any]) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesdict[str, Any]See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.summarize_fhir_resource

Return a compact, inspectable summary for one FHIR resource.

Import path: fyron.fhir.builder.summarize_fhir_resource

python
summarize_fhir_resource(resource: dict[str, Any]) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesdict[str, Any]See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.ucum_quantity

Build a UCUM Quantity.

Import path: fyron.fhir.builder.ucum_quantity

python
ucum_quantity(value: int | float, unit: str, code: str | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
valueyesint or floatSee signature.
unityesstrSee signature.
codenostr or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.validate_fhir_bundle

Lightweight structural validation for a FHIR Bundle.

Import path: fyron.fhir.builder.validate_fhir_bundle

python
validate_fhir_bundle(bundle: dict[str, Any], version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesdict[str, Any]See signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.validate_fhir_references

Inspect local references inside a FHIR Bundle without mutating it.

Import path: fyron.fhir.builder.validate_fhir_references

python
validate_fhir_references(bundle: dict[str, Any]) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesdict[str, Any]See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.validate_fhir_resource

Lightweight structural validation for a FHIR resource dictionary.

Import path: fyron.fhir.builder.validate_fhir_resource

python
validate_fhir_resource(resource: dict[str, Any], version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesdict[str, Any]See signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.builder.write_fhir_json

Write a FHIR JSON payload to disk.

Import path: fyron.fhir.builder.write_fhir_json

python
write_fhir_json(payload: dict[str, Any], path: StrPath) -> Path

Parameters

ParameterRequiredTypeDefaultDescription
payloadyesdict[str, Any]See signature.
pathyesStrPathSee signature.

Returns

Path

See also: FHIR module guide.

fyron.fhir.mapping.build_bundle_from_dataframe

Dispatch DataFrame-to-FHIR conversion by resource type.

Import path: fyron.fhir.mapping.build_bundle_from_dataframe

python
build_bundle_from_dataframe(df: pd.DataFrame, resource_type: str, mapping: dict[str, Any], *, subject_col: str, id_col: str | None = None, study_uid_col: str | None = None, series_uid_col: str | None = None, bundle_type: str = 'collection', transaction_method: str = 'POST', if_none_exist: str | dict[str, str] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameSee signature.
resource_typeyesstrSee signature.
mappingyesdict[str, Any]See signature.
subject_colyesstrSee signature.
id_colnostr or NoneNoneSee signature.
study_uid_colnostr or NoneNoneSee signature.
series_uid_colnostr or NoneNoneSee signature.
bundle_typenostr'collection'See signature.
transaction_methodnostr'POST'See signature.
if_none_existnostr or dict[str, str] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.build_conditions_from_dataframe

Build Condition resources and a Bundle from a DataFrame.

Import path: fyron.fhir.mapping.build_conditions_from_dataframe

python
build_conditions_from_dataframe(df: pd.DataFrame, mapping: dict[str, Any], *, subject_col: str, id_col: str | None = None, bundle_type: str = 'collection', transaction_method: str = 'POST', if_none_exist: str | dict[str, str] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameSee signature.
mappingyesdict[str, Any]See signature.
subject_colyesstrSee signature.
id_colnostr or NoneNoneSee signature.
bundle_typenostr'collection'See signature.
transaction_methodnostr'POST'See signature.
if_none_existnostr or dict[str, str] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.build_document_references_from_dataframe

Build DocumentReference resources and a Bundle from a DataFrame.

Import path: fyron.fhir.mapping.build_document_references_from_dataframe

python
build_document_references_from_dataframe(df: pd.DataFrame, mapping: dict[str, Any], *, subject_col: str, id_col: str | None = None, bundle_type: str = 'collection', transaction_method: str = 'POST', if_none_exist: str | dict[str, str] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameSee signature.
mappingyesdict[str, Any]See signature.
subject_colyesstrSee signature.
id_colnostr or NoneNoneSee signature.
bundle_typenostr'collection'See signature.
transaction_methodnostr'POST'See signature.
if_none_existnostr or dict[str, str] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.build_imaging_measurements_from_dataframe

Build imaging-measurement resources and a Bundle from a DataFrame.

Import path: fyron.fhir.mapping.build_imaging_measurements_from_dataframe

python
build_imaging_measurements_from_dataframe(df: pd.DataFrame, mapping: dict[str, Any], *, subject_col: str, study_uid_col: str, series_uid_col: str | None = None, id_col: str | None = None, bundle_type: str = 'collection', transaction_method: str = 'POST', if_none_exist: str | dict[str, str] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameSee signature.
mappingyesdict[str, Any]See signature.
subject_colyesstrSee signature.
study_uid_colyesstrSee signature.
series_uid_colnostr or NoneNoneSee signature.
id_colnostr or NoneNoneSee signature.
bundle_typenostr'collection'See signature.
transaction_methodnostr'POST'See signature.
if_none_existnostr or dict[str, str] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.build_observations_from_dataframe

Build Observation resources and a Bundle from a DataFrame.

Import path: fyron.fhir.mapping.build_observations_from_dataframe

python
build_observations_from_dataframe(df: pd.DataFrame, mapping: dict[str, Any], *, subject_col: str, id_col: str | None = None, bundle_type: str = 'collection', transaction_method: str = 'POST', if_none_exist: str | dict[str, str] | None = None, version: str = FHIR_R4) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameSee signature.
mappingyesdict[str, Any]See signature.
subject_colyesstrSee signature.
id_colnostr or NoneNoneSee signature.
bundle_typenostr'collection'See signature.
transaction_methodnostr'POST'See signature.
if_none_existnostr or dict[str, str] or NoneNoneSee signature.
versionnostrFHIR_R4See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.extract_coding_summary

Extract all Coding entries from a resource or Bundle into a DataFrame.

Import path: fyron.fhir.mapping.extract_coding_summary

python
extract_coding_summary(payload: dict[str, Any]) -> pd.DataFrame

Parameters

ParameterRequiredTypeDefaultDescription
payloadyesdict[str, Any]See signature.

Returns

pd.DataFrame

See also: FHIR module guide.

fyron.fhir.mapping.fhir_validation_report

Return a structured validation report for a FHIR Bundle.

Import path: fyron.fhir.mapping.fhir_validation_report

python
fhir_validation_report(bundle: dict[str, Any]) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesdict[str, Any]See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.read_fhir_mapping

Read a Fyron FHIR mapping JSON file.

Import path: fyron.fhir.mapping.read_fhir_mapping

python
read_fhir_mapping(path: StrPath) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
pathyesStrPathSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.validate_coding_systems

Check coding-system presence and optional allow-list consistency.

Import path: fyron.fhir.mapping.validate_coding_systems

python
validate_coding_systems(payload: dict[str, Any], allowed_systems: set[str] | list[str] | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
payloadyesdict[str, Any]See signature.
allowed_systemsnoset[str] or list[str] or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.validate_fhir_mapping

Validate a Fyron FHIR mapping dictionary and optional source DataFrame.

Import path: fyron.fhir.mapping.validate_fhir_mapping

python
validate_fhir_mapping(mapping: dict[str, Any], df: pd.DataFrame | None = None, required_columns: list[str | None] | None = None) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
mappingyesdict[str, Any]See signature.
dfnopd.DataFrame or NoneNoneSee signature.
required_columnsnolist[str or None] or NoneNoneSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.validate_fhir_mapping_result

Validate a mapping result object returned by this module.

Import path: fyron.fhir.mapping.validate_fhir_mapping_result

python
validate_fhir_mapping_result(result: dict[str, Any]) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resultyesdict[str, Any]See signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.validate_fhir_payload

Return a structured lightweight validation report for a resource or Bundle.

Import path: fyron.fhir.mapping.validate_fhir_payload

python
validate_fhir_payload(payload: dict[str, Any], *, version: str = FHIR_R4, strict: bool = False) -> dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
payloadyesdict[str, Any]See signature.
versionnostrFHIR_R4See signature.
strictnoboolFalseSee signature.

Returns

dict[str, Any]

See also: FHIR module guide.

fyron.fhir.mapping.write_fhir_mapping

Write a Fyron FHIR mapping JSON file.

Import path: fyron.fhir.mapping.write_fhir_mapping

python
write_fhir_mapping(mapping: dict[str, Any], path: StrPath) -> Path

Parameters

ParameterRequiredTypeDefaultDescription
mappingyesdict[str, Any]See signature.
pathyesStrPathSee signature.

Returns

Path

See also: FHIR module guide.

fyron.fhir.path_presets.get_fhir_path_preset

Return a copy of the default FHIRPath extraction preset for a resource.

Import path: fyron.fhir.path_presets.get_fhir_path_preset

python
get_fhir_path_preset(resource_type: str) -> list[tuple[str, str]]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type name, for example `"Patient", "Observation", "Condition", or "ImagingStudy"`.

Returns

list[tuple[str, str]] - A mutable list of `(column_name, fhir_path) pairs suitable for FHIRRestClient.search_df(..., fhir_paths=...)`.

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient

Simple FHIR REST client focused on bundle retrieval and DataFrame conversion.

Import path: fyron.fhir.rest.FHIRRestClient

python
FHIRRestClient(self, base_url: Optional[str] = None, auth_url: Optional[str] = None, auth: Optional[Union[Auth, requests.Session]] = None, num_processes: int = 4, request_timeout: int = 30, request_params: Optional[Dict[str, Any]] = None, bearer_token: Optional[str] = None, log_requests: bool = False, log_request_urls: bool = False, extra_headers: Optional[Dict[str, str]] = None, retries: Optional[Retry] = None, return_fhir_obj: bool = False, token_auth_method: Optional[str] = None, cache_ttl_seconds: int = 300, cache_max_entries: int = 1000)

Parameters

ParameterRequiredTypeDefaultDescription
base_urlnoOptional[str]NoneBase FHIR server URL (e.g., https://example.org/fhir).
auth_urlnoOptional[str]NoneToken endpoint for password-based auth. If omitted, uses FHIR_AUTH_URL env.
authnoOptional[Union[Auth, requests.Session]]NoneOptional Auth or requests.Session instance to use.
num_processesnoint4Process count for multiprocessing (>=1).
request_timeoutnoint30Per-request timeout in seconds.
request_paramsnoOptional[Dict[str, Any]]NoneDefault query params merged into every request.
bearer_tokennoOptional[str]NoneToken used for parallel requests (or set FHIR_TOKEN env).
log_requestsnoboolFalseIf True, logs request timing and summaries.
log_request_urlsnoboolFalseIf True, prints each request URL (with query string) to the console.
extra_headersnoOptional[Dict[str, str]]NoneSee signature.
retriesnoOptional[Retry]NoneSee signature.
return_fhir_objnoboolFalseSee signature.
token_auth_methodnoOptional[str]NoneToken auth method for password-based token endpoints ("basic" or "post").
cache_ttl_secondsnoint300In-memory cache TTL for GET responses.
cache_max_entriesnoint1000Maximum number of cached GET responses.

Returns

Class constructor.

See also: FHIR module guide.

Public Methods

fyron.fhir.rest.FHIRRestClient.close

Close the underlying session if owned.

Import path: fyron.fhir.rest.FHIRRestClient.close

python
FHIRRestClient.close(self) -> None

Parameters

No parameters documented.

Returns

None

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.fetch_bundles

Fetch bundles for a resource with pagination.

Import path: fyron.fhir.rest.FHIRRestClient.fetch_bundles

python
FHIRRestClient.fetch_bundles(self, resource_type: str, params: Optional[Dict[str, Any]] = None, max_pages: int = -1, show_progress: bool = True) -> Generator[Dict[str, Any], None, int]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type (e.g., Patient, Observation).
paramsnoOptional[Dict[str, Any]]NoneQuery parameters for the search.
max_pagesnoint-1Maximum number of pages to fetch (-1 for all).
show_progressnoboolTrueWhether to show a tqdm progress bar.

Returns

Generator[Dict[str, Any], None, int]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.fetch_bundles_parallel

Fetch bundles in parallel for multiple parameter sets.

Import path: fyron.fhir.rest.FHIRRestClient.fetch_bundles_parallel

python
FHIRRestClient.fetch_bundles_parallel(self, resource_type: str, param_list: Sequence[Dict[str, Any]], max_pages: int = -1, show_progress: bool = True) -> Generator[Dict[str, Any], None, int]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type.
param_listyesSequence[Dict[str, Any]]List of query param dicts; each runs as a separate job.
max_pagesnoint-1Maximum pages per job (-1 for all).
show_progressnoboolTrueWhether to show a tqdm progress bar.

Returns

Generator[Dict[str, Any], None, int]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.fetch_bundles_partitioned

Fetch bundles by splitting a broad search into date/time partitions.

Import path: fyron.fhir.rest.FHIRRestClient.fetch_bundles_partitioned

python
FHIRRestClient.fetch_bundles_partitioned(self, resource_type: str, partition_param: str, start: Union[str, pd.Timestamp], end: Union[str, pd.Timestamp], params: Optional[Dict[str, Any]] = None, frequency: str = 'YS', window_days: Optional[int] = None, max_pages_per_partition: int = -1, show_progress: bool = True, parallel_fetch: bool = False, auto_sort: bool = True, sort: str = '_id') -> Generator[Dict[str, Any], None, int]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type to search.
partition_paramyesstrDate or dateTime search parameter used for partition windows.
startyesUnion[str, pd.Timestamp]Inclusive start date for the first partition.
endyesUnion[str, pd.Timestamp]Exclusive end date for the final partition.
paramsnoOptional[Dict[str, Any]]NoneBase search parameters merged into every partition.
frequencynostr'YS'Pandas-style partition frequency, for example `YS or MS`.
window_daysnoOptional[int]NoneOptional fixed window size in days; overrides `frequency`.
max_pages_per_partitionnoint-1Maximum pages fetched inside each partition.
show_progressnoboolTrueWhether to show progress bars.
parallel_fetchnoboolFalseWhether to fetch partitions in parallel when supported.
auto_sortnoboolTrueWhether to add a stable `_sort` parameter when one is missing.
sortnostr'_id'Sort field used when `auto_sort` is enabled.

Returns

Generator[Dict[str, Any], None, int]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.bundles_to_dataframe

Convert bundles to DataFrame(s).

Import path: fyron.fhir.rest.FHIRRestClient.bundles_to_dataframe

python
FHIRRestClient.bundles_to_dataframe(self, bundles: Iterable[Dict[str, Any] | FHIRObj], process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, per_bundle_metadata: Optional[List[Dict[str, Any]]] = None) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
bundlesyesIterable[Dict[str, Any] or FHIRObj]Iterable of FHIR Bundle JSON objects.
process_functionnoOptional[ProcessFunc]NoneCustom processing function. Required when mode="custom".
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract fields (requires fhirpathpy).
modenostr'flatten'"flatten" (default) or "custom".
use_multiprocessingnoboolTrueWhether to process bundles with multiprocessing.
per_bundle_metadatanoOptional[List[Dict[str, Any]]]NoneOptional list of dicts, one per bundle; each dict is merged into every row from that bundle (e.g. to attach column_map values).

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.query_to_dataframe_partitioned

Run a partitioned FHIR search and return DataFrame output.

Import path: fyron.fhir.rest.FHIRRestClient.query_to_dataframe_partitioned

python
FHIRRestClient.query_to_dataframe_partitioned(self, resource_type: str, partition_param: str, start: Union[str, pd.Timestamp], end: Union[str, pd.Timestamp], params: Optional[Dict[str, Any]] = None, frequency: str = 'YS', window_days: Optional[int] = None, max_pages_per_partition: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_fetch: bool = False, include_partition_columns: bool = True, deduplicate_by: Optional[Union[str, Sequence[str]]] = None, auto_sort: bool = True, sort: str = '_id', show_progress: bool = True) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type to search.
partition_paramyesstrDate or dateTime search parameter used for partition windows.
startyesUnion[str, pd.Timestamp]Inclusive start date for the first partition.
endyesUnion[str, pd.Timestamp]Exclusive end date for the final partition.
paramsnoOptional[Dict[str, Any]]NoneBase search parameters merged into every partition.
frequencynostr'YS'Pandas-style partition frequency, for example `YS or MS`.
window_daysnoOptional[int]NoneOptional fixed window size in days; overrides `frequency`.
max_pages_per_partitionnoint-1Maximum pages fetched inside each partition.
process_functionnoOptional[ProcessFunc]NoneCustom bundle processing function used in `custom` mode.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract columns from each resource.
modenostr'flatten'DataFrame conversion mode, usually `flatten or custom`.
use_multiprocessingnoboolTrueWhether bundle-to-table conversion can use multiprocessing.
parallel_fetchnoboolFalseWhether partitions may be fetched in parallel.
include_partition_columnsnoboolTrueWhether partition metadata columns are added to result rows.
deduplicate_bynoOptional[Union[str, Sequence[str]]]NoneOptional column or columns used to drop duplicate rows.
auto_sortnoboolTrueWhether to add a stable `_sort` parameter when one is missing.
sortnostr'_id'Sort field used when `auto_sort` is enabled.
show_progressnoboolTrueWhether to show progress bars.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.query_to_dataframe

Run a query and return DataFrame(s).

Import path: fyron.fhir.rest.FHIRRestClient.query_to_dataframe

python
FHIRRestClient.query_to_dataframe(self, resource_type: str, params: Optional[Dict[str, Any]] = None, max_pages: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_params: Optional[Sequence[Dict[str, Any]]] = None) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type.
paramsnoOptional[Dict[str, Any]]NoneQuery parameters for a single request flow.
max_pagesnoint-1Maximum pages to fetch (-1 for all).
process_functionnoOptional[ProcessFunc]NoneCustom processing function.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract fields.
modenostr'flatten'"flatten" (default) or "custom".
use_multiprocessingnoboolTrueWhether to process bundles with multiprocessing.
parallel_paramsnoOptional[Sequence[Dict[str, Any]]]NoneIf provided, runs parallel jobs for each param dict.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.query_from_dataframe

Run one query per DataFrame row and return DataFrame(s).

Import path: fyron.fhir.rest.FHIRRestClient.query_from_dataframe

python
FHIRRestClient.query_from_dataframe(self, df: pd.DataFrame, resource_type: str, column_map: Dict[str, str], params: Optional[Dict[str, Any]] = None, max_pages: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_fetch: bool = False, param_prefix: Optional[Dict[str, str]] = None, include_column_map_columns: bool = False) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameInput DataFrame containing query values.
resource_typeyesstrFHIR resource type.
column_mapyesDict[str, str]Mapping of FHIR param -> DataFrame column. Column values can be scalars or list-like; lists are sent comma-separated for the same param (e.g. code=a,b).
paramsnoOptional[Dict[str, Any]]NoneBase query parameters added to each request. Values may be list-like; multiple values are sent comma-separated (e.g. code=a,b).
max_pagesnoint-1Maximum pages per row (-1 for all).
process_functionnoOptional[ProcessFunc]NoneCustom processing function.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract fields.
modenostr'flatten'"flatten" (default) or "custom".
use_multiprocessingnoboolTrueWhether to process bundles with multiprocessing.
parallel_fetchnoboolFalseWhether to fetch bundles in parallel (uses active Auth token or basic auth).
param_prefixnoOptional[Dict[str, str]]NoneOptional mapping of FHIR param -> prefix to prepend to each value (e.g., {"subject": "Patient/"}).
include_column_map_columnsnoboolFalseIf True, the DataFrame column values used as query params (from column_map) are added as columns to the result so each row can be traced back to the input row. Uses sequential fetch (ignores parallel_fetch) so order is preserved.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.query_df

Short alias for query_to_dataframe.

Import path: fyron.fhir.rest.FHIRRestClient.query_df

python
FHIRRestClient.query_df(self, resource_type: str, params: Optional[Dict[str, Any]] = None, max_pages: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_params: Optional[Sequence[Dict[str, Any]]] = None) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type.
paramsnoOptional[Dict[str, Any]]NoneSearch parameters for one request flow.
max_pagesnoint-1Maximum pages to fetch.
process_functionnoOptional[ProcessFunc]NoneCustom bundle processing function used in `custom` mode.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract columns from each resource.
modenostr'flatten'DataFrame conversion mode, usually `flatten or custom`.
use_multiprocessingnoboolTrueWhether bundle-to-table conversion can use multiprocessing.
parallel_paramsnoOptional[Sequence[Dict[str, Any]]]NoneOptional sequence of parameter dictionaries fetched in parallel.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.search_df

Friendly FHIR search alias returning DataFrame output.

Import path: fyron.fhir.rest.FHIRRestClient.search_df

python
FHIRRestClient.search_df(self, resource_type: str, params: Optional[Dict[str, Any]] = None, max_pages: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_params: Optional[Sequence[Dict[str, Any]]] = None) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type.
paramsnoOptional[Dict[str, Any]]NoneSearch parameters for one request flow.
max_pagesnoint-1Maximum pages to fetch.
process_functionnoOptional[ProcessFunc]NoneCustom bundle processing function used in `custom` mode.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract columns from each resource.
modenostr'flatten'DataFrame conversion mode, usually `flatten or custom`.
use_multiprocessingnoboolTrueWhether bundle-to-table conversion can use multiprocessing.
parallel_paramsnoOptional[Sequence[Dict[str, Any]]]NoneOptional sequence of parameter dictionaries fetched in parallel.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.query_df_partitioned

Short alias for query_to_dataframe_partitioned.

Import path: fyron.fhir.rest.FHIRRestClient.query_df_partitioned

python
FHIRRestClient.query_df_partitioned(self, resource_type: str, partition_param: str, start: Union[str, pd.Timestamp], end: Union[str, pd.Timestamp], params: Optional[Dict[str, Any]] = None, frequency: str = 'YS', window_days: Optional[int] = None, max_pages_per_partition: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_fetch: bool = False, include_partition_columns: bool = True, deduplicate_by: Optional[Union[str, Sequence[str]]] = None, auto_sort: bool = True, sort: str = '_id', show_progress: bool = True) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type to search.
partition_paramyesstrDate or dateTime search parameter used for partition windows.
startyesUnion[str, pd.Timestamp]Inclusive start date for the first partition.
endyesUnion[str, pd.Timestamp]Exclusive end date for the final partition.
paramsnoOptional[Dict[str, Any]]NoneBase search parameters merged into every partition.
frequencynostr'YS'Pandas-style partition frequency.
window_daysnoOptional[int]NoneOptional fixed window size in days.
max_pages_per_partitionnoint-1Maximum pages fetched inside each partition.
process_functionnoOptional[ProcessFunc]NoneCustom bundle processing function used in `custom` mode.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract columns from each resource.
modenostr'flatten'DataFrame conversion mode, usually `flatten or custom`.
use_multiprocessingnoboolTrueWhether bundle-to-table conversion can use multiprocessing.
parallel_fetchnoboolFalseWhether partitions may be fetched in parallel.
include_partition_columnsnoboolTrueWhether partition metadata columns are added to result rows.
deduplicate_bynoOptional[Union[str, Sequence[str]]]NoneOptional column or columns used to drop duplicate rows.
auto_sortnoboolTrueWhether to add a stable `_sort` parameter when one is missing.
sortnostr'_id'Sort field used when `auto_sort` is enabled.
show_progressnoboolTrueWhether to show progress bars.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.search_df_partitioned

Friendly alias for partitioned FHIR search returning DataFrames.

Import path: fyron.fhir.rest.FHIRRestClient.search_df_partitioned

python
FHIRRestClient.search_df_partitioned(self, resource_type: str, partition_param: str, start: Union[str, pd.Timestamp], end: Union[str, pd.Timestamp], params: Optional[Dict[str, Any]] = None, frequency: str = 'YS', window_days: Optional[int] = None, max_pages_per_partition: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_fetch: bool = False, include_partition_columns: bool = True, deduplicate_by: Optional[Union[str, Sequence[str]]] = None, auto_sort: bool = True, sort: str = '_id', show_progress: bool = True) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
resource_typeyesstrFHIR resource type to search.
partition_paramyesstrDate or dateTime search parameter used for partition windows.
startyesUnion[str, pd.Timestamp]Inclusive start date for the first partition.
endyesUnion[str, pd.Timestamp]Exclusive end date for the final partition.
paramsnoOptional[Dict[str, Any]]NoneBase search parameters merged into every partition.
frequencynostr'YS'Pandas-style partition frequency.
window_daysnoOptional[int]NoneOptional fixed window size in days.
max_pages_per_partitionnoint-1Maximum pages fetched inside each partition.
process_functionnoOptional[ProcessFunc]NoneCustom bundle processing function used in `custom` mode.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract columns from each resource.
modenostr'flatten'DataFrame conversion mode, usually `flatten or custom`.
use_multiprocessingnoboolTrueWhether bundle-to-table conversion can use multiprocessing.
parallel_fetchnoboolFalseWhether partitions may be fetched in parallel.
include_partition_columnsnoboolTrueWhether partition metadata columns are added to result rows.
deduplicate_bynoOptional[Union[str, Sequence[str]]]NoneOptional column or columns used to drop duplicate rows.
auto_sortnoboolTrueWhether to add a stable `_sort` parameter when one is missing.
sortnostr'_id'Sort field used when `auto_sort` is enabled.
show_progressnoboolTrueWhether to show progress bars.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.query_df_from

Short alias for query_from_dataframe.

Import path: fyron.fhir.rest.FHIRRestClient.query_df_from

python
FHIRRestClient.query_df_from(self, df: pd.DataFrame, resource_type: str, column_map: Dict[str, str], params: Optional[Dict[str, Any]] = None, max_pages: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_fetch: bool = False, param_prefix: Optional[Dict[str, str]] = None, include_column_map_columns: bool = False) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameInput DataFrame containing query values.
resource_typeyesstrFHIR resource type.
column_mapyesDict[str, str]Mapping from FHIR search parameter to DataFrame column.
paramsnoOptional[Dict[str, Any]]NoneBase query parameters added to every row-wise request.
max_pagesnoint-1Maximum pages per row.
process_functionnoOptional[ProcessFunc]NoneCustom bundle processing function used in `custom` mode.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract columns from each resource.
modenostr'flatten'DataFrame conversion mode, usually `flatten or custom`.
use_multiprocessingnoboolTrueWhether bundle-to-table conversion can use multiprocessing.
parallel_fetchnoboolFalseWhether row-wise requests may be fetched in parallel.
param_prefixnoOptional[Dict[str, str]]NoneOptional prefixes prepended to row values by FHIR parameter.
include_column_map_columnsnoboolFalseWhether input query values are copied into result rows.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.search_df_from

Friendly row-wise FHIR search alias returning DataFrame output.

Import path: fyron.fhir.rest.FHIRRestClient.search_df_from

python
FHIRRestClient.search_df_from(self, df: pd.DataFrame, resource_type: str, column_map: Dict[str, str], params: Optional[Dict[str, Any]] = None, max_pages: int = -1, process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True, parallel_fetch: bool = False, param_prefix: Optional[Dict[str, str]] = None, include_column_map_columns: bool = False) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameInput DataFrame containing query values.
resource_typeyesstrFHIR resource type.
column_mapyesDict[str, str]Mapping from FHIR search parameter to DataFrame column.
paramsnoOptional[Dict[str, Any]]NoneBase query parameters added to every row-wise request.
max_pagesnoint-1Maximum pages per row.
process_functionnoOptional[ProcessFunc]NoneCustom bundle processing function used in `custom` mode.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneFHIRPath expressions to extract columns from each resource.
modenostr'flatten'DataFrame conversion mode, usually `flatten or custom`.
use_multiprocessingnoboolTrueWhether bundle-to-table conversion can use multiprocessing.
parallel_fetchnoboolFalseWhether row-wise requests may be fetched in parallel.
param_prefixnoOptional[Dict[str, str]]NoneOptional prefixes prepended to row values by FHIR parameter.
include_column_map_columnsnoboolFalseWhether input query values are copied into result rows.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.bundles_to_df

Short alias for bundles_to_dataframe.

Import path: fyron.fhir.rest.FHIRRestClient.bundles_to_df

python
FHIRRestClient.bundles_to_df(self, bundles: Iterable[Dict[str, Any] | FHIRObj], process_function: Optional[ProcessFunc] = None, fhir_paths: Optional[Sequence[Union[str, Tuple[str, str]]]] = None, mode: str = 'flatten', use_multiprocessing: bool = True) -> Union[pd.DataFrame, Dict[str, pd.DataFrame]]

Parameters

ParameterRequiredTypeDefaultDescription
bundlesyesIterable[Dict[str, Any] or FHIRObj]See signature.
process_functionnoOptional[ProcessFunc]NoneSee signature.
fhir_pathsnoOptional[Sequence[Union[str, Tuple[str, str]]]]NoneSee signature.
modenostr'flatten'See signature.
use_multiprocessingnoboolTrueSee signature.

Returns

Union[pd.DataFrame, Dict[str, pd.DataFrame]]

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.create_resource

POST a FHIR resource to `/{resourceType}`.

Import path: fyron.fhir.rest.FHIRRestClient.create_resource

python
FHIRRestClient.create_resource(self, resource: Dict[str, Any], resource_type: Optional[str] = None) -> FHIRWriteResult

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesDict[str, Any]See signature.
resource_typenoOptional[str]NoneSee signature.

Returns

FHIRWriteResult

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.update_resource

PUT a FHIR resource to `/{resourceType}/{id}`.

Import path: fyron.fhir.rest.FHIRRestClient.update_resource

python
FHIRRestClient.update_resource(self, resource: Dict[str, Any], resource_id: Optional[str] = None, resource_type: Optional[str] = None) -> FHIRWriteResult

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesDict[str, Any]See signature.
resource_idnoOptional[str]NoneSee signature.
resource_typenoOptional[str]NoneSee signature.

Returns

FHIRWriteResult

See also: FHIR module guide.

fyron.fhir.rest.FHIRRestClient.submit_bundle

POST a transaction FHIR bundle to the server base URL.

Import path: fyron.fhir.rest.FHIRRestClient.submit_bundle

python
FHIRRestClient.submit_bundle(self, bundle: Dict[str, Any]) -> FHIRWriteResult

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesDict[str, Any]See signature.

Returns

FHIRWriteResult

See also: FHIR module guide.

fyron.fhir.rest.FHIRWriteResult

Summary of a FHIR write request.

Import path: fyron.fhir.rest.FHIRWriteResult

python
FHIRWriteResult()

Parameters

No parameters documented.

Returns

Class constructor.

See also: FHIR module guide.

fyron.fhir.rest.QueryJob

See the signature and linked module guide for context.

Import path: fyron.fhir.rest.QueryJob

python
QueryJob()

Parameters

No parameters documented.

Returns

Class constructor.

See also: FHIR module guide.

fyron.fhir.rest.RepeatedParam

Represent repeated FHIR search parameters with the same key.

Import path: fyron.fhir.rest.RepeatedParam

python
RepeatedParam()

Parameters

No parameters documented.

Returns

Class constructor.

See also: FHIR module guide.

fyron.fhir.rest.ResponseCache

Small in-memory TTL cache for GET responses.

Import path: fyron.fhir.rest.ResponseCache

python
ResponseCache(self, ttl_seconds: int = 300, max_entries: int = 1000)

Parameters

ParameterRequiredTypeDefaultDescription
ttl_secondsnoint300See signature.
max_entriesnoint1000See signature.

Returns

Class constructor.

See also: FHIR module guide.

Public Methods

fyron.fhir.rest.ResponseCache.get

See the signature and linked module guide for context.

Import path: fyron.fhir.rest.ResponseCache.get

python
ResponseCache.get(self, key: Tuple[Any, ...], now: float) -> Optional[Tuple[Dict[str, Any], str, int, float]]

Parameters

ParameterRequiredTypeDefaultDescription
keyyesTuple[Any, ...]See signature.
nowyesfloatSee signature.

Returns

Optional[Tuple[Dict[str, Any], str, int, float]]

See also: FHIR module guide.

fyron.fhir.rest.ResponseCache.set

See the signature and linked module guide for context.

Import path: fyron.fhir.rest.ResponseCache.set

python
ResponseCache.set(self, key: Tuple[Any, ...], payload: Tuple[Dict[str, Any], str, int, float], now: float) -> None

Parameters

ParameterRequiredTypeDefaultDescription
keyyesTuple[Any, ...]See signature.
payloadyesTuple[Dict[str, Any], str, int, float]See signature.
nowyesfloatSee signature.

Returns

None

See also: FHIR module guide.

fyron.fhir.rest.build_partition_params

Build FHIR search parameter sets split by a date/dateTime range.

Import path: fyron.fhir.rest.build_partition_params

python
build_partition_params(params: Optional[Dict[str, Any]], partition_param: str, start: Union[str, pd.Timestamp], end: Union[str, pd.Timestamp], *, frequency: str = 'YS', window_days: Optional[int] = None) -> List[Dict[str, Any]]

Parameters

ParameterRequiredTypeDefaultDescription
paramsyesOptional[Dict[str, Any]]See signature.
partition_paramyesstrSee signature.
startyesUnion[str, pd.Timestamp]See signature.
endyesUnion[str, pd.Timestamp]See signature.
frequencynostr'YS'See signature.
window_daysnoOptional[int]NoneSee signature.

Returns

List[Dict[str, Any]]

See also: FHIR module guide.

fyron.fhir.rest.flatten_data

Flatten bundle entries into row dictionaries by resourceType.

Import path: fyron.fhir.rest.flatten_data

python
flatten_data(bundle: Dict[str, Any] | FHIRObj, col_sep: str = '_') -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesDict[str, Any] or FHIRObjSee signature.
col_sepnostr'_'See signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.rest.parse_fhir_path

Extract fields from bundle entries using compiled FHIRPath expressions.

Import path: fyron.fhir.rest.parse_fhir_path

python
parse_fhir_path(bundle: Dict[str, Any] | FHIRObj, compiled_fhir_paths: List[Tuple[str, Any]]) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesDict[str, Any] or FHIRObjSee signature.
compiled_fhir_pathsyesList[Tuple[str, Any]]See signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient

Lightweight SQL client for FHIR-backed databases.

Import path: fyron.fhir.sql.FHIRSQLClient

python
FHIRSQLClient(self, dsn: Optional[str] = None, host: Optional[str] = None, port: Optional[int] = None, dbname: Optional[str] = None, user: Optional[str] = None, password: Optional[str] = None, sslmode: Optional[str] = None, connect_timeout: int = 10, log_queries: bool = False)

Parameters

ParameterRequiredTypeDefaultDescription
dsnnoOptional[str]NoneSee signature.
hostnoOptional[str]NoneSee signature.
portnoOptional[int]NoneSee signature.
dbnamenoOptional[str]NoneSee signature.
usernoOptional[str]NoneSee signature.
passwordnoOptional[str]NoneSee signature.
sslmodenoOptional[str]NoneSee signature.
connect_timeoutnoint10See signature.
log_queriesnoboolFalseSee signature.

Returns

Class constructor.

See also: FHIR module guide.

Public Methods

fyron.fhir.sql.FHIRSQLClient.close

Close the database connection.

Import path: fyron.fhir.sql.FHIRSQLClient.close

python
FHIRSQLClient.close(self) -> None

Parameters

No parameters documented.

Returns

None

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient.query

Execute a SQL query and return rows as dicts.

Import path: fyron.fhir.sql.FHIRSQLClient.query

python
FHIRSQLClient.query(self, sql: str, params: Optional[Dict[str, Any] | Sequence[Any]] = None) -> List[Dict[str, Any]]

Parameters

ParameterRequiredTypeDefaultDescription
sqlyesstrSee signature.
paramsnoOptional[Dict[str, Any] or Sequence[Any]]NoneSee signature.

Returns

List[Dict[str, Any]]

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient.query_to_dataframe

Execute a SQL query and return a DataFrame.

Import path: fyron.fhir.sql.FHIRSQLClient.query_to_dataframe

python
FHIRSQLClient.query_to_dataframe(self, sql: str, params: Optional[Dict[str, Any] | Sequence[Any]] = None, rename: Optional[Dict[str, str]] = None) -> pd.DataFrame

Parameters

ParameterRequiredTypeDefaultDescription
sqlyesstrSQL statement with placeholders.
paramsnoOptional[Dict[str, Any] or Sequence[Any]]NoneOptional parameters (dict for named, sequence for positional).
renamenoOptional[Dict[str, str]]NoneOptional mapping to rename columns in the resulting DataFrame.

Returns

pd.DataFrame

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient.query_df

Backward-compatible alias for query_to_dataframe.

Import path: fyron.fhir.sql.FHIRSQLClient.query_df

python
FHIRSQLClient.query_df(self, sql: str, params: Optional[Dict[str, Any] | Sequence[Any]] = None, rename: Optional[Dict[str, str]] = None) -> pd.DataFrame

Parameters

ParameterRequiredTypeDefaultDescription
sqlyesstrSee signature.
paramsnoOptional[Dict[str, Any] or Sequence[Any]]NoneSee signature.
renamenoOptional[Dict[str, str]]NoneSee signature.

Returns

pd.DataFrame

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient.query_df_stream

Stream a large SQL query as DataFrame chunks.

Import path: fyron.fhir.sql.FHIRSQLClient.query_df_stream

python
FHIRSQLClient.query_df_stream(self, sql: str, params: Optional[Dict[str, Any] | Sequence[Any]] = None, rename: Optional[Dict[str, str]] = None, chunksize: int = 10000) -> Iterator[pd.DataFrame]

Parameters

ParameterRequiredTypeDefaultDescription
sqlyesstrSee signature.
paramsnoOptional[Dict[str, Any] or Sequence[Any]]NoneSee signature.
renamenoOptional[Dict[str, str]]NoneSee signature.
chunksizenoint10000See signature.

Returns

Iterator[pd.DataFrame]

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient.query_df_parallel

Run multiple SQL queries in parallel and merge results.

Import path: fyron.fhir.sql.FHIRSQLClient.query_df_parallel

python
FHIRSQLClient.query_df_parallel(self, jobs: Sequence[Tuple[str, Optional[Dict[str, Any] | Sequence[Any]]]], rename: Optional[Dict[str, str]] = None, max_workers: Optional[int] = None, merge: str = 'concat', unique_on: Optional[Sequence[str]] = None) -> pd.DataFrame

Parameters

ParameterRequiredTypeDefaultDescription
jobsyesSequence[Tuple[str, Optional[Dict[str, Any] or Sequence[Any]]]]List of (sql, params) pairs.
renamenoOptional[Dict[str, str]]NoneOptional mapping to rename output columns.
max_workersnoOptional[int]NoneNumber of worker processes (defaults to CPU count).
mergenostr'concat'See signature.
unique_onnoOptional[Sequence[str]]NoneSee signature.

Returns

pd.DataFrame

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient.query_from_dataframe

Run a query with parameters sourced from a DataFrame.

Import path: fyron.fhir.sql.FHIRSQLClient.query_from_dataframe

python
FHIRSQLClient.query_from_dataframe(self, df: pd.DataFrame, sql: str, column_map: Dict[str, str], rename: Optional[Dict[str, str]] = None, param_limit: int = 50000, chunk_size: Optional[int] = None, parallel: bool = False, max_workers: Optional[int] = None, merge: str = 'concat', unique_on: Optional[Sequence[str]] = None, param_style: str = 'positional', param_safety_factor: float = 0.9) -> pd.DataFrame

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameInput DataFrame containing values.
sqlyesstrSQL statement with {name} placeholder blocks.
column_mapyesDict[str, str]Mapping from placeholder name -> DataFrame column name.
renamenoOptional[Dict[str, str]]NoneOptional mapping to rename output columns.
param_limitnoint50000Max number of parameters per query (Postgres limit is 65535).
chunk_sizenoOptional[int]NoneOptional explicit chunk size for splitting the DataFrame.
parallelnoboolFalseWhether to execute chunks in parallel and merge results.
max_workersnoOptional[int]NoneNumber of worker processes when parallel is True.
mergenostr'concat'How to merge results: "concat" or "drop_duplicates".
unique_onnoOptional[Sequence[str]]NoneColumns to use for duplicate dropping when merge="drop_duplicates".
param_stylenostr'positional'"positional" (default) or "named".
param_safety_factornofloat0.9Fraction of param_limit used for chunk sizing (0.0-1.0).

Returns

pd.DataFrame

See also: FHIR module guide.

fyron.fhir.sql.FHIRSQLClient.query_df_from

Short alias for query_from_dataframe.

Import path: fyron.fhir.sql.FHIRSQLClient.query_df_from

python
FHIRSQLClient.query_df_from(self, df: pd.DataFrame, sql: str, column_map: Dict[str, str], rename: Optional[Dict[str, str]] = None, param_limit: int = 50000, chunk_size: Optional[int] = None, parallel: bool = False, max_workers: Optional[int] = None, merge: str = 'concat', unique_on: Optional[Sequence[str]] = None, param_style: str = 'positional', param_safety_factor: float = 0.9) -> pd.DataFrame

Parameters

ParameterRequiredTypeDefaultDescription
dfyespd.DataFrameSee signature.
sqlyesstrSee signature.
column_mapyesDict[str, str]See signature.
renamenoOptional[Dict[str, str]]NoneSee signature.
param_limitnoint50000See signature.
chunk_sizenoOptional[int]NoneSee signature.
parallelnoboolFalseSee signature.
max_workersnoOptional[int]NoneSee signature.
mergenostr'concat'See signature.
unique_onnoOptional[Sequence[str]]NoneSee signature.
param_stylenostr'positional'See signature.
param_safety_factornofloat0.9See signature.

Returns

pd.DataFrame

See also: FHIR module guide.

fyron.fhir.sql.SQLConfig

See the signature and linked module guide for context.

Import path: fyron.fhir.sql.SQLConfig

python
SQLConfig()

Parameters

No parameters documented.

Returns

Class constructor.

See also: FHIR module guide.

fyron.fhir.types.FHIRObj

Recursively wraps dicts/lists for attribute-style access.

Import path: fyron.fhir.types.FHIRObj

python
FHIRObj(self, **kwargs: Any)

Parameters

ParameterRequiredTypeDefaultDescription
kwargsyesAnySee signature.

Returns

Class constructor.

See also: FHIR module guide.

Public Methods

fyron.fhir.types.FHIRObj.to_json

Serialize the object to JSON.

Import path: fyron.fhir.types.FHIRObj.to_json

python
FHIRObj.to_json(self) -> str

Parameters

No parameters documented.

Returns

str

See also: FHIR module guide.

fyron.fhir.types.FHIRObj.to_dict

Convert the object to a plain dict.

Import path: fyron.fhir.types.FHIRObj.to_dict

python
FHIRObj.to_dict(self) -> Any

Parameters

No parameters documented.

Returns

Any

See also: FHIR module guide.

fyron.fhir.utils.extract_condition

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.extract_condition

python
extract_condition(resource: Any) -> Dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.

Returns

Dict[str, Any]

See also: FHIR module guide.

fyron.fhir.utils.extract_diagnostic_report

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.extract_diagnostic_report

python
extract_diagnostic_report(resource: Any) -> Dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.

Returns

Dict[str, Any]

See also: FHIR module guide.

fyron.fhir.utils.extract_encounter

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.extract_encounter

python
extract_encounter(resource: Any) -> Dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.

Returns

Dict[str, Any]

See also: FHIR module guide.

fyron.fhir.utils.extract_imaging_study

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.extract_imaging_study

python
extract_imaging_study(resource: Any, series: Any = None) -> Dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.
seriesnoAnyNoneSee signature.

Returns

Dict[str, Any]

See also: FHIR module guide.

fyron.fhir.utils.extract_observation

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.extract_observation

python
extract_observation(resource: Any) -> Dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.

Returns

Dict[str, Any]

See also: FHIR module guide.

fyron.fhir.utils.extract_patient

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.extract_patient

python
extract_patient(resource: Any) -> Dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.

Returns

Dict[str, Any]

See also: FHIR module guide.

fyron.fhir.utils.extract_procedure

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.extract_procedure

python
extract_procedure(resource: Any) -> Dict[str, Any]

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.

Returns

Dict[str, Any]

See also: FHIR module guide.

fyron.fhir.utils.process_condition_bundle

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.process_condition_bundle

python
process_condition_bundle(bundle: Any) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesAnySee signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.utils.process_diagnostic_report_bundle

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.process_diagnostic_report_bundle

python
process_diagnostic_report_bundle(bundle: Any) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesAnySee signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.utils.process_encounter_bundle

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.process_encounter_bundle

python
process_encounter_bundle(bundle: Any) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesAnySee signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.utils.process_imaging_study_bundle

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.process_imaging_study_bundle

python
process_imaging_study_bundle(bundle: Any) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesAnySee signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.utils.process_observation_bundle

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.process_observation_bundle

python
process_observation_bundle(bundle: Any) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesAnySee signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.utils.process_patient_bundle

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.process_patient_bundle

python
process_patient_bundle(bundle: Any) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesAnySee signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.utils.process_procedure_bundle

See the signature and linked module guide for context.

Import path: fyron.fhir.utils.process_procedure_bundle

python
process_procedure_bundle(bundle: Any) -> Dict[str, List[Dict[str, Any]]]

Parameters

ParameterRequiredTypeDefaultDescription
bundleyesAnySee signature.

Returns

Dict[str, List[Dict[str, Any]]]

See also: FHIR module guide.

fyron.fhir.utils.safe_get

Safely extract a value from nested FHIR JSON or FHIRObj by path.

Import path: fyron.fhir.utils.safe_get

python
safe_get(resource: Any, path: str | List[Any] | tuple[Any, ...], default: Any = None) -> Any

Parameters

ParameterRequiredTypeDefaultDescription
resourceyesAnySee signature.
pathyesstr or List[Any] or tuple[Any, ...]See signature.
defaultnoAnyNoneSee signature.

Returns

Any

See also: FHIR module guide.