fhirpack.extraction package

Submodules

fhirpack.extraction.base module

class fhirpack.extraction.base.BaseExtractorMixin

Bases: object

__dict__ = mappingproxy({'__module__': 'fhirpack.extraction.base', 'getReferences': <function BaseExtractorMixin.getReferences>, 'getResources': <function BaseExtractorMixin.getResources>, 'searchResources': <function BaseExtractorMixin.searchResources>, 'getConversionPath': <function BaseExtractorMixin.getConversionPath>, 'getAbsolutePaths': <function BaseExtractorMixin.getAbsolutePaths>, 'getURLBytes': <function BaseExtractorMixin.getURLBytes>, 'getFromFiles': <function BaseExtractorMixin.getFromFiles>, 'getDICOMInstances': <function BaseExtractorMixin.getDICOMInstances>, '__dict__': <attribute '__dict__' of 'BaseExtractorMixin' objects>, '__weakref__': <attribute '__weakref__' of 'BaseExtractorMixin' objects>, '__doc__': None, '__annotations__': {}})

__doc__ = None

__module__ = 'fhirpack.extraction.base'

__weakref__

list of weak references to the object (if defined)

getAbsolutePaths(paths: list[str], input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, searchParams: dict | None = None, params: dict | None = None)

getConversionPath(sourceType: str, targetType: str)

This method retrieves the needed fhir serach param (field) and the respective path for a source-target pair from the handler ditcionary

getDICOMInstances(input: list[str] | None = None, operateOnCol: str = 'data', resultInCol: str | None = None, params: dict | None = None, inPlace: dict = False)

getFromFiles(input: list[str])

Creates a Frame object from json files containing fhir resources

getReferences(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, params: dict | None = None, ignoreFrame: bool = False, raw: bool = False)

getResources(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, searchParams: dict | None = None, params: dict | None = None, resourceType: str | None = None, metaResourceType: str | None = None, ignoreFrame: bool = False, raw: bool = False)

getURLBytes(input: list[str] | None = None, operateOnCol: str = 'data', resultInCol: str | None = None, params: dict = {})

searchResources(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, searchParams: dict | None = None, params: dict | None = None, resourceType: str | None = None, metaResourceType: str | None = None, ignoreFrame: bool = True, raw: bool = False)

fhirpack.extraction.base_test module

fhirpack.extraction.base_test.y(request)

fhirpack.extraction.condition module

class fhirpack.extraction.condition.ExtractorConditionMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.condition'

getConditions(*args, **kwargs)

fhirpack.extraction.condition_test module

fhirpack.extraction.diagnosticreport module

class fhirpack.extraction.diagnosticreport.ExtractorDiagnosticReportMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.diagnosticreport'

getDiagnosticReports(*args, **kwargs)

fhirpack.extraction.documentreference module

class fhirpack.extraction.documentreference.ExtractorDocumentReferenceMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.documentreference'

getDocumentReference(*args, **kwargs)

fhirpack.extraction.encounter module

class fhirpack.extraction.encounter.ExtractorEncounterMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.encounter'

getEncounters(*args, **kwargs)

fhirpack.extraction.endpoint module

class fhirpack.extraction.endpoint.ExtractorEndpointMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.endpoint'

getEndpoints(*args, **kwargs)

fhirpack.extraction.episodeofcare module

class fhirpack.extraction.episodeofcare.ExtractorEpisodeOfCareMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.episodeofcare'

getEpisodesOfCare(*args, **kwargs)

fhirpack.extraction.familymemberhistory module

class fhirpack.extraction.familymemberhistory.ExtractorFamilyMemberHistoryMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.familymemberhistory'

getFamilyMemberHistories(*args, **kwargs)

fhirpack.extraction.imagingstudy module

class fhirpack.extraction.imagingstudy.ExtractorImagingStudyMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.imagingstudy'

getImagingStudies(*args, **kwargs)

fhirpack.extraction.list module

class fhirpack.extraction.list.ExtractorListMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.list'

getLists(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, searchParams: dict | None = None, params: dict | None = None, ignoreFrame: bool = False)

fhirpack.extraction.medicationadministration module

class fhirpack.extraction.medicationadministration.ExtractorMedicationAdministrationMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.medicationadministration'

getMedicationAdministrations(*args, **kwargs)

fhirpack.extraction.medicationrequest module

class fhirpack.extraction.medicationrequest.ExtractorMedicationRequestMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.medicationrequest'

getMedicationRequests(*args, **kwargs)

fhirpack.extraction.observation module

class fhirpack.extraction.observation.ExtractorObservationMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.observation'

getObservations(*args, **kwargs)

fhirpack.extraction.patient module

class fhirpack.extraction.patient.ExtractorPatientMixin

Bases: BaseExtractorMixin

__doc__ = None

__module__ = 'fhirpack.extraction.patient'

getLinkedPatients(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, searchParams: dict | None = None, params: dict | None = None, ignoreFrame: bool = False, raw: bool = False)

getPatients(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, searchParams: dict | None = None, params: dict | None = None, ignoreFrame: bool = False, *args, **kwargs)

getRootPatients(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, searchParams: dict | None = None, params: dict | None = None, ignoreFrame: bool = False, raw: bool = False)

fhirpack.extraction.patient_test module

fhirpack.extraction.sample module

class fhirpack.extraction.sample.BaseExtractorMixin

Bases: object

__dict__ = mappingproxy({'__module__': 'fhirpack.extraction.sample', 'getSampleExtractionMethod': <function BaseExtractorMixin.getSampleExtractionMethod>, '__dict__': <attribute '__dict__' of 'BaseExtractorMixin' objects>, '__weakref__': <attribute '__weakref__' of 'BaseExtractorMixin' objects>, '__doc__': None, '__annotations__': {}})

__doc__ = None

__module__ = 'fhirpack.extraction.sample'

__weakref__

list of weak references to the object (if defined)

getSampleExtractionMethod(input: list[str] | list[fhirpy.lib.SyncFHIRReference] | list[fhirpy.lib.SyncFHIRResource] | None = None, params: dict | None = None, ignoreFrame: bool = False)

Module contents

class fhirpack.extraction.ExtractorMixin

Bases: ExtractorObservationMixin, ExtractorPatientMixin, ExtractorConditionMixin, ExtractorDiagnosticReportMixin, ExtractorDocumentReferenceMixin, ExtractorEncounterMixin, ExtractorEpisodeOfCareMixin, ExtractorFamilyMemberHistoryMixin, ExtractorMedicationRequestMixin, ExtractorMedicationAdministrationMixin, ExtractorListMixin, ExtractorImagingStudyMixin, ExtractorEndpointMixin

__doc__ = None

__module__ = 'fhirpack.extraction'