fhirpack.extraction package#

Submodules#

fhirpack.extraction.base module#

class fhirpack.extraction.base.BaseExtractorMixin[source]#

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: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, searchParams: Optional[dict] = None, params: Optional[dict] = None)[source]#
getConversionPath(sourceType: str, targetType: str)[source]#

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

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

Creates a Frame object from json files containing fhir resources

getReferences(input: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, params: Optional[dict] = None, ignoreFrame: bool = False, raw: bool = False)[source]#
getResources(input: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, searchParams: Optional[dict] = None, params: Optional[dict] = None, resourceType: Optional[str] = None, metaResourceType: Optional[str] = None, ignoreFrame: bool = False, raw: bool = False, progressSuffix: str = '')[source]#
getURLBytes(input: Optional[list[str]] = None, operateOnCol: str = 'data', resultInCol: Optional[str] = None, params: dict = {})[source]#
searchResources(input: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, searchParams: Optional[dict] = None, params: Optional[dict] = None, resourceType: Optional[str] = None, metaResourceType: Optional[str] = None, ignoreFrame: bool = True, raw: bool = False, progressSuffix: str = '')[source]#

fhirpack.extraction.base_test module#

fhirpack.extraction.base_test.y(request)[source]#

fhirpack.extraction.condition module#

class fhirpack.extraction.condition.ExtractorConditionMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.condition'#
getConditions(*args, **kwargs)[source]#

fhirpack.extraction.condition_test module#

fhirpack.extraction.diagnosticreport module#

class fhirpack.extraction.diagnosticreport.ExtractorDiagnosticReportMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.diagnosticreport'#
getDiagnosticReports(*args, **kwargs)[source]#

fhirpack.extraction.documentreference module#

class fhirpack.extraction.documentreference.ExtractorDocumentReferenceMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.documentreference'#
getDocumentReferences(*args, **kwargs)[source]#

fhirpack.extraction.encounter module#

class fhirpack.extraction.encounter.ExtractorEncounterMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.encounter'#
getEncounters(*args, **kwargs)[source]#

fhirpack.extraction.endpoint module#

class fhirpack.extraction.endpoint.ExtractorEndpointMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.endpoint'#
getEndpoints(*args, **kwargs)[source]#

fhirpack.extraction.episodeofcare module#

class fhirpack.extraction.episodeofcare.ExtractorEpisodeOfCareMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.episodeofcare'#
getEpisodesOfCare(*args, **kwargs)[source]#

fhirpack.extraction.familymemberhistory module#

class fhirpack.extraction.familymemberhistory.ExtractorFamilyMemberHistoryMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.familymemberhistory'#
getFamilyMemberHistories(*args, **kwargs)[source]#

fhirpack.extraction.imagingstudy module#

class fhirpack.extraction.imagingstudy.ExtractorImagingStudyMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.imagingstudy'#
getImagingStudies(*args, **kwargs)[source]#

fhirpack.extraction.list module#

class fhirpack.extraction.list.ExtractorListMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.list'#
getLists(input: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, searchParams: Optional[dict] = None, params: Optional[dict] = None, ignoreFrame: bool = False)[source]#

fhirpack.extraction.medicationadministration module#

class fhirpack.extraction.medicationadministration.ExtractorMedicationAdministrationMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.medicationadministration'#
getMedicationAdministrations(*args, **kwargs)[source]#

fhirpack.extraction.medicationrequest module#

class fhirpack.extraction.medicationrequest.ExtractorMedicationRequestMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.medicationrequest'#
getMedicationRequests(*args, **kwargs)[source]#

fhirpack.extraction.observation module#

class fhirpack.extraction.observation.ExtractorObservationMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.observation'#
getObservations(*args, **kwargs)[source]#

fhirpack.extraction.patient module#

class fhirpack.extraction.patient.ExtractorPatientMixin[source]#

Bases: fhirpack.extraction.base.BaseExtractorMixin

__doc__ = None#
__module__ = 'fhirpack.extraction.patient'#
getLinkedPatients(input: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, searchParams: Optional[dict] = None, params: Optional[dict] = None, ignoreFrame: bool = False, raw: bool = False)[source]#
getPatients(input: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, searchParams: Optional[dict] = None, params: Optional[dict] = None, ignoreFrame: bool = False, *args, **kwargs)[source]#
getRootPatients(input: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, searchParams: Optional[dict] = None, params: Optional[dict] = None, ignoreFrame: bool = False, raw: bool = False)[source]#

fhirpack.extraction.patient_test module#

fhirpack.extraction.sample module#

class fhirpack.extraction.sample.BaseExtractorMixin[source]#

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: Optional[Union[list[str], list[fhirpy.lib.SyncFHIRReference], list[fhirpy.lib.SyncFHIRResource]]] = None, params: Optional[dict] = None, ignoreFrame: bool = False)[source]#

Module contents#

class fhirpack.extraction.ExtractorMixin[source]#

Bases: fhirpack.extraction.observation.ExtractorObservationMixin, fhirpack.extraction.patient.ExtractorPatientMixin, fhirpack.extraction.condition.ExtractorConditionMixin, fhirpack.extraction.diagnosticreport.ExtractorDiagnosticReportMixin, fhirpack.extraction.documentreference.ExtractorDocumentReferenceMixin, fhirpack.extraction.encounter.ExtractorEncounterMixin, fhirpack.extraction.episodeofcare.ExtractorEpisodeOfCareMixin, fhirpack.extraction.familymemberhistory.ExtractorFamilyMemberHistoryMixin, fhirpack.extraction.medicationrequest.ExtractorMedicationRequestMixin, fhirpack.extraction.medicationadministration.ExtractorMedicationAdministrationMixin, fhirpack.extraction.list.ExtractorListMixin, fhirpack.extraction.imagingstudy.ExtractorImagingStudyMixin, fhirpack.extraction.endpoint.ExtractorEndpointMixin

__doc__ = None#
__module__ = 'fhirpack.extraction'#