Index

_

__CONFIG (fhirpack.config.Config attribute) __configLogger() (fhirpack.config.Config method) __dict__ (fhirpack.auth.Auth attribute) (fhirpack.base.BaseMixin attribute) (fhirpack.config.Config attribute) (fhirpack.custom.base.PluginBaseMixin attribute) (fhirpack.custom.extraction.base.PluginBaseExtractorMixin attribute) (fhirpack.custom.load.base.PluginBaseLoaderMixin attribute) (fhirpack.custom.load.sample.PluginSampleLoaderMixin attribute) (fhirpack.custom.transformation.base.PluginBaseTransformerMixin attribute) (fhirpack.custom.transformation.sample.PluginSampleTransformerMixin attribute) (fhirpack.exceptions.InvalidConfigurationException attribute) (fhirpack.exceptions.InvalidOperationException attribute) (fhirpack.extraction.base.BaseExtractorMixin attribute) (fhirpack.extraction.sample.BaseExtractorMixin attribute) (fhirpack.load.base.BaseLoaderMixin attribute) (fhirpack.transformation.base.BaseTransformerMixin attribute) __doc__ (fhirpack.auth.Auth attribute) (fhirpack.base.BaseMixin attribute) (fhirpack.base.Frame attribute) (fhirpack.config.Config attribute) (fhirpack.constants.SampleEnum attribute) (fhirpack.custom.base.PluginBaseMixin attribute) (fhirpack.custom.extraction.base.PluginBaseExtractorMixin attribute) (fhirpack.custom.extraction.PluginExtractorMixin attribute) (fhirpack.custom.extraction.sample.PluginSampleExtractorMixin attribute) (fhirpack.custom.load.base.PluginBaseLoaderMixin attribute) (fhirpack.custom.load.PluginLoaderMixin attribute) (fhirpack.custom.load.sample.PluginSampleLoaderMixin attribute) (fhirpack.custom.PluginMixin attribute) (fhirpack.custom.transformation.base.PluginBaseTransformerMixin attribute) (fhirpack.custom.transformation.PluginTransformerMixin attribute) (fhirpack.custom.transformation.sample.PluginSampleTransformerMixin attribute) (fhirpack.exceptions.BaseError attribute) (fhirpack.exceptions.ErrorSeverity attribute) (fhirpack.exceptions.InvalidConfigurationException attribute) (fhirpack.exceptions.InvalidInputDataException attribute) (fhirpack.exceptions.InvalidOperationException attribute) (fhirpack.exceptions.InvalidSearchParams attribute) (fhirpack.exceptions.SampleError attribute) (fhirpack.exceptions.ServerConnectionException attribute) (fhirpack.extraction.base.BaseExtractorMixin attribute) (fhirpack.extraction.condition.ExtractorConditionMixin attribute) (fhirpack.extraction.diagnosticreport.ExtractorDiagnosticReportMixin attribute) (fhirpack.extraction.endpoint.ExtractorEndpointMixin attribute) (fhirpack.extraction.episodeofcare.ExtractorEpisodeOfCareMixin attribute) (fhirpack.extraction.ExtractorMixin attribute) (fhirpack.extraction.familymemberhistory.ExtractorFamilyMemberHistoryMixin attribute) (fhirpack.extraction.imagingstudy.ExtractorImagingStudyMixin attribute) (fhirpack.extraction.list.ExtractorListMixin attribute) (fhirpack.extraction.medicationadministration.ExtractorMedicationAdministrationMixin attribute) (fhirpack.extraction.medicationrequest.ExtractorMedicationRequestMixin attribute) (fhirpack.extraction.observation.ExtractorObservationMixin attribute) (fhirpack.extraction.patient.ExtractorPatientMixin attribute) (fhirpack.extraction.sample.BaseExtractorMixin attribute) (fhirpack.load.base.BaseLoaderMixin attribute) (fhirpack.load.condition.LoaderConditionMixin attribute) (fhirpack.load.LoaderMixin attribute) (fhirpack.load.observation.LoaderObservationMixin attribute) (fhirpack.load.patient.LoaderPatientMixin attribute) (fhirpack.pack.PACK attribute) (fhirpack.transformation.base.BaseTransformerMixin attribute) (fhirpack.transformation.condition.TransformerConditionMixin attribute) (fhirpack.transformation.observation.TransformerObservationMixin attribute) (fhirpack.transformation.patient.TransformerPatientMixin attribute) (fhirpack.transformation.TransformerMixin attribute) __DOTENVPATH (fhirpack.config.Config attribute) __gatherSimplePath() (fhirpack.transformation.base.BaseTransformerMixin method) __init__() (fhirpack.base.Frame method) (fhirpack.config.Config method) (fhirpack.pack.PACK method) __module__ (fhirpack.auth.Auth attribute) (fhirpack.base.BaseMixin attribute) (fhirpack.base.Frame attribute) (fhirpack.config.Config attribute) (fhirpack.constants.SampleEnum attribute) (fhirpack.custom.base.PluginBaseMixin attribute) (fhirpack.custom.extraction.base.PluginBaseExtractorMixin attribute) (fhirpack.custom.extraction.PluginExtractorMixin attribute) (fhirpack.custom.extraction.sample.PluginSampleExtractorMixin attribute) (fhirpack.custom.load.base.PluginBaseLoaderMixin attribute) (fhirpack.custom.load.PluginLoaderMixin attribute) (fhirpack.custom.load.sample.PluginSampleLoaderMixin attribute) (fhirpack.custom.PluginMixin attribute) (fhirpack.custom.transformation.base.PluginBaseTransformerMixin attribute) (fhirpack.custom.transformation.PluginTransformerMixin attribute) (fhirpack.custom.transformation.sample.PluginSampleTransformerMixin attribute) (fhirpack.exceptions.BaseError attribute) (fhirpack.exceptions.ErrorSeverity attribute) (fhirpack.exceptions.InvalidConfigurationException attribute) (fhirpack.exceptions.InvalidInputDataException attribute) (fhirpack.exceptions.InvalidOperationException attribute) (fhirpack.exceptions.InvalidSearchParams attribute) (fhirpack.exceptions.SampleError attribute) (fhirpack.exceptions.ServerConnectionException attribute) (fhirpack.extraction.base.BaseExtractorMixin attribute) (fhirpack.extraction.condition.ExtractorConditionMixin attribute) (fhirpack.extraction.diagnosticreport.ExtractorDiagnosticReportMixin attribute) (fhirpack.extraction.endpoint.ExtractorEndpointMixin attribute) (fhirpack.extraction.episodeofcare.ExtractorEpisodeOfCareMixin attribute) (fhirpack.extraction.ExtractorMixin attribute) (fhirpack.extraction.familymemberhistory.ExtractorFamilyMemberHistoryMixin attribute) (fhirpack.extraction.imagingstudy.ExtractorImagingStudyMixin attribute) (fhirpack.extraction.list.ExtractorListMixin attribute) (fhirpack.extraction.medicationadministration.ExtractorMedicationAdministrationMixin attribute) (fhirpack.extraction.medicationrequest.ExtractorMedicationRequestMixin attribute) (fhirpack.extraction.observation.ExtractorObservationMixin attribute) (fhirpack.extraction.patient.ExtractorPatientMixin attribute) (fhirpack.extraction.sample.BaseExtractorMixin attribute) (fhirpack.load.base.BaseLoaderMixin attribute) (fhirpack.load.condition.LoaderConditionMixin attribute) (fhirpack.load.LoaderMixin attribute) (fhirpack.load.observation.LoaderObservationMixin attribute) (fhirpack.load.patient.LoaderPatientMixin attribute) (fhirpack.pack.PACK attribute) (fhirpack.transformation.base.BaseTransformerMixin attribute) (fhirpack.transformation.condition.TransformerConditionMixin attribute) (fhirpack.transformation.observation.TransformerObservationMixin attribute) (fhirpack.transformation.patient.TransformerPatientMixin attribute) (fhirpack.transformation.TransformerMixin attribute)

__setupClient() (fhirpack.pack.PACK method) __weakref__ (fhirpack.auth.Auth attribute) (fhirpack.base.BaseMixin attribute) (fhirpack.config.Config attribute) (fhirpack.custom.base.PluginBaseMixin attribute) (fhirpack.custom.extraction.base.PluginBaseExtractorMixin attribute) (fhirpack.custom.load.base.PluginBaseLoaderMixin attribute) (fhirpack.custom.load.sample.PluginSampleLoaderMixin attribute) (fhirpack.custom.transformation.base.PluginBaseTransformerMixin attribute) (fhirpack.custom.transformation.sample.PluginSampleTransformerMixin attribute) (fhirpack.exceptions.BaseError attribute) (fhirpack.exceptions.InvalidConfigurationException attribute) (fhirpack.exceptions.InvalidInputDataException attribute) (fhirpack.exceptions.InvalidOperationException attribute) (fhirpack.exceptions.InvalidSearchParams attribute) (fhirpack.exceptions.ServerConnectionException attribute) (fhirpack.extraction.base.BaseExtractorMixin attribute) (fhirpack.extraction.sample.BaseExtractorMixin attribute) (fhirpack.load.base.BaseLoaderMixin attribute) (fhirpack.transformation.base.BaseTransformerMixin attribute) _constructor (fhirpack.base.Frame property) _constructor_expanddim (fhirpack.base.Frame property) _metadata (fhirpack.base.Frame attribute) _mgr (fhirpack.base.Frame attribute)

A

Auth (class in fhirpack.auth)

B

BaseError BaseExtractorMixin (class in fhirpack.extraction.base) (class in fhirpack.extraction.sample)

BaseLoaderMixin (class in fhirpack.load.base) BaseMixin (class in fhirpack.base) BaseTransformerMixin (class in fhirpack.transformation.base)

C

cast() (fhirpack.base.Frame method) castOperand() (fhirpack.base.BaseMixin method)

clientFromEnv() (in module fhirpack.utils) Config (class in fhirpack.config) countServerResources() (fhirpack.pack.PACK method)

D

data (fhirpack.config.Config property)

E

envFile() (in module fhirpack.config_test) error (fhirpack.exceptions.ErrorSeverity attribute) ErrorSeverity (class in fhirpack.exceptions) explode() (fhirpack.base.Frame method) ExtractorConditionMixin (class in fhirpack.extraction.condition) ExtractorDiagnosticReportMixin (class in fhirpack.extraction.diagnosticreport) ExtractorEndpointMixin (class in fhirpack.extraction.endpoint) ExtractorEpisodeOfCareMixin (class in fhirpack.extraction.episodeofcare)

ExtractorFamilyMemberHistoryMixin (class in fhirpack.extraction.familymemberhistory) ExtractorImagingStudyMixin (class in fhirpack.extraction.imagingstudy) ExtractorListMixin (class in fhirpack.extraction.list) ExtractorMedicationAdministrationMixin (class in fhirpack.extraction.medicationadministration) ExtractorMedicationRequestMixin (class in fhirpack.extraction.medicationrequest) ExtractorMixin (class in fhirpack.extraction) ExtractorObservationMixin (class in fhirpack.extraction.observation) ExtractorPatientMixin (class in fhirpack.extraction.patient)

F

fatal (fhirpack.exceptions.ErrorSeverity attribute) fhirpack module fhirpack.auth module fhirpack.base module fhirpack.base_test module fhirpack.cli module fhirpack.cli_test module fhirpack.config module fhirpack.config_test module fhirpack.conftest module fhirpack.constants module fhirpack.custom module fhirpack.custom.base module fhirpack.custom.extraction module fhirpack.custom.extraction.base module fhirpack.custom.extraction.sample module fhirpack.custom.load module fhirpack.custom.load.base module fhirpack.custom.load.sample module fhirpack.custom.transformation module fhirpack.custom.transformation.base module fhirpack.custom.transformation.sample module fhirpack.custom.utils module fhirpack.exceptions module fhirpack.extraction module fhirpack.extraction.base module fhirpack.extraction.base_test module fhirpack.extraction.condition module

fhirpack.extraction.condition_test module fhirpack.extraction.diagnosticreport module fhirpack.extraction.endpoint module fhirpack.extraction.episodeofcare module fhirpack.extraction.familymemberhistory module fhirpack.extraction.imagingstudy module fhirpack.extraction.list module fhirpack.extraction.medicationadministration module fhirpack.extraction.medicationrequest module fhirpack.extraction.observation module fhirpack.extraction.patient module fhirpack.extraction.patient_test module fhirpack.extraction.sample module fhirpack.load module fhirpack.load.base module fhirpack.load.condition module fhirpack.load.observation module fhirpack.load.patient module fhirpack.pack module fhirpack.transformation module fhirpack.transformation.base module fhirpack.transformation.base_test module fhirpack.transformation.condition module fhirpack.transformation.observation module fhirpack.transformation.patient module fhirpack.utils module fhirpack.utils_test module flattenList() (in module fhirpack.utils) Frame (class in fhirpack.base)

G

gatherDates() (fhirpack.transformation.base.BaseTransformerMixin method) gatherKeys() (fhirpack.transformation.base.BaseTransformerMixin method) gatherReferences() (fhirpack.transformation.base.BaseTransformerMixin method) gatherSimplePaths() (fhirpack.transformation.base.BaseTransformerMixin method) gatherText() (fhirpack.transformation.base.BaseTransformerMixin method) gatherValuesForKeys() (fhirpack.transformation.base.BaseTransformerMixin method) get() (fhirpack.config.Config method) getAbsolutePaths() (fhirpack.extraction.base.BaseExtractorMixin method) getConditions() (fhirpack.extraction.condition.ExtractorConditionMixin method) getDiagnosticReports() (fhirpack.extraction.diagnosticreport.ExtractorDiagnosticReportMixin method) getDICOMInstances() (fhirpack.extraction.base.BaseExtractorMixin method) getEndpoints() (fhirpack.extraction.endpoint.ExtractorEndpointMixin method) getEpisodesOfCare() (fhirpack.extraction.episodeofcare.ExtractorEpisodeOfCareMixin method) getFamilyMemberHistories() (fhirpack.extraction.familymemberhistory.ExtractorFamilyMemberHistoryMixin method) getFromFiles() (fhirpack.extraction.base.BaseExtractorMixin method) getImagingStudies() (fhirpack.extraction.imagingstudy.ExtractorImagingStudyMixin method) getInstallationPath() (in module fhirpack.utils)

getLinkedPatients() (fhirpack.extraction.patient.ExtractorPatientMixin method) getLists() (fhirpack.extraction.list.ExtractorListMixin method) getLogger() (fhirpack.config.Config method) getMedicationAdministrations() (fhirpack.extraction.medicationadministration.ExtractorMedicationAdministrationMixin method) getMedicationRequests() (fhirpack.extraction.medicationrequest.ExtractorMedicationRequestMixin method) getObservations() (fhirpack.extraction.observation.ExtractorObservationMixin method) getPatients() (fhirpack.extraction.patient.ExtractorPatientMixin method) getReferences() (fhirpack.extraction.base.BaseExtractorMixin method) getResources() (fhirpack.extraction.base.BaseExtractorMixin method) getResourceType (fhirpack.base.Frame property) getRootPatients() (fhirpack.extraction.patient.ExtractorPatientMixin method) getSampleExtractionMethod() (fhirpack.extraction.sample.BaseExtractorMixin method) getToken() (fhirpack.auth.Auth static method) getURLBytes() (fhirpack.extraction.base.BaseExtractorMixin method) globalExceptionHandler() (fhirpack.config.Config method) guessBufferMIMEType() (in module fhirpack.utils) guessOutputResourceType() (fhirpack.base.BaseMixin method)

I

info() (in module fhirpack.cli) information (fhirpack.exceptions.ErrorSeverity attribute) InvalidConfigurationException (class in fhirpack.exceptions)

InvalidInputDataException InvalidOperationException (class in fhirpack.exceptions) InvalidSearchParams isFrame (fhirpack.base.BaseMixin property)

K

keys (fhirpack.base.Frame property)

keys() (in module fhirpack.utils)

L

loadConfig() (fhirpack.config.Config method) LoaderConditionMixin (class in fhirpack.load.condition) LoaderMixin (class in fhirpack.load)

LoaderObservationMixin (class in fhirpack.load.observation) LoaderPatientMixin (class in fhirpack.load.patient) loadToDestination() (in module fhirpack.cli)

M

module fhirpack fhirpack.auth fhirpack.base fhirpack.base_test fhirpack.cli fhirpack.cli_test fhirpack.config fhirpack.config_test fhirpack.conftest fhirpack.constants fhirpack.custom fhirpack.custom.base fhirpack.custom.extraction fhirpack.custom.extraction.base fhirpack.custom.extraction.sample fhirpack.custom.load fhirpack.custom.load.base fhirpack.custom.load.sample fhirpack.custom.transformation fhirpack.custom.transformation.base fhirpack.custom.transformation.sample fhirpack.custom.utils fhirpack.exceptions fhirpack.extraction fhirpack.extraction.base fhirpack.extraction.base_test fhirpack.extraction.condition fhirpack.extraction.condition_test fhirpack.extraction.diagnosticreport fhirpack.extraction.endpoint fhirpack.extraction.episodeofcare fhirpack.extraction.familymemberhistory fhirpack.extraction.imagingstudy fhirpack.extraction.list fhirpack.extraction.medicationadministration fhirpack.extraction.medicationrequest fhirpack.extraction.observation fhirpack.extraction.patient fhirpack.extraction.patient_test fhirpack.extraction.sample fhirpack.load fhirpack.load.base fhirpack.load.condition fhirpack.load.observation fhirpack.load.patient fhirpack.pack fhirpack.transformation fhirpack.transformation.base fhirpack.transformation.base_test fhirpack.transformation.condition fhirpack.transformation.observation fhirpack.transformation.patient fhirpack.utils fhirpack.utils_test

O

oAuthTokenFromJWT() (fhirpack.auth.Auth static method)

observationFrame() (in module fhirpack.conftest) observationResourceList() (in module fhirpack.conftest)

P

PACK (class in fhirpack.pack) packageSessionFixture() (in module fhirpack.conftest) parseReference() (fhirpack.base.BaseMixin method) parseSHIPTokenEndpointResponse() (fhirpack.auth.Auth static method) patientAsDict() (in module fhirpack.conftest) patientFrame() (in module fhirpack.conftest) patientReference() (in module fhirpack.conftest) patientReferenceList() (in module fhirpack.conftest) patientResource() (in module fhirpack.conftest) patientResourceList() (in module fhirpack.conftest) PluginBaseExtractorMixin (class in fhirpack.custom.extraction.base) PluginBaseLoaderMixin (class in fhirpack.custom.load.base) PluginBaseMixin (class in fhirpack.custom.base) PluginBaseTransformerMixin (class in fhirpack.custom.transformation.base)

PluginExtractorMixin (class in fhirpack.custom.extraction) PluginLoaderMixin (class in fhirpack.custom.load) PluginMixin (class in fhirpack.custom) PluginSampleExtractorMixin (class in fhirpack.custom.extraction.sample) PluginSampleLoaderMixin (class in fhirpack.custom.load.sample) PluginSampleTransformerMixin (class in fhirpack.custom.transformation.sample) PluginTransformerMixin (class in fhirpack.custom.transformation) prepareCompositeOutput() (fhirpack.base.BaseMixin method) prepareInput() (fhirpack.base.BaseMixin method) prepareOperationInput() (fhirpack.base.BaseMixin method) prepareOutput() (fhirpack.base.BaseMixin method) prepareReferences() (fhirpack.base.BaseMixin method) pretty (fhirpack.base.Frame property) processParams() (in module fhirpack.cli)

R

referencesToIds() (fhirpack.base.BaseMixin method) referencesToResources() (fhirpack.base.BaseMixin method)

resourceTypeIs() (fhirpack.base.Frame method) run() (in module fhirpack.cli)

S

sample (fhirpack.constants.SampleEnum attribute) SampleEnum (class in fhirpack.constants) SampleError searchResources() (fhirpack.extraction.base.BaseExtractorMixin method) sendBytesToFile() (fhirpack.load.base.BaseLoaderMixin method) sendDICOMToFiles() (fhirpack.load.base.BaseLoaderMixin method)

sendResourcesToFiles() (fhirpack.load.base.BaseLoaderMixin method) sendToTable() (fhirpack.load.base.BaseLoaderMixin method) ServerConnectionException set() (fhirpack.config.Config method) setResourceType() (fhirpack.base.Frame method) setupLogging() (in module fhirpack.cli)

T

textToAscii() (in module fhirpack.utils) tokenViaPasswordGrant() (fhirpack.auth.Auth static method) transformerConditionMethod() (fhirpack.load.condition.LoaderConditionMixin method) (fhirpack.transformation.condition.TransformerConditionMixin method) TransformerConditionMixin (class in fhirpack.transformation.condition) TransformerMixin (class in fhirpack.transformation)

transformerObservationMethod() (fhirpack.load.observation.LoaderObservationMixin method) (fhirpack.transformation.observation.TransformerObservationMixin method) TransformerObservationMixin (class in fhirpack.transformation.observation) transformerPatientMethod() (fhirpack.load.patient.LoaderPatientMixin method) (fhirpack.transformation.patient.TransformerPatientMixin method) TransformerPatientMixin (class in fhirpack.transformation.patient)

U

unimplementedPluginBaseExtractorMethod() (fhirpack.custom.extraction.base.PluginBaseExtractorMixin method) unimplementedPluginBaseLoaderMethod() (fhirpack.custom.load.base.PluginBaseLoaderMixin method) unimplementedPluginBaseMethod() (fhirpack.custom.base.PluginBaseMixin method) unimplementedPluginBaseTransformerMethod() (fhirpack.custom.transformation.base.PluginBaseTransformerMixin method)

unimplementedPluginSampleExtractorMethod() (fhirpack.custom.extraction.sample.PluginSampleExtractorMixin method) unimplementedPluginSampleLoaderMethod() (fhirpack.custom.load.sample.PluginSampleLoaderMixin method) unimplementedPluginSampleTransformerMethod() (fhirpack.custom.transformation.sample.PluginSampleTransformerMixin method) unimplementedPluginUtilsMethod() (in module fhirpack.custom.utils)

V

validate() (fhirpack.transformation.base.BaseTransformerMixin method)

validateFrame() (in module fhirpack.utils) valuesForKeys() (in module fhirpack.utils)

W

warning (fhirpack.exceptions.ErrorSeverity attribute)

Y

y() (in module fhirpack.extraction.base_test)