indivo.rdf.transforms package

Submodules

indivo.rdf.transforms.base module

class indivo.rdf.transforms.base.BaseRDFTransform

Bases: indivo.document_processing.transform.BaseTransform

Base class for SMART RDF transforms.

_format_mappings(mappings, from_field, to_field)

Convenience method for formatting mappings with {from_filed} and {to_field} replacement fields in the key/value pairs

Parameters:

• mappings – dictionary to format
• from_field – substitution value for {from_field}
• to_field – substitution value for {to_field}

Returns:

dictionary of formatted parameters

map_address_field(params, from_field, to_field)

Convenience method for mapping an ~indivo.fields.AddressField

Parameters:

• params – dictionary of params to ty mapping
• from_field – value for {from_field} replacement
• to_field – value for {to_field} replacement

Returns:

dictionary of mapped params

map_code_field(params, from_field, to_field)

Convenience method for mapping a CodeField

Parameters:

• params – dictionary of params to ty mapping
• from_field – value for {from_field} replacement
• to_field – value for {to_field} replacement

Returns:

dictionary of mapped params

map_coded_value_field(params, from_field, to_field)

Convenience method for mapping a ~indivo.fields.CodedValueField

Parameters:

• params – dictionary of params to ty mapping
• from_field – value for {from_field} replacement
• to_field – value for {to_field} replacement

Returns:

dictionary of mapped params

map_name_field(params, from_field, to_field)

Convenience method for mapping a ~indivo.fields.NameField

Parameters:

• params – dictionary of params to ty mapping
• from_field – value for {from_field} replacement
• to_field – value for {to_field} replacement

Returns:

dictionary of mapped params

map_pharmacy_field(params, from_field, to_field)

Convenience method for mapping a ~indivo.fields.PharmacyField

Parameters:

• params – dictionary of params to ty mapping
• from_field – value for {from_field} replacement
• to_field – value for {to_field} replacement

Returns:

dictionary of mapped params

map_provider_field(params, from_field, to_field)

Convenience method for mapping a ~indivo.fields.ProviderField

Parameters:

• params – dictionary of params to ty mapping
• from_field – value for {from_field} replacement
• to_field – value for {to_field} replacement

Returns:

dictionary of mapped params

map_simple_fields(params, mappings)

Map matching params to new keys

Parameters:

• params – dictionary of params to try mapping
• mappings – dictionary of key:new_key mappings

Returns:

dictionary of mapped params

map_value_and_unit_field(params, from_field, to_field)

Convenience method for mapping a ~indivo.fields.ValueAndUnitField

Parameters:

• params – dictionary of params to ty mapping
• from_field – value for {from_field} replacement
• to_field – value for {to_field} replacement

Returns:

dictionary of mapped params

smart_class_dictionary = {'Participant': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5277510>, 'SNOMED': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x43c9b10>, 'ValueAndUnit': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5191490>, 'Coded Value': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5180d50>, 'MedicalRecordNumber': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52eb390>, 'Pref': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5277890>, 'Person': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a7550>, 'Pharmacy': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5267310>, 'Cell': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51bbfd0>, 'Literal': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5180fd0>, 'Call': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52eb350>, 'Social History': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52eb910>, 'AllergyExclusion': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5244e90>, 'Ontology': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d050>, 'ContainerManifest': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52f1090>, 'ParameterSet': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52eb1d0>, 'Parameter': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52f1110>, 'Problem': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5277a50>, 'Lab Panel': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x524e210>, 'ImmunizationProduct': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525fd10>, 'QuantitativeResult': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x524e750>, 'User Preferences': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d0d0>, 'Attribution': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52ebb50>, 'Address': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a7c90>, 'SMART Statement': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x519cd10>, 'Demographics': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x526fc90>, 'TranslationFidelity': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5191090>, 'VCardLabels': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x4833a90>, 'VCard': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a76d0>, 'SmokingStatus': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x526fa10>, 'anyURI': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5180ed0>, 'MediaTypeOrExtent': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525f4d0>, 'AllergySeverity': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523de50>, 'LabResultInterpretation': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x524ed50>, 'Home': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x483ea10>, 'BloodPressure': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5191c10>, 'ProcedureStatus': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5277910>, 'Vital Sign Set': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x4838e10>, 'Clinical Note': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525f210>, 'Encounter': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a70d0>, 'Panel': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5244b10>, 'ImmunizationClass': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525fc10>, 'EncounterType': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a7250>, 'UNII': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d510>, 'LOINC': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5180b50>, 'Name': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a77d0>, 'Provider': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a7450>, 'Component': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x43c9d50>, 'BloodPressureBodySite': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x519c610>, 'User': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52eb4d0>, 'RxNorm_Semantic': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5244a10>, 'Allergy Exclusion': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5244d50>, 'Immunization': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x526f150>, 'Code': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x43c9b90>, 'ProblemStatus': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525fb10>, 'RxNorm_Ingredient': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5244190>, 'CodeProvenance': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5180e10>, 'Organization': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51b4b50>, 'Medical Record': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x519ce10>, 'AllergyCategory': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d910>, 'VitalSign': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x4838a90>, 'BloodPressureMethod': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x519c150>, 'Procedure': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52f1210>, 'SMARTAPI': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x4833bd0>, 'Medication': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525fe50>, 'Tel': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51a7b10>, 'Work': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52eb490>, 'ImmunizationRefusalReason': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x51bb990>, 'DataType': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x43c9cd0>, 'ImmunizationAdministrationStatus': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d1d0>, 'Allergy': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d610>, 'RxNorm': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d410>, 'ValueRatio': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5259d50>, 'NarrativeResult': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x524efd0>, 'dateTime': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x519cc90>, 'ValueRange': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x524e850>, 'NDFRT': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x523d790>, 'App Manifest': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x52ebfd0>, 'Fulfillment': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525ff90>, 'Lab Result': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x524e490>, 'Filter': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525f150>, 'BloodPressureBodyPosition': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5191d50>, 'DocumentWithFormat': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x525f390>, 'LabResultStatus': <smart_common.rdf_tools.rdf_ontology.SMART_Class object at 0x5259250>}

smart_class_to_params(graph, subject, klass, base='')

Extract out a property:value dictionary representing a specific instance of a SMART_Class in the Graph

Parameters:

• graph – RDF Graph to search
• subject – RDF subject to extract
• klass – SMART_Class to extract the subject as
• base – prefix string for keys

Returns:

property:value dictionary representing the subject

smart_classes_to_params(graph, klass)

Extract out a list of property:value dictionaries for all instances of a SMART_Class in the Graph

Parameters:

• graph – RDF Graph to search
• klass – SMART_Class to search for

Returns:

list of property:value dictionaries for all instances of type klass found

indivo.rdf.transforms.fulfillment module

class indivo.rdf.transforms.fulfillment.FulfillmentForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.util.ErrorList'>, label_suffix=':', empty_permitted=False, instance=None)

Bases: django.forms.models.ModelForm

class Meta

model

alias of Fill

FulfillmentForm._meta = <django.forms.models.ModelFormOptions object at 0x52f8550>

FulfillmentForm.base_fields = {'id': <django.forms.fields.CharField object at 0x52f85d0>, 'document': <django.forms.models.ModelChoiceField object at 0x52f8850>, 'record': <django.forms.models.ModelChoiceField object at 0x52f8a10>, 'date': <django.forms.fields.DateTimeField object at 0x52f8990>, 'dispenseDaysSupply': <django.forms.fields.FloatField object at 0x52f8a90>, 'pbm': <django.forms.fields.CharField object at 0x52f8b10>, 'medication': <django.forms.models.ModelChoiceField object at 0x52f8d90>, 'pharmacy_org': <django.forms.fields.CharField object at 0x52f8d10>, 'pharmacy_adr_postalcode': <django.forms.fields.CharField object at 0x52f8e50>, 'pharmacy_adr_country': <django.forms.fields.CharField object at 0x52f8f10>, 'pharmacy_adr_region': <django.forms.fields.CharField object at 0x52f8fd0>, 'pharmacy_adr_street': <django.forms.fields.CharField object at 0x52fd0d0>, 'pharmacy_adr_city': <django.forms.fields.CharField object at 0x52fd190>, 'pharmacy_ncpdpid': <django.forms.fields.CharField object at 0x52fd250>, 'provider_bday': <django.forms.fields.DateField object at 0x52fd310>, 'provider_dea_number': <django.forms.fields.CharField object at 0x52fd390>, 'provider_ethnicity': <django.forms.fields.CharField object at 0x52fd450>, 'provider_npi_number': <django.forms.fields.CharField object at 0x52fd510>, 'provider_adr_postalcode': <django.forms.fields.CharField object at 0x52fd5d0>, 'provider_adr_country': <django.forms.fields.CharField object at 0x52fd690>, 'provider_adr_region': <django.forms.fields.CharField object at 0x52fd750>, 'provider_adr_street': <django.forms.fields.CharField object at 0x52fd810>, 'provider_adr_city': <django.forms.fields.CharField object at 0x52fd8d0>, 'provider_name_middle': <django.forms.fields.CharField object at 0x52fd990>, 'provider_name_given': <django.forms.fields.CharField object at 0x52fda50>, 'provider_name_prefix': <django.forms.fields.CharField object at 0x52fdb10>, 'provider_name_family': <django.forms.fields.CharField object at 0x52fdbd0>, 'provider_name_suffix': <django.forms.fields.CharField object at 0x52fdc90>, 'provider_preferred_language': <django.forms.fields.CharField object at 0x52fdd50>, 'provider_tel_2_type': <django.forms.fields.TypedChoiceField object at 0x52fde10>, 'provider_tel_2_number': <django.forms.fields.CharField object at 0x52fde90>, 'provider_tel_2_preferred_p': <django.forms.fields.BooleanField object at 0x52fdf50>, 'provider_tel_1_type': <django.forms.fields.TypedChoiceField object at 0x52fdfd0>, 'provider_tel_1_number': <django.forms.fields.CharField object at 0x52ff090>, 'provider_tel_1_preferred_p': <django.forms.fields.BooleanField object at 0x52ff150>, 'provider_race': <django.forms.fields.CharField object at 0x52ff1d0>, 'provider_gender': <django.forms.fields.TypedChoiceField object at 0x52ff2d0>, 'provider_email': <django.forms.fields.EmailField object at 0x52ff390>, 'quantityDispensed_unit': <django.forms.fields.CharField object at 0x52ff450>, 'quantityDispensed_value': <django.forms.fields.CharField object at 0x52ff510>}

FulfillmentForm.declared_fields = {}

FulfillmentForm.media

class indivo.rdf.transforms.fulfillment.FulfillmentTransform

Bases: indivo.rdf.transforms.base.BaseRDFTransform

param_map = {'date': 'date', 'pbm': 'pbm', 'dispenseDaysSupply': 'dispenseDaysSupply'}

params_to_facts(param_list)

to_facts(rdf_graph)

Extract Fulfillment Facts from an RDF graph

indivo.rdf.transforms.medication module

class indivo.rdf.transforms.medication.MedicationForm(data=None, files=None, auto_id='id_%s', prefix=None, initial=None, error_class=<class 'django.forms.util.ErrorList'>, label_suffix=':', empty_permitted=False, instance=None)

Bases: django.forms.models.ModelForm

class Meta

model

alias of Medication

MedicationForm._meta = <django.forms.models.ModelFormOptions object at 0x52f8590>

MedicationForm.base_fields = {'id': <django.forms.fields.CharField object at 0x52ff610>, 'document': <django.forms.models.ModelChoiceField object at 0x52ff890>, 'record': <django.forms.models.ModelChoiceField object at 0x52ffa50>, 'endDate': <django.forms.fields.DateField object at 0x52ff9d0>, 'instructions': <django.forms.fields.CharField object at 0x52ffad0>, 'startDate': <django.forms.fields.DateField object at 0x52ffb90>, 'name_provenance_source_code': <django.forms.fields.CharField object at 0x52ffc10>, 'name_provenance_translation_fidelity': <django.forms.fields.CharField object at 0x52ffcd0>, 'name_provenance_title': <django.forms.fields.CharField object at 0x52ffd90>, 'name_code_identifier': <django.forms.fields.CharField object at 0x52ffe50>, 'name_code_system': <django.forms.fields.CharField object at 0x52fff10>, 'name_code_title': <django.forms.fields.CharField object at 0x5302050>, 'name_title': <django.forms.fields.CharField object at 0x5302110>, 'provenance_identifier': <django.forms.fields.CharField object at 0x53021d0>, 'provenance_system': <django.forms.fields.CharField object at 0x5302290>, 'provenance_title': <django.forms.fields.CharField object at 0x5302350>, 'frequency_unit': <django.forms.fields.CharField object at 0x5302450>, 'frequency_value': <django.forms.fields.CharField object at 0x5302550>, 'quantity_unit': <django.forms.fields.CharField object at 0x5302610>, 'quantity_value': <django.forms.fields.CharField object at 0x5302710>}

MedicationForm.declared_fields = {}

MedicationForm.media

class indivo.rdf.transforms.medication.MedicationTransform

Bases: indivo.rdf.transforms.base.BaseRDFTransform

param_map = {'startDate': 'startDate', 'endDate': 'endDate', 'instructions': 'instructions'}

params_to_facts(param_list)

to_facts(rdf_graph)

Extract Medication Facts from an RDF graph

indivo.rdf.transforms.problem module

indivo.rdf.transforms.problem.from_rdf(rdf)

Module contents