Index

A

add_code_cell() (phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder method) (phenopacket_mapper.utils.NotebookBuilder method)

add_markdown_cell() (phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder method) (phenopacket_mapper.utils.NotebookBuilder method)

C

code (phenopacket_mapper.data_standards.code.Coding attribute) (phenopacket_mapper.data_standards.Coding attribute) CodeableConcept (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.code) CodeSystem (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.code_system)

Coding (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.code) coding (phenopacket_mapper.data_standards.code.CodeableConcept attribute) (phenopacket_mapper.data_standards.CodeableConcept attribute)

D

data_model (phenopacket_mapper.data_standards.data_model.DataModelInstance attribute) (phenopacket_mapper.data_standards.DataModelInstance attribute) data_model_name (phenopacket_mapper.data_standards.data_model.DataModel attribute) (phenopacket_mapper.data_standards.DataModel attribute) data_type (phenopacket_mapper.data_standards.data_model.DataField attribute) (phenopacket_mapper.data_standards.DataField attribute) DataField (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.data_model) DataFieldValue (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.data_model) DataModel (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.data_model)

DataModel2PhenopacketSchema (class in phenopacket_mapper.data_standards.DataModel2PhenopacketSchema) DataModelInstance (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.data_model) Date (class in phenopacket_mapper.data_standards) (class in phenopacket_mapper.data_standards.date) day (phenopacket_mapper.data_standards.Date attribute) (phenopacket_mapper.data_standards.date.Date attribute) description (phenopacket_mapper.data_standards.data_model.DataField attribute) (phenopacket_mapper.data_standards.DataField attribute) display (phenopacket_mapper.data_standards.code.Coding attribute) (phenopacket_mapper.data_standards.Coding attribute)

F

field (phenopacket_mapper.data_standards.data_model.DataFieldValue attribute) (phenopacket_mapper.data_standards.DataFieldValue attribute) fields (phenopacket_mapper.data_standards.data_model.DataModel attribute) (phenopacket_mapper.data_standards.DataModel attribute) formatted_string() (phenopacket_mapper.data_standards.Date method) (phenopacket_mapper.data_standards.date.Date method)

from_datetime() (phenopacket_mapper.data_standards.Date static method) (phenopacket_mapper.data_standards.date.Date static method) from_iso_8601() (phenopacket_mapper.data_standards.Date static method) (phenopacket_mapper.data_standards.date.Date static method)

G

get_field_name() (in module phenopacket_mapper.utils.get_field_name)

H

hour (phenopacket_mapper.data_standards.Date attribute) (phenopacket_mapper.data_standards.date.Date attribute)

I

iri_prefix (phenopacket_mapper.data_standards.code_system.CodeSystem attribute) (phenopacket_mapper.data_standards.CodeSystem attribute)

iso_8601_datestring() (phenopacket_mapper.data_standards.Date method) (phenopacket_mapper.data_standards.date.Date method)

L

load_data() (phenopacket_mapper.PhenopacketMapper method), [1] (phenopacket_mapper.pipeline.mapper.PhenopacketMapper method) (phenopacket_mapper.pipeline.PhenopacketMapper method)

loc_default() (in module phenopacket_mapper.utils) (in module phenopacket_mapper.utils.pandas_utils)

M

main() (in module phenopacket_mapper.cli.main) (in module phenopacket_mapper.cli.mapping_command) (in module phenopacket_mapper.cli.quickstart_command) (in module phenopacket_mapper.cli.validate_command) map() (phenopacket_mapper.PhenopacketMapper method), [1] (phenopacket_mapper.pipeline.mapper.PhenopacketMapper method) (phenopacket_mapper.pipeline.PhenopacketMapper method) mapping() (in module phenopacket_mapper.pipeline.mapper) minute (phenopacket_mapper.data_standards.Date attribute) (phenopacket_mapper.data_standards.date.Date attribute) module phenopacket_mapper, [1] phenopacket_mapper.cli phenopacket_mapper.cli.main phenopacket_mapper.cli.mapping_command phenopacket_mapper.cli.quickstart_command phenopacket_mapper.cli.validate_command phenopacket_mapper.data_standards phenopacket_mapper.data_standards.code phenopacket_mapper.data_standards.code_system phenopacket_mapper.data_standards.data_model phenopacket_mapper.data_standards.data_models phenopacket_mapper.data_standards.data_models.erdri_cds phenopacket_mapper.data_standards.data_models.rarelink_datamodel phenopacket_mapper.data_standards.DataModel2PhenopacketSchema phenopacket_mapper.data_standards.date phenopacket_mapper.pipeline phenopacket_mapper.pipeline.input phenopacket_mapper.pipeline.mapper phenopacket_mapper.pipeline.output phenopacket_mapper.pipeline.validate phenopacket_mapper.utils phenopacket_mapper.utils.create_ipynb_in_code phenopacket_mapper.utils.get_field_name phenopacket_mapper.utils.pandas_utils phenopacket_mapper.utils.parsing phenopacket_mapper.utils.parsing.parse_data_type phenopacket_mapper.utils.parsing.parse_ordinal

month (phenopacket_mapper.data_standards.Date attribute) (phenopacket_mapper.data_standards.date.Date attribute)

N

name (phenopacket_mapper.data_standards.code_system.CodeSystem attribute) (phenopacket_mapper.data_standards.CodeSystem attribute) (phenopacket_mapper.data_standards.data_model.DataField attribute) (phenopacket_mapper.data_standards.DataField attribute) namespace_prefix (phenopacket_mapper.data_standards.code_system.CodeSystem attribute) (phenopacket_mapper.data_standards.CodeSystem attribute)

notebook_content (phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder attribute) (phenopacket_mapper.utils.NotebookBuilder attribute) NotebookBuilder (class in phenopacket_mapper.utils) (class in phenopacket_mapper.utils.create_ipynb_in_code)

O

ordinal (phenopacket_mapper.data_standards.data_model.DataField attribute) (phenopacket_mapper.data_standards.DataField attribute)

P

parse_data_type() (in module phenopacket_mapper.data_standards.data_models) (in module phenopacket_mapper.utils.parsing) (in module phenopacket_mapper.utils.parsing.parse_data_type) parse_ordinal() (in module phenopacket_mapper.utils.parsing) (in module phenopacket_mapper.utils.parsing.parse_ordinal) phenopacket_mapper module, [1] phenopacket_mapper.cli module phenopacket_mapper.cli.main module phenopacket_mapper.cli.mapping_command module phenopacket_mapper.cli.quickstart_command module phenopacket_mapper.cli.validate_command module phenopacket_mapper.data_standards module phenopacket_mapper.data_standards.code module phenopacket_mapper.data_standards.code_system module phenopacket_mapper.data_standards.data_model module phenopacket_mapper.data_standards.data_models module phenopacket_mapper.data_standards.data_models.erdri_cds module phenopacket_mapper.data_standards.data_models.rarelink_datamodel module

phenopacket_mapper.data_standards.DataModel2PhenopacketSchema module phenopacket_mapper.data_standards.date module phenopacket_mapper.pipeline module phenopacket_mapper.pipeline.input module phenopacket_mapper.pipeline.mapper module phenopacket_mapper.pipeline.output module phenopacket_mapper.pipeline.validate module phenopacket_mapper.utils module phenopacket_mapper.utils.create_ipynb_in_code module phenopacket_mapper.utils.get_field_name module phenopacket_mapper.utils.pandas_utils module phenopacket_mapper.utils.parsing module phenopacket_mapper.utils.parsing.parse_data_type module phenopacket_mapper.utils.parsing.parse_ordinal module PhenopacketMapper (class in phenopacket_mapper), [1] (class in phenopacket_mapper.pipeline) (class in phenopacket_mapper.pipeline.mapper)

R

read_data_model() (in module phenopacket_mapper.pipeline) (in module phenopacket_mapper.pipeline.input) read_file() (in module phenopacket_mapper.pipeline) (in module phenopacket_mapper.pipeline.input) read_phenopackets() (in module phenopacket_mapper.pipeline) (in module phenopacket_mapper.pipeline.input)

read_redcap_api() (in module phenopacket_mapper.pipeline) (in module phenopacket_mapper.pipeline.input) read_validate() (in module phenopacket_mapper.pipeline.validate) required (phenopacket_mapper.data_standards.data_model.DataField attribute) (phenopacket_mapper.data_standards.DataField attribute) resources (phenopacket_mapper.data_standards.data_model.DataModel attribute) (phenopacket_mapper.data_standards.DataModel attribute)

S

second (phenopacket_mapper.data_standards.Date attribute) (phenopacket_mapper.data_standards.date.Date attribute) section (phenopacket_mapper.data_standards.data_model.DataField attribute) (phenopacket_mapper.data_standards.DataField attribute) set_version() (phenopacket_mapper.data_standards.code_system.CodeSystem method) (phenopacket_mapper.data_standards.CodeSystem method)

specification (phenopacket_mapper.data_standards.data_model.DataField attribute) (phenopacket_mapper.data_standards.DataField attribute) synonyms (phenopacket_mapper.data_standards.code_system.CodeSystem attribute) (phenopacket_mapper.data_standards.CodeSystem attribute) system (phenopacket_mapper.data_standards.code.Coding attribute) (phenopacket_mapper.data_standards.Coding attribute)

T

text (phenopacket_mapper.data_standards.code.CodeableConcept attribute) (phenopacket_mapper.data_standards.code.Coding attribute) (phenopacket_mapper.data_standards.CodeableConcept attribute) (phenopacket_mapper.data_standards.Coding attribute)

U

url (phenopacket_mapper.data_standards.code_system.CodeSystem attribute) (phenopacket_mapper.data_standards.CodeSystem attribute)

V

validate() (in module phenopacket_mapper.pipeline.validate) (phenopacket_mapper.pipeline.validate.Validator method) Validator (class in phenopacket_mapper.pipeline.validate) value (phenopacket_mapper.data_standards.data_model.DataFieldValue attribute) (phenopacket_mapper.data_standards.DataFieldValue attribute)

values (phenopacket_mapper.data_standards.data_model.DataModelInstance attribute) (phenopacket_mapper.data_standards.DataModelInstance attribute) version (phenopacket_mapper.data_standards.code_system.CodeSystem attribute) (phenopacket_mapper.data_standards.CodeSystem attribute)

W

write() (in module phenopacket_mapper.pipeline) (in module phenopacket_mapper.pipeline.output) (phenopacket_mapper.PhenopacketMapper method), [1] (phenopacket_mapper.pipeline.mapper.PhenopacketMapper method) (phenopacket_mapper.pipeline.PhenopacketMapper method)

write_to_file() (phenopacket_mapper.utils.create_ipynb_in_code.NotebookBuilder method) (phenopacket_mapper.utils.NotebookBuilder method)

Y

year (phenopacket_mapper.data_standards.Date attribute) (phenopacket_mapper.data_standards.date.Date attribute)