fhiry package

Submodules

fhiry.base_fhiry module

Copyright (c) 2020 Bell Eapen

This software is released under the MIT License. https://opensource.org/licenses/MIT

class fhiry.base_fhiry.BaseFhiry(config_json=None)

Bases: object

add_patient_id()

Create a patientId column with the resource.id if a Patient resource or with the resource.subject.reference if other resource type

check_subject_reference(row)

convert_object_to_list()

property delete_col_raw_coding

delete_unwanted_cols()

property df

drop_empty_cols()

Drop columns that are completely empty (all NaN values) from the dataframe.

empty_list_to_nan()

Convert empty lists in the dataframe to NaN.

get_info()

llm_query(query, llm, embed_model=None, verbose=True)

Execute a query using llama_index

Parameters:

• query (str) – The natural language query

• llm (Any) – The Language Model

• embed_model (str, optional) – The embedding model string from HuggingFace. Defaults to None.

• verbose (bool, optional) – Verbose or not. Defaults to True.

Raises:

• Exception – Llama_index not installed

• Exception – Dataframe is empty

Returns:

Results of the query

Return type:

Any

process_bundle_dict(bundle_dict)

process_df()

process_list(myList)

Extracts the codes from a list of objects

Parameters:

myList (list) – A list of objects

Returns:

A list of codes

Return type:

list

read_bundle_from_bundle_dict(bundle_dict)

remove_string_from_columns(string_to_remove='resource.')

Removes a string from all column names in a Pandas DataFrame.

Parameters:

• df (pd.DataFrame) – The input DataFrame.

• string_to_remove (str) – The string to remove from column names.

Returns:

A new DataFrame with modified column names.

Return type:

pd.DataFrame

rename_cols()

fhiry.bqsearch module

Copyright (c) 2023 Bell Eapen

This software is released under the MIT License. https://opensource.org/licenses/MIT

class fhiry.bqsearch.BQsearch(config_json=None)

Bases: BaseFhiry

search(query=None)

fhiry.fhirndjson module

Copyright (c) 2020 Bell Eapen

This software is released under the MIT License. https://opensource.org/licenses/MIT

class fhiry.fhirndjson.Fhirndjson(config_json=None)

Bases: BaseFhiry

property df

property folder

process_file(file)

process_source()

Read a single JSON resource or a directory full of JSON resources ONLY COMMON FIELDS IN ALL resources will be mapped

read_resource_from_line(line)

fhiry.fhirsearch module

class fhiry.fhirsearch.Fhirsearch(fhir_base_url, config_json=None)

Bases: BaseFhiry

search(resource_type='Patient', search_parameters={})

fhiry.fhirsearch.get_next_page_url(bundle_dict)

fhiry.fhiry module

Copyright (c) 2020 Bell Eapen

This software is released under the MIT License. https://opensource.org/licenses/MIT

class fhiry.fhiry.Fhiry(config_json=None)

Bases: BaseFhiry

property delete_col_raw_coding

property df

property filename

property folder

process_bundle_dict(bundle_dict)

process_file(filename)

process_source()

Read a single JSON resource or a directory full of JSON resources ONLY COMMON FIELDS IN ALL resources will be mapped

read_bundle_from_file(filename)

fhiry.flattenfhir module

Copyright (c) 2024 Bell Eapen

This software is released under the MIT License. https://opensource.org/licenses/MIT

class fhiry.flattenfhir.FlattenFhir(fhirobject={}, config_json=None)

Bases: ABC

property fhirobject

flatten()

flatten_allergyintolerance(allergyintolerance) → str

Flatten the allergyintolerance object into a string representation.

Parameters:

allergyintolerance (AllergyIntolerance) – The allergyintolerance object to be flattened.

Returns:

The flattened string representation of the allergyintolerance object.

Return type:

str

flatten_condition(condition) → str

Flatten the condition object into a string representation.

Parameters:

condition (Condition) – The condition object to be flattened.

Returns:

The flattened string representation of the condition object.

Return type:

str

flatten_documentreference(documentreference) → str

Flatten the documentreference object into a string representation.

Parameters:

documentreference (DocumentReference) – The documentreference object to be flattened.

Returns:

The flattened string representation of the documentreference object.

Return type:

str

flatten_medication(medication) → str

Flatten the medication object into a string representation.

Parameters:

medication (Medication) – The medication object to be flattened.

Returns:

The flattened string representation of the medication object.

Return type:

str

flatten_observation(observation) → str

Flatten the observation object into a string representation.

Parameters:

observation (Observation) – The observation object to be flattened.

Returns:

The flattened string representation of the observation object.

Return type:

str

flatten_patient(patient) → str

Flatten the patient object into a string representation.

Parameters:

patient (Patient) – The patient object to be flattened.

Returns:

The flattened string representation of the patient object.

Return type:

str

flatten_procedure(procedure) → str

Flatten the procedure object into a string representation.

Parameters:

procedure (Procedure) – The procedure object to be flattened.

Returns:

The flattened string representation of the procedure object.

Return type:

str

property flattened

get_flattened_text(entry)

get_timeago(datestring) → str

Returns a string representing the time elapsed since the given date.

Parameters:

datestring (datetime) – The date to calculate the time ago from.

Returns:

A string representing the time elapsed since the given date.

Return type:

str

fhiry.main module

Copyright (c) 2025 Bell Eapen

This software is released under the MIT License. https://opensource.org/licenses/MIT

fhiry.parallel module

fhiry.parallel.ndjson(folder, config_json=None)

fhiry.parallel.process(folder, config_json=None)

Module contents