mtbp3.health.emt

Classes

Emt

A class representing MedDRA terms.

Module Contents

class mtbp3.health.emt.Emt(folder_name='')[source]

A class representing MedDRA terms.

This class provides methods to interact with the Emt object, including listing files associated with the Emt.

folder_name

The folder name associated with the Emt.

Type:: str

lsrt

An instance of the LsrTree class for listing files.

Type:: LsrTree

month

The month of the version published.

Type:: str

year

The year of the version published.

Type:: str

version_number = '00.0'

version_number_us = '00_0'

readme_file = None

year = ''

month = ''

language = ''

mdhier = None

llt = None

smq_list = None

smq_content = None

fmq_list = None

fmq_list_unique = None

fmq_list_default = None

expected_file_lists()[source]

Get the three lists of files associated with the Emt.

Returns:: A tuple containing three lists of file names.
Return type:: tuple

find_files()[source]

Find all expected files associated with the Emt.

Returns:: A list of missing file names.
Return type:: list

load_llt(unique=True)[source]

list_files()[source]

List all files associated with the Emt.

Returns:: A list of file names.
Return type:: list

find_soc(terms=[], ignore_case=False)[source]

Find all unique SOC (System Organ Class) terms.

Parameters:

terms (list, optional) – The specific SOC name(s) to filter the results. Defaults to an empty list.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A list of unique SOC terms. If terms is provided, it returns the corresponding ids.

Return type:

list

Raises:

AssertionError – If terms is not a list.

find_hlgt(terms=[], ignore_case=False)[source]

Find all unique HLGT terms.

Parameters:

terms (list, optional) – The specific HLGT name(s) to filter the results. Defaults to an empty list.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A list of unique HLGT terms. If terms is provided, it returns the corresponding ids.

Return type:

list

Raises:

AssertionError – If terms is not a list.

find_hlt(terms=[], ignore_case=False)[source]

Find all unique HLT terms.

Parameters:

terms (list, optional) – The specific HLT name(s) to filter the results. Defaults to an empty list.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A list of unique HLT terms. If terms is provided, it returns the corresponding ids.

Return type:

list

Raises:

AssertionError – If terms is not a list.

find_pt(terms=[], ignore_case=False)[source]

Find all unique PT terms.

Parameters:

terms (list, optional) – The specific PT name(s) to filter the results. Defaults to an empty list.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A list of unique PT terms. If terms is provided, it returns the corresponding ids.

Return type:

list

Raises:

AssertionError – If terms is not a list.

find_llt(terms=[], ignore_case=False, llt_current_only=True)[source]

Find all unique LLT terms.

Parameters:

terms (list, optional) – The specific LLT name(s) to filter the results. Defaults to an empty list.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A list of unique LLT terms. If terms is provided, it returns the corresponding ids.

Return type:

list

Raises:

AssertionError – If terms is not a list.

all_str_digit(lst=[])[source]

Check if all elements in a given list are strings containing only digits.

Parameters:: fin (list) – The list to check.
Returns:: True if all elements in the list are strings containing only digits, False otherwise.
Return type:: bool

assert_terms(input, remove_none=False)[source]

Assert that the input is either a string or a list. If the input is a string, it is converted to a length one list. All elements in the list are converted to strings and empty elements are removed.

Parameters:: input (str or list) – The input to be validated.
Returns:: The validated list.
Return type:: list
Raises:: AssertionError – If the input is neither a string nor a list.

find_term_wi_level(terms=[], ignore_case=False, level=1, llt_current_only=True)[source]

Find all unique terms.

Parameters:

terms (list, optional) – The specific SOC name(s) to filter the results. Defaults to an empty list.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.
level (int, optional) – The level of the SOC hierarchy to consider. Defaults to 1.

Returns:

A list of unique terms. If terms is provided, it returns the corresponding ids.

Return type:

list

Raises:

AssertionError – If terms is not a list.

find_pt_given_soc(soc=[], primary_soc_only=False, ignore_case=False)[source]

Find all PTs (Preferred Terms) given a SOC (System Organ Class) name.

Parameters:

soc (str or list) – The name of the SOC or a list of SOC names.
primary_soc_only (bool, optional) – If True, only return PTs associated with the primary SOC. Defaults to False.

Returns:

A DataFrame containing the PTs associated with the given SOC.: Each row represents a PT and contains the PT code and PT name.

Return type:

pandas.DataFrame

find_llt_given_pt(pt=[], ignore_case=False, llt_current_only=True)[source]

Find all LLTs (Lowest Level Terms) given a PT (Preferred Term) name or a list of PT names.

Parameters:

pt (str or list) – The name of the PT or a list of PT names.

Returns:

A DataFrame containing the LLTs associated with the given PT(s).: Each row represents an LLT and contains the LLT code and LLT name.

Return type:

pandas.DataFrame

find_llt_given_soc(soc=[], primary_soc_only=False, ignore_case=False, llt_current_only=True)[source]

Find all LLTs (Lowest Level Terms) given a SOC (System Organ Class) name.

Parameters:

soc_name (str) – The name of the SOC.
primary_soc_only (bool, optional) – If True, only return LLTs associated with the primary SOC. Defaults to False.

Returns:

A DataFrame containing the LLTs associated with the given SOC.: Each row represents an LLT and contains the LLT code and LLT name.

Return type:

pandas.DataFrame

find_soc_given_pt(pt=[], primary_only=True, ignore_case=False)[source]

Find the SOC (System Organ Class) given a list of PT (Preferred Term) names.

Parameters:: pt (list) – A list of PT names.
Returns:: The name of the primary SOC.
Return type:: str
Raises:: AssertionError – If pt is not a list.

load_smq()[source]

find_smq(terms=[], with_detail=False, ignore_case=False)[source]

Find all unique SMQ (Standard MedDRA Queries) terms.

Parameters:

terms (list, optional) – The specific SMQ name(s) to filter the results. Defaults to an empty list.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A list of unique SMQ terms. If terms is provided, it returns the corresponding ids.

Return type:

list

Raises:

AssertionError – If terms is not a list.

find_terms_given_smq(smq=[], ignore_case=False, active_only=True, narrow_only=True, llt_only=False, llt_current_only=True)[source]

Find all terms related an SMQ (Standard MedDRA Query) name or a list of SMQ names.

Parameters:

smq (str or list) – The name of the SMQ or a list of SMQ names.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A DataFrame containing the terms associated with the given SMQ(s).

Return type:

pandas.DataFrame

find_terms_given_smq_sub(subset_df, keep_columns, llt_only, llt_current_only)[source]

load_fmq_default()[source]

load_fmq()[source]

find_fmq_file(file_path='')[source]

save_fmq_consolidated_list_csv(folder_path='')[source]

Save the CSV file in the specified folder.

Parameters:: folder_path (str) – The path of the folder where the CSV file should be saved.

find_fmq(fmq=[], narrow_only=True)[source]

Find all unique FMQ (FDA Medical Queries) terms.

Parameters:: fmq (list, optional) – The specific FMQ name(s) to filter the results. Defaults to an empty list.
Returns:: A list of unique FMQ terms. If fmq is provided, it returns the corresponding ids.
Return type:: list
Raises:: AssertionError – If fmq is not a list.

find_terms_given_fmq(fmq=[], ignore_case=False, narrow_only=True)[source]

Find all terms related to an FMQ (FDA Medical Query) name or a list of FMQ names.

Parameters:

fmq (str or list) – The name of the FMQ or a list of FMQ names.
ignore_case (bool, optional) – Flag to indicate whether to ignore case sensitivity when filtering terms. Defaults to False.

Returns:

A DataFrame containing the terms associated with the given FMQ(s).

Return type:

pandas.DataFrame

show_fmq_tree(fmq=[], with_soc=False, ignore_case=False, to_right=False)[source]