From fd717e5aca057956dae017f17514e37939f60140 Mon Sep 17 00:00:00 2001 From: Benjamin Mouncer Date: Mon, 23 Jan 2023 21:06:04 +0000 Subject: [PATCH 01/34] Added proxy parameter to all api calls. --- fingertips_py/api_calls.py | 34 +++++++++++++++++++--------------- 1 file changed, 19 insertions(+), 15 deletions(-) diff --git a/fingertips_py/api_calls.py b/fingertips_py/api_calls.py index 4a8c746..0b5bca8 100644 --- a/fingertips_py/api_calls.py +++ b/fingertips_py/api_calls.py @@ -11,16 +11,17 @@ from io import StringIO -def make_request(url, attr=None): +def make_request(url, attr=None, proxies=None): """ :param url: A url to make a request :param attr: The attribute that needs to be returned + :proxies: proxies info to access the data :return: a dict of the attribute and associated data """ try: - req = requests.get(url) + req = requests.get(url, proxies=proxies) except requests.exceptions.SSLError: - req = requests.get(url, verify=False) + req = requests.get(url, verify=False, proxies=proxies) json_response = json.loads(req.content.decode('utf-8')) data = {} for item in json_response: @@ -29,29 +30,31 @@ def make_request(url, attr=None): return data -def get_json(url): +def get_json(url, proxies=None): """ :param url: A url to make a request + :proxies: proxies info to access the data :return: A parsed JSON object """ try: - req = requests.get(url) + req = requests.get(url, proxies=proxies) except requests.exceptions.SSLError: - req = requests.get(url, verify=False) + req = requests.get(url, verify=False, proxies=proxies) json_resp = json.loads(req.content.decode('utf-8')) return json_resp -def get_json_return_df(url, transpose=True): +def get_json_return_df(url, transpose=True, proxies=None): """ :param url: A url to make a request :param transpose: [OPTIONAL] transposes dataframe. Default True. + :proxies: proxies info to access the data :return: Dataframe generated from JSON response. """ try: - req = requests.get(url) + req = requests.get(url, proxies=proxies) except requests.exceptions.SSLError: - req = requests.get(url, verify=False) + req = requests.get(url, verify=False, proxies=proxies) try: df = pd.read_json(req.content, encoding='utf-8') except ValueError: @@ -61,16 +64,16 @@ def get_json_return_df(url, transpose=True): return df -def get_data_in_tuple(url): +def get_data_in_tuple(url, proxies=None): """ - :param url: A url to make a request + :proxies: proxies info to access the data :return: A tuple of returned data """ try: - req = requests.get(url) + req = requests.get(url, proxies=proxies) except requests.exceptions.SSLError: - req = requests.get(url, verify=False) + req = requests.get(url, verify=False, proxies=proxies) json_resp = json.loads(req.content.decode('utf-8')) tup = [tuple(d.values()) for d in json_resp] if isinstance(tup[0][0], str): @@ -79,12 +82,13 @@ def get_data_in_tuple(url): return tup -def deal_with_url_error(url): +def deal_with_url_error(url, proxies=None): """ :param url: A url that returns a URL Error based on SSL errors + :proxies: proxies info to access the data :return: A dataframe from the URL with varify set to false. """ - req = requests.get(url, verify=False) + req = requests.get(url, verify=False, proxies=proxies) s = str(req.content, 'utf-8') data = StringIO(s) df = pd.read_csv(data) From 107578786bb02915f8af108193ed0273653dc068 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Tue, 24 Jan 2023 19:39:12 +0000 Subject: [PATCH 02/34] Added proxy variable to api_calls.py --- fingertips_py/api_calls.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/fingertips_py/api_calls.py b/fingertips_py/api_calls.py index 0b5bca8..7266f1f 100644 --- a/fingertips_py/api_calls.py +++ b/fingertips_py/api_calls.py @@ -15,7 +15,7 @@ def make_request(url, attr=None, proxies=None): """ :param url: A url to make a request :param attr: The attribute that needs to be returned - :proxies: proxies info to access the data + :param proxies: proxies info to access the data :return: a dict of the attribute and associated data """ try: @@ -33,7 +33,7 @@ def make_request(url, attr=None, proxies=None): def get_json(url, proxies=None): """ :param url: A url to make a request - :proxies: proxies info to access the data + :param proxies: proxies info to access the data :return: A parsed JSON object """ try: @@ -48,7 +48,7 @@ def get_json_return_df(url, transpose=True, proxies=None): """ :param url: A url to make a request :param transpose: [OPTIONAL] transposes dataframe. Default True. - :proxies: proxies info to access the data + :param proxies: proxies info to access the data :return: Dataframe generated from JSON response. """ try: @@ -67,7 +67,7 @@ def get_json_return_df(url, transpose=True, proxies=None): def get_data_in_tuple(url, proxies=None): """ :param url: A url to make a request - :proxies: proxies info to access the data + :param proxies: proxies info to access the data :return: A tuple of returned data """ try: @@ -85,7 +85,7 @@ def get_data_in_tuple(url, proxies=None): def deal_with_url_error(url, proxies=None): """ :param url: A url that returns a URL Error based on SSL errors - :proxies: proxies info to access the data + :param proxies: proxies info to access the data :return: A dataframe from the URL with varify set to false. """ req = requests.get(url, verify=False, proxies=proxies) From 4cef47eaab6aaf83c25e8539ec930d533d7787bf Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Tue, 24 Jan 2023 19:42:20 +0000 Subject: [PATCH 03/34] Corrected wording of variable. --- fingertips_py/api_calls.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/fingertips_py/api_calls.py b/fingertips_py/api_calls.py index 7266f1f..74e151f 100644 --- a/fingertips_py/api_calls.py +++ b/fingertips_py/api_calls.py @@ -15,7 +15,7 @@ def make_request(url, attr=None, proxies=None): """ :param url: A url to make a request :param attr: The attribute that needs to be returned - :param proxies: proxies info to access the data + :param proxies: proxy info to access the data :return: a dict of the attribute and associated data """ try: @@ -33,7 +33,7 @@ def make_request(url, attr=None, proxies=None): def get_json(url, proxies=None): """ :param url: A url to make a request - :param proxies: proxies info to access the data + :param proxies: proxy info to access the data :return: A parsed JSON object """ try: @@ -48,7 +48,7 @@ def get_json_return_df(url, transpose=True, proxies=None): """ :param url: A url to make a request :param transpose: [OPTIONAL] transposes dataframe. Default True. - :param proxies: proxies info to access the data + :param proxies: proxy info to access the data :return: Dataframe generated from JSON response. """ try: @@ -67,7 +67,7 @@ def get_json_return_df(url, transpose=True, proxies=None): def get_data_in_tuple(url, proxies=None): """ :param url: A url to make a request - :param proxies: proxies info to access the data + :param proxies: proxy info to access the data :return: A tuple of returned data """ try: @@ -85,7 +85,7 @@ def get_data_in_tuple(url, proxies=None): def deal_with_url_error(url, proxies=None): """ :param url: A url that returns a URL Error based on SSL errors - :param proxies: proxies info to access the data + :param proxies: proxy info to access the data :return: A dataframe from the URL with varify set to false. """ req = requests.get(url, verify=False, proxies=proxies) From 7f936d4226721f15c2174027978677a722963d89 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Tue, 24 Jan 2023 19:53:11 +0000 Subject: [PATCH 04/34] Added proxies variable to functions retrieving the metadata. --- fingertips_py/metadata.py | 82 ++++++++++++++++++++++++++------------- 1 file changed, 55 insertions(+), 27 deletions(-) diff --git a/fingertips_py/metadata.py b/fingertips_py/metadata.py index fe2994d..6e215d6 100644 --- a/fingertips_py/metadata.py +++ b/fingertips_py/metadata.py @@ -10,11 +10,12 @@ from .api_calls import get_data_in_tuple, base_url, make_request, get_json, get_json_return_df, deal_with_url_error -def get_all_ages(is_test=False): +def get_all_ages(is_test=False, proxies=None): """ Returns a dictionary of all the age categories and their IDs. :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param proxies: proxy info to access the data :return: Age codes used in Fingertips in a tuple """ ages = get_data_in_tuple(base_url + 'ages') @@ -23,10 +24,11 @@ def get_all_ages(is_test=False): return ages -def get_all_areas(is_test=False): +def get_all_areas(is_test=False, proxies=None): """ Retreives all area types. + :param proxies: proxy info to access the data :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A dictionary of all area types used in Fingertips """ @@ -36,10 +38,11 @@ def get_all_areas(is_test=False): return areas -def get_age_id(age, is_test=False): +def get_age_id(age, is_test=False, proxies=None): """ Returns an ID for a given age. + :param proxies: proxy info to access the data :param age: Search term of an age or age range as a string :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: Code used in Fingertips to represent the age or age range as a string @@ -50,10 +53,11 @@ def get_age_id(age, is_test=False): return ages[age]['Id'] -def get_age_from_id(age_id, is_test=False): +def get_age_from_id(age_id, is_test=False, proxies=None): """ Returns an age name from given id. + :param proxies: proxy info to access the data :param age_id: Age id used in Fingertips as an integer :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: Age or age range as a string @@ -64,10 +68,11 @@ def get_age_from_id(age_id, is_test=False): return ages[age_id]['Name'] -def get_all_sexes(is_test=False): +def get_all_sexes(is_test=False, proxies=None): """ Returns a tuple of all sex categories and their IDs. + :param proxies: proxy info to access the data :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: Sex categories used in Fingertips with associated codes as a tuple """ @@ -77,10 +82,11 @@ def get_all_sexes(is_test=False): return sexes -def get_sex_id(sex, is_test=False): +def get_sex_id(sex, is_test=False, proxies=None): """ Returns an ID for a given sex. + :param proxies: proxy info to access the data :param sex: Sex category as string (Case sensitive) :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: ID used in Fingertips to represent the sex as integer @@ -91,10 +97,11 @@ def get_sex_id(sex, is_test=False): return sexes[sex]['Id'] -def get_sex_from_id(sex_id, is_test=False): +def get_sex_from_id(sex_id, is_test=False, proxies=None): """ Returns a sex name given an id. + :param proxies: proxy info to access the data :param sex_id: ID used in Fingertips to represent the sex as integer :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: Sex category as string @@ -105,10 +112,11 @@ def get_sex_from_id(sex_id, is_test=False): return sexes[sex_id]['Name'] -def get_all_value_notes(is_test=False): +def get_all_value_notes(is_test=False, proxies=None): """ Returns a dictionary of all value notes and their IDs. + :param proxies: proxy info to access the data :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: Data value notes and their associated codes that are used in Fingertips as a list of tuples """ @@ -118,10 +126,11 @@ def get_all_value_notes(is_test=False): return value_notes -def get_value_note_id(value_note, is_test=False): +def get_value_note_id(value_note, is_test=False, proxies=None): """ Returns a value note ID for a given value note. + :param proxies: proxy info to access the data :param value_note: Value note as string :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: ID used in Fingertips to represent the value note as integer @@ -132,24 +141,28 @@ def get_value_note_id(value_note, is_test=False): return value_notes[value_note]['Id'] -def get_areas_for_area_type(area_type_id, is_test=False): +def get_areas_for_area_type(area_type_id, is_test=False, proxies=None): """ Returns a dictionary of areas that match an area type id given the id as integer or string. + :param proxies: proxy info to access the data :param area_type_id: ID of area type (ID of General Practice is 7 etc) used in Fingertips as integer or string :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A dictionary of dictionaries with area codes and the names of those areas """ - areas = make_request(base_url + 'areas/by_area_type?area_type_id=' + str(area_type_id), 'Code') + areas = make_request( + base_url + 'areas/by_area_type?area_type_id=' + str(area_type_id), + 'Code') if is_test: return areas, base_url + 'areas/by_area_type?area_type_id=' + str(area_type_id) return areas -def get_metadata_for_indicator(indicator_number, is_test=False): +def get_metadata_for_indicator(indicator_number, is_test=False, proxies=None): """ Returns the metadata for an indicator given the indicator number as integer or string. + :param proxies: proxy info to access the data :param indicator_number: Number used to identify an indicator within Fingertips as integer or string :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A dictionary of metadata for the given indicator @@ -160,10 +173,11 @@ def get_metadata_for_indicator(indicator_number, is_test=False): return metadata -def get_metadata_for_all_indicators_from_csv(is_test=False): +def get_metadata_for_all_indicators_from_csv(is_test=False, proxies=None): """ Returns a dataframe from the csv of all metadata for all indicators. + :param proxies: proxy info to access the data :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A dataframe of all metadata for all indicators """ @@ -176,10 +190,11 @@ def get_metadata_for_all_indicators_from_csv(is_test=False): return metadata -def get_metadata_for_all_indicators(include_definition='no', include_system_content='no', is_test=False): +def get_metadata_for_all_indicators(include_definition='no', include_system_content='no', is_test=False, proxies=None): """ Returns the metadata for all indicators in a dataframe. + :param proxies: proxy info to access the data :param include_definition: optional to include definitions :param include_system_content: optional to include system content :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data @@ -193,10 +208,11 @@ def get_metadata_for_all_indicators(include_definition='no', include_system_cont return metadata_df -def get_multiplier_and_calculation_for_indicator(indicator_number): +def get_multiplier_and_calculation_for_indicator(indicator_number, proxies=None): """ Returns the multiplier and calculation method for a given indicator. + :param proxies: proxy info to access the data :param indicator_number: Number used to identify an indicator within Fingertips as integer or string :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A tuple of multiplier and calculation method from Fingetips metadata @@ -213,10 +229,11 @@ def get_multiplier_and_calculation_for_indicator(indicator_number): return multiplier, calc -def get_area_types_as_dict(is_test=False): +def get_area_types_as_dict(is_test=False, proxies=None): """ Returns all area types and related information such as ID and name. + :param proxies: proxy info to access the data :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A dictionary of area types """ @@ -226,10 +243,11 @@ def get_area_types_as_dict(is_test=False): return areas -def get_profile_by_id(profile_id, is_test=False): +def get_profile_by_id(profile_id, is_test=False, proxies=None): """ Returns a profile as an dictionary which contains information about domains and sequencing. + :param proxies: proxy info to access the data :param profile_id: ID used in Fingertips to identify a profile as integer or string :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A dictionary of information about the profile @@ -240,10 +258,11 @@ def get_profile_by_id(profile_id, is_test=False): return get_json(base_url + 'profile?profile_id=' + str(profile_id)) -def get_all_profiles(is_test=False): +def get_all_profiles(is_test=False, proxies=None): """ Returns all profiles. + :param proxies: proxy info to access the data :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A dictionary of all profiles in Fingertips including information on domains and sequencing """ @@ -253,10 +272,11 @@ def get_all_profiles(is_test=False): return profiles -def get_domains_in_profile(profile_id): +def get_domains_in_profile(profile_id, proxies=None): """ Returns the domain IDs for a given profile. + :param proxies: proxy info to access the data :param profile_id: ID used in Fingertips to identify a profile as integer or string :return: A list of domain IDs """ @@ -264,10 +284,11 @@ def get_domains_in_profile(profile_id): return profile['GroupIds'] -def get_area_types_for_profile(profile_id, is_test=False): +def get_area_types_for_profile(profile_id, is_test=False, proxies=None): """ Retrieves all the area types that have data for a given profile. + :param proxies: proxy info to access the data :param profile_id: ID used in Fingertips to identify a profile as integer or string :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data :return: A list of dictionaries of area types with relevant information @@ -278,10 +299,11 @@ def get_area_types_for_profile(profile_id, is_test=False): return get_json(base_url + 'area_types?profile_ids=' + str(profile_id)) -def get_area_type_ids_for_profile(profile_id): +def get_area_type_ids_for_profile(profile_id, proxies=None): """ Returns a list of area types used within a given profile. + :param proxies: proxy info to access the data :param profile_id: ID used in Fingertips to identify a profile as integer or string :return: A list of area types used within a given profile """ @@ -292,10 +314,11 @@ def get_area_type_ids_for_profile(profile_id): return area_type_list -def get_profile_by_name(profile_name): +def get_profile_by_name(profile_name, proxies=None): """ Returns a profile object given a name to search - try to be specific to get better results. + :param proxies: proxy info to access the data :param profile_name: A string or part of a string that is used as the profile name :return: A dictionary of the profile metadata including domain information or an error message """ @@ -310,12 +333,13 @@ def get_profile_by_name(profile_name): return profile_obj -def get_profile_by_key(profile_key): +def get_profile_by_key(profile_key, proxies=None): """ Returns a profile object given a key (as the stub following 'profile' in the website URL). For example, give, a URL of the form `https://fingertips.phe.org.uk/profile/general-practice/data#page/3/gid/2000...`, the key is 'general-practice'. + :param proxies: proxy info to access the data :param profile_key: The exact key for the profile. :return: A dictionary of the profile metadata including domain information or an error message """ @@ -326,10 +350,11 @@ def get_profile_by_key(profile_key): return 'Profile could not be found' -def get_metadata_for_indicator_as_dataframe(indicator_ids, is_test=False): +def get_metadata_for_indicator_as_dataframe(indicator_ids, is_test=False, proxies=None): """ Returns a dataframe of metadata for a given indicator ID or list of indicator IDs. + :param proxies: proxy info to access the data :param indicator_ids: Number or list of numbers used to identify an indicator within Fingertips as integer or string :return: Dataframe object with metadate for the indicator ID """ @@ -347,10 +372,11 @@ def get_metadata_for_indicator_as_dataframe(indicator_ids, is_test=False): return df -def get_metadata_for_domain_as_dataframe(group_ids, is_test=False): +def get_metadata_for_domain_as_dataframe(group_ids, is_test=False, proxies=None): """ Returns a dataframe of metadata for a given domain ID or list of domain IDs. + :param proxies: proxy info to access the data :param group_ids: Number or list of numbers used to identify a domain within Fingertips as integer or string :return: Dataframe object with metadata for the indicators for a given domain ID """ @@ -376,10 +402,11 @@ def get_metadata_for_domain_as_dataframe(group_ids, is_test=False): return df -def get_metadata_for_profile_as_dataframe(profile_ids): +def get_metadata_for_profile_as_dataframe(profile_ids, proxies=None): """ Returns a dataframe of metadata for a given profile ID or list of profile IDs. + :param proxies: proxy info to access the data :param profile_ids: ID or list of IDs used in Fingertips to identify a profile as integer or string :return: Dataframe object with metadata for the indicators for a given group ID """ @@ -403,11 +430,12 @@ def get_metadata_for_profile_as_dataframe(profile_ids): return df -def get_metadata(indicator_ids=None, domain_ids=None, profile_ids=None): +def get_metadata(indicator_ids=None, domain_ids=None, profile_ids=None, proxies=None): """ Returns a dataframe object of metadata for a given indicator, domain, and/or profile given the relevant IDs. At least one of these IDs has to be given otherwise an error is raised. + :param proxies: proxy info to access the data :param indicator_ids: [OPTIONAL] Number used to identify an indicator within Fingertips as integer or string :param domain_ids: [OPTIONAL] Number used to identify a domain within Fingertips as integer or string :param profile_ids: [OPTIONAL] ID used in Fingertips to identify a profile as integer or string From e84fb8683561ac06e4de23208918224b01525681 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Wed, 25 Jan 2023 11:01:01 +0000 Subject: [PATCH 05/34] started changing function definitions. --- fingertips_py/api_calls.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/fingertips_py/api_calls.py b/fingertips_py/api_calls.py index 74e151f..a07e226 100644 --- a/fingertips_py/api_calls.py +++ b/fingertips_py/api_calls.py @@ -11,17 +11,17 @@ from io import StringIO -def make_request(url, attr=None, proxies=None): +def make_request(url, attr=None, proxy=None): """ :param url: A url to make a request :param attr: The attribute that needs to be returned - :param proxies: proxy info to access the data + :param proxy: proxy info to access the data :return: a dict of the attribute and associated data """ try: - req = requests.get(url, proxies=proxies) + req = requests.get(url, proxies=proxy) except requests.exceptions.SSLError: - req = requests.get(url, verify=False, proxies=proxies) + req = requests.get(url, verify=False, proxies=proxy) json_response = json.loads(req.content.decode('utf-8')) data = {} for item in json_response: From c6dd7813ec4e30bed568e77f7f6dddeee36ae5ab Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Wed, 25 Jan 2023 20:28:58 +0000 Subject: [PATCH 06/34] Added proxy variable to all functions in metadata.py and refactored several functions. --- fingertips_py/api_calls.py | 52 +++-- fingertips_py/metadata.py | 463 +++++++++++++++++++++---------------- 2 files changed, 302 insertions(+), 213 deletions(-) diff --git a/fingertips_py/api_calls.py b/fingertips_py/api_calls.py index a07e226..03d7cd5 100644 --- a/fingertips_py/api_calls.py +++ b/fingertips_py/api_calls.py @@ -4,7 +4,6 @@ A group of functions to query the Fingertips api and retrieve data in a variety of formats. """ - import requests import json import pandas as pd @@ -15,7 +14,7 @@ def make_request(url, attr=None, proxy=None): """ :param url: A url to make a request :param attr: The attribute that needs to be returned - :param proxy: proxy info to access the data + :param proxy: proxy given to the get request used to access the API :return: a dict of the attribute and associated data """ try: @@ -30,31 +29,31 @@ def make_request(url, attr=None, proxy=None): return data -def get_json(url, proxies=None): +def get_json(url, proxy=None): """ :param url: A url to make a request - :param proxies: proxy info to access the data + :param proxy: proxy given to the get request used to access the API :return: A parsed JSON object """ try: - req = requests.get(url, proxies=proxies) + req = requests.get(url, proxies=proxy) except requests.exceptions.SSLError: - req = requests.get(url, verify=False, proxies=proxies) + req = requests.get(url, verify=False, proxies=proxy) json_resp = json.loads(req.content.decode('utf-8')) return json_resp -def get_json_return_df(url, transpose=True, proxies=None): +def get_json_return_df(url, transpose=True, proxy=None): """ :param url: A url to make a request :param transpose: [OPTIONAL] transposes dataframe. Default True. - :param proxies: proxy info to access the data + :param proxy: proxy given to the get request used to access the API :return: Dataframe generated from JSON response. """ try: - req = requests.get(url, proxies=proxies) + req = requests.get(url, proxies=proxy) except requests.exceptions.SSLError: - req = requests.get(url, verify=False, proxies=proxies) + req = requests.get(url, verify=False, proxies=proxy) try: df = pd.read_json(req.content, encoding='utf-8') except ValueError: @@ -64,16 +63,16 @@ def get_json_return_df(url, transpose=True, proxies=None): return df -def get_data_in_tuple(url, proxies=None): +def get_data_in_tuple(url, proxy=None): """ :param url: A url to make a request - :param proxies: proxy info to access the data + :param proxy: proxy given to the get request used to access the API :return: A tuple of returned data """ try: - req = requests.get(url, proxies=proxies) + req = requests.get(url, proxies=proxy) except requests.exceptions.SSLError: - req = requests.get(url, verify=False, proxies=proxies) + req = requests.get(url, verify=False, proxies=proxy) json_resp = json.loads(req.content.decode('utf-8')) tup = [tuple(d.values()) for d in json_resp] if isinstance(tup[0][0], str): @@ -82,13 +81,28 @@ def get_data_in_tuple(url, proxies=None): return tup -def deal_with_url_error(url, proxies=None): +def get_csv(url, proxy=None): + """ + :param url: A url to make a request + :param proxy: proxy given to the get request used to access the API + :return: A pandas df of the csv file + """ + try: + req = requests.get(url, proxies=proxy).text + + except requests.exceptions.SSLError: + req = requests.get(url, verify=False, proxies=proxy).text + + return pd.read_csv(StringIO(req)) + + +def deal_with_url_error(url, proxy=None): """ :param url: A url that returns a URL Error based on SSL errors - :param proxies: proxy info to access the data - :return: A dataframe from the URL with varify set to false. + :param proxy: proxy given to the get request used to access the API + :return: A dataframe from the URL with verify set to false. """ - req = requests.get(url, verify=False, proxies=proxies) + req = requests.get(url, verify=False, proxies=proxy) s = str(req.content, 'utf-8') data = StringIO(s) df = pd.read_csv(data) @@ -96,5 +110,3 @@ def deal_with_url_error(url, proxies=None): base_url = 'http://fingertips.phe.org.uk/api/' - - diff --git a/fingertips_py/metadata.py b/fingertips_py/metadata.py index 6e215d6..ee59659 100644 --- a/fingertips_py/metadata.py +++ b/fingertips_py/metadata.py @@ -1,223 +1,255 @@ """ metadata.py ================================== -Calls used to retrieve metadata about areas, ages, sexes, value notes, calculation methods, rates, and indicator -metadata. +Calls used to retrieve metadata about areas, ages, sexes, value notes, +calculation methods, rates, and indicator metadata. """ import pandas as pd from urllib.error import HTTPError, URLError -from .api_calls import get_data_in_tuple, base_url, make_request, get_json, get_json_return_df, deal_with_url_error +from .api_calls import get_data_in_tuple, base_url, make_request, get_json, \ + get_json_return_df, get_csv, deal_with_url_error -def get_all_ages(is_test=False, proxies=None): +def get_all_ages(is_test=False, proxy=None): """ Returns a dictionary of all the age categories and their IDs. - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data - :param proxies: proxy info to access the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: Age codes used in Fingertips in a tuple """ - ages = get_data_in_tuple(base_url + 'ages') + ages = get_data_in_tuple(base_url + 'ages', proxy) if is_test: return ages, base_url + 'ages' return ages -def get_all_areas(is_test=False, proxies=None): +def get_all_areas(is_test=False, proxy=None): """ - Retreives all area types. + Retrieves all area types. - :param proxies: proxy info to access the data - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: A dictionary of all area types used in Fingertips """ - areas = make_request(base_url + 'area_types', 'Id') + areas = make_request(base_url + 'area_types', 'Id', proxy) if is_test: return areas, base_url + 'area_types' return areas -def get_age_id(age, is_test=False, proxies=None): +def get_age_id(age, is_test=False, proxy=None): """ Returns an ID for a given age. - :param proxies: proxy info to access the data :param age: Search term of an age or age range as a string - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: Code used in Fingertips to represent the age or age range as a string """ - ages = make_request(base_url + 'ages', 'Name') + ages = make_request(base_url + 'ages', 'Name', proxy) if is_test: return ages[age]['Id'], base_url + 'ages' return ages[age]['Id'] -def get_age_from_id(age_id, is_test=False, proxies=None): +def get_age_from_id(age_id, is_test=False, proxy=None): """ Returns an age name from given id. - :param proxies: proxy info to access the data :param age_id: Age id used in Fingertips as an integer - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: Age or age range as a string """ - ages = make_request(base_url + 'ages', 'Id') + ages = make_request(base_url + 'ages', 'Id', proxy) if is_test: return ages[age_id]['Name'], base_url + 'ages' return ages[age_id]['Name'] -def get_all_sexes(is_test=False, proxies=None): +def get_all_sexes(is_test=False, proxy=None): """ Returns a tuple of all sex categories and their IDs. - :param proxies: proxy info to access the data - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: Sex categories used in Fingertips with associated codes as a tuple """ - sexes = get_data_in_tuple(base_url + 'sexes') + sexes = get_data_in_tuple(base_url + 'sexes', proxy) if is_test: return sexes, base_url + 'sexes' return sexes -def get_sex_id(sex, is_test=False, proxies=None): +def get_sex_id(sex, is_test=False, proxy=None): """ Returns an ID for a given sex. - :param proxies: proxy info to access the data :param sex: Sex category as string (Case sensitive) - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: ID used in Fingertips to represent the sex as integer """ - sexes = make_request(base_url + 'sexes', 'Name') + sexes = make_request(base_url + 'sexes', 'Name', proxy) if is_test: return sexes[sex]['Id'], base_url + 'sexes' return sexes[sex]['Id'] -def get_sex_from_id(sex_id, is_test=False, proxies=None): +def get_sex_from_id(sex_id, is_test=False, proxy=None): """ Returns a sex name given an id. - :param proxies: proxy info to access the data :param sex_id: ID used in Fingertips to represent the sex as integer - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: Sex category as string """ - sexes = make_request(base_url + 'sexes', 'Id') + sexes = make_request(base_url + 'sexes', 'Id', proxy) if is_test: return sexes[sex_id]['Name'], base_url + 'sexes' return sexes[sex_id]['Name'] -def get_all_value_notes(is_test=False, proxies=None): +def get_all_value_notes(is_test=False, proxy=None): """ Returns a dictionary of all value notes and their IDs. - :param proxies: proxy info to access the data - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data - :return: Data value notes and their associated codes that are used in Fingertips as a list of tuples + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API + :return: Data value notes and their associated codes that are used in + Fingertips as a list of tuples """ - value_notes = get_data_in_tuple(base_url + 'value_notes') + value_notes = get_data_in_tuple(base_url + 'value_notes', proxy) if is_test: return value_notes, base_url + 'value_notes' return value_notes -def get_value_note_id(value_note, is_test=False, proxies=None): +def get_value_note_id(value_note, is_test=False, proxy=None): """ Returns a value note ID for a given value note. - :param proxies: proxy info to access the data :param value_note: Value note as string - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: ID used in Fingertips to represent the value note as integer """ - value_notes = make_request(base_url + 'value_notes', 'Text') + value_notes = make_request(base_url + 'value_notes', 'Text', proxy) if is_test: return value_notes[value_note]['Id'], base_url + 'value_notes' return value_notes[value_note]['Id'] -def get_areas_for_area_type(area_type_id, is_test=False, proxies=None): +def get_areas_for_area_type(area_type_id, is_test=False, proxy=None): """ - Returns a dictionary of areas that match an area type id given the id as integer or string. + Returns a dictionary of areas that match an area type id given the id as + integer or string. - :param proxies: proxy info to access the data - :param area_type_id: ID of area type (ID of General Practice is 7 etc) used in Fingertips as integer or string - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data - :return: A dictionary of dictionaries with area codes and the names of those areas + :param area_type_id: ID of area type (ID of General Practice is 7 etc) used + in Fingertips as integer or string + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API + :return: A dictionary of dictionaries with area codes and the names of + those areas """ areas = make_request( base_url + 'areas/by_area_type?area_type_id=' + str(area_type_id), - 'Code') + 'Code', proxy) if is_test: return areas, base_url + 'areas/by_area_type?area_type_id=' + str(area_type_id) return areas -def get_metadata_for_indicator(indicator_number, is_test=False, proxies=None): +def get_metadata_for_indicator(indicator_number, is_test=False, proxy=None): """ - Returns the metadata for an indicator given the indicator number as integer or string. + Returns the metadata for an indicator given the indicator number as integer + or string. - :param proxies: proxy info to access the data - :param indicator_number: Number used to identify an indicator within Fingertips as integer or string - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param indicator_number: Number used to identify an indicator within + Fingertips as integer or string + :param proxy: proxy given to the get request used to access the API + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data :return: A dictionary of metadata for the given indicator """ - metadata = get_json(base_url + 'indicator_metadata/by_indicator_id?indicator_ids=' + str(indicator_number)) + metadata = get_json(base_url + + 'indicator_metadata/by_indicator_id?indicator_ids=' + + str(indicator_number), proxy) if is_test: - return metadata, base_url + 'indicator_metadata/by_indicator_id?indicator_ids=' + str(indicator_number) + return metadata, base_url + \ + 'indicator_metadata/by_indicator_id?indicator_ids=' \ + + str(indicator_number) return metadata -def get_metadata_for_all_indicators_from_csv(is_test=False, proxies=None): +def get_metadata_for_all_indicators_from_csv(is_test=False, proxy=None): """ Returns a dataframe from the csv of all metadata for all indicators. - :param proxies: proxy info to access the data - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: A dataframe of all metadata for all indicators """ try: - metadata = pd.read_csv(base_url + 'indicator_metadata/csv/all') + metadata = get_csv(base_url + 'indicator_metadata/csv/all', proxy) + except URLError: - metadata = deal_with_url_error(base_url + 'indicator_metadata/csv/all') + metadata = deal_with_url_error( + base_url + 'indicator_metadata/csv/all', proxy) + if is_test: return metadata, base_url + 'indicator_metadata/csv/all' return metadata -def get_metadata_for_all_indicators(include_definition='no', include_system_content='no', is_test=False, proxies=None): +def get_metadata_for_all_indicators(include_definition='no', + include_system_content='no', + is_test=False, proxy=None): """ Returns the metadata for all indicators in a dataframe. - :param proxies: proxy info to access the data :param include_definition: optional to include definitions :param include_system_content: optional to include system content - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: dataframe of all indicators """ url = 'indicator_metadata/all?include_definition={}&include_system_content={}' url_suffix = url.format(include_definition, include_system_content) - metadata_df = get_json_return_df(base_url + url_suffix) + metadata_df = get_json_return_df(base_url + url_suffix, proxy) if is_test: return metadata_df, base_url + url_suffix return metadata_df -def get_multiplier_and_calculation_for_indicator(indicator_number, proxies=None): +def get_multiplier_and_calculation_for_indicator(indicator_number, proxy=None): """ Returns the multiplier and calculation method for a given indicator. - :param proxies: proxy info to access the data - :param indicator_number: Number used to identify an indicator within Fingertips as integer or string - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data - :return: A tuple of multiplier and calculation method from Fingetips metadata + :param indicator_number: Number used to identify an indicator within + Fingertips as integer or string + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy info to access the data + :return: A tuple of multiplier and calculation method from Fingertips + metadata """ - metadata = get_metadata_for_indicator(indicator_number) + metadata = get_metadata_for_indicator(indicator_number, proxy=proxy) multiplier = metadata[str(indicator_number)]['Unit']['Value'] calc_metadata = metadata[str(indicator_number)]['ConfidenceIntervalMethod']['Name'] if 'wilson' in calc_metadata.lower(): @@ -229,100 +261,119 @@ def get_multiplier_and_calculation_for_indicator(indicator_number, proxies=None) return multiplier, calc -def get_area_types_as_dict(is_test=False, proxies=None): +def get_area_types_as_dict(is_test=False, proxy=None): """ Returns all area types and related information such as ID and name. - :param proxies: proxy info to access the data - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy info to access the data :return: A dictionary of area types """ - areas = get_json(base_url + 'area_types') + areas = get_json(base_url + 'area_types', proxy) if is_test: return areas, base_url + 'area_types' return areas -def get_profile_by_id(profile_id, is_test=False, proxies=None): +def get_profile_by_id(profile_id, is_test=False, proxy=None): """ - Returns a profile as an dictionary which contains information about domains and sequencing. + Returns a profile as an dictionary which contains information about domains + and sequencing. - :param proxies: proxy info to access the data - :param profile_id: ID used in Fingertips to identify a profile as integer or string - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param profile_id: ID used in Fingertips to identify a profile as integer + or string + :param proxy: proxy info to access the data + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data :return: A dictionary of information about the profile """ + + tmp_url = base_url + 'profile?profile_id=' + str(profile_id) + if is_test: - return get_json(base_url + 'profile?profile_id=' + str(profile_id)), base_url + 'profile?profile_id=' + \ - str(profile_id) - return get_json(base_url + 'profile?profile_id=' + str(profile_id)) + return get_json(tmp_url, proxy), tmp_url + return get_json(tmp_url, proxy) -def get_all_profiles(is_test=False, proxies=None): + +def get_all_profiles(is_test=False, proxy=None): """ Returns all profiles. - :param proxies: proxy info to access the data - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data - :return: A dictionary of all profiles in Fingertips including information on domains and sequencing + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy info to access the data + :return: A dictionary of all profiles in Fingertips including information + on domains and sequencing """ - profiles = get_json(base_url + 'profiles') + profiles = get_json(base_url + 'profiles', proxy) if is_test: return profiles, base_url + 'profiles' return profiles -def get_domains_in_profile(profile_id, proxies=None): +def get_domains_in_profile(profile_id, proxy=None): """ Returns the domain IDs for a given profile. - :param proxies: proxy info to access the data - :param profile_id: ID used in Fingertips to identify a profile as integer or string + :param profile_id: ID used in Fingertips to identify a profile as integer + or string + :param proxy: proxy given to the get request used to access the API :return: A list of domain IDs """ - profile = get_profile_by_id(profile_id) + profile = get_profile_by_id(profile_id, proxy=proxy) return profile['GroupIds'] -def get_area_types_for_profile(profile_id, is_test=False, proxies=None): +def get_area_types_for_profile(profile_id, is_test=False, proxy=None): """ Retrieves all the area types that have data for a given profile. - :param proxies: proxy info to access the data - :param profile_id: ID used in Fingertips to identify a profile as integer or string - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param profile_id: ID used in Fingertips to identify a profile as integer + or string + :param proxy: proxy given to the get request used to access the API + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data :return: A list of dictionaries of area types with relevant information """ + + tmp_url = base_url + 'area_types?profile_ids=' + str(profile_id) + if is_test: - return get_json(base_url + 'area_types?profile_ids=' + str(profile_id)), base_url + 'area_types?profile_ids=' + \ - str(profile_id) - return get_json(base_url + 'area_types?profile_ids=' + str(profile_id)) + return get_json(tmp_url, proxy), tmp_url + + return get_json(tmp_url, proxy) -def get_area_type_ids_for_profile(profile_id, proxies=None): +def get_area_type_ids_for_profile(profile_id, proxy=None): """ Returns a list of area types used within a given profile. - :param proxies: proxy info to access the data - :param profile_id: ID used in Fingertips to identify a profile as integer or string + :param profile_id: ID used in Fingertips to identify a profile as integer + or string + :param proxy: proxy given to the get request used to access the API :return: A list of area types used within a given profile """ - area_type_obj = get_area_types_for_profile(profile_id) + area_type_obj = get_area_types_for_profile(profile_id, proxy=proxy) area_type_list = [] for area_type in area_type_obj: area_type_list.append(area_type['Id']) return area_type_list -def get_profile_by_name(profile_name, proxies=None): +def get_profile_by_name(profile_name, proxy=None): """ - Returns a profile object given a name to search - try to be specific to get better results. + Returns a profile object given a name to search - try to be specific to get + better results. - :param proxies: proxy info to access the data - :param profile_name: A string or part of a string that is used as the profile name - :return: A dictionary of the profile metadata including domain information or an error message + :param profile_name: A string or part of a string that is used as the + profile name + :param proxy: proxy given to the get request used to access the API + :return: A dictionary of the profile metadata including domain information + or an error message """ - all_profiles = get_all_profiles() + all_profiles = get_all_profiles(proxy=proxy) profile_obj = '' for profile in all_profiles: if profile_name.lower() in profile['Name'].lower(): @@ -333,135 +384,161 @@ def get_profile_by_name(profile_name, proxies=None): return profile_obj -def get_profile_by_key(profile_key, proxies=None): +def get_profile_by_key(profile_key, proxy=None): """ - Returns a profile object given a key (as the stub following 'profile' in the website URL). For example, - give, a URL of the form `https://fingertips.phe.org.uk/profile/general-practice/data#page/3/gid/2000...`, + Returns a profile object given a key (as the stub following 'profile' in the + website URL). For example, give, a URL of the form + `https://fingertips.phe.org.uk/profile/general-practice/data#page/3/gid/2000...`, the key is 'general-practice'. - :param proxies: proxy info to access the data :param profile_key: The exact key for the profile. - :return: A dictionary of the profile metadata including domain information or an error message + :param proxy: proxy info to access the data + :return: A dictionary of the profile metadata including domain information + or an error message """ - all_profiles = get_all_profiles() + all_profiles = get_all_profiles(proxy=proxy) for profile in all_profiles: if profile['Key'] == profile_key: return profile return 'Profile could not be found' -def get_metadata_for_indicator_as_dataframe(indicator_ids, is_test=False, proxies=None): +def get_metadata_for_indicator_as_dataframe(indicator_ids, is_test=False, + proxy=None): """ - Returns a dataframe of metadata for a given indicator ID or list of indicator IDs. + Returns a dataframe of metadata for a given indicator ID or list of + indicator IDs. - :param proxies: proxy info to access the data - :param indicator_ids: Number or list of numbers used to identify an indicator within Fingertips as integer or string + :param indicator_ids: Number or list of numbers used to identify an + indicator within Fingertips as integer or string + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: Dataframe object with metadate for the indicator ID """ - url_suffix = "indicator_metadata/csv/by_indicator_id?indicator_ids={}" + if isinstance(indicator_ids, list): indicator_ids = ','.join(list(map(str, indicator_ids))) + else: + indicator_ids = str(indicator_ids) + + tmp_url = base_url + f"indicator_metadata/csv/by_indicator_id?" \ + f"indicator_ids={indicator_ids}" try: - df = pd.read_csv(base_url + url_suffix.format(str(indicator_ids))) + df = get_csv(tmp_url, proxy) except HTTPError: - raise NameError('Indicator {} does not exist'.format(indicator_ids)) + raise NameError(f"Indicator {indicator_ids} does not exist") except URLError: - df = deal_with_url_error(base_url + url_suffix.format(str(indicator_ids))) + df = deal_with_url_error(tmp_url, proxy) + if is_test: - return df, base_url + url_suffix.format(str(indicator_ids)) + return df, tmp_url return df -def get_metadata_for_domain_as_dataframe(group_ids, is_test=False, proxies=None): +def get_metadata_for_domain_as_dataframe(group_ids, is_test=False, proxy=None): """ - Returns a dataframe of metadata for a given domain ID or list of domain IDs. + Returns a dataframe of metadata for a given domain ID or list of domain + IDs. - :param proxies: proxy info to access the data - :param group_ids: Number or list of numbers used to identify a domain within Fingertips as integer or string - :return: Dataframe object with metadata for the indicators for a given domain ID + :param group_ids: Number or list of numbers used to identify a domain + within Fingertips as integer or string + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API + :return: Dataframe object with metadata for the indicators for a given + domain ID """ - url_suffix = "indicator_metadata/csv/by_group_id?group_id={}" - if isinstance(group_ids, list): - df = pd.DataFrame() - for group_id in group_ids: - try: - df = df.append(pd.read_csv(base_url + url_suffix.format(str(group_id)))) - except HTTPError: - raise NameError('Domain {} does not exist'.format(group_id)) - except URLError: - df = deal_with_url_error(base_url + url_suffix.format(str(group_id))) - else: + if not isinstance(group_ids, list): + group_ids = [group_ids] + + list_of_df = [] + + for group_id in group_ids: + + tmp_url = base_url + f"indicator_metadata/csv/by_group_id" \ + f"?group_id={group_id}" try: - df = pd.read_csv(base_url + url_suffix.format(str(group_ids))) + list_of_df.append(get_csv(tmp_url, proxy)) except HTTPError: - raise NameError('Domain {} does not exist'.format(group_ids)) + raise NameError(f"Domain {group_id} does not exist") except URLError: - df = deal_with_url_error(base_url + url_suffix.format(str(group_ids))) + list_of_df.append(deal_with_url_error(tmp_url, proxy)) + else: + df = pd.concat(list_of_df) + if is_test: - return df, base_url + url_suffix.format(str(group_ids)) + return df, tmp_url return df -def get_metadata_for_profile_as_dataframe(profile_ids, proxies=None): +def get_metadata_for_profile_as_dataframe(profile_ids, proxy=None): """ - Returns a dataframe of metadata for a given profile ID or list of profile IDs. + Returns a dataframe of metadata for a given profile ID or list of profile + IDs. - :param proxies: proxy info to access the data - :param profile_ids: ID or list of IDs used in Fingertips to identify a profile as integer or string - :return: Dataframe object with metadata for the indicators for a given group ID + :param profile_ids: ID or list of IDs used in Fingertips to identify a + profile as integer or string + :param proxy: proxy given to the get request used to access the API + :return: Dataframe object with metadata for the indicators for a given + group ID """ url_suffix = "indicator_metadata/csv/by_profile_id?profile_id={}" - if isinstance(profile_ids, list): - df = pd.DataFrame() - for profile_id in profile_ids: - try: - df = df.append(pd.read_csv(base_url + url_suffix.format(str(profile_id)))) - except HTTPError: - raise NameError('Profile {} does not exist'.format(profile_id)) - except URLError: - df = deal_with_url_error(base_url + url_suffix.format(str(profile_id))) - else: + + if not isinstance(profile_ids, list): + profile_ids = [profile_ids] + + list_of_df = [] + + for profile_id in profile_ids: + + tmp_url = base_url + f"indicator_metadata/csv/by_profile_id" \ + f"?profile_id={profile_id}" try: - df = pd.read_csv(base_url + url_suffix.format(str(profile_ids))) + list_of_df.append(get_csv(tmp_url, proxy)) except HTTPError: - raise NameError('Profile {} does not exist'.format(profile_ids)) + raise NameError(f"Profile {profile_id} does not exist") except URLError: - df = deal_with_url_error(base_url + url_suffix.format(str(profile_ids))) - return df + list_of_df.append(deal_with_url_error((tmp_url, proxy))) + return pd.concat(list_of_df) -def get_metadata(indicator_ids=None, domain_ids=None, profile_ids=None, proxies=None): + +def get_metadata(indicator_ids=None, domain_ids=None, profile_ids=None, + proxy=None): """ - Returns a dataframe object of metadata for a given indicator, domain, and/or profile given the relevant IDs. At + Returns a dataframe object of metadata for a given indicator, domain, + and/or profile given the relevant IDs. At least one of these IDs has to be given otherwise an error is raised. - :param proxies: proxy info to access the data - :param indicator_ids: [OPTIONAL] Number used to identify an indicator within Fingertips as integer or string - :param domain_ids: [OPTIONAL] Number used to identify a domain within Fingertips as integer or string - :param profile_ids: [OPTIONAL] ID used in Fingertips to identify a profile as integer or string - :return: A dataframe object with metadata for the given IDs or an error if nothing is specified - """ - if indicator_ids and domain_ids and profile_ids: - df = get_metadata_for_profile_as_dataframe(profile_ids) - df = df.append(get_metadata_for_domain_as_dataframe(domain_ids)) - df = df.append(get_metadata_for_indicator_as_dataframe(indicator_ids)) - return df - if indicator_ids and domain_ids: - df = get_metadata_for_domain_as_dataframe(domain_ids) - df = df.append(get_metadata_for_indicator_as_dataframe(indicator_ids)) - return df - if indicator_ids and profile_ids: - df = get_metadata_for_profile_as_dataframe(profile_ids) - df = df.append(get_metadata_for_indicator_as_dataframe(indicator_ids)) - return df - if domain_ids and profile_ids: - df = get_metadata_for_profile_as_dataframe(profile_ids) - df = df.append(get_metadata_for_domain_as_dataframe(domain_ids)) - return df - if profile_ids: - return get_metadata_for_profile_as_dataframe(profile_ids) - if domain_ids: - return get_metadata_for_domain_as_dataframe(domain_ids) + :param indicator_ids: [OPTIONAL] Number used to identify an indicator + within Fingertips as integer or string + :param domain_ids: [OPTIONAL] Number used to identify a domain within + Fingertips as integer or string + :param profile_ids: [OPTIONAL] ID used in Fingertips to identify a profile + as integer or string + :param proxy: proxy info to access the data + :return: A dataframe object with metadata for the given IDs or an error if + nothing is specified + """ + + # Works as long as there is no id that equals zero + if not any([indicator_ids, domain_ids, profile_ids]): + raise NameError( + 'Must use a valid indicator IDs, domain IDs or profile IDs') + + list_of_df = [] + if indicator_ids: - return get_metadata_for_indicator_as_dataframe(indicator_ids) - raise NameError('Must use a valid indicator IDs, domain IDs or profile IDs') + list_of_df.append(get_metadata_for_profile_as_dataframe( + profile_ids, proxy)) + + if domain_ids: + list_of_df.append(get_metadata_for_domain_as_dataframe( + domain_ids, proxy)) + + if profile_ids: + list_of_df.append(get_metadata_for_indicator_as_dataframe( + indicator_ids, proxy)) + + return pd.concat(list_of_df) From 7e344023562468fa86623f29100310a814da7f0a Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Wed, 25 Jan 2023 21:24:59 +0000 Subject: [PATCH 07/34] Added proxy variable to functions. --- fingertips_py/retrieve_data.py | 204 ++++++++++++++++++++------------- 1 file changed, 124 insertions(+), 80 deletions(-) diff --git a/fingertips_py/retrieve_data.py b/fingertips_py/retrieve_data.py index 6d33c93..5fd4634 100644 --- a/fingertips_py/retrieve_data.py +++ b/fingertips_py/retrieve_data.py @@ -1,162 +1,206 @@ """ retrieve_data.py ================================== -A group of functions to retrieve data from Fingertips by indicator, profile, domain (group), or geography. +A group of functions to retrieve data from Fingertips by indicator, profile, +domain (group), or geography. """ - import pandas as pd from urllib.error import URLError, HTTPError from .api_calls import base_url, get_json_return_df, deal_with_url_error -from .metadata import get_area_type_ids_for_profile, get_metadata_for_all_indicators, get_all_areas +from .metadata import get_area_type_ids_for_profile, get_csv, \ + get_metadata_for_all_indicators, get_all_areas -def get_data_by_indicator_ids(indicator_ids, area_type_id, parent_area_type_id=15, profile_id=None, - include_sortable_time_periods=None, is_test=False): +def get_data_by_indicator_ids(indicator_ids, area_type_id, + parent_area_type_id=15, profile_id=None, + include_sortable_time_periods=None, + is_test=False, + proxy=None): """ - Returns a dataframe of indicator data given a list of indicators and area types. + Returns a dataframe of indicator data given a list of indicators and area + types. :param indicator_ids: List of indicator IDs as strings - :param area_type_id: ID of area type (eg. CCG, Upper Tier Local Authority) used in Fingertips as integer or string - :param parent_area_type_id: Area type of parent area - defaults to England value + :param area_type_id: ID of area type (eg. CCG, Upper Tier Local Authority) + used in Fingertips as integer or string + :param parent_area_type_id: Area type of parent area - defaults to England + value :param profile_id: ID of profile to select by as either int or string - :param include_sortable_time_periods: Boolean as to whether to include a sort-friendly data field - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param include_sortable_time_periods: Boolean as to whether to include a + sort-friendly data field + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: A dataframe of data relating to the given indicators """ + url_append = "" + + if profile_id: + url_append += f"&profile_id={profile_id}" + + if include_sortable_time_periods: + url_append += "&include_sortable_time_periods=yes" - url_suffix = 'all_data/csv/by_indicator_id?indicator_ids={}&child_area_type_id={}&parent_area_type_id={}' - if profile_id and not include_sortable_time_periods: - url_addition = '&profile_id={}'.format(str(profile_id)) - url_suffix = url_suffix + url_addition - elif include_sortable_time_periods and not profile_id: - url_addition = '&include_sortable_time_periods=yes' - url_suffix = url_suffix + url_addition - elif profile_id and include_sortable_time_periods: - url_addition = '&profile_id={}&include_sortable_time_periods=yes'.format(str(profile_id)) - url_suffix = url_suffix + url_addition if isinstance(indicator_ids, list): - if any(isinstance(ind, int) for ind in indicator_ids): - indicator_ids = ','.join(str(ind) for ind in indicator_ids) - else: - indicator_ids = ','.join(indicator_ids) - else: - indicator_ids = str(indicator_ids) - populated_url = url_suffix.format(indicator_ids, str(area_type_id), parent_area_type_id) + indicator_ids = ','.join(list(map(str, indicator_ids))) + + tmp_url = base_url + f"all_data/csv/by_indicator_id?indicator_ids" \ + f"={indicator_ids}&child_area_type_id" \ + f"={area_type_id}&parent_area_type_id" \ + f"={parent_area_type_id}" + url_append try: - df = pd.read_csv(base_url + populated_url) + df = get_csv(tmp_url, proxy) except URLError: - df = deal_with_url_error(base_url + populated_url) + df = deal_with_url_error(tmp_url, proxy) if is_test: - return df, base_url + populated_url + return df, tmp_url return df -def get_all_data_for_profile(profile_id, parent_area_type_id=15, area_type_id=None, filter_by_area_codes=None, - is_test=False): +def get_all_data_for_profile(profile_id, parent_area_type_id=15, + area_type_id=None, filter_by_area_codes=None, + is_test=False, + proxy=None): """ Returns a dataframe of data for all indicators within a profile. - :param profile_id: ID used in Fingertips to identify a profile as integer or string - :param parent_area_type_id: Area type of parent area - defaults to England value - :param area_type_id: Option to only return data for a given area type. Area type ids are string, int or a list. - :param filter_by_area_codes: Option to limit returned data to areas. Areas as either string or list of strings. - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data - :return: A dataframe of data for all indicators within a profile with any filters applied + :param profile_id: ID used in Fingertips to identify a profile as integer + or string. + :param parent_area_type_id: Area type of parent area - defaults to England. + value + :param area_type_id: Option to only return data for a given area type. Area + type ids are string, int or a list. + :param filter_by_area_codes: Option to limit returned data to areas. Areas + as either string or list of strings. + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API + :return: A dataframe of data for all indicators within a profile with any + filters applied. """ if area_type_id: - area_types = area_type_id + area_types = [area_type_id] else: - area_types = get_area_type_ids_for_profile(profile_id) - url_suffix = 'all_data/csv/by_profile_id?child_area_type_id={}&parent_area_type_id={}&profile_id={}' - df = pd.DataFrame() + area_types = get_area_type_ids_for_profile(profile_id, proxy) + + list_of_df = [] + for area in area_types: - populated_url = url_suffix.format(area, parent_area_type_id, profile_id) + + tmp_url = base_url + f"all_data/csv/by_profile_id?child_area_type_id" \ + f"={area}&parent_area_type_id={parent_area_type_id}" \ + f"&profile_id={profile_id}" try: - df_returned = pd.read_csv(base_url + populated_url) - except HTTPError: - raise Exception('There has been a server error with Fingertips for this request. ') + list_of_df.append(get_csv(tmp_url, proxy)) + except URLError: - df_returned = deal_with_url_error(base_url + populated_url) - df = df.append(df_returned) + list_of_df.append(deal_with_url_error(tmp_url, proxy)) + else: + df = pd.concat(list_of_df) + if filter_by_area_codes: if isinstance(filter_by_area_codes, list): df = df.loc[df['Area Code'].isin(filter_by_area_codes)] elif isinstance(filter_by_area_codes, str): df = df.loc[df['Area Code'] == filter_by_area_codes] df = df.reset_index() + if is_test: - return df, base_url + populated_url + return df, tmp_url return df -def get_all_data_for_indicators(indicators, area_type_id, parent_area_type_id=15, filter_by_area_codes=None, - is_test=False): +def get_all_data_for_indicators(indicators, area_type_id, + parent_area_type_id=15, + filter_by_area_codes=None, + is_test=False, + proxy=None): """ Returns a dataframe of data for given indicators at an area. :param indicators: List or integer or string of indicator Ids - :param area_type_id: ID of area type (eg. ID of General Practice is 7 etc) used in Fingertips as integer or string - :param parent_area_type_id: Area type of parent area - defaults to England value - :param filter_by_area_codes: Option to limit returned data to areas. Areas as either string or list of strings - :param is_test: Used for testing. Returns a tuple of expected return and the URL called to retrieve the data + :param area_type_id: ID of area type (eg. ID of General Practice is 7 etc) + used in Fingertips as integer or string + :param parent_area_type_id: Area type of parent area - defaults to England + value + :param filter_by_area_codes: Option to limit returned data to areas. Areas + as either string or list of strings + :param is_test: Used for testing. Returns a tuple of expected return and + the URL called to retrieve the data + :param proxy: proxy given to the get request used to access the API :return: Dataframe of data for given indicators at an area """ - url_suffix = 'all_data/csv/by_indicator_id?indicator_ids={}&child_area_type_id={}&parent_area_type_id={}' if isinstance(indicators, list): - if any(isinstance(ind, int) for ind in indicators): - indicators = ','.join(str(ind) for ind in indicators) - else: - indicators = ','.join(indicators) - else: - indicators = str(indicators) - populated_url = url_suffix.format(indicators, str(area_type_id), str(parent_area_type_id)) + indicators = ','.join(list(map(str, indicators))) + + tmp_url = base_url + f"all_data/csv/by_indicator_id?indicator_ids" \ + f"={indicators}&child_area_type_id={area_type_id}" \ + f"&parent_area_type_id={parent_area_type_id}" try: - df = pd.read_csv(base_url + populated_url) + df = get_csv(tmp_url, proxy) except URLError: - df = deal_with_url_error(base_url + populated_url) - df.reset_index() + df = deal_with_url_error(tmp_url, proxy) + if filter_by_area_codes: if isinstance(filter_by_area_codes, list): df = df.loc[df['Area Code'].isin(filter_by_area_codes)] elif isinstance(filter_by_area_codes, str): df = df.loc[df['Area Code'] == filter_by_area_codes] - df = df.reset_index() + + df.reset_index(inplace=True) + if is_test: - return df, base_url + populated_url + return df, tmp_url return df -def get_all_areas_for_all_indicators(): +def get_all_areas_for_all_indicators(proxy=None): """ Returns a dataframe of all indicators and their geographical breakdowns. + :param proxy: proxy given to the get request used to access the API :return: Dataframe of all indicators and their geographical breakdowns """ url_suffix = 'available_data' - df = get_json_return_df(base_url + url_suffix, transpose=False) - indicator_metadata = get_metadata_for_all_indicators() - df = pd.merge(df, indicator_metadata[['Descriptive']], left_on='IndicatorId', right_index=True) + + df = get_json_return_df(base_url + url_suffix, transpose=False, + proxy=proxy) + + indicator_metadata = get_metadata_for_all_indicators(proxy=proxy) + + df = pd.merge(df, indicator_metadata[['Descriptive']], + left_on='IndicatorId', right_index=True) + df['IndicatorName'] = df.apply(lambda x: x['Descriptive']['Name'], axis=1) - areas = get_all_areas() - df['GeographicalArea'] = df.apply(lambda x: areas[x['AreaTypeId']]['Name'], axis=1) + + areas = get_all_areas(proxy=proxy) + + df['GeographicalArea'] = df.apply(lambda x: areas[x['AreaTypeId']]['Name'], + axis=1) df = df[['IndicatorId', 'IndicatorName', 'GeographicalArea', 'AreaTypeId']] + return df -def get_data_for_indicator_at_all_available_geographies(indicator_id): +def get_data_for_indicator_at_all_available_geographies(indicator_id, + proxy=None): """ - Returns a dataframe of all data for an indicator for all available geographies. + Returns a dataframe of all data for an indicator for all available + geographies. :param indicator_id: Indicator id - :return: Dataframe of data for indicator for all available areas for all time periods + :param proxy: proxy given to the get request used to access the API + :return: Dataframe of data for indicator for all available areas for all + time periods """ - all_area_for_all_indicators = get_all_areas_for_all_indicators() - areas_for_indicator = all_area_for_all_indicators[all_area_for_all_indicators['IndicatorId'] == indicator_id] + all_area_for_all_indicators = get_all_areas_for_all_indicators(proxy) + areas_for_indicator = all_area_for_all_indicators[ + all_area_for_all_indicators['IndicatorId'] == indicator_id] areas_to_get = areas_for_indicator['AreaTypeId'].unique() df = pd.DataFrame() for area in areas_to_get: - df_temp = get_data_by_indicator_ids(indicator_id, area) + df_temp = get_data_by_indicator_ids(indicator_id, area, proxy=proxy) df = df.append(df_temp) df.drop_duplicates(inplace=True) return df From d2401bf84fcebe254e9f5615faa8698274f4f06a Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Wed, 25 Jan 2023 21:28:01 +0000 Subject: [PATCH 08/34] Added HTTP error exception to get_csv. --- fingertips_py/api_calls.py | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/fingertips_py/api_calls.py b/fingertips_py/api_calls.py index 03d7cd5..e75a698 100644 --- a/fingertips_py/api_calls.py +++ b/fingertips_py/api_calls.py @@ -8,6 +8,7 @@ import json import pandas as pd from io import StringIO +import urllib def make_request(url, attr=None, proxy=None): @@ -93,6 +94,10 @@ def get_csv(url, proxy=None): except requests.exceptions.SSLError: req = requests.get(url, verify=False, proxies=proxy).text + except urllib.error.HTTPError: + raise Exception( + 'There has been a server error with Fingertips for this request.') + return pd.read_csv(StringIO(req)) From 4cfbd2af20adbdd73b774e52505709d125057c9b Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Wed, 25 Jan 2023 21:29:53 +0000 Subject: [PATCH 09/34] Removed extraneous lines and cleaned up text. --- fingertips_py/metadata.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/fingertips_py/metadata.py b/fingertips_py/metadata.py index ee59659..4e393ea 100644 --- a/fingertips_py/metadata.py +++ b/fingertips_py/metadata.py @@ -386,8 +386,8 @@ def get_profile_by_name(profile_name, proxy=None): def get_profile_by_key(profile_key, proxy=None): """ - Returns a profile object given a key (as the stub following 'profile' in the - website URL). For example, give, a URL of the form + Returns a profile object given a key (as the stub following 'profile' in + the website URL). For example, give, a URL of the form `https://fingertips.phe.org.uk/profile/general-practice/data#page/3/gid/2000...`, the key is 'general-practice'. @@ -419,8 +419,6 @@ def get_metadata_for_indicator_as_dataframe(indicator_ids, is_test=False, if isinstance(indicator_ids, list): indicator_ids = ','.join(list(map(str, indicator_ids))) - else: - indicator_ids = str(indicator_ids) tmp_url = base_url + f"indicator_metadata/csv/by_indicator_id?" \ f"indicator_ids={indicator_ids}" From 16c87d6f48b2f008f595808d66d95d20daf36cca Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Wed, 25 Jan 2023 22:11:50 +0000 Subject: [PATCH 10/34] Added proxy variable to deprivation_decile. --- fingertips_py/area_data.py | 63 +++++++++++++++++++++++--------------- 1 file changed, 38 insertions(+), 25 deletions(-) diff --git a/fingertips_py/area_data.py b/fingertips_py/area_data.py index 7c48e4b..f9a00ed 100644 --- a/fingertips_py/area_data.py +++ b/fingertips_py/area_data.py @@ -4,13 +4,13 @@ Functions to retrieve data that are specific to areas and relevant to all indicators. For example: Deprivation decile. """ - import pandas as pd import warnings from .retrieve_data import get_data_by_indicator_ids -def defined_qcut(df, value_series, number_of_bins, bins_for_extras, labels=False): +def defined_qcut(df, value_series, number_of_bins, bins_for_extras, + labels=False): """ Allows users to define how values are split into bins when clustering. @@ -21,15 +21,18 @@ def defined_qcut(df, value_series, number_of_bins, bins_for_extras, labels=False :param labels: Optional. Labels for bins if required :return: A dataframe with a new column 'bins' which contains the cluster numbers """ - if max(bins_for_extras) > number_of_bins or any(x < 0 for x in bins_for_extras): + if max(bins_for_extras) > number_of_bins or any( + x < 0 for x in bins_for_extras): raise ValueError('Attempted to allocate to a bin that doesnt exist') - base_number, number_of_values_to_allocate = divmod(df[value_series].count(), number_of_bins) + base_number, number_of_values_to_allocate = divmod( + df[value_series].count(), number_of_bins) bins_for_extras = bins_for_extras[:number_of_values_to_allocate] if number_of_values_to_allocate == 0: df['bins'] = pd.qcut(df[value_series], number_of_bins, labels=labels) return df elif number_of_values_to_allocate > len(bins_for_extras): - raise ValueError('There are more values to allocate than the list provided, please select more bins') + raise ValueError( + 'There are more values to allocate than the list provided, please select more bins') bins = {} for i in range(number_of_bins): number_of_values_in_bin = base_number @@ -43,7 +46,8 @@ def defined_qcut(df, value_series, number_of_bins, bins_for_extras, labels=False row_to_end_allocate = 0 for bin_number, number_in_bin in bins.items(): row_to_end_allocate += number_in_bin - bins.update({bin_number: [number_in_bin, row_to_start_allocate, row_to_end_allocate]}) + bins.update({bin_number: [number_in_bin, row_to_start_allocate, + row_to_end_allocate]}) row_to_start_allocate = row_to_end_allocate conditions = [df['rank'].iloc[v[1]: v[2]] for k, v in bins.items()] series_to_add = pd.Series() @@ -69,18 +73,24 @@ def defined_qcut(df, value_series, number_of_bins, bins_for_extras, labels=False } -def deprivation_decile(area_type_id, year='2015', area_code=None): +def deprivation_decile(area_type_id, year='2015', area_code=None, proxy=None): """ - Takes in an area type id and returns a pandas series of deprivation deciles for those areas (with the areas as an - index. If a specific area is requested, it returns just the deprivation decile value. + Takes in an area type id and returns a pandas series of deprivation deciles + for those areas (with the areas as an index. If a specific area is + requested, it returns just the deprivation decile value. :param area_type_id: Area type id as denoted by the Fingertips API :param year: Year of deprivation score - :param area_code: Optional. Area code for area type to return a single value for that area - :return: A pandas series of deprivation scores with area codes as the index. Or single value if area is specified. + :param area_code: Optional. Area code for area type to return a single + value for that area + :param proxy: proxy given to the get request used to access the API + :return: A pandas series of deprivation scores with area codes as the + index. Or single value if area is specified. """ - warnings.warn('Caution, the deprivation deciles are being calculated on the fly and might show some inconsistencies' - ' from the live Fingertips site.') + warnings.warn('Caution, the deprivation deciles are being calculated on ' + 'the fly and might show some inconsistencies from the live ' + 'Fingertips site.') + acceptable_deprivation_years_la = ['2010', '2015'] acceptable_deprivation_years_gp = ['2015'] acceptable_area_types = [3, 101, 102, 7, 153] @@ -88,34 +98,37 @@ def deprivation_decile(area_type_id, year='2015', area_code=None): if not isinstance(year, str): year = str(year) if year not in acceptable_deprivation_years_la and area_type_id is not 7: - raise ValueError \ - ('The acceptable years are 2010 and 2015 for local authorities and CCGs, please select one of these') + raise ValueError('The acceptable years are 2010 and 2015 for local ' + 'authorities and CCGs, please select one of these') elif year not in acceptable_deprivation_years_gp: raise ValueError('The acceptable years are 2015, please select this') if area_type_id not in acceptable_area_types: - raise ValueError('Currently, we support deprivation decile for District & UA, County & UA, MSOA and GP area ' - 'types') + raise ValueError('Currently, we support deprivation decile for' + ' District & UA, County & UA, MSOA and GP area types') if area_type_id == 3: indicator_id = 93275 - area_dep_dec = get_data_by_indicator_ids(indicator_id, area_type_id, parent_area_type_id=101, profile_id=143, - include_sortable_time_periods=True) + area_dep_dec = get_data_by_indicator_ids(indicator_id, area_type_id, + parent_area_type_id=101, + profile_id=143, + include_sortable_time_periods=True, + proxy=proxy) else: indicator_id = 91872 - area_dep_dec = get_data_by_indicator_ids(indicator_id, area_type_id) + area_dep_dec = get_data_by_indicator_ids(indicator_id, area_type_id, + proxy=proxy) if area_type_id == 102: order_of_extra_values = [0, 9, 1, 2, 3, 4, 5, 6, 7, 8] area_dep_dec = area_dep_dec[area_dep_dec['Area Code'] != 'E92000001'] if not order_of_extra_values: order_of_extra_values = extra_areas[area_dep_dec['Value'].count() % 10] - area_dep_dec = defined_qcut(area_dep_dec, 'Value', 10, order_of_extra_values) + area_dep_dec = defined_qcut(area_dep_dec, 'Value', 10, + order_of_extra_values) area_dep_dec.set_index('Area Code', inplace=True) if area_code: try: return area_dep_dec.loc[area_code, 'decile'] except KeyError: - raise KeyError('This area is not available at in this area type. Please try another area type') + raise KeyError('This area is not available at in this area type. ' + 'Please try another area type') return area_dep_dec['bins'] - - - From 3abb3eb27eac31765c96afcbae287287ea9f8e89 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Fri, 27 Jan 2023 21:32:57 +0000 Subject: [PATCH 11/34] Changed function used to process JSONs to pd dataframes. --- fingertips_py/api_calls.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fingertips_py/api_calls.py b/fingertips_py/api_calls.py index e75a698..ab5fd81 100644 --- a/fingertips_py/api_calls.py +++ b/fingertips_py/api_calls.py @@ -56,7 +56,7 @@ def get_json_return_df(url, transpose=True, proxy=None): except requests.exceptions.SSLError: req = requests.get(url, verify=False, proxies=proxy) try: - df = pd.read_json(req.content, encoding='utf-8') + df = pd.DataFrame.from_dict(req.json()) except ValueError: df = pd.DataFrame.from_dict([req.json()]) if transpose: From 1f6823a28d78def42ca543711397871d6cf39f1b Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Fri, 27 Jan 2023 22:08:36 +0000 Subject: [PATCH 12/34] Updated test for get_all_areas as the area '1' has been removed. Changed it to look for the England area type. --- fingertips_py/unit_tests/tests.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/fingertips_py/unit_tests/tests.py b/fingertips_py/unit_tests/tests.py index 92b6a93..68833d1 100644 --- a/fingertips_py/unit_tests/tests.py +++ b/fingertips_py/unit_tests/tests.py @@ -44,9 +44,18 @@ def test_get_all_data_for_profile(): def test_get_all_areas(): data = get_all_areas(is_test=True) + + # Check the function output is a tuple + assert isinstance(data, tuple) is True + + # Check the standard output for the function is a dict assert isinstance(data[0], dict) is True - assert isinstance(data[0][1], dict) is True - assert isinstance(data[0][1]['Name'], str) is True + + # See if the England area type is there + assert 15 in data[0] + assert data[0][15]["Name"] == "England" + + # Check the correct URL is being used assert data[1] == 'http://fingertips.phe.org.uk/api/area_types' From 202bfb2b62f9a4e4d8db4588aad3e86b91846c4f Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Fri, 27 Jan 2023 22:27:40 +0000 Subject: [PATCH 13/34] Updated test for 'get_all_data_for_indicators()' as the number of columns had changed since test was written. --- fingertips_py/unit_tests/tests.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/fingertips_py/unit_tests/tests.py b/fingertips_py/unit_tests/tests.py index 68833d1..d4fd642 100644 --- a/fingertips_py/unit_tests/tests.py +++ b/fingertips_py/unit_tests/tests.py @@ -61,8 +61,17 @@ def test_get_all_areas(): def test_get_all_data_for_indicators(): data = get_all_data_for_indicators([92949, 247], area_type_id=102, is_test=True) + + # Check that what the functon returns a pd dataframe assert isinstance(data[0], pd.DataFrame) is True - assert data[0].shape[1] == 26 + + # Check one of the columns is named "Indicator ID" + assert "Indicator ID" in data[0].columns + + # Check that only 92949 and 247 are in the "Indicator ID" column + assert all(data[0]["Indicator ID"].isin([92949, 247])) + + # Check the correct URL is being used assert data[1] == 'http://fingertips.phe.org.uk/api/all_data/csv/by_indicator_id?indicator_ids=92949,247&child_area_type_id=102&parent_area_type_id=15' From 80084f07383043c83477839a15556113326dc99e Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Fri, 27 Jan 2023 22:33:26 +0000 Subject: [PATCH 14/34] Updated test for 'get_data_by_indicator_ids()' as the number of columns had changed since test was written. --- fingertips_py/unit_tests/tests.py | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/fingertips_py/unit_tests/tests.py b/fingertips_py/unit_tests/tests.py index d4fd642..98d7eee 100644 --- a/fingertips_py/unit_tests/tests.py +++ b/fingertips_py/unit_tests/tests.py @@ -77,8 +77,17 @@ def test_get_all_data_for_indicators(): def test_get_data_by_indicator_ids(): data = get_data_by_indicator_ids([92949, 247], 102, is_test=True) + + # Check that what the functon returns a pd dataframe assert isinstance(data[0], pd.DataFrame) is True - assert data[0].shape[1] == 26 + + # Check one of the columns is named "Indicator ID" + assert "Indicator ID" in data[0].columns + + # Check that only 92949 and 247 are in the "Indicator ID" column + assert all(data[0]["Indicator ID"].isin([92949, 247])) + + # Check the correct URL is being used assert data[1] == 'http://fingertips.phe.org.uk/api/all_data/csv/by_indicator_id?indicator_ids=92949,247&child_area_type_id=102&parent_area_type_id=15' From fed8f7aada32ccfa3eea5069ea9a131bdb0314ec Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Sat, 28 Jan 2023 22:31:26 +0000 Subject: [PATCH 15/34] Refactored 'get_metadata_for_all_indicators()' so all the columns are expanded out and the function uses bool inputs rather than strings. --- fingertips_py/metadata.py | 59 +++++++++++++++++++++++++++++++++------ 1 file changed, 51 insertions(+), 8 deletions(-) diff --git a/fingertips_py/metadata.py b/fingertips_py/metadata.py index 4e393ea..67d0d29 100644 --- a/fingertips_py/metadata.py +++ b/fingertips_py/metadata.py @@ -210,14 +210,14 @@ def get_metadata_for_all_indicators_from_csv(is_test=False, proxy=None): except URLError: metadata = deal_with_url_error( base_url + 'indicator_metadata/csv/all', proxy) - + if is_test: return metadata, base_url + 'indicator_metadata/csv/all' return metadata -def get_metadata_for_all_indicators(include_definition='no', - include_system_content='no', +def get_metadata_for_all_indicators(include_definition=False, + include_system_content=False, is_test=False, proxy=None): """ Returns the metadata for all indicators in a dataframe. @@ -229,12 +229,55 @@ def get_metadata_for_all_indicators(include_definition='no', :param proxy: proxy given to the get request used to access the API :return: dataframe of all indicators """ - url = 'indicator_metadata/all?include_definition={}&include_system_content={}' - url_suffix = url.format(include_definition, include_system_content) - metadata_df = get_json_return_df(base_url + url_suffix, proxy) + url_suffix = "indicator_metadata/all?include_definition=" + + if include_definition: + url_suffix += "yes" + else: + url_suffix += "no" + + if include_system_content: + url_suffix += "&include_system_content=yes" + else: + url_suffix += "&include_system_content=no" + + df = get_json_return_df(base_url + url_suffix, proxy) + + # Transpose to get the Indicator ID as a column + df = df.transpose() + df.reset_index(inplace=True) + df.rename(columns={'index': 'Indicator ID'}, inplace=True) + + # Detect columns that contain any dictionaries + dict_cols = [] + + for col_name in df.columns: + if any(df[col_name].apply(lambda x: isinstance(x, dict))): + dict_cols.append(col_name) + + # Expand the dictionary columns of the metadata df + expanded_dfs = [] + + for col_name in dict_cols: + + # Extract the Dict column + tmp_df = pd.json_normalize(df[col_name]) + + # Change the new column names to be unique + tmp_df = tmp_df.add_prefix(col_name + "_") + + expanded_dfs.append(tmp_df) + + # Remove the dictionary columns + df.drop(dict_cols, axis=1, inplace=True) + + # Combine all the columns together + df0 = pd.concat(expanded_dfs, axis=1) + df = pd.concat([df, df0], axis=1) + if is_test: - return metadata_df, base_url + url_suffix - return metadata_df + return df, base_url + url_suffix + return df def get_multiplier_and_calculation_for_indicator(indicator_number, proxy=None): From e1fa5cd1a32125a811f9ef87e552ae1ac43c4bca Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Sun, 29 Jan 2023 03:05:57 +0000 Subject: [PATCH 16/34] Updated 'get_all_areas_for_all_indicators()' to merge correctly. --- fingertips_py/retrieve_data.py | 20 ++++++++++++++------ 1 file changed, 14 insertions(+), 6 deletions(-) diff --git a/fingertips_py/retrieve_data.py b/fingertips_py/retrieve_data.py index 5fd4634..b0e3517 100644 --- a/fingertips_py/retrieve_data.py +++ b/fingertips_py/retrieve_data.py @@ -6,6 +6,7 @@ """ import pandas as pd +import numpy as np from urllib.error import URLError, HTTPError from .api_calls import base_url, get_json_return_df, deal_with_url_error from .metadata import get_area_type_ids_for_profile, get_csv, \ @@ -164,20 +165,27 @@ def get_all_areas_for_all_indicators(proxy=None): """ url_suffix = 'available_data' - df = get_json_return_df(base_url + url_suffix, transpose=False, - proxy=proxy) + df_avail = get_json_return_df(base_url + url_suffix, transpose=False, + proxy=proxy) - indicator_metadata = get_metadata_for_all_indicators(proxy=proxy) + df_meta = get_metadata_for_all_indicators(proxy=proxy) - df = pd.merge(df, indicator_metadata[['Descriptive']], - left_on='IndicatorId', right_index=True) + # Get the descriptive columns + df_meta = df_meta.loc[:, + df_meta.columns.str.contains('Descriptive_|Indicator ID')] + df_meta['Indicator ID'] = df_meta['Indicator ID'].astype(np.int64) - df['IndicatorName'] = df.apply(lambda x: x['Descriptive']['Name'], axis=1) + df = pd.merge(df_avail, df_meta, + left_on='IndicatorId', + right_on='Indicator ID') areas = get_all_areas(proxy=proxy) df['GeographicalArea'] = df.apply(lambda x: areas[x['AreaTypeId']]['Name'], axis=1) + + df.rename(columns={'Descriptive_Name': 'IndicatorName'}, + inplace=True) df = df[['IndicatorId', 'IndicatorName', 'GeographicalArea', 'AreaTypeId']] return df From 44ab2a974440832ef4a005f1d12febacf2d1aae4 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Sun, 29 Jan 2023 17:50:01 +0000 Subject: [PATCH 17/34] Updated tests for 'get_data_for_indicator_at_all_available_geographies()'. --- fingertips_py/unit_tests/tests.py | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/fingertips_py/unit_tests/tests.py b/fingertips_py/unit_tests/tests.py index 98d7eee..cca0432 100644 --- a/fingertips_py/unit_tests/tests.py +++ b/fingertips_py/unit_tests/tests.py @@ -98,9 +98,17 @@ def test_get_all_areas_for_all_indicators(): def test_get_data_for_indicator_at_all_available_geographies(): + data = get_data_for_indicator_at_all_available_geographies(247) + + # Check that a pandas dataframe is returned by the function assert isinstance(data, pd.DataFrame) is True - assert data.shape[1] == 26 + + # Check one of the columns is named "Indicator ID" + assert "Indicator ID" in data[0].columns + + # Check that only `247` is in the "Indicator ID" column + assert all(data[0]["Indicator ID"].isin([247])) def test_get_metadata_for_profile_as_dataframe(): From 76cac54e6446eeb8bacafe2af39c3c3b95edc357 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Sun, 29 Jan 2023 18:00:04 +0000 Subject: [PATCH 18/34] Updated tests to match changes in API. --- fingertips_py/unit_tests/tests.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/fingertips_py/unit_tests/tests.py b/fingertips_py/unit_tests/tests.py index cca0432..df2066c 100644 --- a/fingertips_py/unit_tests/tests.py +++ b/fingertips_py/unit_tests/tests.py @@ -105,10 +105,10 @@ def test_get_data_for_indicator_at_all_available_geographies(): assert isinstance(data, pd.DataFrame) is True # Check one of the columns is named "Indicator ID" - assert "Indicator ID" in data[0].columns + assert "Indicator ID" in data.columns # Check that only `247` is in the "Indicator ID" column - assert all(data[0]["Indicator ID"].isin([247])) + assert all(data["Indicator ID"].isin([247])) def test_get_metadata_for_profile_as_dataframe(): @@ -264,8 +264,12 @@ def test_get_value_note_id(): def test_get_metadata_for_all_indicators(): data = get_metadata_for_all_indicators() + + # Check that a pandas dataframe is returned by the function assert isinstance(data, pd.DataFrame) is True - assert data.shape[1] == 11 + + # Check one of the columns is named "Indicator ID" + assert "Indicator ID" in data.columns def test_get_metadata_for_all_indicators_from_csv(): From 7d7ab2e33efdb3dec2e3cc3af57c4088e09e105b Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Sun, 29 Jan 2023 18:28:25 +0000 Subject: [PATCH 19/34] Updated test for 'get_all_data_for_profile()' to match changes in API. --- fingertips_py/unit_tests/tests.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/fingertips_py/unit_tests/tests.py b/fingertips_py/unit_tests/tests.py index df2066c..25c0f25 100644 --- a/fingertips_py/unit_tests/tests.py +++ b/fingertips_py/unit_tests/tests.py @@ -36,10 +36,16 @@ def test_get_json_return_df(): # need to think about this one def test_get_all_data_for_profile(): + data = get_all_data_for_profile(84, is_test=True) + + # Check output of the function is a pandas df assert isinstance(data[0], pd.DataFrame) is True - assert data[1] == base_url + 'all_data/csv/by_profile_id?child_area_type_id=154&parent_area_type_id=15&profile_id=84' - assert data[0].shape[1] == 26 + + # Check the df has some of the required columns + assert "Indicator ID" in data[0].columns + assert "Indicator Name" in data[0].columns + assert "Value" in data[0].columns def test_get_all_areas(): From cad84fbe567e5e9ce35eee1a78f4ff7358c3b3cb Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Sun, 29 Jan 2023 18:56:26 +0000 Subject: [PATCH 20/34] Corrected mistake in 'get_metadata()'. --- fingertips_py/metadata.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/fingertips_py/metadata.py b/fingertips_py/metadata.py index 67d0d29..f1444f9 100644 --- a/fingertips_py/metadata.py +++ b/fingertips_py/metadata.py @@ -571,15 +571,15 @@ def get_metadata(indicator_ids=None, domain_ids=None, profile_ids=None, list_of_df = [] if indicator_ids: - list_of_df.append(get_metadata_for_profile_as_dataframe( - profile_ids, proxy)) + list_of_df.append(get_metadata_for_indicator_as_dataframe( + indicator_ids, proxy)) if domain_ids: list_of_df.append(get_metadata_for_domain_as_dataframe( domain_ids, proxy)) if profile_ids: - list_of_df.append(get_metadata_for_indicator_as_dataframe( - indicator_ids, proxy)) + list_of_df.append(get_metadata_for_profile_as_dataframe( + profile_ids, proxy)) return pd.concat(list_of_df) From 94ef5a64909c9702914c821f9958e66d7b11543f Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Mon, 30 Jan 2023 23:20:37 +0000 Subject: [PATCH 21/34] Rewrote 'deprivation_decile()' to fix errors. --- fingertips_py/area_data.py | 120 +++++++++++++++++++++++-------------- 1 file changed, 76 insertions(+), 44 deletions(-) diff --git a/fingertips_py/area_data.py b/fingertips_py/area_data.py index f9a00ed..0bbb7b0 100644 --- a/fingertips_py/area_data.py +++ b/fingertips_py/area_data.py @@ -6,7 +6,10 @@ import pandas as pd import warnings -from .retrieve_data import get_data_by_indicator_ids +from .retrieve_data import get_data_by_indicator_ids, \ + get_all_areas_for_all_indicators +from .api_calls import get_json +from .metadata import get_metadata def defined_qcut(df, value_series, number_of_bins, bins_for_extras, @@ -73,7 +76,7 @@ def defined_qcut(df, value_series, number_of_bins, bins_for_extras, } -def deprivation_decile(area_type_id, year='2015', area_code=None, proxy=None): +def deprivation_decile(area_type_id, year=None, area_code=None, proxy=None): """ Takes in an area type id and returns a pandas series of deprivation deciles for those areas (with the areas as an index. If a specific area is @@ -87,48 +90,77 @@ def deprivation_decile(area_type_id, year='2015', area_code=None, proxy=None): :return: A pandas series of deprivation scores with area codes as the index. Or single value if area is specified. """ - warnings.warn('Caution, the deprivation deciles are being calculated on ' - 'the fly and might show some inconsistencies from the live ' - 'Fingertips site.') - - acceptable_deprivation_years_la = ['2010', '2015'] - acceptable_deprivation_years_gp = ['2015'] - acceptable_area_types = [3, 101, 102, 7, 153] - order_of_extra_values = [] - if not isinstance(year, str): - year = str(year) - if year not in acceptable_deprivation_years_la and area_type_id is not 7: - raise ValueError('The acceptable years are 2010 and 2015 for local ' - 'authorities and CCGs, please select one of these') - elif year not in acceptable_deprivation_years_gp: - raise ValueError('The acceptable years are 2015, please select this') - if area_type_id not in acceptable_area_types: - raise ValueError('Currently, we support deprivation decile for' - ' District & UA, County & UA, MSOA and GP area types') - if area_type_id == 3: - indicator_id = 93275 - area_dep_dec = get_data_by_indicator_ids(indicator_id, area_type_id, - parent_area_type_id=101, - profile_id=143, - include_sortable_time_periods=True, - proxy=proxy) + + # find all the indicator IDs that are deprivation indexes + search_url = "https://fingertips.phe.org.uk/api/indicator_search" \ + "?search_text=index%20AND%20deprivation%20" \ + "AND%20score%20AND%20IMD" + + ind_area_dict = get_json(search_url, proxy=proxy) + valid_ind = list(set([y for x in ind_area_dict.values() for y in x])) + + # Find the valid area types for the indicator IDs + df = get_all_areas_for_all_indicators(proxy=proxy) + df = df.loc[df["IndicatorId"].isin(valid_ind)] + + # Add in the year column + meta_df = get_metadata(indicator_ids=valid_ind, proxy=proxy) + meta_df["year"] = meta_df["Definition"].str.extract(r"(20[0-9]{2})") + meta_df = meta_df[["year", "Indicator ID"]] + + df = pd.merge(df, meta_df, + how='left', + left_on="IndicatorId", + right_on="Indicator ID").sort_values("year", ascending=False) + + # Check the users choices + if int(area_type_id) not in df["AreaTypeId"].values: + raise ValueError(f"Invalid Area Type: {area_type_id} is not a " + f"supported area type. The supported types are" + f": {', '.join(set(df['AreaTypeId'].values))}.") + + elif year is not None and str(year) not in df["year"].values: + raise ValueError(f"Invalid Year: {year} is not a " + f"supported year. The supported years are" + f": {', '.join(set(df['year'].values))}.") + + # Filter down to the right indicator ID + if year is not None: + df0 = df[(df["year"] == str(year)) + & (df["AreaTypeId"] == int(area_type_id))] else: - indicator_id = 91872 - area_dep_dec = get_data_by_indicator_ids(indicator_id, area_type_id, - proxy=proxy) - if area_type_id == 102: - order_of_extra_values = [0, 9, 1, 2, 3, 4, 5, 6, 7, 8] + df0 = df[df["AreaTypeId"] == int(area_type_id)] + + # Check the year, area type is a valid a combination + if df0.empty: + err_str = f"Invalid Combination: {year} and {area_type_id} are not " \ + f"a valid combination. The following are: \n\n" + err_str += df.to_string(columns=['GeographicalArea', + 'AreaTypeId', + 'year'], index=False) + raise ValueError(err_str) + + # Extract the indicator data from the API + area_dep_dec = get_data_by_indicator_ids(df0["Indicator ID"].values[0], + area_type_id, proxy=proxy) + + # Remove England from the data area_dep_dec = area_dep_dec[area_dep_dec['Area Code'] != 'E92000001'] - if not order_of_extra_values: - order_of_extra_values = extra_areas[area_dep_dec['Value'].count() % 10] - area_dep_dec = defined_qcut(area_dep_dec, 'Value', 10, - order_of_extra_values) - area_dep_dec.set_index('Area Code', inplace=True) - if area_code: - try: - return area_dep_dec.loc[area_code, 'decile'] - except KeyError: - raise KeyError('This area is not available at in this area type. ' - 'Please try another area type') - return area_dep_dec['bins'] + + # Create the decile column + area_dep_dec["decile"] = pd.qcut(area_dep_dec["Value"], q=10, + labels=[str(x) for x in range(1, 11)]) + + if area_code is None: + return area_dep_dec + + elif area_code in area_dep_dec["Area Code"].values: + return area_dep_dec[area_dep_dec["Area Code"] == area_code, \ + 'decile'].values[0] + + else: + raise LookupError(f"Area Code {area_code} not in the data. Possible " + f"areas are: " + f"{', '.join(area_dep_dec['Area Code'].values)}.") + From c0378b43d69db36c3fd39855d86668f70fab4b9b Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Mon, 30 Jan 2023 23:22:12 +0000 Subject: [PATCH 22/34] Removed uneeded dict 'extra_areas'. --- fingertips_py/area_data.py | 14 -------------- 1 file changed, 14 deletions(-) diff --git a/fingertips_py/area_data.py b/fingertips_py/area_data.py index 0bbb7b0..c822fcb 100644 --- a/fingertips_py/area_data.py +++ b/fingertips_py/area_data.py @@ -62,20 +62,6 @@ def defined_qcut(df, value_series, number_of_bins, bins_for_extras, df = df.reset_index() return df - -extra_areas = { - 1: [0], - 2: [0, 5], - 3: [0, 3, 7], - 4: [0, 2, 6, 8], - 5: [0, 2, 4, 6, 8], - 6: [0, 1, 3, 5, 6, 8], - 7: [0, 1, 2, 4, 5, 7, 8], - 8: [0, 1, 2, 3, 5, 6, 7, 8], - 9: [0, 1, 2, 3, 4, 5, 6, 7, 8] -} - - def deprivation_decile(area_type_id, year=None, area_code=None, proxy=None): """ Takes in an area type id and returns a pandas series of deprivation deciles From 0d3f3e66b66d0dab99edd477bf9e0bbde750ea13 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Mon, 30 Jan 2023 23:24:39 +0000 Subject: [PATCH 23/34] Removed obsolete function 'defined_qcut()'. --- fingertips_py/area_data.py | 50 -------------------------------------- 1 file changed, 50 deletions(-) diff --git a/fingertips_py/area_data.py b/fingertips_py/area_data.py index c822fcb..8441a31 100644 --- a/fingertips_py/area_data.py +++ b/fingertips_py/area_data.py @@ -12,56 +12,6 @@ from .metadata import get_metadata -def defined_qcut(df, value_series, number_of_bins, bins_for_extras, - labels=False): - """ - Allows users to define how values are split into bins when clustering. - - :param df: Dataframe of values - :param value_series: Name of value column to rank upon - :param number_of_bins: Integer of number of bins to create - :param bins_for_extras: Ordered list of bin numbers to assign uneven splits - :param labels: Optional. Labels for bins if required - :return: A dataframe with a new column 'bins' which contains the cluster numbers - """ - if max(bins_for_extras) > number_of_bins or any( - x < 0 for x in bins_for_extras): - raise ValueError('Attempted to allocate to a bin that doesnt exist') - base_number, number_of_values_to_allocate = divmod( - df[value_series].count(), number_of_bins) - bins_for_extras = bins_for_extras[:number_of_values_to_allocate] - if number_of_values_to_allocate == 0: - df['bins'] = pd.qcut(df[value_series], number_of_bins, labels=labels) - return df - elif number_of_values_to_allocate > len(bins_for_extras): - raise ValueError( - 'There are more values to allocate than the list provided, please select more bins') - bins = {} - for i in range(number_of_bins): - number_of_values_in_bin = base_number - if i in bins_for_extras: - number_of_values_in_bin += 1 - bins[i] = number_of_values_in_bin - df['rank'] = df[value_series].rank() - df = df.sort_values(by=['rank']) - df['bins'] = 0 - row_to_start_allocate = 0 - row_to_end_allocate = 0 - for bin_number, number_in_bin in bins.items(): - row_to_end_allocate += number_in_bin - bins.update({bin_number: [number_in_bin, row_to_start_allocate, - row_to_end_allocate]}) - row_to_start_allocate = row_to_end_allocate - conditions = [df['rank'].iloc[v[1]: v[2]] for k, v in bins.items()] - series_to_add = pd.Series() - for idx, series in enumerate(conditions): - series[series > -1] = idx - series_to_add = series_to_add.append(series) - df['bins'] = series_to_add - df['bins'] = df['bins'] + 1 - df = df.reset_index() - return df - def deprivation_decile(area_type_id, year=None, area_code=None, proxy=None): """ Takes in an area type id and returns a pandas series of deprivation deciles From 7f5f5053206bcb02447d1273f11bf5b8ce96624b Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Mon, 30 Jan 2023 23:27:16 +0000 Subject: [PATCH 24/34] Removed uneeded import and cleaned description. --- fingertips_py/area_data.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/fingertips_py/area_data.py b/fingertips_py/area_data.py index 8441a31..ddd76a3 100644 --- a/fingertips_py/area_data.py +++ b/fingertips_py/area_data.py @@ -1,11 +1,11 @@ """ area_data.py ================================== -Functions to retrieve data that are specific to areas and relevant to all indicators. For example: Deprivation decile. +Functions to retrieve data that are specific to areas and relevant to all +indicators. For example: Deprivation decile. """ import pandas as pd -import warnings from .retrieve_data import get_data_by_indicator_ids, \ get_all_areas_for_all_indicators from .api_calls import get_json From 468b6ac8e88d7e5c2fd70311c398d555654f88b2 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Tue, 31 Jan 2023 19:16:37 +0000 Subject: [PATCH 25/34] Updated unit test for 'deprivation_decile()'. --- fingertips_py/unit_tests/tests.py | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/fingertips_py/unit_tests/tests.py b/fingertips_py/unit_tests/tests.py index 25c0f25..8d57c26 100644 --- a/fingertips_py/unit_tests/tests.py +++ b/fingertips_py/unit_tests/tests.py @@ -286,4 +286,11 @@ def test_get_metadata_for_all_indicators_from_csv(): def test_deprivation_decile(): data = deprivation_decile(7) - assert len(data.unique()) == 10 + + # Check one of the columns is named "Indicator ID" and one is called + # "Area Type". + assert "Indicator ID" in data.columns + assert "Area Type" in data.columns + + # Check that the only value in the "Indicator ID" column is "GPs" + assert all(data["Area Type"].isin(["GPs"])) From 8d0d46b04eb13ab2627ae9c306f7b0028f25c479 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Tue, 31 Jan 2023 22:05:55 +0000 Subject: [PATCH 26/34] Changed doc strings to render correctly in Sphinx. --- .../__pycache__/__init__.cpython-311.pyc | Bin 0 -> 1910 bytes .../__pycache__/api_calls.cpython-311.pyc | Bin 0 -> 6341 bytes .../__pycache__/area_data.cpython-311.pyc | Bin 0 -> 5343 bytes .../__pycache__/metadata.cpython-311.pyc | Bin 0 -> 24247 bytes .../__pycache__/retrieve_data.cpython-311.pyc | Bin 0 -> 9669 bytes fingertips_py/api_calls.py | 2 +- fingertips_py/area_data.py | 3 +- fingertips_py/metadata.py | 117 ++++++------------ fingertips_py/retrieve_data.py | 45 +++---- .../__pycache__/__init__.cpython-311.pyc | Bin 0 -> 182 bytes .../tests.cpython-311-pytest-7.2.1.pyc | Bin 0 -> 87657 bytes 11 files changed, 56 insertions(+), 111 deletions(-) create mode 100644 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+++++++++++++++++++++++++++++++++++++++++++++++++++-- 1 file changed, 157 insertions(+), 4 deletions(-) diff --git a/.gitignore b/.gitignore index de0d65e..b0b6f3a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,7 +1,160 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] +*$py.class -.idea -*.iml -out -gen +# C extensions +*.so + +# Distribution / packaging +.Python +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +share/python-wheels/ +*.egg-info/ +.installed.cfg +*.egg +MANIFEST + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.nox/ +.coverage +.coverage.* +.cache +nosetests.xml +coverage.xml +*.cover +*.py,cover +.hypothesis/ +.pytest_cache/ +cover/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py +db.sqlite3 +db.sqlite3-journal + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +.pybuilder/ +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# IPython +profile_default/ +ipython_config.py + +# pyenv +# For a library or package, you might want to ignore these files since the code is +# intended to run in multiple environments; otherwise, check them in: +# .python-version + +# pipenv +# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. +# However, in case of collaboration, if having platform-specific dependencies or dependencies +# having no cross-platform support, pipenv may install dependencies that don't work, or not +# install all needed dependencies. +#Pipfile.lock + +# poetry +# Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control. +# This is especially recommended for binary packages to ensure reproducibility, and is more +# commonly ignored for libraries. +# https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control +#poetry.lock + +# pdm +# Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control. +#pdm.lock +# pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it +# in version control. +# https://pdm.fming.dev/#use-with-ide +.pdm.toml + +# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm +__pypackages__/ + +# Celery stuff +celerybeat-schedule +celerybeat.pid + +# SageMath parsed files +*.sage.py + +# Environments +.env +.venv +env/ venv/ +ENV/ +env.bak/ +venv.bak/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ +.dmypy.json +dmypy.json + +# Pyre type checker +.pyre/ + +# pytype static type analyzer +.pytype/ + +# Cython debug symbols +cython_debug/ +# PyCharm +# JetBrains specific template is maintained in a separate JetBrains.gitignore that can +# be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore +# and can be added to the global gitignore or merged into this file. 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build/html/_static/css/badge_only.css | 2 +- build/html/_static/css/theme.css | 4 +- build/html/_static/doctools.js | 381 +++------ build/html/_static/documentation_options.js | 4 +- build/html/_static/jquery.js | 4 +- build/html/_static/js/theme.js | 2 +- build/html/_static/language_data.js | 102 +-- build/html/_static/pygments.css | 34 +- build/html/_static/searchtools.js | 820 +++++++++++--------- build/html/genindex.html | 167 +--- build/html/index.html | 636 +++++++-------- build/html/objects.inv | Bin 635 -> 632 bytes build/html/py-modindex.html | 157 +--- build/html/search.html | 163 +--- build/html/searchindex.js | 2 +- source/index.rst | 62 +- source/index.rst.bak | 127 +++ 22 files changed, 1184 insertions(+), 1566 deletions(-) create mode 100644 source/index.rst.bak diff --git a/build/doctrees/environment.pickle b/build/doctrees/environment.pickle index 031eb614d39911b6b07ae24fd4bbffe311c00ce3..9cdf04715fc64566d88d188d93421103e38df992 100644 GIT binary patch literal 45694 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' + _('Hide Search Matches') + '

') - .appendTo($('#searchbox')); - } - }, - - /** - * init the domain index toggle buttons - */ - initIndexTable : function() { - var togglers = $('img.toggler').click(function() { - var src = $(this).attr('src'); - var idnum = $(this).attr('id').substr(7); - $('tr.cg-' + idnum).toggle(); - if (src.substr(-9) === 'minus.png') - $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); - else - $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); - }).css('display', ''); - if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { - togglers.click(); - } - }, + }; - /** - * helper function to hide the search marks again - */ - hideSearchWords : function() { - $('#searchbox .highlight-link').fadeOut(300); - $('span.highlighted').removeClass('highlighted'); + const togglerElements = document.querySelectorAll("img.toggler"); + togglerElements.forEach((el) => + el.addEventListener("click", (event) => toggler(event.currentTarget)) + ); + togglerElements.forEach((el) => (el.style.display = "")); + if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler); }, - /** - * make the url absolute - */ - makeURL : function(relativeURL) { - return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; - }, - - /** - * get the current relative url - */ - getCurrentURL : function() { - var path = document.location.pathname; - var parts = path.split(/\//); - $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { - if (this === '..') - parts.pop(); - }); - var url = parts.join('/'); - return path.substring(url.lastIndexOf('/') + 1, path.length - 1); - }, - - initOnKeyListeners: function() { - $(document).keydown(function(event) { - var activeElementType = document.activeElement.tagName; - // don't navigate when in search box, textarea, dropdown or button - if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT' - && activeElementType !== 'BUTTON' && !event.altKey && !event.ctrlKey && !event.metaKey - && !event.shiftKey) { - switch (event.keyCode) { - case 37: // left - var prevHref = $('link[rel="prev"]').prop('href'); - if (prevHref) { - window.location.href = prevHref; - return false; + initOnKeyListeners: () => { + // only install a listener if it is really needed + if ( + !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS && + !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS + ) + return; + + document.addEventListener("keydown", (event) => { + // bail for input elements + if (BLACKLISTED_KEY_CONTROL_ELEMENTS.has(document.activeElement.tagName)) return; + // bail with special keys + if (event.altKey || event.ctrlKey || event.metaKey) return; + + if (!event.shiftKey) { + switch (event.key) { + case "ArrowLeft": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const prevLink = document.querySelector('link[rel="prev"]'); + if (prevLink && prevLink.href) { + window.location.href = prevLink.href; + event.preventDefault(); } break; - case 39: // right - var nextHref = $('link[rel="next"]').prop('href'); - if (nextHref) { - window.location.href = nextHref; - return false; + case "ArrowRight": + if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break; + + const nextLink = document.querySelector('link[rel="next"]'); + if (nextLink && nextLink.href) { + window.location.href = nextLink.href; + event.preventDefault(); } break; } } + + // some keyboard layouts may need Shift to get / + switch (event.key) { + case "/": + if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break; + Documentation.focusSearchBar(); + event.preventDefault(); + } }); - } + }, }; // quick alias for translations -_ = Documentation.gettext; +const _ = Documentation.gettext; -$(document).ready(function() { - Documentation.init(); -}); +_ready(Documentation.init); diff --git a/build/html/_static/documentation_options.js b/build/html/_static/documentation_options.js index 84728ea..081dc3c 100644 --- a/build/html/_static/documentation_options.js +++ 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Please make sure that all words are spelled correctly and that you've selected enough categories." + ); + else + Search.status.innerText = _( + `Search finished, found ${resultCount} page(s) matching the search query.` + ); +}; +const _displayNextItem = ( + results, + resultCount, + searchTerms +) => { + // results left, load the summary and display it + // this is intended to be dynamic (don't sub resultsCount) + if (results.length) { + _displayItem(results.pop(), searchTerms); + setTimeout( + () => _displayNextItem(results, resultCount, searchTerms), + 5 + ); + } + // search finished, update title and status message + else _finishSearch(resultCount); +}; + +/** + * Default splitQuery function. Can be overridden in ``sphinx.search`` with a + * custom function per language. + * + * The regular expression works by splitting the string on consecutive characters + * that are not Unicode letters, numbers, underscores, or emoji characters. + * This is the same as ``\W+`` in Python, preserving the surrogate pair area. + */ +if (typeof splitQuery === "undefined") { + var splitQuery = (query) => query + .split(/[^\p{Letter}\p{Number}_\p{Emoji_Presentation}]+/gu) + .filter(term => term) // remove remaining empty strings } /** * Search Module */ -var Search = { - - _index : null, - _queued_query : null, - _pulse_status : -1, - - htmlToText : function(htmlString) { - var virtualDocument = document.implementation.createHTMLDocument('virtual'); - var htmlElement = $(htmlString, virtualDocument); - htmlElement.find('.headerlink').remove(); - docContent = htmlElement.find('[role=main]')[0]; - if(docContent === undefined) { - console.warn("Content block not found. Sphinx search tries to obtain it " + - "via '[role=main]'. Could you check your theme or template."); - return ""; - } - return docContent.textContent || docContent.innerText; +const Search = { + _index: null, + _queued_query: null, + _pulse_status: -1, + + htmlToText: (htmlString) => { + const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); + htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() }); + const docContent = htmlElement.querySelector('[role="main"]'); + if (docContent !== undefined) return docContent.textContent; + console.warn( + "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template." + ); + return ""; }, - init : function() { - var params = $.getQueryParameters(); - if (params.q) { - var query = params.q[0]; - $('input[name="q"]')[0].value = query; - this.performSearch(query); - } + init: () => { + const query = new URLSearchParams(window.location.search).get("q"); + document + .querySelectorAll('input[name="q"]') + .forEach((el) => (el.value = query)); + if (query) Search.performSearch(query); }, - loadIndex : function(url) { - $.ajax({type: "GET", url: url, data: null, - dataType: "script", cache: true, - complete: function(jqxhr, textstatus) { - if (textstatus != "success") { - document.getElementById("searchindexloader").src = url; - } - }}); - }, + loadIndex: (url) => + (document.body.appendChild(document.createElement("script")).src = url), - setIndex : function(index) { - var q; - this._index = index; - if ((q = this._queued_query) !== null) { - this._queued_query = null; - Search.query(q); + setIndex: (index) => { + Search._index = index; + if (Search._queued_query !== null) { + const query = Search._queued_query; + Search._queued_query = null; + Search.query(query); } }, - hasIndex : function() { - return this._index !== null; - }, + hasIndex: () => Search._index !== null, - deferQuery : function(query) { - this._queued_query = query; - }, + deferQuery: (query) => (Search._queued_query = query), - stopPulse : function() { - this._pulse_status = 0; - }, + stopPulse: () => (Search._pulse_status = -1), - startPulse : function() { - if (this._pulse_status >= 0) - return; - function pulse() { - var i; + startPulse: () => { + if (Search._pulse_status >= 0) return; + + const pulse = () => { Search._pulse_status = (Search._pulse_status + 1) % 4; - var dotString = ''; - for (i = 0; i < Search._pulse_status; i++) - dotString += '.'; - Search.dots.text(dotString); - if (Search._pulse_status > -1) - window.setTimeout(pulse, 500); - } + Search.dots.innerText = ".".repeat(Search._pulse_status); + if (Search._pulse_status >= 0) window.setTimeout(pulse, 500); + }; pulse(); }, /** * perform a search for something (or wait until index is loaded) */ - performSearch : function(query) { + performSearch: (query) => { // create the required interface elements - this.out = $('#search-results'); - this.title = $('

' + _('Searching') + '

').appendTo(this.out); - this.dots = $('').appendTo(this.title); - this.status = $('

 

').appendTo(this.out); - this.output = $(' @@ -240,15 +149,17 @@

G

  • get_area_types_for_profile() (in module fingertips_py.metadata)
  • get_areas_for_area_type() (in module fingertips_py.metadata) +
    • +
  • get_csv() (in module fingertips_py.api_calls)
  • get_data_by_indicator_ids() (in module fingertips_py.retrieve_data)
  • get_data_for_indicator_at_all_available_geographies() (in module fingertips_py.retrieve_data) -
    • -
  • get_data_in_tuple() (in module fingertips_py.api_calls)
    • - - - -
    - - -
    - - - - - - - - + + window.dataLayer = window.dataLayer || []; + function gtag(){dataLayer.push(arguments);} + gtag('js', new Date()); - - + gtag('config', 'UA-XXXXXXX-1', { + 'anonymize_ip': false, + }); + \ No newline at end of file diff --git a/build/html/objects.inv b/build/html/objects.inv index 5bf3ee146ef18321fc609576fa681b6db7addc7e..3f4b4f73f040df3b380ef2715d6af348f6ab37f7 100644 GIT binary patch delta 479 zcmV<50U-YS1o#Aye=^)45XbNP6iAKK)2^Cp-k^s{k$UJ6O<-)(U?6-dsH~a0px~5%)lU?G;%eoxz(~()OTC$c?QwtmW;j0+g*$VUSb_h}MVCV3sCu zCxrT1LOYR@Cc9Qhks6tYmq@ydj(yTHNBc0=^zsGe z5yw3+rY39Dj;p6zW>m=E`uUXEtM_w~MfYR_lHQb_YJ-AMNG|*c#lZAyS??{W99dFreo&4DM{CRkDlU8J> zg~u<{!qSzAmaU@y8W=gJ9!;Fu#(_%b!g6jr&OZw8N2$89@Z#?WvimW1w8@n^Ab8QO Vg~e7hKg<7ndJG;0UH}F`<&=`i^)mnf delta 482 zcmV<80UiGM1p5S#e=_7C49D;D6iB<$o@Ufu`vyI%RA~=;L@qc9TLP4iZ1eUtp_wMz z(N+`ETV(kEFt)MNk+BsRcEgmB_;TuEufG-B@jE*nn#;C6ZIEkg4&|<38ZC$2;S`z}2@B+KHSr*|kFQ)W|&kMABt+>=TyR+sCn{ zmoF$!IPQTlHBqB>Ts_?~qeA}P&#$D=uaQ?c;I{vim3loTD?7@6W%9=twI_5#H~vVR zXt})4Z=R;(4#`{eKM(KQ zq!oG7V#jaP!qSt8maV-15g2VwJ(@VRjRTd=h2z|KoEHl3XQ{e!@M857*~1t+y5ve7 Y5WMKt!eT3$UuFFXfqn)LuY!~3eixYZT>t<8 diff --git a/build/html/py-modindex.html b/build/html/py-modindex.html index 9a77b21..34a6769 100644 --- a/build/html/py-modindex.html +++ b/build/html/py-modindex.html @@ -1,44 +1,22 @@ - - - - Python Module Index — fingertips_py 0.2 documentation - - - - - - - - - - - - - - - - - + + - - + - - - - + + @@ -46,29 +24,13 @@ - - - +
    - -
    - - -
    - - - - - - - + - - - + gtag('config', 'UA-XXXXXXX-1', { + 'anonymize_ip': false, + }); + \ No newline at end of file diff --git a/build/html/search.html b/build/html/search.html index b57e0e3..377109e 100644 --- a/build/html/search.html +++ b/build/html/search.html @@ -1,74 +1,36 @@ - - - - Search — fingertips_py 0.2 documentation - - - - - - - - - - - - - - - - - + + - - + - - - - - - + + + + - - - +
    - -
    - - -
    - - - - - - - + - - - - - + diff --git a/build/html/searchindex.js b/build/html/searchindex.js index 7080279..7dd3db0 100644 --- a/build/html/searchindex.js +++ b/build/html/searchindex.js @@ -1 +1 @@ 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"fingertips_py.api_calls.make_request"]], "module": [[0, "module-fingertips_py.api_calls"], [0, "module-fingertips_py.area_data"], [0, "module-fingertips_py.metadata"], [0, "module-fingertips_py.retrieve_data"]]}}) \ No newline at end of file diff --git a/source/index.rst b/source/index.rst index caebc1e..a22414f 100644 --- a/source/index.rst +++ b/source/index.rst @@ -11,7 +11,7 @@ Introduction This is a python package to interact with Public Health England's -[Fingertips](https://fingertips.phe.org.uk/) data tool. Fingertips is a +`Fingertips `_ data tool. Fingertips is a major repository of population and public health indicators for England. The site presents the information in many ways to improve accessibility for a wide range of audiences ranging from public health professionals @@ -30,15 +30,15 @@ Installation This packaged should be installed using pip: -``` -pip install fingertips_py -``` +.. code-block:: console + + pip install fingertips_py Or it can be compiled from source (still requires pip): -``` -pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git -``` +.. code-block:: console + + pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git Usage ***** @@ -47,20 +47,18 @@ fingertips_py should be imported and used in line with standard python conventions. It is suggested that if the whole package is to be imported then the following convention is used: -``` -import fingertips_py as ftp -``` +>>> import fingertips_py as ftp The package returns data in a variety of types dependent on the function. For more information on any function, you can use: -``` -help(*fingertips_py function name*) -``` +>>> help(*fingertips_py function name*) + + +Or you can view the documents `here `_. -Or you can view the documents [here](https://fingertips-py.readthedocs.io/en/latest/). Example ******* @@ -69,32 +67,40 @@ This is an example of a workflow for retrieving data for the indicator on *Healthy Life Expectancy at Birth* from the *Public Health Outcomes Framework* profile. -``` -import fingertips_py as ftp +.. code-block:: python + :linenos: + import fingertips_py as ftp -phof = ftp.get_profile_by_name('public health outcomes framework') -phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id']) -indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')] -print(indicator_meta) + # Extract the metadata for a particular profile + phof = ftp.get_profile_by_name('public health outcomes framework') + phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id']) + + # Extract metadata for indicators containing the string "Healthy" + indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')] + + print(indicator_meta) + +.. code-block:: + :linenos: + + Indicator ID Indicator ... + 90362 0.1i - Healthy life expectancy at birth ... + 92543 2.05ii - Proportion of children aged 2-2½yrs r ... - Indicator ID Indicator ... -0 90362 0.1i - Healthy life expectancy at birth ... -55 92543 2.05ii - Proportion of children aged 2-2½yrs r... ... -``` We can see that the *Healthy life expectancy at birth* indicator has an id of 90362. The data for this indicator at all geographical breakdowns can be retrieved using `get_data_for_indicator_at_all_available_geographies()` -``` -healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362) -``` + +>>> healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362) + Licence ******* -This project is released under the [GPL-3](https://opensource.org/licenses/GPL-3.0) +This project is released under the `GPL-3 `_ licence. .. automodule:: fingertips_py.metadata diff --git a/source/index.rst.bak b/source/index.rst.bak new file mode 100644 index 0000000..c4d1dc3 --- /dev/null +++ b/source/index.rst.bak @@ -0,0 +1,127 @@ +.. fingertips_py documentation master file, created by + sphinx-quickstart on Mon Feb 25 08:34:07 2019. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to fingertips_py's documentation +========================================= + +Introduction +============ + + +This is a python package to interact with Public Health England's +`Fingertips `_ data tool. Fingertips is a +major repository of population and public health indicators for England. +The site presents the information in many ways to improve accessibility +for a wide range of audiences ranging from public health professionals +and researchers to the general public. The information presented is a +mixture of data available from other public sources, and those that are +available through user access agreements with other organisations. The +source of each indicator presented is available using the +`get_metadata_for_indicator()` function. + + +This package can be used to load data from the Fingertips API into +python for further use. + +Installation +************ + +This packaged should be installed using pip: + +.. code-block:: console + + pip install fingertips_py + +Or it can be compiled from source (still requires pip): + +.. code-block:: console + + pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git + +Usage +***** + +fingertips_py should be imported and used in line with standard python +conventions. It is suggested that if the whole package is to be imported + then the following convention is used: + +>>> import fingertips_py as ftp + +The package returns data in a variety of types dependent on the +function. + +For more information on any function, you can use: + +>>> help(*fingertips_py function name*) + + +Or you can view the documents [here](https://fingertips-py.readthedocs.io/en/latest/). + + +Example +******* + +This is an example of a workflow for retrieving data for the indicator +on *Healthy Life Expectancy at Birth* from the *Public Health Outcomes +Framework* profile. + +.. code-block:: python + :linenos: + + import fingertips_py as ftp + + # Extract the metadata for a particular profile + phof = ftp.get_profile_by_name('public health outcomes framework') + phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id']) + + # Extract metadata for indicators containing the string "Healthy" + indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')] + + print(indicator_meta) + +.. code-block:: + :linenos: + + Indicator ID Indicator ... + 90362 0.1i - Healthy life expectancy at birth ... + 92543 2.05ii - Proportion of children aged 2-2½yrs r ... + + +We can see that the *Healthy life expectancy at birth* indicator has an +id of 90362. The data for this indicator at all geographical breakdowns +can be retrieved using `get_data_for_indicator_at_all_available_geographies()` + + +>>> healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362) + + +Licence +******* + +This project is released under the `GPL-3 ` +licence. + +.. automodule:: fingertips_py.metadata + :members: +.. automodule:: fingertips_py.api_calls + :members: +.. automodule:: fingertips_py.retrieve_data + :members: +.. automodule:: fingertips_py.area_data + :members: + +.. toctree:: + :maxdepth: 3 + :caption: Contents: + + fingertips_py/readme.md + + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` From 7b475a42348432bcca7cebc42ec341e85ce57827 Mon Sep 17 00:00:00 2001 From: xn4224nx Date: Wed, 1 Feb 2023 20:15:49 +0000 Subject: [PATCH 30/34] Made sure the eadme.md and index.rst were consistent. --- build/doctrees/environment.pickle | Bin 45694 -> 45694 bytes build/doctrees/index.doctree | Bin 205420 -> 205296 bytes build/html/_sources/index.rst.txt | 29 ++++--- build/html/index.html | 26 +++--- build/html/searchindex.js | 2 +- readme.md | 43 +++++----- source/index.rst | 29 ++++--- source/index.rst.bak | 127 ------------------------------ 8 files changed, 63 insertions(+), 193 deletions(-) delete mode 100644 source/index.rst.bak diff --git a/build/doctrees/environment.pickle b/build/doctrees/environment.pickle index 9cdf04715fc64566d88d188d93421103e38df992..0fedb1d962db8b252d4f67cffe447ba08049b6c4 100644 GIT binary patch delta 47 zcmV+~0MP&b2Tlf1ZjRx1OFJm!*-Zi7}A>Ud3Jt$cI|fLxy%?koMLojZiZHp?Ux!O6A4l8nKdyVZ6wGe&QA)ly+(OqiUdeT*?>v!PBQ6Jy%u z#d?_+S%JD{i%!3&$fP^foza_fDkB3hw18l;V3zdOwT$`yr{}$8{COTgZZW&Q3RX705p24^Yn?FOuk!xG3T)` z7ERA&WuC^EGL4P-8FN)>(&US06}NM-GY2v<)=ZD#VAf}>+1|s!+{VaS3)E^qJpm+S zJ$(WPv*-2+T+GIdtaU)~LXfyNn3)Tbv!1@2m6>bu2Rni3zC6q_K%=sFn9~`nrW^7w M%WeO_!(1Z@03eT_-2eap delta 658 zcmexxnCHzA9+n2ysf-(0+7&owGBPkIfWTxyC0SMoOHauF%8FBRhO!pISx=Olpkivu zK2X*NMOmtuBsRH2*=X_;Rl&&zlnsSGgPr7=my(&BSdw3);OR0+#eA}Y3M-$Uo*oxi z($c`#%xJQjs+};Hix4+5H8Gx?uWGLZ6Q7d79y=vNu!kCkO27?mozgg^c8W#@YX)0} zSeEGIgR07ESwc(<3>_IyIy0X3u&1P^C6?xtOv!j&JEb&3HRDQ#dWJ@Zrgz9@ezl#< zj4_)}YN{|YCQg2*b&N4}^H%LbCdTy5>UxIWyn7-gYWBKHU?OfCQ{xPy`HDIa%N?I!cHGuSd3{shX;XhOGbbTgf&aI}*+gTWk zr@v)kp2nCuy@i$e8FO`M(qzWjirf3xm;)IZYo|Y8XVzz|-7dhv+{VaS2lR^l^gwoI z`N<2!c)(n1Fn3Z7_jEfBX8G+RT+GIdto1;3g$Q*ZZZ5Jq!Rhv_%v_TN`UIw5>!LphF diff --git a/build/html/_sources/index.rst.txt b/build/html/_sources/index.rst.txt index a22414f..abd72a2 100644 --- a/build/html/_sources/index.rst.txt +++ b/build/html/_sources/index.rst.txt @@ -68,25 +68,24 @@ on *Healthy Life Expectancy at Birth* from the *Public Health Outcomes Framework* profile. .. code-block:: python - :linenos: - import fingertips_py as ftp + import fingertips_py as ftp + + # Extract the metadata for a particular profile + phof = ftp.get_profile_by_name('public health outcomes framework') + phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id']) + + # Extract metadata for indicators containing the string "Healthy" + indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')] - # Extract the metadata for a particular profile - phof = ftp.get_profile_by_name('public health outcomes framework') - phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id']) - - # Extract metadata for indicators containing the string "Healthy" - indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')] - - print(indicator_meta) + print(indicator_meta) -.. code-block:: +.. code-block:: console :linenos: - - Indicator ID Indicator ... - 90362 0.1i - Healthy life expectancy at birth ... - 92543 2.05ii - Proportion of children aged 2-2½yrs r ... + + Indicator ID Indicator ... + 90362 0.1i - Healthy life expectancy at birth ... + 92543 2.05ii - Proportion of children aged 2-2½yrs r ... We can see that the *Healthy life expectancy at birth* indicator has an diff --git a/build/html/index.html b/build/html/index.html index 3c5b50e..0e29faf 100644 --- a/build/html/index.html +++ b/build/html/index.html @@ -169,21 +169,21 @@

    Example
     1     import fingertips_py as ftp
- 2
- 3     # Extract the metadata for a particular profile
- 4     phof = ftp.get_profile_by_name('public health outcomes framework')
- 5     phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id'])
- 6
- 7     # Extract metadata for indicators containing the string "Healthy"
- 8     indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')]
- 9
-10     print(indicator_meta)
+
    import fingertips_py as ftp
+
+# Extract the metadata for a particular profile
+phof = ftp.get_profile_by_name('public health outcomes framework')
+phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id'])
+
+# Extract metadata for indicators containing the string "Healthy"
+indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')]
+
+print(indicator_meta)
 
    
 
    
-
    1     Indicator ID    Indicator                                               ...
-2     90362           0.1i - Healthy life expectancy at birth                 ...
-3     92543           2.05ii - Proportion of children aged 2-2½yrs r          ...
+
    1Indicator ID      Indicator                                          ...
+290362             0.1i - Healthy life expectancy at birth            ...
+392543             2.05ii - Proportion of children aged 2-2½yrs r     ...
 
    
 
    
 
    We can see that the Healthy life expectancy at birth indicator has an
diff --git a/build/html/searchindex.js b/build/html/searchindex.js
index 7dd3db0..b83ed4b 100644
--- a/build/html/searchindex.js
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"fingertips_py.metadata.get_multiplier_and_calculation_for_indicator"]], "get_profile_by_id() (in module fingertips_py.metadata)": [[0, "fingertips_py.metadata.get_profile_by_id"]], "get_profile_by_key() (in module fingertips_py.metadata)": [[0, "fingertips_py.metadata.get_profile_by_key"]], "get_profile_by_name() (in module fingertips_py.metadata)": [[0, "fingertips_py.metadata.get_profile_by_name"]], "get_sex_from_id() (in module fingertips_py.metadata)": [[0, "fingertips_py.metadata.get_sex_from_id"]], "get_sex_id() (in module fingertips_py.metadata)": [[0, "fingertips_py.metadata.get_sex_id"]], "get_value_note_id() (in module fingertips_py.metadata)": [[0, "fingertips_py.metadata.get_value_note_id"]], "make_request() (in module fingertips_py.api_calls)": [[0, "fingertips_py.api_calls.make_request"]], "module": [[0, "module-fingertips_py.api_calls"], [0, "module-fingertips_py.area_data"], [0, "module-fingertips_py.metadata"], [0, "module-fingertips_py.retrieve_data"]]}})
\ No newline at end of file
diff --git a/readme.md b/readme.md
index c332cba..d48ad99 100644
--- a/readme.md
+++ b/readme.md
@@ -19,34 +19,29 @@ python for further use.
  
 This packaged should be installed using pip:
 
-```
-pip install fingertips_py
-``` 
+    
+    pip install fingertips_py 
 
 Or it can be compiled from source (still requires pip):
 
-```
-pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git
-```
+
+    pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git
+
 
 ## Usage
 
 fingertips_py should be imported and used in line with standard python
 conventions. It is suggested that if the whole package is to be imported
  then the following convention is used:
- 
-```
-import fingertips_py as ftp
-```
+
+    >>> import fingertips_py as ftp
 
 The package returns data in a variety of types dependent on the 
 function. 
 
 For more information on any function, you can use:
 
-```
-help(*fingertips_py function name*)
-```
+    >>> help(*fingertips_py function name*)
 
 Or you can view the documents [here](https://fingertips-py.readthedocs.io/en/latest/).
 
@@ -56,27 +51,31 @@ This is an example of a workflow for retrieving data for the indicator
 on *Healthy Life Expectancy at Birth* from the *Public Health Outcomes 
 Framework* profile. 
 
-```
+```python
 import fingertips_py as ftp
 
-
+# Extract the metadata for a particular profile 
 phof = ftp.get_profile_by_name('public health outcomes framework')
 phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id'])
+
+# Extract metadata for indicators containing the string "Healthy"
 indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')]
-print(indicator_meta)
 
-    Indicator ID                                          Indicator  ...   
-0          90362            0.1i - Healthy life expectancy at birth  ... 
-55         92543  2.05ii - Proportion of children aged 2-2½yrs r...  ...
+print(indicator_meta)
+```
+```
+Indicator ID     Indicator                                          ...   
+90362            0.1i - Healthy life expectancy at birth            ... 
+92543            2.05ii - Proportion of children aged 2-2½yrs r     ...
 ```
 
 We can see that the *Healthy life expectancy at birth* indicator has an 
 id of 90362. The data for this indicator at all geographical breakdowns 
 can be retrieved using `get_data_for_indicator_at_all_available_geographies()`
 
-```
-healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362)
-```
+
+    >>> healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362)
+
 
 ## Licence
 
diff --git a/source/index.rst b/source/index.rst
index a22414f..abd72a2 100644
--- a/source/index.rst
+++ b/source/index.rst
@@ -68,25 +68,24 @@ on *Healthy Life Expectancy at Birth* from the *Public Health Outcomes
 Framework* profile.
 
 .. code-block:: python
-   :linenos:
 
-	import fingertips_py as ftp
+   import fingertips_py as ftp
+
+   # Extract the metadata for a particular profile
+   phof = ftp.get_profile_by_name('public health outcomes framework')
+   phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id'])
+
+   # Extract metadata for indicators containing the string "Healthy"
+   indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')]
 
-	# Extract the metadata for a particular profile 
-	phof = ftp.get_profile_by_name('public health outcomes framework')
-	phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id'])
-	
-	# Extract metadata for indicators containing the string "Healthy"
-	indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')]
-	
-	print(indicator_meta)
+   print(indicator_meta)
 
-.. code-block::
+.. code-block:: console
    :linenos:
-   
-	Indicator ID	Indicator  						...
-	90362		0.1i - Healthy life expectancy at birth  		...
-	92543  		2.05ii - Proportion of children aged 2-2½yrs r		... 
+
+   Indicator ID	     Indicator  					...
+   90362	     0.1i - Healthy life expectancy at birth  		...
+   92543	     2.05ii - Proportion of children aged 2-2½yrs r	...
 
 
 We can see that the *Healthy life expectancy at birth* indicator has an
diff --git a/source/index.rst.bak b/source/index.rst.bak
deleted file mode 100644
index c4d1dc3..0000000
--- a/source/index.rst.bak
+++ /dev/null
@@ -1,127 +0,0 @@
-.. fingertips_py documentation master file, created by
-   sphinx-quickstart on Mon Feb 25 08:34:07 2019.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-Welcome to fingertips_py's documentation
-=========================================
-
-Introduction
-============
-
-
-This is a python package to interact with Public Health England's
-`Fingertips `_ data tool. Fingertips is a
-major repository of population and public health indicators for England.
-The site presents the information in many ways to improve accessibility
-for a wide range of audiences ranging from public health professionals
-and researchers to the general public. The information presented is a
-mixture of data available from other public sources, and those that are
-available through user access agreements with other organisations. The
-source of each indicator presented is available using the
-`get_metadata_for_indicator()` function.
-
-
-This package can be used to load data from the Fingertips API into
-python for further use.
-
-Installation
-************
-
-This packaged should be installed using pip:
-
-.. code-block:: console
-
-	pip install fingertips_py
-
-Or it can be compiled from source (still requires pip):
-
-.. code-block:: console
-
-	pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git
-
-Usage
-*****
-
-fingertips_py should be imported and used in line with standard python
-conventions. It is suggested that if the whole package is to be imported
- then the following convention is used:
-
->>> import fingertips_py as ftp
-
-The package returns data in a variety of types dependent on the
-function.
-
-For more information on any function, you can use:
-
->>> help(*fingertips_py function name*)
-
-
-Or you can view the documents [here](https://fingertips-py.readthedocs.io/en/latest/).
-
-
-Example
-*******
-
-This is an example of a workflow for retrieving data for the indicator
-on *Healthy Life Expectancy at Birth* from the *Public Health Outcomes
-Framework* profile.
-
-.. code-block:: python
-   :linenos:
-
-	import fingertips_py as ftp
-
-	# Extract the metadata for a particular profile 
-	phof = ftp.get_profile_by_name('public health outcomes framework')
-	phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id'])
-	
-	# Extract metadata for indicators containing the string "Healthy"
-	indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')]
-	
-	print(indicator_meta)
-
-.. code-block::
-   :linenos:
-   
-	Indicator ID	Indicator  						...
-	90362		0.1i - Healthy life expectancy at birth  		...
-	92543  		2.05ii - Proportion of children aged 2-2½yrs r		... 
-
-
-We can see that the *Healthy life expectancy at birth* indicator has an
-id of 90362. The data for this indicator at all geographical breakdowns
-can be retrieved using `get_data_for_indicator_at_all_available_geographies()`
-
-
->>> healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362)
-
-
-Licence
-*******
-
-This project is released under the `GPL-3 `
-licence.
-
-.. automodule:: fingertips_py.metadata
-   :members:
-.. automodule:: fingertips_py.api_calls
-   :members:
-.. automodule:: fingertips_py.retrieve_data
-   :members:
-.. automodule:: fingertips_py.area_data
-   :members:
-
-.. toctree::
-   :maxdepth: 3
-   :caption: Contents:
-
-   fingertips_py/readme.md
-
-
-Indices and tables
-==================
-
-* :ref:`genindex`
-* :ref:`modindex`
-* :ref:`search`

From 5ab748937232ec5588134fbd7c7eb2a32ed5c68a Mon Sep 17 00:00:00 2001
From: xn4224nx 
Date: Wed, 1 Feb 2023 20:43:21 +0000
Subject: [PATCH 31/34] Fixed incorrect documentation.

---
 .gitignore                        |   3 ++
 build/doctrees/environment.pickle | Bin 45694 -> 45694 bytes
 build/doctrees/index.doctree      | Bin 205296 -> 205251 bytes
 build/html/index.html             |  64 ++++++++++++++----------------
 build/html/searchindex.js         |   2 +-
 fingertips_py/area_data.py        |   3 +-
 fingertips_py/metadata.py         |  37 ++++++-----------
 fingertips_py/retrieve_data.py    |   3 +-
 8 files changed, 49 insertions(+), 63 deletions(-)

diff --git a/.gitignore b/.gitignore
index b0b6f3a..41ae443 100644
--- a/.gitignore
+++ b/.gitignore
@@ -3,6 +3,9 @@ __pycache__/
 *.py[cod]
 *$py.class
 
+# Google Drive backup files
+*.bak
+
 # C extensions
 *.so
 
diff --git a/build/doctrees/environment.pickle b/build/doctrees/environment.pickle
index 0fedb1d962db8b252d4f67cffe447ba08049b6c4..dfa385e327cfd7a922a5995bc2a7b8aad77b2cf2 100644
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diff --git a/build/html/index.html b/build/html/index.html
index 0e29faf..6e059f0 100644
--- a/build/html/index.html
+++ b/build/html/index.html
@@ -228,13 +228,14 @@ 
    metadata.pyParameters
 
      
 
    • age -- Search term of an age or age range as a string
      • 
-
    • is_test -- Used for testing. Returns a tuple of expected return and
      • 
+
    • is_test -- Used for testing. Returns a tuple of expected return and the URL called to retrieve the data
      • 
+
    • proxy -- proxy given to the get request used to access the API
      • 
 
    
 
    
+
    Returns
    
+
    Code used in Fingertips to represent the age or age range as a string
    
+
    
 
-
    the URL called to retrieve the data
-:param proxy: proxy given to the get request used to access the API
-:return: Code used in Fingertips to represent the age or age range as a string
    
 
 
 
    
@@ -243,12 +244,15 @@ 
    metadata.py
 
    Parameters
    
-
    is_test -- Used for testing. Returns a tuple of expected return and
    
+
      
+
    • is_test -- Used for testing. Returns a tuple of expected return and the URL called to retrieve the data
      • 
+
    • proxy -- proxy given to the get request used to access the API
      • 
+
    
+
    
+
    Returns
    
+
    Age codes used in Fingertips in a tuple
    
 
    
 
    
-
    the URL called to retrieve the data
-:param proxy: proxy given to the get request used to access the API
-:return: Age codes used in Fingertips in a tuple
    
 
 
 
    
@@ -257,12 +261,15 @@ 
    metadata.py
 
    Parameters
    
-
    is_test -- Used for testing. Returns a tuple of expected return and
    
+
      
+
    • is_test -- Used for testing. Returns a tuple of expected return and the URL called to retrieve the data
      • 
+
    • proxy -- proxy given to the get request used to access the API
      • 
+
    
+
    
+
    Returns
    
+
    A dictionary of all area types used in Fingertips
    
 
    
 
    
-
    the URL called to retrieve the data
-:param proxy: proxy given to the get request used to access the API
-:return: A dictionary of all area types used in Fingertips
    
 
 
 
    
@@ -311,10 +318,9 @@ 
    metadata.pyReturns
-
    Data value notes and their associated codes that are used in
    
+
    Data value notes and their associated codes that are used in Fingertips as a list of tuples
    
 
    
 
    
-
    Fingertips as a list of tuples
    
 
 
 
    
@@ -359,8 +365,8 @@ 
    metadata.pyParameters
 
      
 
    • profile_id -- ID used in Fingertips to identify a profile as integer or string
      • 
-
    • proxy -- proxy given to the get request used to access the API
      • 
 
    • is_test -- Used for testing. Returns a tuple of expected return and the URL called to retrieve the data
      • 
+
    • proxy -- proxy given to the get request used to access the API
      • 
 
    
 
    
 
    Returns
    
@@ -417,7 +423,7 @@ 
    metadata.pyReturns
@@ -484,16 +490,13 @@ 
    metadata.py
 
    
 fingertips_py.metadata.get_metadata_for_indicator(indicator_number, is_test=False, proxy=None)
    
-
    
-
    Returns the metadata for an indicator given the indicator number as integer
    or string.
    
-
    
-
    
+
    Returns the metadata for an indicator given the indicator number as integer or string.
    
 
    
 
    Parameters
    
 
      
 
    • indicator_number -- Number used to identify an indicator within Fingertips as integer or string
      • 
-
    • proxy -- proxy given to the get request used to access the API
      • 
 
    • is_test -- Used for testing. Returns a tuple of expected return and the URL called to retrieve the data
      • 
+
    • proxy -- proxy given to the get request used to access the API
      • 
 
    
 
    
 
    Returns
    
@@ -505,8 +508,7 @@ 
    metadata.py
 
    
 fingertips_py.metadata.get_metadata_for_indicator_as_dataframe(indicator_ids, is_test=False, proxy=None)
    
-
    Returns a dataframe of metadata for a given indicator ID or list of 
-indicator IDs.
    
+
    Returns a dataframe of metadata for a given indicator ID or list of indicator IDs.
    
 
    
 
    Parameters

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Fingertips is a major repository of population and public health indicators for England. The site presents the information in many ways to improve accessibility for a wide range of audiences ranging from public health professionals @@ -30,15 +30,15 @@ Installation This packaged should be installed using pip: -``` -pip install fingertips_py -``` +.. code-block:: console + + pip install fingertips_py Or it can be compiled from source (still requires pip): -``` -pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git -``` +.. code-block:: console + + pip install git+https://github.com/PublicHealthEngland/PHDS_fingertips_py.git Usage ***** @@ -47,20 +47,18 @@ fingertips_py should be imported and used in line with standard python conventions. It is suggested that if the whole package is to be imported then the following convention is used: -``` -import fingertips_py as ftp -``` +>>> import fingertips_py as ftp The package returns data in a variety of types dependent on the function. For more information on any function, you can use: -``` -help(*fingertips_py function name*) -``` +>>> help(*fingertips_py function name*) + + +Or you can view the documents `here `_. -Or you can view the documents [here](https://fingertips-py.readthedocs.io/en/latest/). Example ******* @@ -69,32 +67,40 @@ This is an example of a workflow for retrieving data for the indicator on *Healthy Life Expectancy at Birth* from the *Public Health Outcomes Framework* profile. -``` -import fingertips_py as ftp +.. code-block:: python + :linenos: + import fingertips_py as ftp -phof = ftp.get_profile_by_name('public health outcomes framework') -phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id']) -indicator_meta = phof_indicators[phof_meta['Indicator'].str.contains('Healthy')] -print(indicator_meta) + # Extract the metadata for a particular profile + phof = ftp.get_profile_by_name('public health outcomes framework') + phof_meta = ftp.get_metadata_for_profile_as_dataframe(phof['Id']) + + # Extract metadata for indicators containing the string "Healthy" + indicator_meta = phof_meta[phof_meta['Indicator'].str.contains('Healthy')] + + print(indicator_meta) + +.. code-block:: + :linenos: + + Indicator ID Indicator ... + 90362 0.1i - Healthy life expectancy at birth ... + 92543 2.05ii - Proportion of children aged 2-2½yrs r ... - Indicator ID Indicator ... -0 90362 0.1i - Healthy life expectancy at birth ... -55 92543 2.05ii - Proportion of children aged 2-2½yrs r... ... -``` We can see that the *Healthy life expectancy at birth* indicator has an id of 90362. The data for this indicator at all geographical breakdowns can be retrieved using `get_data_for_indicator_at_all_available_geographies()` -``` -healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362) -``` + +>>> healthy_life_data = ftp.get_data_for_indicator_at_all_available_geographies(90362) + Licence ******* -This project is released under the [GPL-3](https://opensource.org/licenses/GPL-3.0) +This project is released under the `GPL-3 `_ licence. .. automodule:: fingertips_py.metadata diff --git a/build/html/_static/basic.css b/build/html/_static/basic.css index 912859b..eeb0519 100644 --- a/build/html/_static/basic.css +++ b/build/html/_static/basic.css @@ -4,7 +4,7 @@ * * Sphinx stylesheet -- basic theme. * - * :copyright: Copyright 2007-2021 by the Sphinx team, see AUTHORS. + * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS. * :license: BSD, see LICENSE for details. * */ @@ -222,7 +222,7 @@ table.modindextable td { /* -- general body 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"group", "groupEnd", "time", "timeEnd", "count", "trace", - "profile", "profileEnd"]; - window.console = {}; - for (var i = 0; i < names.length; ++i) - window.console[names[i]] = function() {}; -} - */ - -/** - * small helper function to urldecode strings - * - * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL - */ -jQuery.urldecode = function(x) { - if (!x) { - return x - } - return decodeURIComponent(x.replace(/\+/g, ' ')); -}; - -/** - * small helper function to urlencode strings - */ -jQuery.urlencode = encodeURIComponent; - -/** - * This function returns the parsed url parameters of the - * current request. Multiple values per key are supported, - * it will always return arrays of strings for the value parts. - */ -jQuery.getQueryParameters = function(s) { - if (typeof s === 'undefined') - s = document.location.search; - var parts = s.substr(s.indexOf('?') + 1).split('&'); - var result = {}; - for (var i = 0; i < parts.length; i++) { - var tmp = parts[i].split('=', 2); - var key = jQuery.urldecode(tmp[0]); - var value = jQuery.urldecode(tmp[1]); - if (key in result) - result[key].push(value); - else - result[key] = [value]; +"use strict"; + +const BLACKLISTED_KEY_CONTROL_ELEMENTS = new Set([ + "TEXTAREA", + "INPUT", + "SELECT", + "BUTTON", +]); + +const _ready = (callback) => { + if (document.readyState !== "loading") { + callback(); + } else { + document.addEventListener("DOMContentLoaded", callback); } - return result; }; -/** - * highlight a given string on a jquery object by wrapping it in - * span elements with the given class name. - */ -jQuery.fn.highlightText = function(text, className) { - function highlight(node, addItems) { - if (node.nodeType === 3) { - var val = node.nodeValue; - var pos = val.toLowerCase().indexOf(text); - if (pos >= 0 && - !jQuery(node.parentNode).hasClass(className) && - !jQuery(node.parentNode).hasClass("nohighlight")) { - var span; - var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg"); - if (isInSVG) { - span = document.createElementNS("http://www.w3.org/2000/svg", "tspan"); - } else { - span = document.createElement("span"); - span.className = className; - } - span.appendChild(document.createTextNode(val.substr(pos, text.length))); - node.parentNode.insertBefore(span, node.parentNode.insertBefore( - document.createTextNode(val.substr(pos + text.length)), - node.nextSibling)); - node.nodeValue = val.substr(0, pos); - if (isInSVG) { - var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect"); - var bbox = node.parentElement.getBBox(); - rect.x.baseVal.value = bbox.x; - rect.y.baseVal.value = bbox.y; - rect.width.baseVal.value = bbox.width; - rect.height.baseVal.value = bbox.height; - rect.setAttribute('class', className); - addItems.push({ - "parent": node.parentNode, - "target": rect}); - } - } - } - else if (!jQuery(node).is("button, select, textarea")) { - jQuery.each(node.childNodes, function() { - highlight(this, addItems); - }); - } - } - var addItems = []; - var result = this.each(function() { - highlight(this, addItems); - }); - for (var i = 0; i < addItems.length; ++i) { - jQuery(addItems[i].parent).before(addItems[i].target); - } - return result; -}; - -/* - * backward compatibility for jQuery.browser - * This will be supported until firefox bug is fixed. - */ -if (!jQuery.browser) { - jQuery.uaMatch = function(ua) { - ua = ua.toLowerCase(); - - var match = /(chrome)[ \/]([\w.]+)/.exec(ua) || - /(webkit)[ \/]([\w.]+)/.exec(ua) || - /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) || - /(msie) ([\w.]+)/.exec(ua) || - ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) || - []; - - return { - browser: match[ 1 ] || "", - version: match[ 2 ] || "0" - }; - }; - jQuery.browser = {}; - jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true; -} - /** * Small JavaScript module for the documentation. */ -var Documentation = { - - init : function() { - this.fixFirefoxAnchorBug(); - this.highlightSearchWords(); - this.initIndexTable(); - if (DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) { - this.initOnKeyListeners(); - } +const Documentation = { + init: () => { + Documentation.initDomainIndexTable(); + Documentation.initOnKeyListeners(); }, /** * i18n support */ - TRANSLATIONS : {}, - PLURAL_EXPR : function(n) { return n === 1 ? 0 : 1; }, - LOCALE : 'unknown', + TRANSLATIONS: {}, + PLURAL_EXPR: (n) => (n === 1 ? 0 : 1), + LOCALE: "unknown", // gettext and ngettext don't access this so that the functions // can safely bound to a different name (_ = Documentation.gettext) - gettext : function(string) { - var translated = Documentation.TRANSLATIONS[string]; - if (typeof translated === 'undefined') - return string; - return (typeof translated === 'string') ? translated : translated[0]; + gettext: (string) => { + const translated = Documentation.TRANSLATIONS[string]; + switch (typeof translated) { + case "undefined": + return string; // no translation + case "string": + return translated; // translation exists + default: + return translated[0]; // (singular, plural) translation tuple exists + } }, - ngettext : function(singular, plural, n) { - var translated = Documentation.TRANSLATIONS[singular]; - if (typeof translated === 'undefined') - return (n == 1) ? singular : plural; - return translated[Documentation.PLURALEXPR(n)]; + ngettext: (singular, plural, n) => { + const translated = Documentation.TRANSLATIONS[singular]; + if (typeof translated !== "undefined") + return translated[Documentation.PLURAL_EXPR(n)]; + return n === 1 ? singular : plural; }, - addTranslations : function(catalog) { - for (var key in catalog.messages) - this.TRANSLATIONS[key] = catalog.messages[key]; - this.PLURAL_EXPR = new Function('n', 'return +(' + catalog.plural_expr + ')'); - this.LOCALE = catalog.locale; + addTranslations: (catalog) => { + Object.assign(Documentation.TRANSLATIONS, catalog.messages); + Documentation.PLURAL_EXPR = new Function( + "n", + `return (${catalog.plural_expr})` + ); + Documentation.LOCALE = catalog.locale; }, /** - * add context elements like header anchor links + * helper function to focus on search bar */ - addContextElements : function() { - $('div[id] > :header:first').each(function() { - $('\u00B6'). - attr('href', '#' + this.id). - attr('title', _('Permalink to this headline')). - appendTo(this); - }); - $('dt[id]').each(function() { - $('\u00B6'). - attr('href', '#' + this.id). - attr('title', _('Permalink to this definition')). - appendTo(this); - }); + focusSearchBar: () => { + document.querySelectorAll("input[name=q]")[0]?.focus(); }, /** - * workaround a firefox stupidity - * see: https://bugzilla.mozilla.org/show_bug.cgi?id=645075 + * Initialise the domain index toggle buttons */ - fixFirefoxAnchorBug : function() { - if (document.location.hash && $.browser.mozilla) - window.setTimeout(function() { - document.location.href += ''; - }, 10); - }, - - /** - * highlight the search words provided in the url in the text - */ - highlightSearchWords : function() { - var params = $.getQueryParameters(); - var terms = (params.highlight) ? params.highlight[0].split(/\s+/) : []; - if (terms.length) { - var body = $('div.body'); - if (!body.length) { - body = $('body'); + initDomainIndexTable: () => { + const toggler = (el) => { + const idNumber = el.id.substr(7); + const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`); + if (el.src.substr(-9) === "minus.png") { + el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`; + toggledRows.forEach((el) => (el.style.display = "none")); + } else { + el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`; + toggledRows.forEach((el) => (el.style.display = "")); } - window.setTimeout(function() { - $.each(terms, function() { - body.highlightText(this.toLowerCase(), 'highlighted'); - }); - }, 10); - $('