2024-06-04 13:57:32 +00:00
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defmodule Growth.Indicators.Download do
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@moduledoc """
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2024-06-06 22:49:52 +00:00
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To calculate z-scores for the different growth measurements, the system must:
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1. Fetch indicators from World Health Organization
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2. Extract data from excel sheets
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3. Convert the data into proper format, specially, handle with decimal values
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3. Add metadata to make search for the parameters possible
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The following indicators to construct z-scores are fetched:
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2024-06-04 13:57:32 +00:00
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* [height for age 0 to 5 years](https://www.who.int/tools/child-growth-standards/standards/length-height-for-age)
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* [height for age 5 to 19 years](https://www.who.int/tools/growth-reference-data-for-5to19-years/indicators/height-for-age)
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* [weight for age 0 to 5 years](https://www.who.int/tools/child-growth-standards/standards/weight-for-age)
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* [weight for age 5 to 10 years](https://www.who.int/tools/growth-reference-data-for-5to19-years/indicators/weight-for-age-5to10-years)
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* [weight for height](https://www.who.int/tools/child-growth-standards/standards/weight-for-length-height)
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* [body mass index (bmi) for age 0 to 5 years](https://www.who.int/toolkits/child-growth-standards/standards/body-mass-index-for-age-bmi-for-age)
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* [body mass index (bmi) for age 5 to 19 years](https://www.who.int/tools/growth-reference-data-for-5to19-years/indicators/bmi-for-age)
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* [head circumference for age 0 to 5 years](https://www.who.int/tools/child-growth-standards/standards/head-circumference-for-age)
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* [arm circumference for age 3 months to 5 years](https://www.who.int/tools/child-growth-standards/standards/arm-circumference-for-age)
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* [subscapular skinfold for age 3 months to 5 years](https://www.who.int/tools/child-growth-standards/standards/subscapular-skinfold-for-age)
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* [triceps skinfold for age 3 months to 5 years](https://www.who.int/tools/child-growth-standards/standards/triceps-skinfold-for-age)
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"""
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NimbleCSV.define(IndicatorParser, separator: ",", escape: "\"")
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@urls %{
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height_for_age: %{
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female: %{
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age_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/lhfa_girls_0-to-13-weeks_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/lhfa_girls_0-to-2-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/lhfa_girls_2-to-5-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/height-for-age-(5-19-years)/hfa-girls-z-who-2007-exp.xlsx
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],
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expanded_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/expandable-tables/lhfa-girls-zscore-expanded-tables.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/height-for-age-(5-19-years)/hfa-girls-z-who-2007-exp.xlsx
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]
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},
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male: %{
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age_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/lhfa_boys_0-to-13-weeks_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/lhfa_boys_0-to-2-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/lhfa_boys_2-to-5-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/height-for-age-(5-19-years)/hfa-boys-z-who-2007-exp.xlsx
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],
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expanded_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/length-height-for-age/expandable-tables/lhfa-boys-zscore-expanded-tables.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/height-for-age-(5-19-years)/hfa-boys-z-who-2007-exp.xlsx
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]
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}
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},
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weight_for_age: %{
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female: %{
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age_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-age/wfa_girls_0-to-13-weeks_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-age/wfa_girls_0-to-5-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/weight-for-age-(5-10-years)/hfa-girls-z-who-2007-exp_7ea58763-36a2-436d-bef0-7fcfbadd2820.xlsx
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],
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expanded_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-age/expanded-tables/wfa-girls-zscore-expanded-tables.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/weight-for-age-(5-10-years)/hfa-girls-z-who-2007-exp_7ea58763-36a2-436d-bef0-7fcfbadd2820.xlsx
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]
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},
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male: %{
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age_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-age/wfa_boys_0-to-13-weeks_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-age/wfa_boys_0-to-5-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/weight-for-age-(5-10-years)/hfa-boys-z-who-2007-exp_0ff9c43c-8cc0-4c23-9fc6-81290675e08b.xlsx
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],
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expanded_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-age/expanded-tables/wfa-boys-zscore-expanded-tables.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/weight-for-age-(5-10-years)/hfa-boys-z-who-2007-exp_0ff9c43c-8cc0-4c23-9fc6-81290675e08b.xlsx
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]
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}
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},
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weight_for_height: %{
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female: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/wfl_girls_0-to-2-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/wfh_girls_2-to-5-years_zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/expanded-tables/wfl-girls-zscore-expanded-table.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/expanded-tables/wfh-girls-zscore-expanded-tables.xlsx
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)
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},
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male: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/wfl_boys_0-to-2-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/wfh_boys_2-to-5-years_zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/expanded-tables/wfl-boys-zscore-expanded-table.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/weight-for-length-height/expanded-tables/wfh-boys-zscore-expanded-tables.xlsx
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)
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}
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},
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bmi_for_age: %{
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female: %{
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age_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/bmi_girls_0-to-13-weeks_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/bmi_girls_0-to-2-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/bmi_girls_2-to-5-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/bmi-for-age-(5-19-years)/bmi-girls-z-who-2007-exp.xlsx
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],
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expanded_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/expanded-tables/bfa-girls-zscore-expanded-tables.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/bmi-for-age-(5-19-years)/bmi-girls-z-who-2007-exp.xlsx
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]
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},
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male: %{
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age_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/bmi_boys_0-to-13-weeks_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/bmi_boys_0-to-2-years_zcores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/bmi_boys_2-to-5-years_zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/bmi-for-age-(5-19-years)/bmi-boys-z-who-2007-exp.xlsx
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],
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expanded_tables: ~w[
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/body-mass-index-for-age/expanded-tables/bfa-boys-zscore-expanded-tables.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/growth-reference-5-19-years/bmi-for-age-(5-19-years)/bmi-boys-z-who-2007-exp.xlsx
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]
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}
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},
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head_circumference_for_age: %{
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female: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/head-circumference-for-age/hcfa-girls-0-13-zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/head-circumference-for-age/hcfa-girls-0-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/head-circumference-for-age/expanded-tables/hcfa-girls-zscore-expanded-tables.xlsx
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)
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},
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male: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/head-circumference-for-age/hcfa-boys-0-13-zscores.xlsx
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/head-circumference-for-age/hcfa-boys-0-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/head-circumference-for-age/expanded-tables/hcfa-boys-zscore-expanded-tables.xlsx
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)
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}
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},
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arm_circumference_for_age: %{
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female: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/arm-circumference-for-age/acfa-girls-3-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/arm-circumference-for-age/expanded-tables/acfa-girls-zscore-expanded-tables.xlsx
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)
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},
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male: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/arm-circumference-for-age/acfa-boys-3-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/arm-circumference-for-age/expanded-tables/acfa-boys-zscore-expanded-tables.xlsx
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)
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}
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},
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subscapular_skinfold_for_age: %{
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female: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/subscapular-skinfold-for-age/ssfa-girls-3-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/subscapular-skinfold-for-age/expanded-tables/ssfa-girls-zscore-expanded-table.xlsx
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)
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},
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male: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/subscapular-skinfold-for-age/ssfa-boys-3-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/subscapular-skinfold-for-age/expanded-tables/ssfa-boys-zscore-expanded-table.xlsx
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)
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}
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},
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triceps_skinfold_for_age: %{
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female: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/triceps-skinfold-for-age/tsfa-girls-3-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/triceps-skinfold-for-age/expanded-tables/tsfa-girls-zscore-expanded-tables.xlsx
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)
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},
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male: %{
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age_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/triceps-skinfold-for-age/tsfa-boys-3-5-zscores.xlsx
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),
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expanded_tables: ~w(
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https://cdn.who.int/media/docs/default-source/child-growth/child-growth-standards/indicators/triceps-skinfold-for-age/expanded-tables/tsfa-boys-zscore-expanded-tables.xlsx
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)
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}
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}
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}
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def process_all do
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@urls
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|> Enum.map(&Task.async(__MODULE__, :process_measure, [&1]))
|
|
|
|
|
|> Task.await_many()
|
|
|
|
|
end
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|
|
|
|
|
|
|
|
|
def process_measure(
|
|
|
|
|
{measure,
|
|
|
|
|
%{
|
2024-06-06 22:49:52 +00:00
|
|
|
female: %{age_tables: female_urls, expanded_tables: e_female_urls},
|
|
|
|
|
male: %{age_tables: male_urls, expanded_tables: e_male_urls}
|
2024-06-04 13:57:32 +00:00
|
|
|
}}
|
|
|
|
|
) do
|
2024-06-06 22:49:52 +00:00
|
|
|
[
|
|
|
|
|
{:female, :age, female_urls},
|
|
|
|
|
{:male, :age, male_urls},
|
|
|
|
|
{:female, :expanded, e_female_urls},
|
|
|
|
|
{:male, :expanded, e_male_urls}
|
|
|
|
|
]
|
2024-06-04 13:57:32 +00:00
|
|
|
|> Enum.map(&Task.async(__MODULE__, :process_gender, [&1]))
|
|
|
|
|
|> Task.await_many()
|
|
|
|
|
|> merge()
|
|
|
|
|
|> as_csv()
|
|
|
|
|
|> save(measure)
|
|
|
|
|
end
|
|
|
|
|
|
2024-06-06 22:49:52 +00:00
|
|
|
def process_gender({gender, category, urls}) do
|
2024-06-04 13:57:32 +00:00
|
|
|
urls
|
2024-06-06 22:49:52 +00:00
|
|
|
|> Enum.map(&Task.async(__MODULE__, :process, [gender, category, &1]))
|
2024-06-04 13:57:32 +00:00
|
|
|
|> Task.await_many()
|
|
|
|
|
|> merge()
|
|
|
|
|
end
|
|
|
|
|
|
2024-06-06 22:49:52 +00:00
|
|
|
def process(gender, category, url) do
|
2024-06-04 13:57:32 +00:00
|
|
|
url
|
|
|
|
|
|> fetch!()
|
|
|
|
|
|> extract!(url)
|
2024-06-06 22:49:52 +00:00
|
|
|
|> convert(gender, category, url)
|
2024-06-04 13:57:32 +00:00
|
|
|
end
|
|
|
|
|
|
|
|
|
|
def fetch!(url) do
|
2024-10-07 19:16:46 +00:00
|
|
|
req =
|
|
|
|
|
[url: url]
|
|
|
|
|
|> Keyword.merge(
|
|
|
|
|
:wabanex
|
|
|
|
|
|> Application.get_env(__MODULE__, [])
|
|
|
|
|
|> Keyword.get(:who_req_options, [])
|
|
|
|
|
)
|
|
|
|
|
|> Req.new()
|
|
|
|
|
|
|
|
|
|
case Req.get(req) do
|
2024-06-04 14:36:20 +00:00
|
|
|
{:ok, %{status: 200, body: body}} ->
|
|
|
|
|
body
|
|
|
|
|
|
|
|
|
|
_ ->
|
|
|
|
|
raise("fetch failed for url #{url}")
|
2024-06-04 13:57:32 +00:00
|
|
|
end
|
|
|
|
|
end
|
|
|
|
|
|
|
|
|
|
def extract!(content, url) do
|
|
|
|
|
with {:ok, package} <- XlsxReader.open(content, source: :binary),
|
|
|
|
|
[sheet_name | _] <- XlsxReader.sheet_names(package),
|
|
|
|
|
{:ok, data} <- XlsxReader.sheet(package, sheet_name) do
|
|
|
|
|
data
|
|
|
|
|
else
|
|
|
|
|
_ -> raise("failed to extract excel for #{url}")
|
|
|
|
|
end
|
|
|
|
|
end
|
|
|
|
|
|
2024-06-06 22:49:52 +00:00
|
|
|
@common_header ~w(source category gender age_unit age l m s sd3neg sd2neg sd1neg sd0 sd1 sd2 sd3)
|
2024-06-04 23:55:03 +00:00
|
|
|
|
2024-06-04 23:56:27 +00:00
|
|
|
# FIX: (jpd) weight for lenght/height does not have an age in the header row
|
2024-06-06 22:49:52 +00:00
|
|
|
def convert([header | rows], gender, category, url) do
|
2024-06-04 23:55:03 +00:00
|
|
|
age_unit = header |> hd() |> String.downcase()
|
2024-06-04 13:57:32 +00:00
|
|
|
|
|
|
|
|
fixed_header = header |> tl() |> Enum.map(&String.downcase/1) |> Enum.map(&String.trim/1)
|
|
|
|
|
|
2024-06-06 22:49:52 +00:00
|
|
|
parsed_header = ["source" | ["category" | ["gender" | ["age_unit" | ["age" | fixed_header]]]]]
|
2024-06-04 13:57:32 +00:00
|
|
|
|
2024-06-04 23:55:03 +00:00
|
|
|
# NOTE: (jpd): parsing the rows consist in:
|
|
|
|
|
# 1. convert row values to decimal
|
|
|
|
|
# 2. prepend the values url source, gender, and age unit
|
|
|
|
|
# 3. convert row to keyword list using the parsed header
|
|
|
|
|
# 4. convert from keyword list to map
|
|
|
|
|
# 5. fetch common values based on common headers
|
|
|
|
|
# 6. sort row values based on common headers
|
2024-06-04 13:57:32 +00:00
|
|
|
parsed_rows =
|
2024-06-04 23:55:03 +00:00
|
|
|
rows
|
|
|
|
|
|> Stream.map(fn row -> Enum.map(row, &Decimal.new/1) end)
|
2024-06-06 22:49:52 +00:00
|
|
|
|> Stream.map(&[url | [category | [gender | [age_unit | &1]]]])
|
2024-06-04 23:55:03 +00:00
|
|
|
|> Stream.map(&Enum.zip(parsed_header, &1))
|
|
|
|
|
|> Stream.map(&Map.new/1)
|
|
|
|
|
|> Stream.map(&Map.take(&1, @common_header))
|
|
|
|
|
|> Enum.map(fn row ->
|
|
|
|
|
Enum.map(@common_header, fn key -> Map.get(row, key) end)
|
2024-06-04 13:57:32 +00:00
|
|
|
end)
|
|
|
|
|
|
2024-06-04 23:55:03 +00:00
|
|
|
[@common_header | parsed_rows]
|
2024-06-04 13:57:32 +00:00
|
|
|
end
|
|
|
|
|
|
|
|
|
|
def merge(datum) do
|
2024-06-04 23:55:03 +00:00
|
|
|
datum
|
|
|
|
|
|> Stream.with_index()
|
|
|
|
|
|> Stream.map(fn
|
|
|
|
|
{data, 0} ->
|
|
|
|
|
data
|
|
|
|
|
|
|
|
|
|
{[_ | data], _} ->
|
|
|
|
|
data
|
|
|
|
|
end)
|
|
|
|
|
|> Enum.reduce([], fn data, accum ->
|
2024-06-04 13:57:32 +00:00
|
|
|
Enum.concat(accum, data)
|
|
|
|
|
end)
|
|
|
|
|
end
|
|
|
|
|
|
|
|
|
|
def as_csv(data) do
|
|
|
|
|
IndicatorParser.dump_to_iodata(data)
|
|
|
|
|
end
|
|
|
|
|
|
|
|
|
|
def save(data, measurement) do
|
|
|
|
|
File.write("priv/growth/indicators/#{measurement}.csv", data)
|
|
|
|
|
end
|
|
|
|
|
end
|
