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ryanraaschCDCryanraaschCDC
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Merge pull request #55 from cdcent/rr-54-vaxfitting-scripts
Rr 54 vaxfitting scripts
2 parents d017461 + 2cfae68 commit 38519f4

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‎cfa/scenarios/dataops/datasets/covid19_vax_coverage_adult.toml‎

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# This dataset is static, and thus only needs to be extracted in it's raw form
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# once and saved to blob storage. For a human viewable we format, see:
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# https://data.cdc.gov/Vaccinations/Weekly-Cumulative-COVID-19-Vaccination-Coverage-an/ksfb-ug5d/about_data
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# Raw (extracted) and transformed (loaded) data will be stored in azure blob storage
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# which requires the account, container and path for access
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[properties]
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name = "covid19_vax_coverage_adult"
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automate = false
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transform_template = "covid19_vax_coverage_adult.sql"
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schema = "datasets/schemas/covid19_vax_coverage_adult.py"
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[source]
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url = "https://data.cdc.gov/resource/ksfb-ug5d.csv"
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pagination = {limit = 1000}
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[extract]
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account = "cfadatalakeprd"
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container = "cfapredict"
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prefix = "dataops/scenarios/raw/covid19_vax_coverage_adult"
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[load]
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account = "cfadatalakeprd"
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container = "cfapredict"
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prefix = "dataops/scenarios/transformed/covid19_vax_coverage_adult"
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# TODO: add some data schema validation

‎cfa/scenarios/dataops/datasets/covid19_vax_coverage_child.toml‎

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# This dataset is static, and thus only needs to be extracted in it's raw form
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# once and saved to blob storage. For a human viewable we format, see:
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# https://data.cdc.gov/Child-Vaccinations/Weekly-Parental-Intent-for-Vaccination-and-Cumulat/ker6-gs6z/about_data
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# Raw (extracted) and transformed (loaded) data will be stored in azure blob storage
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# which requires the account, container and path for access
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[properties]
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name = "covid19_vax_coverage_child"
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automate = false
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transform_template = "covid19_vax_coverage_child.sql"
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schema = "datasets/schemas/covid19_vax_coverage_child.py"
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[source]
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url = "https://data.cdc.gov/resource/ker6-gs6z.csv"
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pagination = {limit = 1000}
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[extract]
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account = "cfadatalakeprd"
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container = "cfapredict"
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prefix = "dataops/scenarios/raw/covid19_vax_coverage_child"
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[load]
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account = "cfadatalakeprd"
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container = "cfapredict"
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prefix = "dataops/scenarios/transformed/covid19_vax_coverage_child"

‎cfa/scenarios/dataops/datasets/covid_rd18_vax_curves.toml‎

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# This dataset is static, and thus only needs to be extracted in it's raw form
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# once and saved to blob storage.
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# Raw (extracted) and transformed (loaded) data will be stored in azure blob storage
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# which requires the account, container and path for access
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[properties]
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name = "covid_rd18_vax_curves"
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automate = false
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transform_template = ""
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schema = ""
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[source]
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url = ""
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pagination = 0
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[extract]
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account = "cfadatalakeprd"
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container = "cfapredict"
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prefix = "dataops/scenarios/raw/covid_rd18_vax_curves"
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[load]
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account = "cfadatalakeprd"
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container = "cfapredict"
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prefix = "dataops/scenarios/transformed/covid_rd18_vax_curves"
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# TODO: add some data schema validation

‎cfa/scenarios/dataops/datasets/schemas/covid19_vax_coverage_adult.py‎

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import random
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import pandas as pd
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import pandera.pandas as pa
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from faker import Faker
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fake = Faker()
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df_len = 100
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extract_schema = pa.DataFrameSchema(
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{
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"vaccine": pa.Column(str),
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"geographic_level": pa.Column(str),
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"geographic_name": pa.Column(str),
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"demographic_level": pa.Column(str),
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"demographic_name": pa.Column(str),
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"indicator_label": pa.Column(str),
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"indicator_category_label": pa.Column(str),
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"month_week": pa.Column(str),
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"week_ending": pa.Column(str),
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"estimate": pa.Column(float, nullable=True),
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"ci_half_width_95pct": pa.Column(float, nullable=True),
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"unweighted_sample_size": pa.Column(int, nullable=True),
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"current_season_week_ending": pa.Column(str, nullable=True),
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"covid_season": pa.Column(str),
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"suppression_flag": pa.Column(int),
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}
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)
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load_schema = pa.DataFrameSchema(
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{
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"vaccine": pa.Column(str),
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"geographic_level": pa.Column(str),
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"geographic_name": pa.Column(str),
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"demographic_level": pa.Column(str),
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"demographic_name": pa.Column(str),
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"indicator_label": pa.Column(str),
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"indicator_category_label": pa.Column(str),
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"month_week": pa.Column(str),
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"week_ending": pa.Column(str),
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"estimate": pa.Column(
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float, checks=pa.Check.in_range(0, 100), nullable=True
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),
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"ci_half_width_95pct": pa.Column(
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float, checks=pa.Check.in_range(0, 100), nullable=True
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),
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"unweighted_sample_size": pa.Column(
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int, checks=pa.Check.in_range(0, 10_000_000), nullable=True
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),
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"covid_season": pa.Column(str),
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"suppression_flag": pa.Column(int),
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"date": pa.Column(str),
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"date1": pa.Column(str),
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}
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)
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geo_name_opts = [
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"National",
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"Region 7",
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"Pennsylvania-Rest of State",
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"Oregon",
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"Tennessee",
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"Region 3",
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"Iowa",
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"New Jersey",
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"Pennsylvania",
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"New York-New York City",
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"New York",
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"Michigan",
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"Rhode Island",
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"Colorado",
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"Delaware",
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"New York-Rest of State",
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"Arkansas",
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"Arizona",
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"Illinois-City of Chicago",
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"Region 9",
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"North Carolina",
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"Nevada",
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"Utah",
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"West Virginia",
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"Alaska",
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"Pennsylvania-Philadelphia County",
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"Region 10",
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"Region 4",
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"Wisconsin",
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"Texas-City of Houston",
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"Maine",
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"Nebraska",
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"Kentucky",
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"Region 2",
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"Florida",
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"Texas-Bexar County",
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"Virginia",
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"New Hampshire",
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"Georgia",
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"Wyoming",
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"Region 5",
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"New Mexico",
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"Louisiana",
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"Mississippi",
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"Puerto Rico",
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"Missouri",
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"Kansas",
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"Oklahoma",
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"Texas",
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"Alabama",
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"Indiana",
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"Massachusetts",
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"South Dakota",
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"Minnesota",
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"District of Columbia",
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"Texas-Rest of State",
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"Ohio",
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"Illinois-Rest of State",
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"Region 1",
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"North Dakota",
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"Washington",
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"South Carolina",
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"Connecticut",
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"Montana",
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"Illinois",
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"Idaho",
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"Region 6",
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"Vermont",
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"Hawaii",
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"Region 8",
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"California",
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"Maryland",
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"U.S. Virgin Islands",
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"Guam",
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]
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demo_level_opts = [
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"Race and Ethnicity",
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"Urbanicity",
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"Overall",
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"Age",
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"Sexual Orientation",
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"Sex",
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"Disability Status",
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"Poverty Status",
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"Health Insurance",
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"Health Insurance Among 18-64 Years",
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]
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demo_name_opts = [
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"Multiple Race/Other (Excludes Asian, AIAN, PI/NH), Non-Hispanic",
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"Rural (Non-MSA)",
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"Asian, Non-Hispanic",
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"White, Non-Hispanic",
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"18+ years",
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"65+ years",
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"Other, Non-Hispanic",
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"Gay/Lesbian/Bisexual/Other",
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"65-74 years",
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"Urban MSA Principal City",
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"Female",
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"75+ years",
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"Yes",
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"30-39 years",
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"Don't Know/Refused",
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"American Indian/Alaska Native, Non-Hispanic",
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"Straight",
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"Above Poverty, Income < $75k",
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"Male",
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"Above Poverty, Income >= $75k",
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"No",
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"Uninsured",
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"Below Poverty",
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"Pacific Islander/Native Hawaiian, Non-Hispanic",
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"50-64 years",
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"60+ years",
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"Insured",
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"Poverty Status Unknown",
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"Suburban (MSA Non-Principal City)",
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"18-49 years",
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"40-49 years",
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"Black, Non-Hispanic",
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"18-29 years",
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"Hispanic",
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]
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ind_label_opts = ["4-level vaccination and intent", "Up-to-date"]
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ind_cat_label_opts = [
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"Definitely will get a vaccine",
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"Received a vaccination",
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"Yes",
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"Probably will get a vaccine or are unsure",
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"Definitely or probably will not get a vaccine",
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]
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year_opts = ["2023-2024", "2024-2025"]
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raw_synth_data = pd.DataFrame()
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raw_synth_data = raw_synth_data.assign(
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vaccine=["COVID" for _ in range(df_len)],
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geographic_level=[
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random.choice(["National", "Region", "Substate", "State"])
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for _ in range(df_len)
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],
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geographic_name=[random.choice(geo_name_opts) for _ in range(df_len)],
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demographic_level=[random.choice(demo_level_opts) for _ in range(df_len)],
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demographic_name=[random.choice(demo_name_opts) for _ in range(df_len)],
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indicator_label=[random.choice(ind_label_opts) for _ in range(df_len)],
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indicator_category_label=[
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random.choice(ind_cat_label_opts) for _ in range(df_len)
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],
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month_week=[
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fake.month_name() + " " + str(random.randint(1, 52))
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for _ in range(df_len)
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],
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week_ending=[str(fake.date_this_year()) for _ in range(df_len)],
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estimate=[random.uniform(0, 100) for _ in range(df_len)],
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ci_half_width_95pct=[random.uniform(0, 100) for _ in range(df_len)],
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unweighted_sample_size=[
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random.randint(1, 10_000_000) for _ in range(df_len)
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],
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current_season_week_ending=[
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str(fake.date_this_year()) for _ in range(df_len)
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],
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covid_season=[random.choice(year_opts) for _ in range(df_len)],
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suppression_flag=[random.randint(0, 99) for _ in range(df_len)],
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)
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tf_synth_data = raw_synth_data.copy()
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tf_synth_data["date"] = tf_synth_data["week_ending"]
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tf_synth_data["date1"] = tf_synth_data["week_ending"]

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