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#358 Add tests for the cli (#554)
* #358 Add tests for the cli * #358 Add tests for the cli * #358 Add tests for the cli - Fixed naming style. Co-authored-by: Kristof <[email protected]> Co-authored-by: Brian Ross <[email protected]>
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‎src/penn_chime/cli.py

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from .model.parameters import Parameters
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from .model.sir import Sir
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def main():
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"""Main."""
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p = Parameters.create(os.environ, sys.argv[1:])
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def run(argv):
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p = Parameters.create(os.environ, argv[1:])
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m = Sir(p)
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for df, name in (
@@ -18,3 +16,7 @@ def main():
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(m.census_df, "projected_census"),
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):
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df.to_csv(f"{p.current_date}_{name}.csv")
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def main():
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"""Main."""
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run(sys.argv)

‎tests/penn_chime/test_cli.py

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import pytest
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import penn_chime.cli
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from datetime import date, timedelta
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def test_main_with_doubling_time():
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""""
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Tests a run via CLI with the minimum amount of parameters. Exponential
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factor is defined by doubling-time.
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"""
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arguments = [
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"pytest",
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"--current-hospitalized", "1",
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"--doubling-time", "2.5",
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"--hospitalized-days", "5",
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"--hospitalized-rate", "0.01",
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"--icu-days", "10",
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"--icu-rate", "0.5",
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"--market-share", "0.1",
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"--infectious-days", "5",
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"--max-y-axis", "10000",
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"--n-days", "200",
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"--recovered", "10",
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"--relative-contact-rate", "0.1",
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"--population", "1000000",
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"--ventilated-days", "5",
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"--ventilated-rate", "0.025"
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]
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penn_chime.cli.run(arguments)
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def test_main_with_date_first_hospitalized():
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""""
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Tests a run via CLI with the minimum amount of parameters. Exponential
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factor is defined by date-first-hospitalized.
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"""
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arguments = [
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"pytest",
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"--current-hospitalized", "69",
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"--current-date", "2020-04-14",
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"--date-first-hospitalized", "2020-04-01",
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"--hospitalized-days", "5",
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"--hospitalized-rate", "0.025",
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"--icu-days", "9",
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"--icu-rate", "0.075",
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"--market-share", "0.1",
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"--infectious-days", "14",
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"--max-y-axis", "1000",
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"--n-days", "30",
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"--recovered", "0",
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"--relative-contact-rate", "0.1",
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"--population", "1000000",
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"--ventilated-days", "10",
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"--ventilated-rate", "0.005"
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]
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penn_chime.cli.run(arguments)
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def test_failure_on_missing_parameters():
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"""Negative test to verify that an error is given when neither defining
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doubling-time nor date-first-hospitalized."""
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arguments = [
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"pytest",
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"--current-hospitalized", "69",
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"--hospitalized-days", "5",
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"--hospitalized-rate", "0.025",
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"--icu-days", "9",
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"--icu-rate", "0.075",
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"--market-share", "0.1",
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"--infectious-days", "14",
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"--max-y-axis", "1000",
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"--n-days", "30",
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"--recovered", "0",
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"--relative-contact-rate", "0.1",
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"--population", "1000000",
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"--ventilated-days", "10",
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"--ventilated-rate", "0.005"
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]
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with pytest.raises(AssertionError):
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penn_chime.cli.run(arguments)
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def test_main_with_csv_verification():
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"""Integration test for CLI. Runs a five-day simulation and verifies the
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content of the resulting csv files."""
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current_date = date.today().strftime("%Y-%m-%d")
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n_days = 5
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arguments = [
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"pytest",
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"--current-hospitalized", "1",
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"--current-date", current_date,
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"--doubling-time", "2.5",
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"--hospitalized-days", "5",
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"--hospitalized-rate", "0.01",
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"--icu-days", "10",
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"--icu-rate", "0.5",
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"--market-share", "0.1",
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"--infectious-days", "5",
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"--max-y-axis", "10000",
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"--n-days", str(n_days),
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"--recovered", "10",
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"--relative-contact-rate", "0.1",
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"--population", "1000000",
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"--ventilated-days", "5",
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"--ventilated-rate", "0.025"
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]
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penn_chime.cli.run(arguments)
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#Verify content of projected_admits.csv
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projected_admits_content = [
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[None, None, None],
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[0.5195079107728944,25.97539553864472,1.298769776932236],
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[0.6851383215271454,34.25691607635727,1.7128458038178636],
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[0.8129161146846768,40.64580573423383,2.0322902867116914],
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[1.029120162473117,51.456008123655835,2.5728004061827923],
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[1.3021513067257287,65.10756533628646,3.255378266814322],
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[1.6465388184586223,82.32694092293116,4.116347046146558],
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[2.0802813033400414,104.01406516700195,5.200703258350099]
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]
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__validate_file(projected_admits_content, ",day,date,admits_hospitalized,admits_icu,admits_ventilated\n", current_date + "_projected_admits.csv")
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#Verify content of projected_admits.csv
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projected_census_content = [
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[0.0,0.0,0.0],
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[0.5195079107728944,25.97539553864472,1.298769776932236],
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[1.2046462323000398,60.23231161500199,3.0116155807500995],
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[2.0175623469847164,100.87811734923582,5.043905867461791],
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[3.0466825094578334,152.33412547289166,7.616706273644583],
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[4.3488338161835625,217.4416908091781,10.872084540458905],
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[5.47586472386929,299.76863173210927,13.689661809673227],
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[6.871007705682186,403.7826968991112,17.17751926420546]
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]
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__validate_file(projected_census_content, ",day,date,census_hospitalized,census_icu,census_ventilated\n", current_date + "_projected_census.csv")
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#Verify content of sim_sir_w_date.csv
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sim_sir_w_date_content = [
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[999000.0,1000.0,10.0],
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[998480.4920892271,1319.5079107728943,210.0],
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[997795.3537677001,1740.7446501454608,473.901582154579],
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[996982.4376530153,2205.5118348010456,822.0505121836709],
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[995953.3174905422,2793.529630313953,1263.15287914388],
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[994651.1661838164,3536.9750109768916,1821.8588052066705],
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[993004.6273653577,4476.118827240136,2529.2538074020486],
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[990924.346062018,5661.176365132148,3424.4775728500767]
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]
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__validate_file(sim_sir_w_date_content, ",day,date,susceptible,infected,recovered\n", current_date + "_sim_sir_w_date.csv")
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def __validate_file(reference_file_content, reference_file_header, reference_file_name):
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with open(reference_file_name, "r") as f:
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lines = f.readlines()
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assert len(lines) == len(reference_file_content) + 1
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assert lines[0] == reference_file_header
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for i, row in enumerate(lines[1:]):
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reference_row = reference_file_content[i]
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tokens = row.split(",")
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row_date = date.today() + timedelta(days=i-2)
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assert int(tokens[0]) == i, f"Failed for file {reference_file_name} row {i+1}."
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assert int(tokens[1]) == i-2, f"Failed for file {reference_file_name} row {i+1}."
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assert tokens[2] == row_date.strftime("%Y-%m-%d"), f"Failed for file {reference_file_name} row {i+1}."
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print(f"'{tokens[3]},{tokens[4]},{tokens[5]}'")
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assert not tokens[3].strip() or float(tokens[3]) == pytest.approx(reference_row[0], 1e-10, 1e-1), f"Failed for file {reference_file_name} row {i+1}."
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assert not tokens[4].strip() or float(tokens[4]) == pytest.approx(reference_row[1], 1e-10, 1e-2), f"Failed for file {reference_file_name} row {i+1}."
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assert not tokens[5].strip() or float(tokens[5]) == pytest.approx(reference_row[2], 1e-10, 1e-3), f"Failed for file {reference_file_name} row {i+1}."
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