diff --git a/google_health/delphi_google_health/constants.py b/google_health/delphi_google_health/constants.py new file mode 100644 index 000000000..4d9dc5a87 --- /dev/null +++ b/google_health/delphi_google_health/constants.py @@ -0,0 +1,13 @@ +""" +REGISTRY FOR SIGNAL NAMES, GEO TYPES +""" +RAW = "raw_search" +SMOOTHED = "smoothed_search" +STATE = "state" +HRR = "hrr" +MSA = "msa" +DMA = "dma" + +SIGNALS = [RAW, SMOOTHED] +GEO_TYPES = [STATE, HRR, MSA, DMA] + diff --git a/google_health/delphi_google_health/run.py b/google_health/delphi_google_health/run.py index d7b9ec42d..2156ed432 100644 --- a/google_health/delphi_google_health/run.py +++ b/google_health/delphi_google_health/run.py @@ -9,10 +9,11 @@ import logging from delphi_utils import read_params - +import covidcast from .pull_api import GoogleHealthTrends, get_counts_states, get_counts_dma from .map_values import derived_counts_from_dma from .export import export_csv +from .constants import * def run_module(): @@ -31,6 +32,7 @@ def run_module(): static_dir = params["static_file_dir"] export_dir = params["export_dir"] cache_dir = params["cache_dir"] + wip_signal = params["wip_signal"] # if missing end_date, set to today (GMT) minus 5 days if end_date == "": @@ -53,17 +55,71 @@ def run_module(): ) df_hrr, df_msa = derived_counts_from_dma(df_dma, static_dir=static_dir) - #  export each geographic region, with both smoothed and unsmoothed data - export_csv(df_state, "state", "raw_search", smooth=False, receiving_dir=export_dir) - export_csv( - df_state, "state", "smoothed_search", smooth=True, receiving_dir=export_dir - ) - - export_csv(df_dma, "dma", "raw_search", smooth=False, receiving_dir=export_dir) - export_csv(df_dma, "dma", "smoothed_search", smooth=True, receiving_dir=export_dir) - - export_csv(df_hrr, "hrr", "raw_search", smooth=False, receiving_dir=export_dir) - export_csv(df_hrr, "hrr", "smoothed_search", smooth=True, receiving_dir=export_dir) + signal_names = add_prefix(SIGNALS, wip_signal, prefix) + + for signal in signal_names: + if signal.endswith(SMOOTHED): + #  export each geographic region, with both smoothed and unsmoothed data + export_csv(df_state, STATE, signal, smooth=True, receiving_dir=export_dir) + export_csv(df_dma, DMA, signal, smooth=True, receiving_dir=export_dir) + export_csv(df_hrr, HRR, signal, smooth=True, receiving_dir=export_dir) + export_csv(df_msa, MSA, signal, smooth=True, receiving_dir=export_dir) + elif signal.endswith(RAW): + export_csv(df_state, STATE, signal, smooth=False, receiving_dir=export_dir) + export_csv(df_dma, DMA, signal, smooth=False, receiving_dir=export_dir) + export_csv(df_hrr, HRR, signal, smooth=False, receiving_dir=export_dir) + export_csv(df_msa, MSA, signal, smooth=False, receiving_dir=export_dir) + + +def add_prefix(signal_names, wip_signal, prefix="wip_"): + """Adds prefix to signal if there is a WIP signal + Parameters + ---------- + signal_names: List[str] + Names of signals to be exported + prefix : 'wip_' + prefix for new/non public signals + wip_signal : List[str] or bool + a list of wip signals: [], OR + all signals in the registry: True OR + only signals that have never been published: False + Returns + ------- + List of signal names + wip/non wip signals for further computation + """ - export_csv(df_msa, "msa", "raw_search", smooth=False, receiving_dir=export_dir) - export_csv(df_msa, "msa", "smoothed_search", smooth=True, receiving_dir=export_dir) + if wip_signal is True: + return [prefix + signal for signal in signal_names] + if isinstance(wip_signal, list): + make_wip = set(wip_signal) + return [ + (prefix if signal in make_wip else "") + signal + for signal in signal_names + ] + if wip_signal in {False, ""}: + return [ + signal if public_signal(signal) + else prefix + signal + for signal in signal_names + ] + raise ValueError("Supply True | False or '' or [] | list()") + + +def public_signal(signal_): + """Checks if the signal name is already public using COVIDcast + Parameters + ---------- + signal_ : str + Name of the signal + Returns + ------- + bool + True if the signal is present + False if the signal is not present + """ + epidata_df = covidcast.metadata() + for index in range(len(epidata_df)): + if epidata_df['signal'][index] == signal_: + return True + return False diff --git a/google_health/params.json.template b/google_health/params.json.template index 38e1af91c..6ad142b33 100644 --- a/google_health/params.json.template +++ b/google_health/params.json.template @@ -5,4 +5,5 @@ "start_date": "2020-02-01", "end_date": "2020-05-15", "ght_key": "" + "wip_signal" : "" } diff --git a/google_health/setup.py b/google_health/setup.py index d5265219a..89acabdb4 100644 --- a/google_health/setup.py +++ b/google_health/setup.py @@ -8,7 +8,8 @@ "pytest", "pytest-cov", "pylint", - "delphi-utils" + "delphi-utils", + "covidcast" ] setup( diff --git a/google_health/tests/params.json.template b/google_health/tests/params.json.template index 0d8b542b6..d7cc3ea49 100644 --- a/google_health/tests/params.json.template +++ b/google_health/tests/params.json.template @@ -4,5 +4,6 @@ "cache_dir": "../cache", "start_date": "2020-02-11", "end_date": "2020-04-30", - "ght_key": "" + "ght_key": "", + "wip_signal": "" } diff --git a/google_health/tests/receiving_test/20200419_dma_wip_raw_search.csv b/google_health/tests/receiving_test/20200419_dma_wip_raw_search.csv new file mode 100644 index 000000000..48c88ca4b --- /dev/null +++ b/google_health/tests/receiving_test/20200419_dma_wip_raw_search.csv @@ -0,0 +1,211 @@ +geo_id,val,se,sample_size +500,0.00000000,NA,NA +501,25.65377897,NA,NA +502,334.67202142,NA,NA +503,175.13134851,NA,NA +504,25.48638218,NA,NA +505,49.01260746,NA,NA +506,12.96612475,NA,NA +507,0.00000000,NA,NA +508,16.92307270,NA,NA +509,0.00000000,NA,NA +510,0.00000000,NA,NA +511,11.13817408,NA,NA +512,46.18495205,NA,NA +513,0.00000000,NA,NA +514,29.04986504,NA,NA +515,0.00000000,NA,NA +516,0.00000000,NA,NA +517,14.20797575,NA,NA +518,0.00000000,NA,NA 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a/google_health/tests/receiving_test/20200419_state_wip_smoothed_search.csv b/google_health/tests/receiving_test/20200419_state_wip_smoothed_search.csv new file mode 100644 index 000000000..b0148acaa --- /dev/null +++ b/google_health/tests/receiving_test/20200419_state_wip_smoothed_search.csv @@ -0,0 +1,52 @@ +geo_id,val,se,sample_size +al,15.13537103,NA,NA +ak,3.05758293,NA,NA +az,7.63543805,NA,NA +ar,17.78133051,NA,NA +ca,14.38890892,NA,NA +co,14.63339668,NA,NA +ct,23.79769031,NA,NA +dc,24.66390149,NA,NA +de,19.84905721,NA,NA +fl,16.64671115,NA,NA +ga,19.43158509,NA,NA +hi,33.26304799,NA,NA +id,14.32245483,NA,NA +il,21.15996990,NA,NA +in,19.26979021,NA,NA +ia,6.76960827,NA,NA +ks,10.61452078,NA,NA +ky,5.02391796,NA,NA +la,12.79162533,NA,NA +me,4.49408940,NA,NA +md,16.39471199,NA,NA +ma,10.22453908,NA,NA +mi,18.06730292,NA,NA +mn,24.17631975,NA,NA +ms,0.00000000,NA,NA +mo,12.71915958,NA,NA +mt,76.53672025,NA,NA +ne,14.12332330,NA,NA +nv,11.80378493,NA,NA +nh,8.16206060,NA,NA +nj,34.93674516,NA,NA +nm,12.29115010,NA,NA +ny,22.02682601,NA,NA +nc,11.81857680,NA,NA +nd,21.08917704,NA,NA +oh,9.57561833,NA,NA +ok,16.76462957,NA,NA +or,8.66004285,NA,NA +pa,15.70623325,NA,NA +ri,5.64461777,NA,NA +sc,3.68524387,NA,NA +sd,0.00000000,NA,NA +tn,14.97463626,NA,NA +tx,12.44232812,NA,NA +ut,10.61684988,NA,NA +vt,15.03279548,NA,NA +va,19.26624098,NA,NA +wa,14.58253303,NA,NA +wv,27.07164771,NA,NA +wi,12.80124249,NA,NA +wy,18.14137134,NA,NA diff --git a/google_health/tests/test_handle_signal_name.py b/google_health/tests/test_handle_signal_name.py new file mode 100644 index 000000000..95a2dcd3d --- /dev/null +++ b/google_health/tests/test_handle_signal_name.py @@ -0,0 +1,22 @@ +import unittest +from delphi_google_health.run import add_prefix, public_signal +from delphi_google_health.constants import SIGNALS + + +class MyTestCase(unittest.TestCase): + def test_handle_signal_name(self): + # Test wip_signal = True, add prefix to all signals + signal_names = add_prefix(SIGNALS, True, prefix="wip_") + assert all(s.startswith("wip_") for s in signal_names) + # Test wip_signal = list, add prefix to listed signals + signal_names = add_prefix(SIGNALS, [SIGNALS[0]], prefix="wip_") + assert signal_names[0].startswith("wip_") + assert all(not s.startswith("wip_") for s in signal_names[1:]) + # Test wip_signal = False, add prefix to unpublished signals + signal_names = add_prefix(["xyzzy", SIGNALS[0]], False, prefix="wip_") + assert signal_names[0].startswith("wip_") + assert all(not s.startswith("wip_") for s in signal_names[1:]) + + +if __name__ == '__main__': + unittest.main() diff --git a/google_health/tests/test_pull_api.py b/google_health/tests/test_pull_api.py index 638e1bd4d..fdc4db5f1 100644 --- a/google_health/tests/test_pull_api.py +++ b/google_health/tests/test_pull_api.py @@ -36,7 +36,7 @@ def test_class_state(self): ] assert len(res["lines"][0]["points"]) == 2 - assert [x for x in res["lines"][0]["points"][0].keys()] == ["date", "value"] + assert set([x for x in res["lines"][0]["points"][0].keys()]) == {"date", "value"} assert res["lines"][0]["points"][0]["date"] == "May 05 2020" assert res["lines"][0]["points"][1]["date"] == "May 06 2020" @@ -55,7 +55,7 @@ def test_class_dma(self): ] assert len(res["lines"][0]["points"]) == 2 - assert [x for x in res["lines"][0]["points"][0].keys()] == ["date", "value"] + assert set([x for x in res["lines"][0]["points"][0].keys()]) == {"date", "value"} assert res["lines"][0]["points"][0]["date"] == "May 05 2020" assert res["lines"][0]["points"][1]["date"] == "May 06 2020" diff --git a/google_health/tests/test_run.py b/google_health/tests/test_run.py index b17539d25..4221f6d33 100644 --- a/google_health/tests/test_run.py +++ b/google_health/tests/test_run.py @@ -4,45 +4,75 @@ import pandas as pd from pandas.testing import assert_frame_equal -from delphi_google_health.run import run_module +from delphi_google_health.run import run_module, add_prefix, public_signal +from delphi_google_health.constants import SIGNALS +from delphi_utils import read_params class TestRunModule: - def test_class(self, run_as_module): - assert exists(join("receiving", "20200419_hrr_raw_search.csv")) - assert exists(join("receiving", "20200419_msa_raw_search.csv")) - assert exists(join("receiving", "20200419_state_raw_search.csv")) - assert exists(join("receiving", "20200419_dma_raw_search.csv")) + def test_class(self, run_as_module, wip_signal=read_params()["wip_signal"]): + if wip_signal is True: + assert exists(join("receiving", "20200419_hrr_wip_raw_search.csv")) + assert exists(join("receiving", "20200419_msa_wip_raw_search.csv")) + assert exists(join("receiving", "20200419_state_wip_raw_search.csv")) + assert exists(join("receiving", "20200419_dma_wip_raw_search.csv")) - assert exists(join("receiving", "20200315_hrr_raw_search.csv")) - assert exists(join("receiving", "20200315_msa_raw_search.csv")) - assert exists(join("receiving", "20200315_state_raw_search.csv")) - assert exists(join("receiving", "20200315_dma_raw_search.csv")) + assert exists(join("receiving", "20200315_hrr_wip_raw_search.csv")) + assert exists(join("receiving", "20200315_msa_wip_raw_search.csv")) + assert exists(join("receiving", "20200315_state_wip_raw_search.csv")) + assert exists(join("receiving", "20200315_dma_wip_raw_search.csv")) + else: + assert exists(join("receiving", "20200419_hrr_raw_search.csv")) + assert exists(join("receiving", "20200419_msa_raw_search.csv")) + assert exists(join("receiving", "20200419_state_raw_search.csv")) + assert exists(join("receiving", "20200419_dma_raw_search.csv")) - def test_match_old_raw_output(self, run_as_module): + assert exists(join("receiving", "20200315_hrr_raw_search.csv")) + assert exists(join("receiving", "20200315_msa_raw_search.csv")) + assert exists(join("receiving", "20200315_state_raw_search.csv")) + assert exists(join("receiving", "20200315_dma_raw_search.csv")) - files = [ - "20200419_hrr_raw_search.csv", - "20200419_msa_raw_search.csv", - "20200419_state_raw_search.csv", - "20200419_dma_raw_search.csv", - ] + def test_match_old_raw_output(self, run_as_module, wip_signal=read_params()["wip_signal"]): + if wip_signal is True: + files = [ + "20200419_hrr_wip_raw_search.csv", + "20200419_msa_wip_raw_search.csv", + "20200419_state_wip_raw_search.csv", + "20200419_dma_wip_raw_search.csv", + ] + else: + files = [ + "20200419_hrr_raw_search.csv", + "20200419_msa_raw_search.csv", + "20200419_state_raw_search.csv", + "20200419_dma_raw_search.csv", + ] for fname in files: test_df = pd.read_csv(join("receiving_test", fname)) + print(test_df) new_df = pd.read_csv(join("receiving", fname)) + print(new_df) assert_frame_equal(test_df, new_df, check_less_precise=5) - def test_match_old_smoothed_output(self, run_as_module): + def test_match_old_smoothed_output(self, run_as_module, wip_signal=read_params()["wip_signal"]): + if wip_signal is True: - files = [ - "20200419_hrr_smoothed_search.csv", - "20200419_msa_smoothed_search.csv", - "20200419_state_smoothed_search.csv", - "20200419_dma_smoothed_search.csv", - ] + files = [ + "20200419_hrr_wip_smoothed_search.csv", + "20200419_msa_wip_smoothed_search.csv", + "20200419_state_wip_smoothed_search.csv", + "20200419_dma_wip_smoothed_search.csv", + ] + else: + files = [ + "20200419_hrr_smoothed_search.csv", + "20200419_msa_smoothed_search.csv", + "20200419_state_smoothed_search.csv", + "20200419_dma_smoothed_search.csv", + ] for fname in files: test_df = pd.read_csv(join("receiving_test", fname))