def test_column_present_with_no_data():
region_tx = Region.from_state("TX")
ds = test_helpers.build_dataset(
{region_tx: {CommonFields.TOTAL_TESTS: [100, 200, 400]}},
timeseries_columns=[CommonFields.POSITIVE_TESTS],
)
method = DivisionMethod(
DatasetName("method2"),
CommonFields.POSITIVE_TESTS,
CommonFields.TOTAL_TESTS,
recent_days=1,
)
with pytest.raises(test_positivity.NoColumnsWithDataException):
AllMethods.run(ds, [method], diff_days=1)
def test_provenance():
region_as = Region.from_state("AS")
region_tx = Region.from_state("TX")
metrics_as = {
CommonFields.POSITIVE_TESTS: TimeseriesLiteral([0, 2, 4, 6], provenance="pt_src1"),
CommonFields.TOTAL_TESTS: [100, 200, 300, 400],
}
metrics_tx = {
CommonFields.POSITIVE_TESTS: TimeseriesLiteral([1, 2, 3, 4], provenance="pt_src2"),
CommonFields.POSITIVE_TESTS_VIRAL: TimeseriesLiteral(
[10, 20, 30, 40], provenance="pos_viral"
),
CommonFields.TOTAL_TESTS: [100, 200, 300, 400],
}
dataset_in = test_helpers.build_dataset({region_as: metrics_as, region_tx: metrics_tx})
methods = [
DivisionMethod(
DatasetName("method1"), CommonFields.POSITIVE_TESTS_VIRAL, CommonFields.TOTAL_TESTS
),
DivisionMethod(
DatasetName("method2"), CommonFields.POSITIVE_TESTS, CommonFields.TOTAL_TESTS
),
]
all_methods = AllMethods.run(dataset_in, methods, diff_days=3)
expected_as = {CommonFields.TEST_POSITIVITY: TimeseriesLiteral([0.02], provenance=["pt_src1"])}
expected_tx = {CommonFields.TEST_POSITIVITY: TimeseriesLiteral([0.1], provenance="pos_viral")}
expected_positivity = test_helpers.build_dataset(
{region_as: expected_as, region_tx: expected_tx}, start_date="2020-04-04"
)
test_helpers.assert_dataset_like(all_methods.test_positivity, expected_positivity)
def test_missing_column_for_one_method():
ds = test_helpers.build_default_region_dataset(
{
CommonFields.POSITIVE_TESTS: [1, 2, 3, 4],
CommonFields.POSITIVE_TESTS_VIRAL: TimeseriesLiteral(
[10, 20, 30, 40], provenance="pos_viral"
),
CommonFields.TOTAL_TESTS: [100, 200, 300, 400],
}
)
methods = [
DivisionMethod(
DatasetName("method1"), CommonFields.POSITIVE_TESTS_VIRAL, CommonFields.TOTAL_TESTS
),
DivisionMethod(
DatasetName("method2"), CommonFields.POSITIVE_TESTS, CommonFields.TOTAL_TESTS
),
DivisionMethod(
DatasetName("method3"),
CommonFields.POSITIVE_TESTS,
CommonFields.TOTAL_TESTS_PEOPLE_VIRAL,
),
]
methods = _replace_methods_attribute(methods, recent_days=4)
assert (
AllMethods.run(ds, methods, diff_days=1)
.test_positivity.provenance.loc[test_helpers.DEFAULT_REGION.location_id]
.at[CommonFields.TEST_POSITIVITY]
== "pos_viral"
)
def test_missing_columns_for_all_tests():
ds = test_helpers.build_default_region_dataset(
{FieldName("m1"): [1, 2, 3, 4], FieldName("m2"): [10, 20, 30, 40]}
)
methods = [
DivisionMethod(
DatasetName("method1"), CommonFields.POSITIVE_TESTS_VIRAL, CommonFields.TOTAL_TESTS
),
DivisionMethod(
DatasetName("method2"), CommonFields.POSITIVE_TESTS, CommonFields.TOTAL_TESTS
),
DivisionMethod(
DatasetName("method3"),
CommonFields.POSITIVE_TESTS,
CommonFields.TOTAL_TESTS_PEOPLE_VIRAL,
),
]
methods = _replace_methods_attribute(methods, recent_days=4)
with pytest.raises(test_positivity.NoMethodsWithRelevantColumns):
AllMethods.run(ds, methods, diff_days=1)
def test_all_columns_na():
# MultiRegionDataset.from_csv drops columns with no real values so make a DataFrame
# to pass to from_timeseries_df.
ts_df = common_df.read_csv(
io.StringIO(
"location_id,date,positive_tests,total_tests\n"
"iso1:us#iso2:tx,2020-04-01,,\n"
"iso1:us#iso2:tx,2020-04-02,,\n"
"iso1:us#iso2:tx,2020-04-04,,\n"
),
set_index=False,
)
ts_df[CommonFields.POSITIVE_TESTS] = pd.NA
ts = timeseries.MultiRegionDataset.from_geodata_timeseries_df(ts_df)
methods = [
DivisionMethod(
DatasetName("method2"),
CommonFields.POSITIVE_TESTS,
CommonFields.TOTAL_TESTS,
recent_days=1,
),
]
with pytest.raises(test_positivity.NoRealTimeseriesValuesException):
AllMethods.run(ts, methods, diff_days=1)
def test_recent_pos_neg_tests_has_positivity_ratio(pos_neg_tests_recent):
# positive_tests and negative_tests appear on 8/10 and 8/11. They will be used when
# that is within 10 days of 'today'.
dataset_in = test_helpers.build_default_region_dataset(
{
CommonFields.TEST_POSITIVITY_7D: TimeseriesLiteral(
[0.02, 0.03, 0.04, 0.05, 0.06, 0.07], provenance="CDCTesting"
),
CommonFields.POSITIVE_TESTS: TimeseriesLiteral(
[1, 2, None, None, None, None], provenance="pos"
),
CommonFields.NEGATIVE_TESTS: [10, 20, None, None, None, None],
},
start_date="2020-08-10",
)
if pos_neg_tests_recent:
freeze_date = "2020-08-21"
# positive_tests and negative_tests are used
expected_metrics = {
CommonFields.TEST_POSITIVITY: TimeseriesLiteral(
[pd.NA, 0.0909, pd.NA, pd.NA, pd.NA, pd.NA], provenance="pos"
)
}
expected = test_helpers.build_default_region_dataset(
expected_metrics, start_date="2020-08-10"
)
else:
freeze_date = "2020-08-22"
# positive_tests and negative_tests no longer recent so test_positivity_7d is copied to
# output.
expected_metrics = {
CommonFields.TEST_POSITIVITY: TimeseriesLiteral(
[0.02, 0.03, 0.04, 0.05, 0.06, 0.07], provenance="CDCTesting"
)
}
expected = test_helpers.build_default_region_dataset(
expected_metrics, start_date="2020-08-10"
)
with freeze_time(freeze_date):
all_methods = AllMethods.run(dataset_in)
# check_less_precise so only 3 digits need match for testPositivityRatio
test_helpers.assert_dataset_like(all_methods.test_positivity, expected, check_less_precise=True)
def test_preserve_tags():
region_as = Region.from_state("AS")
region_tx = Region.from_state("TX")
tag1 = test_helpers.make_tag(type=TagType.CUMULATIVE_LONG_TAIL_TRUNCATED, date="2020-04-04")
tag2 = test_helpers.make_tag(type=TagType.CUMULATIVE_TAIL_TRUNCATED, date="2020-04-04")
tag_drop = test_helpers.make_tag(type=TagType.ZSCORE_OUTLIER, date="2020-04-01")
tag3 = test_helpers.make_tag(type=TagType.ZSCORE_OUTLIER, date="2020-04-04")
tag4 = test_helpers.make_tag(type=TagType.ZSCORE_OUTLIER, date="2020-04-03")
metrics_as = {
CommonFields.POSITIVE_TESTS: TimeseriesLiteral(
[1, 2, 3, 4], annotation=[tag1], provenance="pos"
),
CommonFields.TOTAL_TESTS: TimeseriesLiteral([100, 200, 300, 400], annotation=[tag2]),
}
metrics_tx = {
CommonFields.POSITIVE_TESTS: TimeseriesLiteral([None, None, 3, 4], annotation=[tag_drop]),
CommonFields.POSITIVE_TESTS_VIRAL: [10, 20, 30, 40],
CommonFields.TOTAL_TESTS: TimeseriesLiteral([100, 200, 300, 400], annotation=[tag3, tag4]),
}
dataset_in = test_helpers.build_dataset({region_as: metrics_as, region_tx: metrics_tx})
methods = [
DivisionMethod(
DatasetName("method1"), CommonFields.POSITIVE_TESTS, CommonFields.TOTAL_TESTS
),
DivisionMethod(
DatasetName("method2"), CommonFields.POSITIVE_TESTS_VIRAL, CommonFields.TOTAL_TESTS
),
]
all_methods = AllMethods.run(dataset_in, methods, diff_days=3)
expected_as = {
CommonFields.TEST_POSITIVITY: TimeseriesLiteral(
[0.01], provenance="pos", annotation=[tag1, tag2]
)
}
expected_tx = {CommonFields.TEST_POSITIVITY: TimeseriesLiteral([0.1], annotation=[tag3, tag4])}
expected_positivity = test_helpers.build_dataset(
{region_as: expected_as, region_tx: expected_tx}, start_date="2020-04-04"
)
test_helpers.assert_dataset_like(all_methods.test_positivity, expected_positivity)
def test_default_positivity_methods():
# This test intentionally doesn't pass any methods to AllMethods.run to run the methods used
# in production.
region_as = Region.from_state("AS")
region_tx = Region.from_state("TX")
metrics_as = {
CommonFields.POSITIVE_TESTS: TimeseriesLiteral([0, 1, 2, 3, 4, 5, 6, 7], provenance="src1"),
CommonFields.NEGATIVE_TESTS: TimeseriesLiteral(
[10, 19, 28, 37, 46, 55, 64, 73], provenance="src1"
),
}
metrics_tx = {
CommonFields.POSITIVE_TESTS_VIRAL: TimeseriesLiteral(
[2, 4, 6, 8, 10, 12, 14, 16], provenance="pos_tests"
),
CommonFields.TOTAL_TESTS_VIRAL: [10, 20, 30, 40, 50, 60, 70, 80],
}
dataset_in = test_helpers.build_dataset({region_as: metrics_as, region_tx: metrics_tx})
# TODO(tom): Once test positivity code seems stable remove call to datetime.today() in
# has_recent_data and remove this freeze_time.
with freeze_time("2020-04-14"):
all_methods = AllMethods.run(dataset_in, diff_days=1)
expected_as = {
CommonFields.TEST_POSITIVITY: TimeseriesLiteral(
[0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1], provenance="src1",
)
}
expected_tx = {
CommonFields.TEST_POSITIVITY: TimeseriesLiteral(
[0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2], provenance="pos_tests"
)
}
expected_positivity = test_helpers.build_dataset(
{region_as: expected_as, region_tx: expected_tx}, start_date="2020-04-02",
)
test_helpers.assert_dataset_like(all_methods.test_positivity, expected_positivity)
def test_recent_days():
region_as = Region.from_state("AS")
region_tx = Region.from_state("TX")
metrics_as = {
CommonFields.POSITIVE_TESTS: TimeseriesLiteral([0, 2, 4, 6], provenance="pos"),
CommonFields.POSITIVE_TESTS_VIRAL: TimeseriesLiteral(
[0, 20, None, None], provenance="pos_viral"
),
CommonFields.TOTAL_TESTS: TimeseriesLiteral([100, 200, 300, 400]),
}
metrics_tx = {
CommonFields.POSITIVE_TESTS: TimeseriesLiteral([1, 2, 3, 4], provenance="pos"),
CommonFields.POSITIVE_TESTS_VIRAL: TimeseriesLiteral(
[10, 20, 30, 40], provenance="pos_viral"
),
CommonFields.TOTAL_TESTS: TimeseriesLiteral([100, 200, 300, 400]),
}
ds = test_helpers.build_dataset({region_as: metrics_as, region_tx: metrics_tx})
methods = [
DivisionMethod(
DatasetName("method1"), CommonFields.POSITIVE_TESTS_VIRAL, CommonFields.TOTAL_TESTS
),
DivisionMethod(
DatasetName("method2"), CommonFields.POSITIVE_TESTS, CommonFields.TOTAL_TESTS
),
]
methods = _replace_methods_attribute(methods, recent_days=2)
all_methods = AllMethods.run(ds, methods, diff_days=1)
expected_positivity = test_helpers.build_dataset(
{
region_as: {
CommonFields.TEST_POSITIVITY: TimeseriesLiteral(
[0.02, 0.02, 0.02], provenance="pos"
)
},
region_tx: {
CommonFields.TEST_POSITIVITY: TimeseriesLiteral(
[0.1, 0.1, 0.1], provenance="pos_viral"
)
},
},
start_date="2020-04-02",
)
test_helpers.assert_dataset_like(all_methods.test_positivity, expected_positivity)
assert all_methods.test_positivity.get_one_region(region_as).provenance == {
CommonFields.TEST_POSITIVITY: ["pos"]
}
assert all_methods.test_positivity.get_one_region(region_tx).provenance == {
CommonFields.TEST_POSITIVITY: ["pos_viral"]
}
methods = _replace_methods_attribute(methods, recent_days=3)
all_methods = AllMethods.run(ds, methods, diff_days=1)
positivity_provenance = all_methods.test_positivity.provenance
assert positivity_provenance.loc["iso1:us#iso2:us-as"].to_dict() == {
CommonFields.TEST_POSITIVITY: "pos_viral"
}
assert positivity_provenance.loc["iso1:us#iso2:us-tx"].to_dict() == {
CommonFields.TEST_POSITIVITY: "pos_viral"
}