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b/tests/labelers/test_TimeHorizonEventLabeler.py |
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# flake8: noqa: E402 |
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import datetime |
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import os |
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import pathlib |
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import sys |
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import warnings |
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from typing import List |
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import meds |
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from femr_test_tools import EventsWithLabels, run_test_for_labeler |
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from femr.labelers import TimeHorizon, TimeHorizonEventLabeler |
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class DummyLabeler(TimeHorizonEventLabeler): |
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"""Dummy labeler that returns True if the event's `code` is in `self.outcome_codes`.""" |
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def __init__(self, outcome_codes: List[int], time_horizon: TimeHorizon, allow_same_time: bool = True): |
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self.outcome_codes: List[str] = [str(a) for a in outcome_codes] |
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self.time_horizon: TimeHorizon = time_horizon |
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self.allow_same_time = allow_same_time |
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def allow_same_time_labels(self) -> bool: |
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return self.allow_same_time |
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def get_prediction_times(self, patient: meds.Patient) -> List[datetime.datetime]: |
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return sorted(list({e["time"] for e in patient["events"]})) |
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def get_time_horizon(self) -> TimeHorizon: |
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return self.time_horizon |
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def get_outcome_times(self, patient: meds.Patient) -> List[datetime.datetime]: |
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times: List[datetime.datetime] = [] |
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for e in patient["events"]: |
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for m in e["measurements"]: |
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if m["code"] in self.outcome_codes: |
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times.append(e["time"]) |
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return times |
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def test_no_outcomes(tmp_path: pathlib.Path): |
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# No outcomes occur in this patient's timeline |
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time_horizon = TimeHorizon(datetime.timedelta(days=0), datetime.timedelta(days=180)) |
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labeler = DummyLabeler([100], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2015, 1, 3), 2, None), "duplicate"), |
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(((2015, 1, 3), 1, None), "duplicate"), |
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(((2015, 1, 3), 3, None), False), |
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(((2015, 10, 5), 1, None), False), |
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(((2018, 1, 3), 2, None), False), |
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(((2018, 3, 3), 1, None), False), |
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(((2018, 5, 3), 2, None), False), |
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(((2018, 5, 3, 11), 1, None), False), |
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(((2018, 5, 4), 1, None), False), |
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(((2018, 12, 4), 1, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_no_outcomes") |
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def test_horizon_0_180_days(tmp_path: pathlib.Path): |
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# (0, 180) days |
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time_horizon = TimeHorizon(datetime.timedelta(days=0), datetime.timedelta(days=180)) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2015, 1, 3), 2, None), "duplicate"), |
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(((2015, 1, 3), 1, None), "duplicate"), |
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(((2015, 1, 3), 3, None), True), |
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(((2015, 10, 5), 1, None), False), |
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(((2018, 1, 3), 2, None), True), |
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(((2018, 3, 3), 1, None), True), |
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(((2018, 5, 3), 2, None), True), |
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(((2018, 5, 3, 11), 1, None), False), |
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(((2018, 5, 4), 1, None), False), |
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(((2018, 12, 4), 1, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_0_180_days") |
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def test_horizon_0_180_days_no_same(tmp_path: pathlib.Path): |
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# (0, 180) days |
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time_horizon = TimeHorizon(datetime.timedelta(days=0), datetime.timedelta(days=180)) |
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labeler = DummyLabeler([2], time_horizon, allow_same_time=False) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2015, 1, 3), 2, None), "duplicate"), |
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(((2015, 1, 3), 1, None), "duplicate"), |
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(((2015, 1, 3), 3, None), "same"), |
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(((2015, 10, 5), 1, None), False), |
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(((2018, 1, 3), 2, None), "same"), |
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(((2018, 3, 3), 1, None), True), |
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(((2018, 5, 3), 2, None), "same"), |
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(((2018, 5, 3, 11), 1, None), False), |
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(((2018, 5, 4), 1, None), False), |
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(((2018, 12, 4), 1, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_0_180_days") |
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def test_horizon_1_180_days(tmp_path: pathlib.Path): |
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# (1, 180) days |
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time_horizon = TimeHorizon(datetime.timedelta(days=1), datetime.timedelta(days=180)) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2015, 1, 3), 2, None), "duplicate"), |
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(((2015, 1, 3), 1, None), "duplicate"), |
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(((2015, 1, 3), 3, None), False), |
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(((2015, 10, 5), 1, None), False), |
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(((2018, 1, 3), 2, None), True), |
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(((2018, 3, 3), 1, None), True), |
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(((2018, 5, 3), 2, None), False), |
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(((2018, 5, 3, 11), 1, None), False), |
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(((2018, 5, 4), 1, None), False), |
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(((2018, 12, 4), 1, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_1_180_days") |
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def test_horizon_180_365_days(tmp_path: pathlib.Path): |
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# (180, 365) days |
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time_horizon = TimeHorizon(datetime.timedelta(days=180), datetime.timedelta(days=365)) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2000, 1, 3), 2, None), True), |
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(((2000, 10, 5), 2, None), False), |
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(((2002, 1, 5), 2, None), True), |
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(((2002, 3, 1), 1, None), True), |
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(((2002, 4, 5), 3, None), True), |
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(((2002, 4, 12), 1, None), True), |
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(((2002, 12, 5), 2, None), False), |
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(((2002, 12, 10), 1, None), False), |
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(((2004, 1, 10), 2, None), False), |
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(((2008, 1, 10), 2, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_180_365_days") |
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def test_horizon_0_0_days(tmp_path: pathlib.Path): |
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# (0, 0) days |
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time_horizon = TimeHorizon(datetime.timedelta(days=0), datetime.timedelta(days=0)) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2015, 1, 3), 2, None), "duplicate"), |
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(((2015, 1, 3), 1, None), True), |
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(((2015, 1, 4), 1, None), False), |
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(((2015, 1, 5), 2, None), True), |
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(((2015, 1, 5, 10), 1, None), False), |
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(((2015, 1, 6), 2, None), True), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_0_0_days") |
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def test_horizon_10_10_days(tmp_path: pathlib.Path): |
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# (10, 10) days |
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time_horizon = TimeHorizon(datetime.timedelta(days=10), datetime.timedelta(days=10)) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2015, 1, 3), 2, None), False), |
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(((2015, 1, 13), 1, None), True), |
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(((2015, 1, 23), 2, None), True), |
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(((2015, 2, 2), 2, None), False), |
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(((2015, 3, 10), 1, None), True), |
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(((2015, 3, 20), 2, None), False), |
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(((2015, 3, 29), 2, None), "out of range"), |
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(((2015, 3, 30), 1, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_10_10_days") |
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def test_horizon_0_1000000_days(tmp_path: pathlib.Path): |
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# (0, 1000000) days |
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time_horizon = TimeHorizon(datetime.timedelta(days=0), datetime.timedelta(days=1000000)) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2000, 1, 3), 2, None), True), |
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(((2001, 10, 5), 1, None), True), |
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(((2020, 10, 5), 2, None), True), |
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(((2021, 10, 5), 1, None), True), |
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(((2050, 1, 10), 2, None), True), |
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(((2051, 1, 10), 1, None), False), |
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(((5000, 1, 10), 1, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_0_1000000_days") |
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def test_horizon_5_10_hours(tmp_path: pathlib.Path): |
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# (5 hours, 10.5 hours) |
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time_horizon = TimeHorizon(datetime.timedelta(hours=5), datetime.timedelta(hours=10, minutes=30)) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((2015, 1, 1, 0, 0), 1, None), True), |
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(((2015, 1, 1, 10, 29), 2, None), False), |
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(((2015, 1, 1, 10, 30), 1, None), False), |
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(((2015, 1, 1, 10, 31), 1, None), False), |
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# |
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(((2016, 1, 1, 0, 0), 1, None), True), |
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(((2016, 1, 1, 10, 29), 1, None), False), |
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(((2016, 1, 1, 10, 30), 2, None), False), |
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(((2016, 1, 1, 10, 31), 1, None), False), |
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# |
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(((2017, 1, 1, 0, 0), 1, None), False), |
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(((2017, 1, 1, 10, 29), 1, None), False), |
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(((2017, 1, 1, 10, 30), 1, None), False), |
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(((2017, 1, 1, 10, 31), 2, None), False), |
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# |
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(((2018, 1, 1, 0, 0), 1, None), False), |
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(((2018, 1, 1, 4, 59, 59), 2, None), False), |
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(((2018, 1, 1, 5), 1, None), False), |
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# |
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(((2019, 1, 1, 0, 0), 1, None), True), |
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(((2019, 1, 1, 4, 59, 59), 1, None), "out of range"), |
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(((2019, 1, 1, 5), 2, None), "out of range"), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_5_10_hours") |
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def test_horizon_infinite(tmp_path: pathlib.Path): |
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# Infinite horizon |
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time_horizon = TimeHorizon( |
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datetime.timedelta(days=10), |
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None, |
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) |
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labeler = DummyLabeler([2], time_horizon) |
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events_with_labels: EventsWithLabels = [ |
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# fmt: off |
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(((1950, 1, 3), 1, None), True), |
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(((2000, 1, 3), 1, None), True), |
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(((2001, 10, 5), 1, None), True), |
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(((2020, 10, 5), 1, None), True), |
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(((2021, 10, 5), 1, None), True), |
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(((2050, 1, 10), 2, None), True), |
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(((2050, 1, 20), 2, None), False), |
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(((2051, 1, 10), 1, None), False), |
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(((5000, 1, 10), 1, None), False), |
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# fmt: on |
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] |
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run_test_for_labeler(labeler, events_with_labels, help_text="test_horizon_infinite") |