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flusurv tests
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@nmdefries
nmdefries committed Sep 15, 2023
1 parent 1e942a5 commit f8a6706
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4 changes: 2 additions & 2 deletions src/acquisition/flusurv/flusurv.py
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Expand Up @@ -253,8 +253,8 @@ def get_data(location, seasonids):
Fetch and parse flu data for the given location.
This method performs the following operations:
- filters location-specific FluSurv data from CDC API response object
- extracts and returns hospitalization rates
- fetch location-specific FluSurv data from CDC API
- extracts and returns hospitalization rates for each epiweek
"""
# fetch
print("[fetching flusurv data...]")
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187 changes: 183 additions & 4 deletions tests/acquisition/flusurv/test_flusurv.py
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Expand Up @@ -2,15 +2,102 @@

# standard library
import unittest
from unittest.mock import MagicMock
from unittest.mock import sentinel
from unittest.mock import (MagicMock, sentinel, patch)

from delphi.epidata.acquisition.flusurv.flusurv import fetch_json
import delphi.epidata.acquisition.flusurv.flusurv as flusurv

# py3tester coverage target
__test_target__ = "delphi.epidata.acquisition.flusurv.flusurv"


# Example location-specific return JSON from CDC GRASP API. Contains
# partial data for "network_all" location and season 49.
network_all_example_data = {
'default_data': [
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 1, 'rate': 20.7, 'weeklyrate': 0.0, 'mmwrid': 2519},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 2, 'rate': 41.3, 'weeklyrate': 0.1, 'mmwrid': 2519},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 1, 'sexid': 0, 'raceid': 0, 'rate': 42, 'weeklyrate': 0.5, 'mmwrid': 2519},

{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 1, 'rate': 4.3, 'weeklyrate': 1.7, 'mmwrid': 2493},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 2, 'rate': 11.6, 'weeklyrate': 3.6, 'mmwrid': 2493},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 3, 'rate': 12.8, 'weeklyrate': 4.8, 'mmwrid': 2493},

{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 1, 'rate': 20.6, 'weeklyrate': 0.1, 'mmwrid': 2516},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 2, 'rate': 40.7, 'weeklyrate': 0.5, 'mmwrid': 2516},

{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 1, 'rate': 20.3, 'weeklyrate': 0.1, 'mmwrid': 2513},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 2, 'rate': 39.6, 'weeklyrate': 0.3, 'mmwrid': 2513},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 0, 'sexid': 0, 'raceid': 3, 'rate': 36.0, 'weeklyrate': 0.1, 'mmwrid': 2513},
]
}

# Example metadata response containing "master_lookup" element only, used
# for mapping between valueids and strata descriptions
master_lookup_metadata = {
'master_lookup': [
{'Variable': 'Age', 'valueid': 1, 'parentid': 97, 'Label': '0-4 yr', 'Color_HexValue': '#d19833', 'Enabled': True},
{'Variable': 'Age', 'valueid': 2, 'parentid': 97, 'Label': '5-17 yr', 'Color_HexValue': '#707070', 'Enabled': True},
{'Variable': 'Age', 'valueid': 3, 'parentid': 98, 'Label': '18-49 yr', 'Color_HexValue': '#44b3c6', 'Enabled': True},
{'Variable': 'Age', 'valueid': 4, 'parentid': 98, 'Label': '50-64 yr', 'Color_HexValue': '#516889', 'Enabled': True},
{'Variable': 'Age', 'valueid': 5, 'parentid': 98, 'Label': '65+ yr', 'Color_HexValue': '#cc5e56', 'Enabled': True},
{'Variable': 'Age', 'valueid': 7, 'parentid': 5, 'Label': '65-74 yr', 'Color_HexValue': '#cc5e56', 'Enabled': True},
{'Variable': 'Age', 'valueid': 8, 'parentid': 5, 'Label': '75-84 yr', 'Color_HexValue': '#cc5e56', 'Enabled': True},
{'Variable': 'Age', 'valueid': 9, 'parentid': 5, 'Label': '85+', 'Color_HexValue': '#cc5e56', 'Enabled': True},
{'Variable': 'Age', 'valueid': 10, 'parentid': 3, 'Label': '18-29 yr', 'Color_HexValue': '#44b3c6', 'Enabled': True},
{'Variable': 'Age', 'valueid': 11, 'parentid': 3, 'Label': '30-39 yr', 'Color_HexValue': '#44b3c6', 'Enabled': True},
{'Variable': 'Age', 'valueid': 12, 'parentid': 3, 'Label': '40-49 yr', 'Color_HexValue': '#44b3c6', 'Enabled': True},
{'Variable': 'Age', 'valueid': 21, 'parentid': 2, 'Label': '5-11 yr', 'Color_HexValue': '#707070', 'Enabled': True},
{'Variable': 'Age', 'valueid': 22, 'parentid': 2, 'Label': '12-17 yr', 'Color_HexValue': '#707070', 'Enabled': True},
{'Variable': 'Age', 'valueid': 97, 'parentid': 0, 'Label': '< 18', 'Color_HexValue': '#000000', 'Enabled': True},
{'Variable': 'Age', 'valueid': 98, 'parentid': 0, 'Label': '>= 18', 'Color_HexValue': '#000000', 'Enabled': True},

{'Variable': 'Race', 'valueid': 1, 'parentid': None, 'Label': 'White', 'Color_HexValue': '#516889', 'Enabled': True},
{'Variable': 'Race', 'valueid': 2, 'parentid': None, 'Label': 'Black', 'Color_HexValue': '#44b3c6', 'Enabled': True},
{'Variable': 'Race', 'valueid': 3, 'parentid': None, 'Label': 'Hispanic/Latino', 'Color_HexValue': '#d19833', 'Enabled': True},
{'Variable': 'Race', 'valueid': 4, 'parentid': None, 'Label': 'Asian/Pacific Islander', 'Color_HexValue': '#cc5e56', 'Enabled': True},
{'Variable': 'Race', 'valueid': 5, 'parentid': None, 'Label': 'American Indian/Alaska Native', 'Color_HexValue': '#007d8e', 'Enabled': True},

{'Variable': 'Sex', 'valueid': 1, 'parentid': None, 'Label': 'Male', 'Color_HexValue': '#44b3c6', 'Enabled': True},
{'Variable': 'Sex', 'valueid': 2, 'parentid': None, 'Label': 'Female', 'Color_HexValue': '#F2775F', 'Enabled': True},

{'Variable': None, 'valueid': 0, 'parentid': 0, 'Label': 'Overall', 'Color_HexValue': '#000000', 'Enabled': True},
],
}

# Map derived from "master_lookup" dictionary above mapping between valueids
# by type and cleaned-up descriptions (no spaces or capital letters, etc)
id_label_map = {
"Age": {
1: "0t4",
2: "5t17",
3: "18t49",
4: "50t64",
5: "65+",
7: "65t74",
8: "75t84",
9: "85+",
10: "18t29",
11: "30t39",
12: "40t49",
21: "5t11",
22: "12t17",
97: "<18",
98: ">=18",
},
"Race": {
1: "white",
2: "black",
3: "hispaniclatino",
4: "asianpacificislander",
5: "americanindianalaskanative",
},
"Sex": {
1: "male",
2: "female",
},
}


class FunctionTests(unittest.TestCase):
"""Tests each function individually."""

Expand All @@ -28,6 +115,98 @@ def test_fetch_json(self):
requests_impl = MagicMock()
requests_impl.get.return_value = response_object

actual = fetch_json(path, payload, requests_impl=requests_impl)
actual = flusurv.fetch_json(path, payload, requests_impl=requests_impl)

self.assertEqual(actual, sentinel.expected)

def test_mmwrid_to_epiweek(self):
# Test epoch
self.assertEqual(flusurv.mmwrid_to_epiweek(2179), 200340)

metadata = flusurv.fetch_flusurv_metadata()
for mmwr in metadata["mmwr"]:
self.assertEqual(flusurv.mmwrid_to_epiweek(mmwr["mmwrid"]), mmwr["yearweek"])

@patch(__test_target__ + ".fetch_flusurv_location")
def test_get_data(self, MockFlusurvLocation):
MockFlusurvLocation.return_value = network_all_example_data

self.assertEqual(flusurv.get_data("network_all", [30, 49]), {
201014: {"rate_race_white": 0.0, "rate_race_black": 0.1, "rate_age_0": 0.5},
200940: {"rate_race_white": 1.7, "rate_race_black": 3.6, "rate_race_hispaniclatino": 4.8},
201011: {"rate_race_white": 0.1, "rate_race_black": 0.5},
201008: {"rate_race_white": 0.1, "rate_race_black": 0.3, "rate_race_hispaniclatino": 0.1},
}
)

@patch(__test_target__ + ".fetch_flusurv_metadata")
def test_group_by_epiweek(self, MockFlusurvMetadata):
# Flusurv metadata is fetched by `make_id_label_map()`.
MockFlusurvMetadata.return_value = master_lookup_metadata

input_data = network_all_example_data
self.assertEqual(flusurv.group_by_epiweek(input_data), {
201014: {"rate_race_white": 0.0, "rate_race_black": 0.1, "rate_age_0": 0.5},
200940: {"rate_race_white": 1.7, "rate_race_black": 3.6, "rate_race_hispaniclatino": 4.8},
201011: {"rate_race_white": 0.1, "rate_race_black": 0.5},
201008: {"rate_race_white": 0.1, "rate_race_black": 0.3, "rate_race_hispaniclatino": 0.1},
}
)

duplicate_input_data = {
'default_data': [
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 1, 'sexid': 0, 'raceid': 0, 'rate': 42, 'weeklyrate': 0.5, 'mmwrid': 2519},
{'networkid': 1, 'catchmentid': 22, 'seasonid': 49, 'ageid': 1, 'sexid': 0, 'raceid': 0, 'rate': 42, 'weeklyrate': 54, 'mmwrid': 2519},
]
}

with self.assertWarnsRegex(Warning, "warning: Multiple rates seen for 201014"):
flusurv.group_by_epiweek(duplicate_input_data)

with self.assertRaisesRegex(Exception, "no data found"):
flusurv.group_by_epiweek({"default_data": []})

@patch('builtins.print')
def test_group_by_epiweek_print_msgs(self, mock_print):
input_data = network_all_example_data
flusurv.group_by_epiweek(input_data)
mock_print.assert_called_with("found data for 4 epiweeks")

def test_get_current_issue(self):
input_data = {
'loaddatetime': 'Sep 12, 2023'
}
self.assertEqual(flusurv.get_current_issue(input_data), 202337)

@patch(__test_target__ + ".fetch_flusurv_metadata")
def test_make_id_label_map(self, MockFlusurvMetadata):
MockFlusurvMetadata.return_value = master_lookup_metadata
self.assertEqual(flusurv.make_id_label_map(), id_label_map)

def test_groupids_to_name(self):
ids = (
(1, 0, 0),
(9, 0, 0),
(0, 2, 0),
(0, 0, 3),
(0, 0, 5),
(0, 0, 0),
)
expected_list = [
"rate_age_0",
"rate_age_7",
"rate_sex_female",
"rate_race_hispaniclatino",
"rate_race_americanindianalaskanative",
"rate_overall",
]

for (ageid, sexid, raceid), expected in zip(ids, expected_list):
self.assertEqual(flusurv.groupids_to_name(ageid, sexid, raceid, id_label_map), expected)

with self.assertRaisesRegex(ValueError, "Ageid cannot be 6"):
flusurv.groupids_to_name(6, 0, 0, id_label_map)
with self.assertRaisesRegex(AssertionError, "At most one groupid can be non-zero"):
flusurv.groupids_to_name(1, 1, 0, id_label_map)
flusurv.groupids_to_name(0, 1, 1, id_label_map)
flusurv.groupids_to_name(1, 1, 1, id_label_map)

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