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Hotfix acquisition: fix dtypes of missing columns #730

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Hotfix acquisition: fix dtypes of missing columns #730

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c9d7045
Hotfix acquisition: fix dtypes of missing columns
dshemetov Oct 4, 2021
cecb6c9
Hotfix acquisition: improve test coverage
dshemetov Oct 4, 2021
d474a39
Update tests/acquisition/covidcast/test_csv_importer.py
dshemetov Oct 5, 2021
8b1232d
Update tests/acquisition/covidcast/test_csv_importer.py
dshemetov Oct 5, 2021
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2 changes: 1 addition & 1 deletion src/acquisition/covidcast/csv_importer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -224,7 +224,7 @@ def validate_missing_code(row, attr_quantity, attr_name):
if hasattr(row, "missing_" + attr_name):
missing_entry = getattr(row, "missing_" + attr_name)
try:
missing_entry = int(missing_entry)
missing_entry = int(float(missing_entry)) # convert from string to float to int
except ValueError:
return None
# A missing code should never contradict the quantity being present,
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54 changes: 25 additions & 29 deletions tests/acquisition/covidcast/test_csv_importer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ def test_find_issue_specific_csv_files(self,os_isdir_mock):
issuedir_match= CsvImporter.PATTERN_ISSUE_DIR.match(path_prefix.lower())
issue_date_value = int(issuedir_match.group(2))
self.assertTrue(CsvImporter.is_sane_day(issue_date_value))

found = set(CsvImporter.find_issue_specific_csv_files(path_prefix, glob=mock_glob))
self.assertTrue(len(found)>0)

Expand Down Expand Up @@ -162,9 +162,9 @@ def make_row(
val='1.23',
se='4.56',
sample_size='100.5',
missing_val=Nans.NOT_MISSING,
missing_se=Nans.NOT_MISSING,
missing_sample_size=Nans.NOT_MISSING):
missing_val=str(float(Nans.NOT_MISSING)),
missing_se=str(float(Nans.NOT_MISSING)),
missing_sample_size=str(float(Nans.NOT_MISSING))):
row = MagicMock(
geo_id=geo_id,
val=val,
Expand Down Expand Up @@ -205,38 +205,34 @@ def make_row(
(make_row(missing_sample_size='missing_val'), 'missing_sample_size'),
(make_row(val='1.2', missing_val=Nans.OTHER), 'missing_val'),
(make_row(se='1.2', missing_se=Nans.OTHER), 'missing_se'),
(make_row(sample_size='1.2', missing_sample_size=Nans.OTHER), 'missing_sample_size')
(make_row(sample_size='1.2', missing_sample_size=Nans.OTHER), 'missing_sample_size'),
(make_row(val='1.2', missing_val=str(float(Nans.OTHER))), 'missing_val'),
(make_row(se='1.2', missing_se=str(float(Nans.OTHER))), 'missing_se'),
(make_row(sample_size='1.2', missing_sample_size=str(float(Nans.OTHER))), 'missing_sample_size'),
]

for ((geo_type, row), field) in failure_cases:
values, error = CsvImporter.extract_and_check_row(row, geo_type)
self.assertIsNone(values)
self.assertEqual(error, field)

# a nominal case without missing values
geo_type, row = make_row()
values, error = CsvImporter.extract_and_check_row(row, geo_type)

self.assertIsInstance(values, CsvImporter.RowValues)
self.assertEqual(str(values.geo_value), row.geo_id)
self.assertEqual(str(values.value), row.val)
self.assertEqual(str(values.stderr), row.se)
self.assertEqual(str(values.sample_size), row.sample_size)
self.assertIsNone(error)

# a nominal case with missing values
geo_type, row = make_row(
se='', sample_size='NA',
missing_se=Nans.OTHER, missing_sample_size=Nans.OTHER
)
values, error = CsvImporter.extract_and_check_row(row, geo_type)

self.assertIsInstance(values, CsvImporter.RowValues)
self.assertEqual(str(values.geo_value), row.geo_id)
self.assertEqual(str(values.value), row.val)
self.assertIsNone(values.stderr)
self.assertIsNone(values.sample_size)
self.assertIsNone(error)
success_cases = [
(make_row(),
CsvImporter.RowValues('vi', 1.23, 4.56, 100.5, Nans.NOT_MISSING, Nans.NOT_MISSING, Nans.NOT_MISSING)),
(make_row(val=None, se=np.nan, sample_size='', missing_val=str(float(Nans.DELETED)), missing_se=str(float(Nans.DELETED)), missing_sample_size=str(float(Nans.DELETED))),
CsvImporter.RowValues('vi', None, None, None, Nans.DELETED, Nans.DELETED, Nans.DELETED)),
(make_row(se='', sample_size='NA', missing_se=str(float(Nans.OTHER)), missing_sample_size=str(float(Nans.OTHER))),
CsvImporter.RowValues('vi', 1.23, None, None, Nans.NOT_MISSING, Nans.OTHER, Nans.OTHER))
]

for ((geo_type, row), field) in success_cases:
values, error = CsvImporter.extract_and_check_row(row, geo_type)
self.assertIsNone(error)
self.assertIsInstance(values, CsvImporter.RowValues)
self.assertEqual(values.geo_value, field.geo_value)
self.assertEqual(values.value, field.value)
self.assertEqual(values.stderr, field.stderr)
self.assertEqual(values.sample_size, field.sample_size)

def test_load_csv_with_invalid_header(self):
"""Bail loading a CSV when the header is invalid."""
Expand Down