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Merged
merged 3 commits into from
Jun 18, 2021
Merged

finish add SQL Query and pass the integrations tests #598

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fdba55b
finish add SQL Query and pass the integrations tests
zhuoran-Cheng16 Jun 16, 2021
040e88f
delete the min_issue part
zhuoran-Cheng16 Jun 16, 2021
34c0fe6
update
zhuoran-Cheng16 Jun 16, 2021
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16 changes: 14 additions & 2 deletions integrations/acquisition/covidcast/test_covidcast_meta_caching.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -67,14 +67,26 @@ def test_caching(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'state', 20200422, 'pa',
123, 1, 2, 3, 456, 1, 20200422, 0, 1, False, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
(0, 'src', 'sig', 'day', 'state', 20200422, 'wa',
789, 1, 2, 3, 456, 1, 20200423, 1, 1, False, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
''')
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(100, 'src', 'wip_sig', 'day', 'state', 20200422, 'pa',
456, 4, 5, 6, 789, -1, 20200422, 0, 1, True, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
''')
Expand Down
32 changes: 28 additions & 4 deletions integrations/client/test_delphi_epidata.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,13 @@ def test_covidcast(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 0, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down Expand Up @@ -331,7 +337,13 @@ def test_geo_value(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down Expand Up @@ -432,7 +444,13 @@ def test_covidcast_meta(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 0, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down Expand Up @@ -562,7 +580,13 @@ def test_covidcast_nowcast(self):
def test_async_epidata(self):
# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down
112 changes: 98 additions & 14 deletions integrations/server/test_covidcast.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -45,7 +45,13 @@ def test_round_trip(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
Expand Down Expand Up @@ -92,7 +98,13 @@ def test_round_trip(self):

# # insert dummy data
# self.cur.execute(f'''
# insert into covidcast values
# INSERT INTO
# `covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
# `time_value`, `geo_value`, `value_updated_timestamp`,
# `value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
# `direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
# `missing_stderr`,`missing_sample_size`)
# VALUES
# (0, 'src', 'sig', 'day', 'county', 20200414, '01234',
# 123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
# {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
Expand Down Expand Up @@ -129,7 +141,13 @@ def test_csv_format(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
Expand Down Expand Up @@ -163,7 +181,13 @@ def test_raw_json_format(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
Expand Down Expand Up @@ -205,7 +229,13 @@ def test_fields(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
Expand Down Expand Up @@ -326,7 +356,13 @@ def test_location_wildcard(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down Expand Up @@ -414,7 +450,13 @@ def test_geo_value(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down Expand Up @@ -530,7 +572,13 @@ def test_location_timeline(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200411, '01234',
123, 10, 11, 12, 456, 13, 20200413, 2, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down Expand Up @@ -618,7 +666,13 @@ def test_unique_key_constraint(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
0, 0, 0, 0, 0, 0, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
Expand All @@ -628,15 +682,27 @@ def test_unique_key_constraint(self):
# fail to insert different dummy data under the same key
with self.assertRaises(mysql.connector.errors.IntegrityError):
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
1, 1, 1, 1, 1, 1, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
''')

# succeed to insert different dummy data under a different issue
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
1, 1, 1, 1, 1, 1, 20200415, 1, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
Expand All @@ -647,7 +713,13 @@ def test_nullable_columns(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
123, 0.123, NULL, NULL, 456, NULL, 20200414, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.OTHER}, {Nans.OTHER})
Expand Down Expand Up @@ -693,7 +765,13 @@ def test_temporal_partitioning(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'hour', 'state', 2020041714, 'vi',
123, 10, 11, 12, 456, 13, 2020041714, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down Expand Up @@ -750,7 +828,13 @@ def test_date_formats(self):

# insert dummy data
self.cur.execute(f'''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, 'src', 'sig', 'day', 'county', 20200411, '01234',
123, 10, 11, 12, 456, 13, 20200413, 0, 1, False,
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
Expand Down
8 changes: 7 additions & 1 deletion integrations/server/test_covidcast_endpoints.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,7 +127,13 @@ def _insert_rows(self, rows: Iterable[CovidcastRow]):
sql = ",\n".join((str(r) for r in rows))
self.cur.execute(
f"""
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
{sql}
"""
)
Expand Down
24 changes: 21 additions & 3 deletions integrations/server/test_covidcast_meta.py
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,13 @@ def test_round_trip(self):

# insert dummy data and accumulate expected results (in sort order)
template = '''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, "%s", "%s", "%s", "%s", %d, "%s", 123,
%d, 0, 0, 456, 0, %d, 0, 1, %d, %d, %d, %d)
'''
Expand Down Expand Up @@ -100,7 +106,13 @@ def test_filter(self):

# insert dummy data and accumulate expected results (in sort order)
template = '''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, "%s", "%s", "%s", "%s", %d, "%s", 123,
%d, 0, 0, 456, 0, %d, 0, 1, %d, %d, %d, %d)
'''
Expand Down Expand Up @@ -218,7 +230,13 @@ def test_suppress_work_in_progress(self):

# insert dummy data and accumulate expected results (in sort order)
template = '''
insert into covidcast values
INSERT INTO
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
`time_value`, `geo_value`, `value_updated_timestamp`,
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
`missing_stderr`,`missing_sample_size`)
VALUES
(0, "%s", "%s", "%s", "%s", %d, "%s", 123,
%d, 0, 0, 456, 0, %d, 0, 1, %d, %d, %d, %d)
'''
Expand Down
6 changes: 5 additions & 1 deletion integrations/server/test_fluview.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,11 @@ def test_round_trip(self):

# insert dummy data
self.cur.execute('''
insert into fluview values
INSERT INTO
`fluview` (`id`, `release_date`, `issue`, `epiweek`, `region`,
`lag`, `num_ili`, `num_patients`, `num_providers`, `wili`, `ili`,
`num_age_0`, `num_age_1`, `num_age_2`, `num_age_3`, `num_age_4`, `num_age_5`)
VALUES
(0, "2020-04-07", 202021, 202020, "nat", 1, 2, 3, 4, 3.14159, 1.41421,
10, 11, 12, 13, 14, 15)
''')
Expand Down
6 changes: 5 additions & 1 deletion integrations/server/test_fluview_meta.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,11 @@ def test_round_trip(self):

# insert dummy data
self.cur.execute('''
insert into fluview values
INSERT INTO
`fluview` (`id`, `release_date`, `issue`, `epiweek`, `region`,
`lag`, `num_ili`, `num_patients`, `num_providers`, `wili`, `ili`,
`num_age_0`, `num_age_1`, `num_age_2`, `num_age_3`, `num_age_4`, `num_age_5`)
VALUES
(0, "2020-04-07", 202021, 202020, "nat", 1, 2, 3, 4, 3.14159, 1.41421,
10, 11, 12, 13, 14, 15),
(0, "2020-04-28", 202022, 202022, "hhs1", 5, 6, 7, 8, 1.11111, 2.22222,
Expand Down