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Merge pull request #598 from cmu-delphi/cheryl-dev
finish add SQL Query and pass the integrations tests
2 parents 8fd0d55 + 34c0fe6 commit e8d33f6

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7 files changed

+178
-26
lines changed

7 files changed

+178
-26
lines changed

‎integrations/acquisition/covidcast/test_covidcast_meta_caching.py

Lines changed: 14 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -67,14 +67,26 @@ def test_caching(self):
6767

6868
# insert dummy data
6969
self.cur.execute(f'''
70-
insert into covidcast values
70+
INSERT INTO
71+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
72+
`time_value`, `geo_value`, `value_updated_timestamp`,
73+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
74+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
75+
`missing_stderr`,`missing_sample_size`)
76+
VALUES
7177
(0, 'src', 'sig', 'day', 'state', 20200422, 'pa',
7278
123, 1, 2, 3, 456, 1, 20200422, 0, 1, False, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
7379
(0, 'src', 'sig', 'day', 'state', 20200422, 'wa',
7480
789, 1, 2, 3, 456, 1, 20200423, 1, 1, False, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
7581
''')
7682
self.cur.execute(f'''
77-
insert into covidcast values
83+
INSERT INTO
84+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
85+
`time_value`, `geo_value`, `value_updated_timestamp`,
86+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
87+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
88+
`missing_stderr`,`missing_sample_size`)
89+
VALUES
7890
(100, 'src', 'wip_sig', 'day', 'state', 20200422, 'pa',
7991
456, 4, 5, 6, 789, -1, 20200422, 0, 1, True, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
8092
''')

‎integrations/client/test_delphi_epidata.py

Lines changed: 28 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,13 @@ def test_covidcast(self):
6767

6868
# insert dummy data
6969
self.cur.execute(f'''
70-
insert into covidcast values
70+
INSERT INTO
71+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
72+
`time_value`, `geo_value`, `value_updated_timestamp`,
73+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
74+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
75+
`missing_stderr`,`missing_sample_size`)
76+
VALUES
7177
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
7278
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 0, False,
7379
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
@@ -331,7 +337,13 @@ def test_geo_value(self):
331337

332338
# insert dummy data
333339
self.cur.execute(f'''
334-
insert into covidcast values
340+
INSERT INTO
341+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
342+
`time_value`, `geo_value`, `value_updated_timestamp`,
343+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
344+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
345+
`missing_stderr`,`missing_sample_size`)
346+
VALUES
335347
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
336348
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
337349
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
@@ -432,7 +444,13 @@ def test_covidcast_meta(self):
432444

433445
# insert dummy data
434446
self.cur.execute(f'''
435-
insert into covidcast values
447+
INSERT INTO
448+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
449+
`time_value`, `geo_value`, `value_updated_timestamp`,
450+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
451+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
452+
`missing_stderr`,`missing_sample_size`)
453+
VALUES
436454
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
437455
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 0, False,
438456
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
@@ -562,7 +580,13 @@ def test_covidcast_nowcast(self):
562580
def test_async_epidata(self):
563581
# insert dummy data
564582
self.cur.execute(f'''
565-
insert into covidcast values
583+
INSERT INTO
584+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
585+
`time_value`, `geo_value`, `value_updated_timestamp`,
586+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
587+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
588+
`missing_stderr`,`missing_sample_size`)
589+
VALUES
566590
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
567591
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
568592
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),

‎integrations/server/test_covidcast.py

Lines changed: 98 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -45,7 +45,13 @@ def test_round_trip(self):
4545

4646
# insert dummy data
4747
self.cur.execute(f'''
48-
insert into covidcast values
48+
INSERT INTO
49+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
50+
`time_value`, `geo_value`, `value_updated_timestamp`,
51+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
52+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
53+
`missing_stderr`,`missing_sample_size`)
54+
VALUES
4955
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
5056
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
5157
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
@@ -92,7 +98,13 @@ def test_round_trip(self):
9298

9399
# # insert dummy data
94100
# self.cur.execute(f'''
95-
# insert into covidcast values
101+
# INSERT INTO
102+
# `covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
103+
# `time_value`, `geo_value`, `value_updated_timestamp`,
104+
# `value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
105+
# `direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
106+
# `missing_stderr`,`missing_sample_size`)
107+
# VALUES
96108
# (0, 'src', 'sig', 'day', 'county', 20200414, '01234',
97109
# 123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
98110
# {Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
@@ -129,7 +141,13 @@ def test_csv_format(self):
129141

130142
# insert dummy data
131143
self.cur.execute(f'''
132-
insert into covidcast values
144+
INSERT INTO
145+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
146+
`time_value`, `geo_value`, `value_updated_timestamp`,
147+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
148+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
149+
`missing_stderr`,`missing_sample_size`)
150+
VALUES
133151
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
134152
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
135153
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
@@ -163,7 +181,13 @@ def test_raw_json_format(self):
163181

164182
# insert dummy data
165183
self.cur.execute(f'''
166-
insert into covidcast values
184+
INSERT INTO
185+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
186+
`time_value`, `geo_value`, `value_updated_timestamp`,
187+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
188+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
189+
`missing_stderr`,`missing_sample_size`)
190+
VALUES
167191
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
168192
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
169193
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
@@ -205,7 +229,13 @@ def test_fields(self):
205229

206230
# insert dummy data
207231
self.cur.execute(f'''
208-
insert into covidcast values
232+
INSERT INTO
233+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
234+
`time_value`, `geo_value`, `value_updated_timestamp`,
235+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
236+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
237+
`missing_stderr`,`missing_sample_size`)
238+
VALUES
209239
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
210240
123, 1.5, 2.5, 3.5, 456, 4, 20200414, 0, 1, False,
211241
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
@@ -326,7 +356,13 @@ def test_location_wildcard(self):
326356

327357
# insert dummy data
328358
self.cur.execute(f'''
329-
insert into covidcast values
359+
INSERT INTO
360+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
361+
`time_value`, `geo_value`, `value_updated_timestamp`,
362+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
363+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
364+
`missing_stderr`,`missing_sample_size`)
365+
VALUES
330366
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
331367
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
332368
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
@@ -414,7 +450,13 @@ def test_geo_value(self):
414450

415451
# insert dummy data
416452
self.cur.execute(f'''
417-
insert into covidcast values
453+
INSERT INTO
454+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
455+
`time_value`, `geo_value`, `value_updated_timestamp`,
456+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
457+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
458+
`missing_stderr`,`missing_sample_size`)
459+
VALUES
418460
(0, 'src', 'sig', 'day', 'county', 20200414, '11111',
419461
123, 10, 11, 12, 456, 13, 20200414, 0, 1, False,
420462
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
@@ -530,7 +572,13 @@ def test_location_timeline(self):
530572

531573
# insert dummy data
532574
self.cur.execute(f'''
533-
insert into covidcast values
575+
INSERT INTO
576+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
577+
`time_value`, `geo_value`, `value_updated_timestamp`,
578+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
579+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
580+
`missing_stderr`,`missing_sample_size`)
581+
VALUES
534582
(0, 'src', 'sig', 'day', 'county', 20200411, '01234',
535583
123, 10, 11, 12, 456, 13, 20200413, 2, 1, False,
536584
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
@@ -618,7 +666,13 @@ def test_unique_key_constraint(self):
618666

619667
# insert dummy data
620668
self.cur.execute(f'''
621-
insert into covidcast values
669+
INSERT INTO
670+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
671+
`time_value`, `geo_value`, `value_updated_timestamp`,
672+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
673+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
674+
`missing_stderr`,`missing_sample_size`)
675+
VALUES
622676
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
623677
0, 0, 0, 0, 0, 0, 20200414, 0, 1, False,
624678
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
@@ -628,15 +682,27 @@ def test_unique_key_constraint(self):
628682
# fail to insert different dummy data under the same key
629683
with self.assertRaises(mysql.connector.errors.IntegrityError):
630684
self.cur.execute(f'''
631-
insert into covidcast values
685+
INSERT INTO
686+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
687+
`time_value`, `geo_value`, `value_updated_timestamp`,
688+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
689+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
690+
`missing_stderr`,`missing_sample_size`)
691+
VALUES
632692
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
633693
1, 1, 1, 1, 1, 1, 20200414, 0, 1, False,
634694
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
635695
''')
636696

637697
# succeed to insert different dummy data under a different issue
638698
self.cur.execute(f'''
639-
insert into covidcast values
699+
INSERT INTO
700+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
701+
`time_value`, `geo_value`, `value_updated_timestamp`,
702+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
703+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
704+
`missing_stderr`,`missing_sample_size`)
705+
VALUES
640706
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
641707
1, 1, 1, 1, 1, 1, 20200415, 1, 1, False,
642708
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING})
@@ -647,7 +713,13 @@ def test_nullable_columns(self):
647713

648714
# insert dummy data
649715
self.cur.execute(f'''
650-
insert into covidcast values
716+
INSERT INTO
717+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
718+
`time_value`, `geo_value`, `value_updated_timestamp`,
719+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
720+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
721+
`missing_stderr`,`missing_sample_size`)
722+
VALUES
651723
(0, 'src', 'sig', 'day', 'county', 20200414, '01234',
652724
123, 0.123, NULL, NULL, 456, NULL, 20200414, 0, 1, False,
653725
{Nans.NOT_MISSING}, {Nans.OTHER}, {Nans.OTHER})
@@ -693,7 +765,13 @@ def test_temporal_partitioning(self):
693765

694766
# insert dummy data
695767
self.cur.execute(f'''
696-
insert into covidcast values
768+
INSERT INTO
769+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
770+
`time_value`, `geo_value`, `value_updated_timestamp`,
771+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
772+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
773+
`missing_stderr`,`missing_sample_size`)
774+
VALUES
697775
(0, 'src', 'sig', 'hour', 'state', 2020041714, 'vi',
698776
123, 10, 11, 12, 456, 13, 2020041714, 0, 1, False,
699777
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),
@@ -750,7 +828,13 @@ def test_date_formats(self):
750828

751829
# insert dummy data
752830
self.cur.execute(f'''
753-
insert into covidcast values
831+
INSERT INTO
832+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
833+
`time_value`, `geo_value`, `value_updated_timestamp`,
834+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
835+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
836+
`missing_stderr`,`missing_sample_size`)
837+
VALUES
754838
(0, 'src', 'sig', 'day', 'county', 20200411, '01234',
755839
123, 10, 11, 12, 456, 13, 20200413, 0, 1, False,
756840
{Nans.NOT_MISSING}, {Nans.NOT_MISSING}, {Nans.NOT_MISSING}),

‎integrations/server/test_covidcast_endpoints.py

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -127,7 +127,13 @@ def _insert_rows(self, rows: Iterable[CovidcastRow]):
127127
sql = ",\n".join((str(r) for r in rows))
128128
self.cur.execute(
129129
f"""
130-
insert into covidcast values
130+
INSERT INTO
131+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
132+
`time_value`, `geo_value`, `value_updated_timestamp`,
133+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
134+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
135+
`missing_stderr`,`missing_sample_size`)
136+
VALUES
131137
{sql}
132138
"""
133139
)

‎integrations/server/test_covidcast_meta.py

Lines changed: 21 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -47,7 +47,13 @@ def test_round_trip(self):
4747

4848
# insert dummy data and accumulate expected results (in sort order)
4949
template = '''
50-
insert into covidcast values
50+
INSERT INTO
51+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
52+
`time_value`, `geo_value`, `value_updated_timestamp`,
53+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
54+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
55+
`missing_stderr`,`missing_sample_size`)
56+
VALUES
5157
(0, "%s", "%s", "%s", "%s", %d, "%s", 123,
5258
%d, 0, 0, 456, 0, %d, 0, 1, %d, %d, %d, %d)
5359
'''
@@ -100,7 +106,13 @@ def test_filter(self):
100106

101107
# insert dummy data and accumulate expected results (in sort order)
102108
template = '''
103-
insert into covidcast values
109+
INSERT INTO
110+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
111+
`time_value`, `geo_value`, `value_updated_timestamp`,
112+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
113+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
114+
`missing_stderr`,`missing_sample_size`)
115+
VALUES
104116
(0, "%s", "%s", "%s", "%s", %d, "%s", 123,
105117
%d, 0, 0, 456, 0, %d, 0, 1, %d, %d, %d, %d)
106118
'''
@@ -218,7 +230,13 @@ def test_suppress_work_in_progress(self):
218230

219231
# insert dummy data and accumulate expected results (in sort order)
220232
template = '''
221-
insert into covidcast values
233+
INSERT INTO
234+
`covidcast` (`id`, `source`, `signal`, `time_type`, `geo_type`,
235+
`time_value`, `geo_value`, `value_updated_timestamp`,
236+
`value`, `stderr`, `sample_size`, `direction_updated_timestamp`,
237+
`direction`, `issue`, `lag`, `is_latest_issue`, `is_wip`,`missing_value`,
238+
`missing_stderr`,`missing_sample_size`)
239+
VALUES
222240
(0, "%s", "%s", "%s", "%s", %d, "%s", 123,
223241
%d, 0, 0, 456, 0, %d, 0, 1, %d, %d, %d, %d)
224242
'''

‎integrations/server/test_fluview.py

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,11 @@ def test_round_trip(self):
4848

4949
# insert dummy data
5050
self.cur.execute('''
51-
insert into fluview values
51+
INSERT INTO
52+
`fluview` (`id`, `release_date`, `issue`, `epiweek`, `region`,
53+
`lag`, `num_ili`, `num_patients`, `num_providers`, `wili`, `ili`,
54+
`num_age_0`, `num_age_1`, `num_age_2`, `num_age_3`, `num_age_4`, `num_age_5`)
55+
VALUES
5256
(0, "2020-04-07", 202021, 202020, "nat", 1, 2, 3, 4, 3.14159, 1.41421,
5357
10, 11, 12, 13, 14, 15)
5458
''')

‎integrations/server/test_fluview_meta.py

Lines changed: 5 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,11 @@ def test_round_trip(self):
4848

4949
# insert dummy data
5050
self.cur.execute('''
51-
insert into fluview values
51+
INSERT INTO
52+
`fluview` (`id`, `release_date`, `issue`, `epiweek`, `region`,
53+
`lag`, `num_ili`, `num_patients`, `num_providers`, `wili`, `ili`,
54+
`num_age_0`, `num_age_1`, `num_age_2`, `num_age_3`, `num_age_4`, `num_age_5`)
55+
VALUES
5256
(0, "2020-04-07", 202021, 202020, "nat", 1, 2, 3, 4, 3.14159, 1.41421,
5357
10, 11, 12, 13, 14, 15),
5458
(0, "2020-04-28", 202022, 202022, "hhs1", 5, 6, 7, 8, 1.11111, 2.22222,

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