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Merge pull request #1786 from MIT-LCP/sqlglot_fixes
Sqlglot fixes
2 parents 72d51fe + 40752b2 commit 3185933

34 files changed

+260
-99
lines changed

‎mimic-iv/concepts_duckdb/demographics/icustay_hourly.sql‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -19,4 +19,4 @@ SELECT
1919
TRY_CAST(hr_unnested AS BIGINT) AS hr,
2020
endtime + TRY_CAST(hr_unnested AS BIGINT) * INTERVAL '1' HOUR AS endtime
2121
FROM all_hours
22-
CROSS JOIN UNNEST(all_hours.hrs) AS _t(hr_unnested)
22+
CROSS JOIN UNNEST(all_hours.hrs) AS _t0(hr_unnested)

‎mimic-iv/concepts_duckdb/medication/antibiotic.sql‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -338,6 +338,8 @@ FROM mimiciv_hosp.prescriptions AS pr
338338
INNER JOIN abx
339339
ON pr.drug = abx.drug AND pr.route = abx.route
340340
LEFT JOIN mimiciv_icu.icustays AS ie
341-
ON pr.hadm_id = ie.hadm_id AND pr.starttime >= ie.intime AND pr.starttime < ie.outtime
341+
ON pr.hadm_id = ie.hadm_id
342+
AND pr.starttime >= ie.intime
343+
AND pr.starttime < ie.outtime
342344
WHERE
343345
abx.antibiotic = 1

‎mimic-iv/concepts_duckdb/medication/vasoactive_agent.sql‎

Lines changed: 21 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -90,18 +90,32 @@ SELECT
9090
mil.vaso_rate AS milrinone
9191
FROM tm_lag AS t
9292
LEFT JOIN mimiciv_derived.dobutamine AS dob
93-
ON t.stay_id = dob.stay_id AND t.starttime >= dob.starttime AND t.endtime <= dob.endtime
93+
ON t.stay_id = dob.stay_id
94+
AND t.starttime >= dob.starttime
95+
AND t.endtime <= dob.endtime
9496
LEFT JOIN mimiciv_derived.dopamine AS dop
95-
ON t.stay_id = dop.stay_id AND t.starttime >= dop.starttime AND t.endtime <= dop.endtime
97+
ON t.stay_id = dop.stay_id
98+
AND t.starttime >= dop.starttime
99+
AND t.endtime <= dop.endtime
96100
LEFT JOIN mimiciv_derived.epinephrine AS epi
97-
ON t.stay_id = epi.stay_id AND t.starttime >= epi.starttime AND t.endtime <= epi.endtime
101+
ON t.stay_id = epi.stay_id
102+
AND t.starttime >= epi.starttime
103+
AND t.endtime <= epi.endtime
98104
LEFT JOIN mimiciv_derived.norepinephrine AS nor
99-
ON t.stay_id = nor.stay_id AND t.starttime >= nor.starttime AND t.endtime <= nor.endtime
105+
ON t.stay_id = nor.stay_id
106+
AND t.starttime >= nor.starttime
107+
AND t.endtime <= nor.endtime
100108
LEFT JOIN mimiciv_derived.phenylephrine AS phe
101-
ON t.stay_id = phe.stay_id AND t.starttime >= phe.starttime AND t.endtime <= phe.endtime
109+
ON t.stay_id = phe.stay_id
110+
AND t.starttime >= phe.starttime
111+
AND t.endtime <= phe.endtime
102112
LEFT JOIN mimiciv_derived.vasopressin AS vas
103-
ON t.stay_id = vas.stay_id AND t.starttime >= vas.starttime AND t.endtime <= vas.endtime
113+
ON t.stay_id = vas.stay_id
114+
AND t.starttime >= vas.starttime
115+
AND t.endtime <= vas.endtime
104116
LEFT JOIN mimiciv_derived.milrinone AS mil
105-
ON t.stay_id = mil.stay_id AND t.starttime >= mil.starttime AND t.endtime <= mil.endtime
117+
ON t.stay_id = mil.stay_id
118+
AND t.starttime >= mil.starttime
119+
AND t.endtime <= mil.endtime
106120
WHERE
107121
NOT t.endtime IS NULL

‎mimic-iv/concepts_duckdb/organfailure/kdigo_uo.sql‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -60,4 +60,6 @@ SELECT
6060
uo_tm_24hr
6161
FROM uo_stg2 AS ur
6262
LEFT JOIN mimiciv_derived.weight_durations AS wd
63-
ON ur.stay_id = wd.stay_id AND ur.charttime >= wd.starttime AND ur.charttime < wd.endtime
63+
ON ur.stay_id = wd.stay_id
64+
AND ur.charttime >= wd.starttime
65+
AND ur.charttime < wd.endtime

‎mimic-iv/concepts_duckdb/score/apsiii.sql‎

Lines changed: 11 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,9 @@ WITH pa AS (
88
ROW_NUMBER() OVER (PARTITION BY ie.stay_id ORDER BY bg.po2 DESC) AS rn
99
FROM mimiciv_derived.bg AS bg
1010
INNER JOIN mimiciv_icu.icustays AS ie
11-
ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
11+
ON bg.hadm_id = ie.hadm_id
12+
AND bg.charttime >= ie.intime
13+
AND bg.charttime < ie.outtime
1214
LEFT JOIN mimiciv_derived.ventilation AS vd
1315
ON ie.stay_id = vd.stay_id
1416
AND bg.charttime >= vd.starttime
@@ -27,7 +29,9 @@ WITH pa AS (
2729
ROW_NUMBER() OVER (PARTITION BY ie.stay_id ORDER BY bg.aado2 DESC) AS rn
2830
FROM mimiciv_derived.bg AS bg
2931
INNER JOIN mimiciv_icu.icustays AS ie
30-
ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
32+
ON bg.hadm_id = ie.hadm_id
33+
AND bg.charttime >= ie.intime
34+
AND bg.charttime < ie.outtime
3135
INNER JOIN mimiciv_derived.ventilation AS vd
3236
ON ie.stay_id = vd.stay_id
3337
AND bg.charttime >= vd.starttime
@@ -62,7 +66,9 @@ WITH pa AS (
6266
END AS acidbase_score
6367
FROM mimiciv_derived.bg AS bg
6468
INNER JOIN mimiciv_icu.icustays AS ie
65-
ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
69+
ON bg.hadm_id = ie.hadm_id
70+
AND bg.charttime >= ie.intime
71+
AND bg.charttime < ie.outtime
6672
WHERE
6773
NOT ph IS NULL AND NOT pco2 IS NULL AND bg.specimen = 'ART.'
6874
), acidbase_max AS (
@@ -608,7 +614,8 @@ WITH pa AS (
608614
WHEN ABS(heart_rate_max - 75) = ABS(heart_rate_min - 75)
609615
AND smax.hr_score >= smin.hr_score
610616
THEN smax.hr_score
611-
WHEN ABS(heart_rate_max - 75) = ABS(heart_rate_min - 75) AND smax.hr_score < smin.hr_score
617+
WHEN ABS(heart_rate_max - 75) = ABS(heart_rate_min - 75)
618+
AND smax.hr_score < smin.hr_score
612619
THEN smin.hr_score
613620
END AS hr_score,
614621
CASE

‎mimic-iv/concepts_duckdb/score/lods.sql‎

Lines changed: 6 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -35,14 +35,18 @@ WITH cpap AS (
3535
CASE WHEN NOT cp.stay_id IS NULL THEN 1 ELSE 0 END AS cpap
3636
FROM mimiciv_derived.bg AS bg
3737
INNER JOIN mimiciv_icu.icustays AS ie
38-
ON bg.hadm_id = ie.hadm_id AND bg.charttime >= ie.intime AND bg.charttime < ie.outtime
38+
ON bg.hadm_id = ie.hadm_id
39+
AND bg.charttime >= ie.intime
40+
AND bg.charttime < ie.outtime
3941
LEFT JOIN mimiciv_derived.ventilation AS vd
4042
ON ie.stay_id = vd.stay_id
4143
AND bg.charttime >= vd.starttime
4244
AND bg.charttime <= vd.endtime
4345
AND vd.ventilation_status = 'InvasiveVent'
4446
LEFT JOIN cpap AS cp
45-
ON ie.stay_id = cp.stay_id AND bg.charttime >= cp.starttime AND bg.charttime <= cp.endtime
47+
ON ie.stay_id = cp.stay_id
48+
AND bg.charttime >= cp.starttime
49+
AND bg.charttime <= cp.endtime
4650
), pafi2 AS (
4751
SELECT
4852
stay_id,

‎mimic-iv/concepts_duckdb/score/sapsii.sql‎

Lines changed: 17 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,9 @@ WITH co AS (
1717
MAX(CASE WHEN REGEXP_MATCHES(LOWER(ce.value), '(cpap mask|bipap)') THEN 1 ELSE 0 END) AS cpap
1818
FROM co
1919
INNER JOIN mimiciv_icu.chartevents AS ce
20-
ON co.stay_id = ce.stay_id AND ce.charttime > co.starttime AND ce.charttime <= co.endtime
20+
ON co.stay_id = ce.stay_id
21+
AND ce.charttime > co.starttime
22+
AND ce.charttime <= co.endtime
2123
WHERE
2224
ce.itemid = 226732 AND REGEXP_MATCHES(LOWER(ce.value), '(cpap mask|bipap)')
2325
GROUP BY
@@ -135,7 +137,9 @@ WITH co AS (
135137
MIN(gcs.gcs) AS mingcs
136138
FROM co
137139
LEFT JOIN mimiciv_derived.gcs AS gcs
138-
ON co.stay_id = gcs.stay_id AND co.starttime < gcs.charttime AND gcs.charttime <= co.endtime
140+
ON co.stay_id = gcs.stay_id
141+
AND co.starttime < gcs.charttime
142+
AND gcs.charttime <= co.endtime
139143
GROUP BY
140144
co.stay_id
141145
), vital AS (
@@ -160,7 +164,9 @@ WITH co AS (
160164
SUM(uo.urineoutput) AS urineoutput
161165
FROM co
162166
LEFT JOIN mimiciv_derived.urine_output AS uo
163-
ON co.stay_id = uo.stay_id AND co.starttime < uo.charttime AND co.endtime >= uo.charttime
167+
ON co.stay_id = uo.stay_id
168+
AND co.starttime < uo.charttime
169+
AND co.endtime >= uo.charttime
164170
GROUP BY
165171
co.stay_id
166172
), labs AS (
@@ -301,7 +307,10 @@ WITH co AS (
301307
THEN 4
302308
WHEN heartrate_min < 70
303309
THEN 2
304-
WHEN heartrate_max >= 70 AND heartrate_max < 120 AND heartrate_min >= 70 AND heartrate_min < 120
310+
WHEN heartrate_max >= 70
311+
AND heartrate_max < 120
312+
AND heartrate_min >= 70
313+
AND heartrate_min < 120
305314
THEN 0
306315
END AS hr_score,
307316
CASE
@@ -371,7 +380,10 @@ WITH co AS (
371380
THEN 3
372381
WHEN potassium_max >= 5.0
373382
THEN 3
374-
WHEN potassium_max >= 3.0 AND potassium_max < 5.0 AND potassium_min >= 3.0 AND potassium_min < 5.0
383+
WHEN potassium_max >= 3.0
384+
AND potassium_max < 5.0
385+
AND potassium_min >= 3.0
386+
AND potassium_min < 5.0
375387
THEN 0
376388
END AS potassium_score,
377389
CASE

‎mimic-iv/concepts_duckdb/score/sofa.sql‎

Lines changed: 27 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,9 @@ WITH co AS (
3333
MIN(vs.mbp) AS meanbp_min
3434
FROM co
3535
LEFT JOIN mimiciv_derived.vitalsign AS vs
36-
ON co.stay_id = vs.stay_id AND co.starttime < vs.charttime AND co.endtime >= vs.charttime
36+
ON co.stay_id = vs.stay_id
37+
AND co.starttime < vs.charttime
38+
AND co.endtime >= vs.charttime
3739
GROUP BY
3840
co.stay_id,
3941
co.hr
@@ -44,7 +46,9 @@ WITH co AS (
4446
MIN(gcs.gcs) AS gcs_min
4547
FROM co
4648
LEFT JOIN mimiciv_derived.gcs AS gcs
47-
ON co.stay_id = gcs.stay_id AND co.starttime < gcs.charttime AND co.endtime >= gcs.charttime
49+
ON co.stay_id = gcs.stay_id
50+
AND co.starttime < gcs.charttime
51+
AND co.endtime >= gcs.charttime
4852
GROUP BY
4953
co.stay_id,
5054
co.hr
@@ -55,7 +59,9 @@ WITH co AS (
5559
MAX(enz.bilirubin_total) AS bilirubin_max
5660
FROM co
5761
LEFT JOIN mimiciv_derived.enzyme AS enz
58-
ON co.hadm_id = enz.hadm_id AND co.starttime < enz.charttime AND co.endtime >= enz.charttime
62+
ON co.hadm_id = enz.hadm_id
63+
AND co.starttime < enz.charttime
64+
AND co.endtime >= enz.charttime
5965
GROUP BY
6066
co.stay_id,
6167
co.hr
@@ -79,7 +85,9 @@ WITH co AS (
7985
MIN(cbc.platelet) AS platelet_min
8086
FROM co
8187
LEFT JOIN mimiciv_derived.complete_blood_count AS cbc
82-
ON co.hadm_id = cbc.hadm_id AND co.starttime < cbc.charttime AND co.endtime >= cbc.charttime
88+
ON co.hadm_id = cbc.hadm_id
89+
AND co.starttime < cbc.charttime
90+
AND co.endtime >= cbc.charttime
8391
GROUP BY
8492
co.stay_id,
8593
co.hr
@@ -109,7 +117,9 @@ WITH co AS (
109117
) AS uo_24hr
110118
FROM co
111119
LEFT JOIN mimiciv_derived.urine_output_rate AS uo
112-
ON co.stay_id = uo.stay_id AND co.starttime < uo.charttime AND co.endtime >= uo.charttime
120+
ON co.stay_id = uo.stay_id
121+
AND co.starttime < uo.charttime
122+
AND co.endtime >= uo.charttime
113123
GROUP BY
114124
co.stay_id,
115125
co.hr
@@ -123,13 +133,21 @@ WITH co AS (
123133
MAX(dob.vaso_rate) AS rate_dobutamine
124134
FROM co
125135
LEFT JOIN mimiciv_derived.epinephrine AS epi
126-
ON co.stay_id = epi.stay_id AND co.endtime > epi.starttime AND co.endtime <= epi.endtime
136+
ON co.stay_id = epi.stay_id
137+
AND co.endtime > epi.starttime
138+
AND co.endtime <= epi.endtime
127139
LEFT JOIN mimiciv_derived.norepinephrine AS nor
128-
ON co.stay_id = nor.stay_id AND co.endtime > nor.starttime AND co.endtime <= nor.endtime
140+
ON co.stay_id = nor.stay_id
141+
AND co.endtime > nor.starttime
142+
AND co.endtime <= nor.endtime
129143
LEFT JOIN mimiciv_derived.dopamine AS dop
130-
ON co.stay_id = dop.stay_id AND co.endtime > dop.starttime AND co.endtime <= dop.endtime
144+
ON co.stay_id = dop.stay_id
145+
AND co.endtime > dop.starttime
146+
AND co.endtime <= dop.endtime
131147
LEFT JOIN mimiciv_derived.dobutamine AS dob
132-
ON co.stay_id = dob.stay_id AND co.endtime > dob.starttime AND co.endtime <= dob.endtime
148+
ON co.stay_id = dob.stay_id
149+
AND co.endtime > dob.starttime
150+
AND co.endtime <= dob.endtime
133151
WHERE
134152
NOT epi.stay_id IS NULL
135153
OR NOT nor.stay_id IS NULL

‎mimic-iv/concepts_postgres/demographics/age.sql‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@ SELECT
77
ad.admittime,
88
pa.anchor_age,
99
pa.anchor_year, /* calculate the age as anchor_age (60) plus difference between */ /* admit year and the anchor year. */ /* the noqa retains the extra long line so the */ /* convert to postgres bash script works */
10-
pa.anchor_age + EXTRACT(EPOCH FROM ad.admittime - TO_TIMESTAMP(TO_CHAR(pa.anchor_year, '0000') || TO_CHAR(1, '00') || TO_CHAR(1, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00'), 'yyyymmddHH24MISS')) / 31556908.8 AS age /* noqa: L016 */
10+
pa.anchor_age + EXTRACT(EPOCH FROM ad.admittime - MAKE_TIMESTAMP(pa.anchor_year, 1, 1, 0, 0, 0)) / 31556908.8 AS age /* noqa: L016 */
1111
FROM mimiciv_hosp.admissions AS ad
1212
INNER JOIN mimiciv_hosp.patients AS pa
1313
ON ad.subject_id = pa.subject_id

‎mimic-iv/concepts_postgres/demographics/icustay_detail.sql‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,7 @@ SELECT
99
adm.admittime,
1010
adm.dischtime,
1111
EXTRACT(EPOCH FROM adm.dischtime - adm.admittime) / 86400.0 AS los_hospital, /* calculate the age as anchor_age (60) plus difference between */ /* admit year and the anchor year. */ /* the noqa retains the extra long line so the */ /* convert to postgres bash script works */
12-
pat.anchor_age + EXTRACT(EPOCH FROM adm.admittime - TO_TIMESTAMP(TO_CHAR(pat.anchor_year, '0000') || TO_CHAR(1, '00') || TO_CHAR(1, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00') || TO_CHAR(0, '00'), 'yyyymmddHH24MISS')) / 31556908.8 AS admission_age, /* noqa: L016 */
12+
pat.anchor_age + EXTRACT(EPOCH FROM adm.admittime - MAKE_TIMESTAMP(pat.anchor_year, 1, 1, 0, 0, 0)) / 31556908.8 AS admission_age, /* noqa: L016 */
1313
adm.race,
1414
adm.hospital_expire_flag,
1515
DENSE_RANK() OVER (PARTITION BY adm.subject_id ORDER BY adm.admittime NULLS FIRST) AS hospstay_seq,

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