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alistairewjalistairewj
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reformat and add noqa comments where needed
This is primarily to ensure the convert to PostgreSQL shell script continues to work by allowing long file lines.
1 parent 9dc14f3 commit 76289ce

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13 files changed

+77
-85
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13 files changed

+77
-85
lines changed

Diff for: ‎mimic-iv/concepts/demographics/age.sql

+5-3
Original file line numberDiff line numberDiff line change
@@ -21,9 +21,11 @@ SELECT
2121
, ad.admittime
2222
, pa.anchor_age
2323
, pa.anchor_year
24-
, DATETIME_DIFF(
25-
ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), YEAR
26-
) + pa.anchor_age AS age
24+
-- calculate the age as anchor_age (60) plus difference between
25+
-- admit year and the anchor year.
26+
-- the noqa retains the extra long line so the
27+
-- convert to postgres bash script works
28+
, pa.anchor_age + DATETIME_DIFF(ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), YEAR) AS age -- noqa: L016
2729
FROM `physionet-data.mimiciv_hosp.admissions` ad
2830
INNER JOIN `physionet-data.mimiciv_hosp.patients` pa
2931
ON ad.subject_id = pa.subject_id

Diff for: ‎mimic-iv/concepts/demographics/icustay_detail.sql

+5-3
Original file line numberDiff line numberDiff line change
@@ -6,9 +6,11 @@ SELECT ie.subject_id, ie.hadm_id, ie.stay_id
66
-- hospital level factors
77
, adm.admittime, adm.dischtime
88
, DATETIME_DIFF(adm.dischtime, adm.admittime, DAY) AS los_hospital
9-
, DATETIME_DIFF(
10-
adm.admittime, DATETIME(pat.anchor_year, 1, 1, 0, 0, 0), YEAR
11-
) + pat.anchor_age AS admission_age
9+
-- calculate the age as anchor_age (60) plus difference between
10+
-- admit year and the anchor year.
11+
-- the noqa retains the extra long line so the
12+
-- convert to postgres bash script works
13+
, pat.anchor_age + DATETIME_DIFF(adm.admittime, DATETIME(pat.anchor_year, 1, 1, 0, 0, 0), YEAR) AS admission_age -- noqa: L016
1214
, adm.race
1315
, adm.hospital_expire_flag
1416
, DENSE_RANK() OVER (

Diff for: ‎mimic-iv/concepts/demographics/icustay_hourly.sql

+1-3
Original file line numberDiff line numberDiff line change
@@ -24,9 +24,7 @@ WITH all_hours AS (
2424
-- create integers for each charttime in hours from admission
2525
-- so 0 is admission time, 1 is one hour after admission, etc, up to ICU disch
2626
-- we allow 24 hours before ICU admission (to grab labs before admit)
27-
, GENERATE_ARRAY(
28-
-24, CEIL(DATETIME_DIFF(it.outtime_hr, it.intime_hr, HOUR))
29-
) AS hrs
27+
, GENERATE_ARRAY(-24, CEIL(DATETIME_DIFF(it.outtime_hr, it.intime_hr, HOUR))) AS hrs -- noqa: L016
3028
FROM `physionet-data.mimiciv_derived.icustay_times` it
3129
)
3230

Diff for: ‎mimic-iv/concepts/firstday/first_day_height.sql

+4-5
Original file line numberDiff line numberDiff line change
@@ -9,11 +9,10 @@ WITH ce AS (
99
c.stay_id
1010
, AVG(valuenum) AS height_chart
1111
FROM `physionet-data.mimiciv_icu.chartevents` c
12-
INNER JOIN `physionet-data.mimiciv_icu.icustays` ie ON
13-
c.stay_id = ie.stay_id
14-
AND c.charttime BETWEEN DATETIME_SUB(
15-
ie.intime, INTERVAL '1' DAY
16-
) AND DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
12+
INNER JOIN `physionet-data.mimiciv_icu.icustays` ie
13+
ON c.stay_id = ie.stay_id
14+
AND c.charttime >= DATETIME_SUB(ie.intime, INTERVAL '1' DAY)
15+
AND c.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
1716
WHERE c.valuenum IS NOT NULL
1817
AND c.itemid IN (226730) -- height
1918
AND c.valuenum != 0

Diff for: ‎mimic-iv/concepts/measurement/bg.sql

+5-6
Original file line numberDiff line numberDiff line change
@@ -155,9 +155,9 @@ WITH bg AS (
155155
-- same hospitalization
156156
ON bg.subject_id = s1.subject_id
157157
-- spo2 occurred at most 2 hours before this blood gas
158-
AND s1.charttime BETWEEN DATETIME_SUB(
159-
bg.charttime, INTERVAL '2' HOUR
160-
) AND bg.charttime
158+
AND s1.charttime
159+
BETWEEN DATETIME_SUB(bg.charttime, INTERVAL '2' HOUR)
160+
AND bg.charttime
161161
WHERE bg.po2 IS NOT NULL
162162
)
163163

@@ -172,9 +172,8 @@ WITH bg AS (
172172
-- same patient
173173
ON bg.subject_id = s2.subject_id
174174
-- fio2 occurred at most 4 hours before this blood gas
175-
AND s2.charttime BETWEEN DATETIME_SUB(
176-
bg.charttime, INTERVAL '4' HOUR
177-
) AND bg.charttime
175+
AND s2.charttime >= DATETIME_SUB(bg.charttime, INTERVAL '4' HOUR)
176+
AND s2.charttime <= bg.charttime
178177
AND s2.fio2_chartevents > 0
179178
-- only the row with the most recent SpO2 (if no SpO2 found lastRowSpO2 = 1)
180179
WHERE bg.lastrowspo2 = 1

Diff for: ‎mimic-iv/concepts/organfailure/kdigo_creatinine.sql

+5-6
Original file line numberDiff line numberDiff line change
@@ -11,9 +11,8 @@ WITH cr AS (
1111
AND le.itemid = 50912
1212
AND le.valuenum IS NOT NULL
1313
AND le.valuenum <= 150
14-
AND le.charttime BETWEEN DATETIME_SUB(
15-
ie.intime, INTERVAL '7' DAY
16-
) AND ie.outtime
14+
AND le.charttime >= DATETIME_SUB(ie.intime, INTERVAL '7' DAY)
15+
AND le.charttime <= ie.outtime
1716
GROUP BY ie.hadm_id, ie.stay_id, le.charttime
1817
)
1918

@@ -41,9 +40,9 @@ WITH cr AS (
4140
FROM cr
4241
-- add in all creatinine values in the last 7 days
4342
LEFT JOIN cr cr7
44-
ON cr.stay_id = cr7.stay_id
45-
AND cr7.charttime < cr.charttime
46-
AND cr7.charttime >= DATETIME_SUB(cr.charttime, INTERVAL '7' DAY)
43+
ON cr.stay_id = cr7.stay_id
44+
AND cr7.charttime < cr.charttime
45+
AND cr7.charttime >= DATETIME_SUB(cr.charttime, INTERVAL '7' DAY)
4746
GROUP BY cr.stay_id, cr.charttime
4847
)
4948

Diff for: ‎mimic-iv/concepts/organfailure/kdigo_stages.sql

+9-11
Original file line numberDiff line numberDiff line change
@@ -45,10 +45,8 @@ WITH cr_stg AS (
4545
, CASE
4646
WHEN uo.uo_rt_6hr IS NULL THEN NULL
4747
-- require patient to be in ICU for at least 6 hours to stage UO
48-
WHEN
49-
uo.charttime <= DATETIME_ADD(
50-
ie.intime, INTERVAL '6' HOUR
51-
) THEN 0
48+
WHEN uo.charttime <= DATETIME_ADD(ie.intime, INTERVAL '6' HOUR)
49+
THEN 0
5250
-- require the UO rate to be calculated over duration specified in KDIGO
5351
-- Stage 3: <0.3 ml/kg/h for >=24 hours
5452
WHEN uo.uo_tm_24hr >= 24 AND uo.uo_rt_24hr < 0.3 THEN 3
@@ -141,14 +139,14 @@ SELECT
141139
FROM `physionet-data.mimiciv_icu.icustays` ie
142140
-- get all possible charttimes as listed in tm_stg
143141
LEFT JOIN tm_stg tm
144-
ON ie.stay_id = tm.stay_id
142+
ON ie.stay_id = tm.stay_id
145143
LEFT JOIN cr_stg cr
146-
ON ie.stay_id = cr.stay_id
147-
AND tm.charttime = cr.charttime
144+
ON ie.stay_id = cr.stay_id
145+
AND tm.charttime = cr.charttime
148146
LEFT JOIN uo_stg uo
149-
ON ie.stay_id = uo.stay_id
150-
AND tm.charttime = uo.charttime
147+
ON ie.stay_id = uo.stay_id
148+
AND tm.charttime = uo.charttime
151149
LEFT JOIN crrt_stg crrt
152-
ON ie.stay_id = crrt.stay_id
153-
AND tm.charttime = crrt.charttime
150+
ON ie.stay_id = crrt.stay_id
151+
AND tm.charttime = crrt.charttime
154152
;

Diff for: ‎mimic-iv/concepts/organfailure/kdigo_uo.sql

+4-10
Original file line numberDiff line numberDiff line change
@@ -2,13 +2,7 @@ WITH uo_stg1 AS (
22
SELECT ie.stay_id, uo.charttime
33
, DATETIME_DIFF(charttime, intime, SECOND) AS seconds_since_admit
44
, COALESCE(
5-
DATETIME_DIFF(
6-
charttime
7-
, LAG(
8-
charttime
9-
) OVER (PARTITION BY ie.stay_id ORDER BY charttime)
10-
, SECOND
11-
) / 3600.0
5+
DATETIME_DIFF(charttime, LAG(charttime) OVER (PARTITION BY ie.stay_id ORDER BY charttime), SECOND) / 3600.0 -- noqa: L016
126
, 1
137
) AS hours_since_previous_row
148
, urineoutput
@@ -108,7 +102,7 @@ SELECT
108102
, uo_tm_24hr
109103
FROM uo_stg2 ur
110104
LEFT JOIN `physionet-data.mimiciv_derived.weight_durations` wd
111-
ON ur.stay_id = wd.stay_id
112-
AND ur.charttime >= wd.starttime
113-
AND ur.charttime < wd.endtime
105+
ON ur.stay_id = wd.stay_id
106+
AND ur.charttime >= wd.starttime
107+
AND ur.charttime < wd.endtime
114108
;

Diff for: ‎mimic-iv/concepts/score/apsiii.sql

+10-7
Original file line numberDiff line numberDiff line change
@@ -193,18 +193,21 @@ WITH pa AS (
193193
FROM `physionet-data.mimiciv_icu.icustays` ie
194194
LEFT JOIN `physionet-data.mimiciv_derived.ventilation` v
195195
ON ie.stay_id = v.stay_id
196+
AND v.ventilation_status = 'InvasiveVent'
196197
AND (
197-
v.starttime BETWEEN ie.intime AND DATETIME_ADD(
198-
ie.intime, INTERVAL '1' DAY
198+
(
199+
v.starttime >= ie.intime
200+
AND v.starttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
199201
)
200-
OR v.endtime BETWEEN ie.intime AND DATETIME_ADD(
201-
ie.intime, INTERVAL '1' DAY
202+
OR (
203+
v.endtime >= ie.intime
204+
AND v.endtime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
202205
)
203-
OR v.starttime <= ie.intime AND v.endtime >= DATETIME_ADD(
204-
ie.intime, INTERVAL '1' DAY
206+
OR (
207+
v.starttime <= ie.intime
208+
AND v.endtime >= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
205209
)
206210
)
207-
AND v.ventilation_status = 'InvasiveVent'
208211
GROUP BY ie.stay_id
209212
)
210213

Diff for: ‎mimic-iv/concepts/score/lods.sql

+2-3
Original file line numberDiff line numberDiff line change
@@ -34,9 +34,8 @@ WITH cpap AS (
3434
FROM `physionet-data.mimiciv_icu.icustays` ie
3535
INNER JOIN `physionet-data.mimiciv_icu.chartevents` ce
3636
ON ie.stay_id = ce.stay_id
37-
AND ce.charttime BETWEEN ie.intime AND DATETIME_ADD(
38-
ie.intime, INTERVAL '1' DAY
39-
)
37+
AND ce.charttime >= ie.intime
38+
AND ce.charttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
4039
WHERE itemid = 226732
4140
AND (
4241
LOWER(ce.value) LIKE '%cpap%' OR LOWER(ce.value) LIKE '%bipap mask%'

Diff for: ‎mimic-iv/concepts/score/oasis.sql

+10-7
Original file line numberDiff line numberDiff line change
@@ -47,18 +47,21 @@ WITH surgflag AS (
4747
FROM `physionet-data.mimiciv_icu.icustays` ie
4848
LEFT JOIN `physionet-data.mimiciv_derived.ventilation` v
4949
ON ie.stay_id = v.stay_id
50+
AND v.ventilation_status = 'InvasiveVent'
5051
AND (
51-
v.starttime BETWEEN ie.intime AND DATETIME_ADD(
52-
ie.intime, INTERVAL '1' DAY
52+
(
53+
v.starttime >= ie.intime
54+
AND v.starttime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
5355
)
54-
OR v.endtime BETWEEN ie.intime AND DATETIME_ADD(
55-
ie.intime, INTERVAL '1' DAY
56+
OR (
57+
v.endtime >= ie.intime
58+
AND v.endtime <= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
5659
)
57-
OR v.starttime <= ie.intime AND v.endtime >= DATETIME_ADD(
58-
ie.intime, INTERVAL '1' DAY
60+
OR (
61+
v.starttime <= ie.intime
62+
AND v.endtime >= DATETIME_ADD(ie.intime, INTERVAL '1' DAY)
5963
)
6064
)
61-
AND v.ventilation_status = 'InvasiveVent'
6265
GROUP BY ie.stay_id
6366
)
6467

Diff for: ‎mimic-iv/concepts/score/sapsii.sql

+15-15
Original file line numberDiff line numberDiff line change
@@ -217,9 +217,9 @@ WITH co AS (
217217
, MAX(vital.temperature) AS tempc_max
218218
FROM co
219219
LEFT JOIN `physionet-data.mimiciv_derived.vitalsign` vital
220-
ON co.subject_id = vital.subject_id
221-
AND co.starttime < vital.charttime
222-
AND co.endtime >= vital.charttime
220+
ON co.subject_id = vital.subject_id
221+
AND co.starttime < vital.charttime
222+
AND co.endtime >= vital.charttime
223223
GROUP BY co.stay_id
224224
)
225225

@@ -229,9 +229,9 @@ WITH co AS (
229229
, SUM(uo.urineoutput) AS urineoutput
230230
FROM co
231231
LEFT JOIN `physionet-data.mimiciv_derived.urine_output` uo
232-
ON co.stay_id = uo.stay_id
233-
AND co.starttime < uo.charttime
234-
AND co.endtime >= uo.charttime
232+
ON co.stay_id = uo.stay_id
233+
AND co.starttime < uo.charttime
234+
AND co.endtime >= uo.charttime
235235
GROUP BY co.stay_id
236236
)
237237

@@ -248,9 +248,9 @@ WITH co AS (
248248
, MAX(labs.bicarbonate) AS bicarbonate_max
249249
FROM co
250250
LEFT JOIN `physionet-data.mimiciv_derived.chemistry` labs
251-
ON co.subject_id = labs.subject_id
252-
AND co.starttime < labs.charttime
253-
AND co.endtime >= labs.charttime
251+
ON co.subject_id = labs.subject_id
252+
AND co.starttime < labs.charttime
253+
AND co.endtime >= labs.charttime
254254
GROUP BY co.stay_id
255255
)
256256

@@ -261,9 +261,9 @@ WITH co AS (
261261
, MAX(cbc.wbc) AS wbc_max
262262
FROM co
263263
LEFT JOIN `physionet-data.mimiciv_derived.complete_blood_count` cbc
264-
ON co.subject_id = cbc.subject_id
265-
AND co.starttime < cbc.charttime
266-
AND co.endtime >= cbc.charttime
264+
ON co.subject_id = cbc.subject_id
265+
AND co.starttime < cbc.charttime
266+
AND co.endtime >= cbc.charttime
267267
GROUP BY co.stay_id
268268
)
269269

@@ -274,9 +274,9 @@ WITH co AS (
274274
, MAX(enz.bilirubin_total) AS bilirubin_max
275275
FROM co
276276
LEFT JOIN `physionet-data.mimiciv_derived.enzyme` enz
277-
ON co.subject_id = enz.subject_id
278-
AND co.starttime < enz.charttime
279-
AND co.endtime >= enz.charttime
277+
ON co.subject_id = enz.subject_id
278+
AND co.starttime < enz.charttime
279+
AND co.endtime >= enz.charttime
280280
GROUP BY co.stay_id
281281
)
282282

Diff for: ‎mimic-iv/concepts/sepsis/suspicion_of_infection.sql

+2-6
Original file line numberDiff line numberDiff line change
@@ -113,18 +113,14 @@ WITH ab_tbl AS (
113113
(
114114
-- if charttime is available, use it
115115
me24.charttime IS NOT NULL
116-
AND ab_tbl.antibiotic_time >= DATETIME_SUB(
117-
me24.charttime, INTERVAL 24 HOUR
118-
)
116+
AND ab_tbl.antibiotic_time >= DATETIME_SUB(me24.charttime, INTERVAL 24 HOUR) -- noqa: L016
119117
AND ab_tbl.antibiotic_time < me24.charttime
120118
)
121119
OR
122120
(
123121
-- if charttime is not available, use chartdate
124122
me24.charttime IS NULL
125-
AND ab_tbl.antibiotic_date >= DATE_SUB(
126-
me24.chartdate, INTERVAL 1 DAY
127-
)
123+
AND ab_tbl.antibiotic_date >= DATE_SUB(me24.chartdate, INTERVAL 1 DAY) -- noqa: L016
128124
AND ab_tbl.antibiotic_date <= me24.chartdate
129125
)
130126
)

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