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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
lines changed

13 files changed

+77
-85
lines changed

‎mimic-iv/concepts/demographics/age.sql‎

Lines changed: 5 additions & 3 deletions
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

‎mimic-iv/concepts/demographics/icustay_detail.sql‎

Lines changed: 5 additions & 3 deletions
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 (

‎mimic-iv/concepts/demographics/icustay_hourly.sql‎

Lines changed: 1 addition & 3 deletions
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

‎mimic-iv/concepts/firstday/first_day_height.sql‎

Lines changed: 4 additions & 5 deletions
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

‎mimic-iv/concepts/measurement/bg.sql‎

Lines changed: 5 additions & 6 deletions
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

‎mimic-iv/concepts/organfailure/kdigo_creatinine.sql‎

Lines changed: 5 additions & 6 deletions
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

‎mimic-iv/concepts/organfailure/kdigo_stages.sql‎

Lines changed: 9 additions & 11 deletions
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
;

‎mimic-iv/concepts/organfailure/kdigo_uo.sql‎

Lines changed: 4 additions & 10 deletions
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
;

‎mimic-iv/concepts/score/apsiii.sql‎

Lines changed: 10 additions & 7 deletions
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

‎mimic-iv/concepts/score/lods.sql‎

Lines changed: 2 additions & 3 deletions
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%'

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