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alistairewjalistairewj
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run sqlfluff fix on mimic-iv concepts
1 parent cef33be commit e56548a

12 files changed

Lines changed: 130 additions & 129 deletions

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‎mimic-iv/concepts/demographics/icustay_detail.sql‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -20,8 +20,8 @@ SELECT ie.subject_id, ie.hadm_id, ie.stay_id
2020
WHEN
2121
DENSE_RANK() OVER (
2222
PARTITION BY adm.subject_id ORDER BY adm.admittime
23-
) = 1 THEN True
24-
ELSE False END AS first_hosp_stay
23+
) = 1 THEN TRUE
24+
ELSE FALSE END AS first_hosp_stay
2525

2626
-- icu level factors
2727
, ie.intime AS icu_intime, ie.outtime AS icu_outtime
@@ -37,8 +37,8 @@ SELECT ie.subject_id, ie.hadm_id, ie.stay_id
3737
WHEN
3838
DENSE_RANK() OVER (
3939
PARTITION BY ie.hadm_id ORDER BY ie.intime
40-
) = 1 THEN True
41-
ELSE False END AS first_icu_stay
40+
) = 1 THEN TRUE
41+
ELSE FALSE END AS first_icu_stay
4242

4343
FROM `physionet-data.mimiciv_icu.icustays` ie
4444
INNER JOIN `physionet-data.mimiciv_hosp.admissions` adm

‎mimic-iv/concepts/measurement/gcs.sql‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -27,15 +27,15 @@ WITH base AS (
2727
, ce.stay_id, ce.charttime
2828
-- pivot each value into its own column
2929
, MAX(
30-
CASE WHEN ce.itemid = 223901 THEN ce.valuenum ELSE null END
30+
CASE WHEN ce.itemid = 223901 THEN ce.valuenum ELSE NULL END
3131
) AS gcsmotor
3232
, MAX(CASE
3333
WHEN ce.itemid = 223900 AND ce.value = 'No Response-ETT' THEN 0
3434
WHEN ce.itemid = 223900 THEN ce.valuenum
35-
ELSE null
35+
ELSE NULL
3636
END) AS gcsverbal
3737
, MAX(
38-
CASE WHEN ce.itemid = 220739 THEN ce.valuenum ELSE null END
38+
CASE WHEN ce.itemid = 220739 THEN ce.valuenum ELSE NULL END
3939
) AS gcseyes
4040
-- convert the data into a number, reserving a value of 0 for ET/Trach
4141
, MAX(CASE
@@ -118,7 +118,7 @@ SELECT
118118
gs.subject_id
119119
, gs.stay_id
120120
, gs.charttime
121-
, gcs AS gcs
121+
, gcs
122122
, gcsmotor AS gcs_motor
123123
, gcsverbal AS gcs_verbal
124124
, gcseyes AS gcs_eyes

‎mimic-iv/concepts/measurement/icp.sql‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@ WITH ce AS (
55
, ce.charttime
66
-- TODO: handle high ICPs when monitoring two ICPs
77
, CASE
8-
WHEN valuenum > 0 AND valuenum < 100 THEN valuenum ELSE null
8+
WHEN valuenum > 0 AND valuenum < 100 THEN valuenum ELSE NULL
99
END AS icp
1010
FROM `physionet-data.mimiciv_icu.chartevents` ce
1111
-- exclude rows marked as error

‎mimic-iv/concepts/measurement/urine_output_rate.sql‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -47,16 +47,16 @@ WITH tm AS (
4747
-- when documentation is done less than hourly
4848
, SUM(CASE WHEN DATETIME_DIFF(io.charttime, iosum.charttime, HOUR) <= 5
4949
THEN iosum.urineoutput
50-
ELSE null END) AS urineoutput_6hr
50+
ELSE NULL END) AS urineoutput_6hr
5151
, SUM(CASE WHEN DATETIME_DIFF(io.charttime, iosum.charttime, HOUR) <= 5
5252
THEN iosum.tm_since_last_uo
53-
ELSE null END) / 60.0 AS uo_tm_6hr
53+
ELSE NULL END) / 60.0 AS uo_tm_6hr
5454
, SUM(CASE WHEN DATETIME_DIFF(io.charttime, iosum.charttime, HOUR) <= 11
5555
THEN iosum.urineoutput
56-
ELSE null END) AS urineoutput_12hr
56+
ELSE NULL END) AS urineoutput_12hr
5757
, SUM(CASE WHEN DATETIME_DIFF(io.charttime, iosum.charttime, HOUR) <= 11
5858
THEN iosum.tm_since_last_uo
59-
ELSE null END) / 60.0 AS uo_tm_12hr
59+
ELSE NULL END) / 60.0 AS uo_tm_12hr
6060
-- 24 hours
6161
, SUM(iosum.urineoutput) AS urineoutput_24hr
6262
, SUM(iosum.tm_since_last_uo) / 60.0 AS uo_tm_24hr

‎mimic-iv/concepts/measurement/ventilator_setting.sql‎

Lines changed: 18 additions & 18 deletions
Original file line numberDiff line numberDiff line change
@@ -15,17 +15,17 @@ WITH ce AS (
1515
THEN valuenum * 100
1616
-- improperly input data - looks like O2 flow in litres
1717
WHEN valuenum > 1 AND valuenum < 20
18-
THEN null
18+
THEN NULL
1919
WHEN valuenum >= 20 AND valuenum <= 100
2020
THEN valuenum
21-
ELSE null END
21+
ELSE NULL END
2222
-- end of fio2 cleaning
2323
-- begin peep cleaning
2424
WHEN itemid IN (220339, 224700)
2525
THEN
2626
CASE
27-
WHEN valuenum > 100 THEN null
28-
WHEN valuenum < 0 THEN null
27+
WHEN valuenum > 100 THEN NULL
28+
WHEN valuenum < 0 THEN NULL
2929
ELSE valuenum END
3030
-- end peep cleaning
3131
ELSE valuenum END AS valuenum
@@ -56,39 +56,39 @@ SELECT
5656
, MAX(stay_id) AS stay_id
5757
, charttime
5858
, MAX(
59-
CASE WHEN itemid = 224688 THEN valuenum ELSE null END
59+
CASE WHEN itemid = 224688 THEN valuenum ELSE NULL END
6060
) AS respiratory_rate_set
6161
, MAX(
62-
CASE WHEN itemid = 224690 THEN valuenum ELSE null END
62+
CASE WHEN itemid = 224690 THEN valuenum ELSE NULL END
6363
) AS respiratory_rate_total
6464
, MAX(
65-
CASE WHEN itemid = 224689 THEN valuenum ELSE null END
65+
CASE WHEN itemid = 224689 THEN valuenum ELSE NULL END
6666
) AS respiratory_rate_spontaneous
6767
, MAX(
68-
CASE WHEN itemid = 224687 THEN valuenum ELSE null END
68+
CASE WHEN itemid = 224687 THEN valuenum ELSE NULL END
6969
) AS minute_volume
7070
, MAX(
71-
CASE WHEN itemid = 224684 THEN valuenum ELSE null END
71+
CASE WHEN itemid = 224684 THEN valuenum ELSE NULL END
7272
) AS tidal_volume_set
7373
, MAX(
74-
CASE WHEN itemid = 224685 THEN valuenum ELSE null END
74+
CASE WHEN itemid = 224685 THEN valuenum ELSE NULL END
7575
) AS tidal_volume_observed
7676
, MAX(
77-
CASE WHEN itemid = 224686 THEN valuenum ELSE null END
77+
CASE WHEN itemid = 224686 THEN valuenum ELSE NULL END
7878
) AS tidal_volume_spontaneous
7979
, MAX(
80-
CASE WHEN itemid = 224696 THEN valuenum ELSE null END
80+
CASE WHEN itemid = 224696 THEN valuenum ELSE NULL END
8181
) AS plateau_pressure
8282
, MAX(
83-
CASE WHEN itemid IN (220339, 224700) THEN valuenum ELSE null END
83+
CASE WHEN itemid IN (220339, 224700) THEN valuenum ELSE NULL END
8484
) AS peep
85-
, MAX(CASE WHEN itemid = 223835 THEN valuenum ELSE null END) AS fio2
86-
, MAX(CASE WHEN itemid = 224691 THEN valuenum ELSE null END) AS flow_rate
87-
, MAX(CASE WHEN itemid = 223849 THEN value ELSE null END) AS ventilator_mode
85+
, MAX(CASE WHEN itemid = 223835 THEN valuenum ELSE NULL END) AS fio2
86+
, MAX(CASE WHEN itemid = 224691 THEN valuenum ELSE NULL END) AS flow_rate
87+
, MAX(CASE WHEN itemid = 223849 THEN value ELSE NULL END) AS ventilator_mode
8888
, MAX(
89-
CASE WHEN itemid = 229314 THEN value ELSE null END
89+
CASE WHEN itemid = 229314 THEN value ELSE NULL END
9090
) AS ventilator_mode_hamilton
91-
, MAX(CASE WHEN itemid = 223848 THEN value ELSE null END) AS ventilator_type
91+
, MAX(CASE WHEN itemid = 223848 THEN value ELSE NULL END) AS ventilator_type
9292
FROM ce
9393
GROUP BY subject_id, charttime
9494
;

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