propagate linting changes to psql concepts

Author: alistairewj

mimic-iv/concepts_postgres/comorbidity/charlson.sql

@@ -17,14 +17,18 @@ DROP TABLE IF EXISTS age; CREATE TABLE age AS
 -- an admission in 2155 will occur in 2010-2012, and so on.
 
 -- Therefore, the age of a patient = hospital admission time - anchor_year + anchor_age
-SELECT 	
-	ad.subject_id
-	, ad.hadm_id
-	, ad.admittime
-	, pa.anchor_age
-	, pa.anchor_year
-	, DATETIME_DIFF(ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), 'YEAR') + pa.anchor_age AS age
+SELECT
+    ad.subject_id
+    , ad.hadm_id
+    , ad.admittime
+    , pa.anchor_age
+    , 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
+    , pa.anchor_age + DATETIME_DIFF(ad.admittime, DATETIME(pa.anchor_year, 1, 1, 0, 0, 0), 'YEAR') AS age -- noqa: L016
 FROM mimiciv_hosp.admissions ad
 INNER JOIN mimiciv_hosp.patients pa
-ON ad.subject_id = pa.subject_id
-;
+    ON ad.subject_id = pa.subject_id
+;

mimic-iv/concepts_postgres/demographics/age.sql

@@ -2,29 +2,45 @@
 DROP TABLE IF EXISTS icustay_detail; CREATE TABLE icustay_detail AS 
 SELECT ie.subject_id, ie.hadm_id, ie.stay_id
 
--- patient level factors
-, pat.gender, pat.dod
+    -- patient level factors
+    , pat.gender, pat.dod
 
--- hospital level factors
-, adm.admittime, adm.dischtime
-, DATETIME_DIFF(adm.dischtime, adm.admittime, 'DAY') as los_hospital
-, DATETIME_DIFF(adm.admittime, DATETIME(pat.anchor_year, 1, 1, 0, 0, 0), 'YEAR') + pat.anchor_age as admission_age
-, adm.race
-, adm.hospital_expire_flag
-, DENSE_RANK() OVER (PARTITION BY adm.subject_id ORDER BY adm.admittime) AS hospstay_seq
-, CASE
-    WHEN DENSE_RANK() OVER (PARTITION BY adm.subject_id ORDER BY adm.admittime) = 1 THEN True
-    ELSE False END AS first_hosp_stay
+    -- hospital level factors
+    , adm.admittime, adm.dischtime
+    , DATETIME_DIFF(adm.dischtime, adm.admittime, 'DAY') 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
+    , pat.anchor_age + DATETIME_DIFF(adm.admittime, DATETIME(pat.anchor_year, 1, 1, 0, 0, 0), 'YEAR') AS admission_age -- noqa: L016
+    , adm.race
+    , adm.hospital_expire_flag
+    , DENSE_RANK() OVER (
+        PARTITION BY adm.subject_id ORDER BY adm.admittime
+    ) AS hospstay_seq
+    , CASE
+        WHEN
+            DENSE_RANK() OVER (
+                PARTITION BY adm.subject_id ORDER BY adm.admittime
+            ) = 1 THEN True
+        ELSE False END AS first_hosp_stay
 
--- icu level factors
-, ie.intime as icu_intime, ie.outtime as icu_outtime
-, ROUND(CAST(DATETIME_DIFF(ie.outtime, ie.intime, 'HOUR')/24.0 AS NUMERIC), 2) as los_icu
-, DENSE_RANK() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) AS icustay_seq
+    -- icu level factors
+    , ie.intime AS icu_intime, ie.outtime AS icu_outtime
+    , ROUND(
+        CAST(DATETIME_DIFF(ie.outtime, ie.intime, 'HOUR') / 24.0 AS NUMERIC), 2
+    ) AS los_icu
+    , DENSE_RANK() OVER (
+        PARTITION BY ie.hadm_id ORDER BY ie.intime
+    ) AS icustay_seq
 
--- first ICU stay *for the current hospitalization*
-, CASE
-    WHEN DENSE_RANK() OVER (PARTITION BY ie.hadm_id ORDER BY ie.intime) = 1 THEN True
-    ELSE False END AS first_icu_stay
+    -- first ICU stay *for the current hospitalization*
+    , CASE
+        WHEN
+            DENSE_RANK() OVER (
+                PARTITION BY ie.hadm_id ORDER BY ie.intime
+            ) = 1 THEN True
+        ELSE False END AS first_icu_stay
 
 FROM mimiciv_icu.icustays ie
 INNER JOIN mimiciv_hosp.admissions adm

mimic-iv/concepts_postgres/demographics/icustay_detail.sql

@@ -9,30 +9,29 @@ DROP TABLE IF EXISTS icustay_hourly; CREATE TABLE icustay_hourly AS
 -- this table can be to other tables on ICUSTAY_ID and (ENDTIME - 1 hour,ENDTIME]
 
 -- get first/last measurement time
-with all_hours as
-(
-select
-  it.stay_id
+WITH all_hours AS (
+    SELECT
+        it.stay_id
 
-  -- ceiling the intime to the nearest hour by adding 59 minutes then truncating
-  -- note thart we truncate by parsing as string, rather than using DATETIME_TRUNC
-  -- this is done to enable compatibility with psql
-  , PARSE_DATETIME(
-      '%Y-%m-%d %H:00:00',
-      FORMAT_DATETIME(
-        '%Y-%m-%d %H:00:00',
-          DATETIME_ADD(it.intime_hr, INTERVAL '59' MINUTE)
-  )) AS endtime
+        -- ceiling the intime to the nearest hour by adding 59 minutes then truncating
+        -- note thart we truncate by parsing as string, rather than using DATETIME_TRUNC
+        -- this is done to enable compatibility with psql
+        , PARSE_DATETIME(
+            '%Y-%m-%d %H:00:00'
+            , FORMAT_DATETIME(
+                '%Y-%m-%d %H:00:00'
+                , DATETIME_ADD(it.intime_hr, INTERVAL '59' MINUTE)
+            )) AS endtime
 
-  -- create integers for each charttime in hours from admission
-  -- so 0 is admission time, 1 is one hour after admission, etc, up to ICU disch
-  --  we allow 24 hours before ICU admission (to grab labs before admit)
-  , ARRAY(SELECT * FROM generate_series(-24, CEIL(DATETIME_DIFF(it.outtime_hr, it.intime_hr, 'HOUR')))) as hrs
-
-  from mimiciv_derived.icustay_times it
+        -- create integers for each charttime in hours from admission
+        -- so 0 is admission time, 1 is one hour after admission, etc, up to ICU disch
+        --  we allow 24 hours before ICU admission (to grab labs before admit)
+        , ARRAY(SELECT * FROM generate_series(-24, CEIL(DATETIME_DIFF(it.outtime_hr, it.intime_hr, 'HOUR')))) AS hrs -- noqa: L016
+    FROM mimiciv_derived.icustay_times it
 )
+
 SELECT stay_id
-, CAST(hr AS bigint) as hr
-, DATETIME_ADD(endtime, interval '1' hour * CAST(hr AS bigint)) as endtime
+    , CAST(hr AS bigint) AS hr
+    , DATETIME_ADD(endtime, interval '1' hour * CAST(hr AS bigint)) AS endtime
 FROM all_hours
-CROSS JOIN UNNEST(all_hours.hrs) AS hr;
+CROSS JOIN UNNEST(all_hours.hrs) AS hr;

mimic-iv/concepts_postgres/demographics/icustay_hourly.sql

@@ -3,21 +3,21 @@ DROP TABLE IF EXISTS icustay_times; CREATE TABLE icustay_times AS
 -- create a table which has fuzzy boundaries on hospital admission
 -- involves first creating a lag/lead version of disch/admit time
 -- get first/last heart rate measurement during hospitalization for each stay_id
-WITH t1 AS
-(
-    select ce.stay_id
-    , min(charttime) as intime_hr
-    , max(charttime) as outtime_hr
+WITH t1 AS (
+    SELECT ce.stay_id
+        , MIN(charttime) AS intime_hr
+        , MAX(charttime) AS outtime_hr
     FROM mimiciv_icu.chartevents ce
     -- only look at heart rate
-    where ce.itemid = 220045
-    group by ce.stay_id
+    WHERE ce.itemid = 220045
+    GROUP BY ce.stay_id
 )
+
 -- add in subject_id/hadm_id
-select
-  ie.subject_id, ie.hadm_id, ie.stay_id
-  , t1.intime_hr
-  , t1.outtime_hr
+SELECT
+    ie.subject_id, ie.hadm_id, ie.stay_id
+    , t1.intime_hr
+    , t1.outtime_hr
 FROM mimiciv_icu.icustays ie
-left join t1
-  on ie.stay_id = t1.stay_id;
+LEFT JOIN t1
+          ON ie.stay_id = t1.stay_id;