Merge pull request #1482 from MIT-LCP/postgres_shell_script_update

Postgres shell script update

Author: alistairewj

mimic-iii/concepts/convert_mimiciii_concepts_bq_to_psql.sh

@@ -150,7 +150,7 @@ do
   if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
     echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "${TARGET_PATH}/${d}/${tbl}.sql"
     echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS " >> "${TARGET_PATH}/${d}/${tbl}.sql"
-    cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${fn}"
+    cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${tbl}.sql"
   fi
   # write out a call to this script in the make concepts file
   echo "\i ${d}/${tbl}.sql" >> $TARGET_PATH/postgres-make-concepts.sql

mimic-iv/concepts/convert_bigquery_to_postgres.sh

@@ -6,8 +6,11 @@ TARGET_PATH='../concepts_postgres'
 mkdir -p $TARGET_PATH
 
 # String replacements are necessary for some queries.
-export REGEX_SCHEMA='s/`physionet-data.(mimiciv_hosp|mimiciv_icu|mimiciv_derived).([A-Za-z0-9_-]+)`/\1.\2/g'
 # Note that these queries are very senstive to changes, e.g. adding whitespaces after comma can already change the behavior.
+
+# Schema replacement: change `physionet-data.<dataset>.<table>` to just <table> (with no backticks)
+export REGEX_SCHEMA='s/`physionet-data.(mimiciv_hosp|mimiciv_icu|mimiciv_derived).([A-Za-z0-9_-]+)`/\1.\2/g'
+# Add single quotes around the date part
 export REGEX_DATETIME_DIFF="s/DATETIME_DIFF\(([^,]+), ?(.*), ?(DAY|MINUTE|SECOND|HOUR|YEAR)\)/DATETIME_DIFF(\1, \2, '\3')/g"
 export REGEX_DATETIME_TRUNC="s/DATETIME_TRUNC\(([^,]+), ?(DAY|MINUTE|SECOND|HOUR|YEAR)\)/DATE_TRUNC('\2', \1)/g"
 # Add necessary quotes to INTERVAL, e.g. "INTERVAL 5 hour" to "INTERVAL '5' hour"
@@ -18,6 +21,24 @@ export REGEX_ARRAY="s/GENERATE_ARRAY\(-24, CEIL\(DATETIME\_DIFF\(it\.outtime_hr,
 export REGEX_HOUR_INTERVAL="s/INTERVAL CAST\(hr AS INT64\) HOUR/interval \'1\' hour * CAST\(hr AS bigint\)/g"
 export REGEX_SECONDS="s/SECOND\)/\'SECOND\'\)/g"
 
+#=== Decide on the order queries are executed
+# Normally, queries will be executed in alphabetical order.
+# However, some tables depend on each other. We specify
+# which queries to run first, and in what order.
+
+# tables we want to run before all other concepts
+# usually because they are used as dependencies
+DIR_AND_TABLES_TO_PREBUILD='demographics.icustay_times demographics.icustay_hourly demographics.weight_durations measurement.urine_output organfailure.kdigo_uo'
+
+# tables which are written directly in postgresql and source code controlled
+# this is usually because there is no trivial conversion between bq/psql syntax
+DIR_AND_TABLES_ALREADY_IN_PSQL=''
+
+# tables which we want to run after all other concepts
+# usually because they depend on one or more other queries
+# these will be generated in the order specified
+DIR_AND_TABLES_TO_SKIP='organfailure.kdigo_stages firstday.first_day_sofa sepsis.sepsis3 medication.vasoactive_agent medication.norepinephrine_equivalent_dose'
+
 # First, we re-create the postgres-make-concepts.sql file.
 echo "\echo ''" > $TARGET_PATH/postgres-make-concepts.sql
 
@@ -37,52 +58,58 @@ echo "-- NOTE: many scripts *require* you to use mimiciv_derived as the schema f
 echo "-- change the search path at your peril!" >> $TARGET_PATH/postgres-make-concepts.sql
 echo "SET search_path TO mimiciv_derived, mimiciv_hosp, mimiciv_icu, mimiciv_ed;" >> $TARGET_PATH/postgres-make-concepts.sql
 
-# reporting to stdout the folder being run
+# ======================================== #
+# === CONCEPTS WHICH WE MUST RUN FIRST === #
+# ======================================== #
 echo -n "Dependencies:"
 
 # output table creation calls to the make-concepts script
 echo "" >> $TARGET_PATH/postgres-make-concepts.sql
 echo "-- dependencies" >> $TARGET_PATH/postgres-make-concepts.sql
 
-for dir_and_table in demographics.icustay_times demographics.weight_durations measurement.urine_output organfailure.kdigo_uo;
+for dir_and_table in $DIR_AND_TABLES_TO_PREBUILD;
 do
   d=`echo ${dir_and_table} | cut -d. -f1`
   tbl=`echo ${dir_and_table} | cut -d. -f2`
 
+  # catch special case when file is in current directory
+  if [[ $d == '' ]]; then
+    d='.'
+  fi
+
   # make the sub-folder for postgres if it does not exist
   mkdir -p "$TARGET_PATH/${d}"
 
   # convert the bigquery script to psql and output it to the appropriate subfolder
   echo -n " ${d}.${tbl} .."
-  echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "$TARGET_PATH/${d}/${tbl}.sql"
-  echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS " >> "$TARGET_PATH/${d}/${tbl}.sql"
 
-  # apply regex to map bigquery syntax to postgres syntax
-  cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" >> "$TARGET_PATH/${d}/${tbl}.sql"
+  # re-write the script into psql using regex
+  # the if statement ensures we do not overwrite tables
+  # for which we already have psql code
+  if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
+    echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "$TARGET_PATH/${d}/${tbl}.sql"
+    echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS" >> "${TARGET_PATH}/${d}/${tbl}.sql"
+
+    # apply regex to map bigquery syntax to postgres syntax
+    cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" >> "$TARGET_PATH/${d}/${tbl}.sql"
+  else
+    echo -n "(psql!) .."
+  fi
 
   # write out a call to this script in the make concepts file
   echo "\i ${d}/${tbl}.sql" >> $TARGET_PATH/postgres-make-concepts.sql
 done
 echo " done!"
 
+# ================================== #
+# === MAIN LOOP FOR ALL CONCEPTS === #
+# ================================== #
+
 # Iterate through each concept subfolder, and:
 # (1) apply the above regular expressions to update the script
 # (2) output to the postgres subfolder
 # (3) add a line to the postgres-make-concepts.sql script to generate this table
 
-# we control the order by skipping tables listed in the below var
-DIR_AND_TABLES_TO_SKIP='demographics.icustay_times demographics.weight_durations measurement.urine_output organfailure.kdigo_uo organfailure.kdigo_stages firstday.first_day_sofa sepsis.sepsis3 medication.vasoactive_agent medication.norepinephrine_equivalent_dose'
-
-# create an array to store tables for which the order of generation matters
-# i.e. these tables cannot be generated in alphabetical order, as done in the later loop
-TABLES_TO_SKIP=()
-for dir_and_table in $DIR_AND_TABLES_TO_SKIP;
-do
-  tbl=`echo ${dir_and_table} | cut -d. -f2`
-  TABLES_TO_SKIP+=($tbl)
-done
-
-echo $TABLES_TO_SKIP
 # the order *only* matters during the conversion step because our loop is
 # inserting table build commands into the postgres-make-concepts.sql file
 for d in demographics measurement comorbidity medication treatment firstday organfailure score sepsis;
@@ -97,28 +124,35 @@ do
         if [[ "${fn: -4}" == ".sql" ]]; then
             # table name is file name minus extension
             tbl="${fn%????}"
-
-            # skip first_day_sofa as it depends on other firstday queries, we'll generate it later
-            # we also skipped tables generated in the "Dependencies" loop above.
-            if [[ "${tbl}" == "first_day_sofa" ]] || [[ "${tbl}" == "icustay_times" ]] || [[ "${tbl}" == "weight_durations" ]] || [[ "${tbl}" == "urine_output" ]] || [[ "${tbl}" == "kdigo_uo" ]] || [[ "${tbl}" == "sepsis3" ]]; then
-                continue
+            echo -n " ${tbl} "
+
+            if [[ "$DIR_AND_TABLES_TO_PREBUILD" =~ "$d.$tbl" ]]; then
+              echo -n "(prebuilt!) .."
+              continue
+            elif [[ "$DIR_AND_TABLES_TO_SKIP" =~ "$d.$tbl" ]]; then
+              echo -n "(skipping!) .."
+              continue
+            else
+              echo -n ".."
             fi
-            echo -n " ${tbl} .."
-            echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "${TARGET_PATH}/${d}/${tbl}.sql"
-            echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS " >> "${TARGET_PATH}/${d}/${tbl}.sql"
-            cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${fn}"
-
-            if [[ ! " ${TABLES_TO_SKIP[*]} " =~ " ${tbl} " ]]; then
-                # this table is *not* in our skip array
-                # therefore, we print it out to the make concepts script
-                echo "\i ${d}/${fn}" >> ${TARGET_PATH}/postgres-make-concepts.sql
+
+            # re-write the script into psql using regex
+            # the if statement ensures we do not overwrite tables which are already written in psql
+            if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
+              echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "${TARGET_PATH}/${d}/${tbl}.sql"
+              echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS" >> "${TARGET_PATH}/${d}/${tbl}.sql"
+              cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" >> "${TARGET_PATH}/${d}/${fn}"
             fi
+            
+            # add statement to generate this table
+            # in the make concepts script
+            echo "\i ${d}/${fn}" >> ${TARGET_PATH}/postgres-make-concepts.sql
         fi
     done
     echo " done!"
 done
 
-# finally generate first_day_sofa which depends on concepts in firstday folder
+# generate remaining concepts
 echo "" >> ${TARGET_PATH}/postgres-make-concepts.sql
 echo "-- final tables which were dependent on one or more prior tables" >> ${TARGET_PATH}/postgres-make-concepts.sql
 
@@ -133,10 +167,12 @@ do
 
   # convert the bigquery script to psql and output it to the appropriate subfolder
   echo -n " ${d}.${tbl} .."
-  echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "$TARGET_PATH/${d}/${tbl}.sql"
-  echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS " >> "$TARGET_PATH/${d}/${tbl}.sql"
+  if ! [[ "$DIR_AND_TABLES_ALREADY_IN_PSQL" =~ "$d.$tbl" ]]; then
+    echo "-- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY." > "$TARGET_PATH/${d}/${tbl}.sql"
+    echo "DROP TABLE IF EXISTS ${tbl}; CREATE TABLE ${tbl} AS" >> "$TARGET_PATH/${d}/${tbl}.sql"
 
-  cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" >> "$TARGET_PATH/${d}/${tbl}.sql"
+    cat "${d}/${tbl}.sql" | sed -r -e "${REGEX_ARRAY}" | sed -r -e "${REGEX_HOUR_INTERVAL}" | sed -r -e "${REGEX_INT}" | sed -r -e "${REGEX_DATETIME_DIFF}" | sed -r -e "${REGEX_DATETIME_TRUNC}" | sed -r -e "${REGEX_SCHEMA}" | sed -r -e "${REGEX_INTERVAL}" | sed -r -e "${REGEX_SECONDS}" >> "$TARGET_PATH/${d}/${tbl}.sql"
+  fi
 
   # write out a call to this script in the make concepts file
   echo "\i ${d}/${tbl}.sql" >> $TARGET_PATH/postgres-make-concepts.sql

mimic-iv/concepts_postgres/comorbidity/charlson.sql

@@ -1,18 +1,22 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS charlson; CREATE TABLE charlson AS 
+DROP TABLE IF EXISTS charlson; CREATE TABLE charlson AS
 -- ------------------------------------------------------------------
--- This query extracts Charlson Comorbidity Index (CCI) based on the recorded ICD-9 and ICD-10 codes.
+-- This query extracts Charlson Comorbidity Index (CCI) based on the
+-- recorded ICD-9 and ICD-10 codes.
 --
 -- Reference for CCI:
--- (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method of classifying prognostic 
--- comorbidity in longitudinal studies: development and validation.J Chronic Dis; 40(5):373-83.
+-- (1) Charlson ME, Pompei P, Ales KL, MacKenzie CR. (1987) A new method
+-- of classifying prognostic comorbidity in longitudinal studies: 
+-- development and validation.J Chronic Dis; 40(5):373-83.
 --
--- (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation of a combined comorbidity 
--- index. J Clin Epidemiol; 47(11):1245-51.
+-- (2) Charlson M, Szatrowski TP, Peterson J, Gold J. (1994) Validation
+-- of a combined comorbidity index. J Clin Epidemiol; 47(11):1245-51.
 -- 
--- Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson Comorbidities:
--- (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for defining Comorbidities in ICD-9-CM
--- and ICD-10 administrative data. Med Care. 2005 Nov; 43(11): 1130-9.
+-- Reference for ICD-9-CM and ICD-10 Coding Algorithms for Charlson
+-- Comorbidities:
+-- (3) Quan H, Sundararajan V, Halfon P, et al. Coding algorithms for
+-- defining Comorbidities in ICD-9-CM and ICD-10 administrative data.
+-- Med Care. 2005 Nov; 43(11): 1130-9.
 -- ------------------------------------------------------------------
 
 WITH diag AS (
@@ -281,7 +285,8 @@ WITH diag AS (
             THEN 1
             ELSE 0 END) AS renal_disease
 
-        -- Any malignancy, including lymphoma and leukemia, except malignant neoplasm of skin
+        -- Any malignancy, including lymphoma and leukemia,
+        -- except malignant neoplasm of skin.
         , MAX(CASE WHEN
             SUBSTR(icd9_code, 1, 3) BETWEEN '140' AND '172'
             OR
@@ -379,8 +384,9 @@ SELECT
     -- Calculate the Charlson Comorbidity Score using the original
     -- weights from Charlson, 1987.
     , age_score
-    + myocardial_infarct + congestive_heart_failure + peripheral_vascular_disease
-    + cerebrovascular_disease + dementia + chronic_pulmonary_disease
+    + myocardial_infarct + congestive_heart_failure
+    + peripheral_vascular_disease + cerebrovascular_disease
+    + dementia + chronic_pulmonary_disease
     + rheumatic_disease + peptic_ulcer_disease
     + GREATEST(mild_liver_disease, 3 * severe_liver_disease)
     + GREATEST(2 * diabetes_with_cc, diabetes_without_cc)

mimic-iv/concepts_postgres/demographics/age.sql

@@ -1,22 +1,24 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS age; CREATE TABLE age AS 
+DROP TABLE IF EXISTS age; CREATE TABLE age AS
 -- This query calculates the age of a patient on admission to the hospital.
 
 -- The columns of the table patients: anchor_age, anchor_year, anchor_year_group
--- provide information regarding the actual patient year for the patient admission, 
--- and the patient's age at that time.
+-- provide information regarding the actual patient year for the patient
+-- admission, and the patient's age at that time.
 
 -- anchor_year is a shifted year for the patient.
--- anchor_year_group is a range of years - the patient's anchor_year occurred during this range.
+-- anchor_year_group is a range of years - the patient's anchor_year occurred
+-- during this range.
 -- anchor_age is the patient's age in the anchor_year.
 -- Example: a patient has an anchor_year of 2153,
 -- anchor_year_group of 2008 - 2010, and an anchor_age of 60.
 -- The year 2153 for the patient corresponds to 2008, 2009, or 2010.
--- The patient was 60 in the shifted year of 2153, i.e. they were 60 in 2008, 2009, or 2010.
+-- The patient was 60 in the shifted year of 2153,
+--  i.e. they were 60 in 2008, 2009, or 2010.
 -- A patient admission in 2154 will occur in 2009-2011, 
 -- 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
+-- Therefore, the age of a patient = admission time - anchor_year + anchor_age
 SELECT
     ad.subject_id
     , ad.hadm_id

mimic-iv/concepts_postgres/demographics/icustay_detail.sql

@@ -1,5 +1,5 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS icustay_detail; CREATE TABLE icustay_detail AS 
+DROP TABLE IF EXISTS icustay_detail; CREATE TABLE icustay_detail AS
 SELECT ie.subject_id, ie.hadm_id, ie.stay_id
 
     -- patient level factors

mimic-iv/concepts_postgres/demographics/icustay_hourly.sql

@@ -1,21 +1,22 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS icustay_hourly; CREATE TABLE icustay_hourly AS 
+DROP TABLE IF EXISTS icustay_hourly; CREATE TABLE icustay_hourly AS
 -- This query generates a row for every hour the patient is in the ICU.
 -- The hours are based on clock-hours (i.e. 02:00, 03:00).
 -- The hour clock starts 24 hours before the first heart rate measurement.
--- Note that the time of the first heart rate measurement is ceilinged to the hour.
+-- Note that the time of the first heart rate measurement is ceilinged to
+-- the hour.
 
 -- this query extracts the cohort and every possible hour they were in the ICU
--- this table can be to other tables on ICUSTAY_ID and (ENDTIME - 1 hour,ENDTIME]
+-- this table can be to other tables on stay_id and (ENDTIME - 1 hour,ENDTIME]
 
 -- get first/last measurement time
 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
+        -- ceiling the intime to the nearest hour by adding 59 minutes,
+        -- then applying truncate by parsing as string
+        -- string truncate is done to enable compatibility with psql
         , PARSE_DATETIME(
             '%Y-%m-%d %H:00:00'
             , FORMAT_DATETIME(
@@ -24,7 +25,8 @@ WITH all_hours AS (
             )) 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
+        -- 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

mimic-iv/concepts_postgres/demographics/icustay_times.sql

@@ -1,5 +1,5 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS icustay_times; CREATE TABLE icustay_times AS 
+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

mimic-iv/concepts_postgres/demographics/weight_durations.sql

@@ -1,5 +1,5 @@
 -- THIS SCRIPT IS AUTOMATICALLY GENERATED. DO NOT EDIT IT DIRECTLY.
-DROP TABLE IF EXISTS weight_durations; CREATE TABLE weight_durations AS 
+DROP TABLE IF EXISTS weight_durations; CREATE TABLE weight_durations AS
 -- This query extracts weights for adult ICU patients with start/stop times
 -- if an admission weight is given, then this is assigned from intime to outtime
 WITH wt_stg AS (
@@ -85,7 +85,8 @@ WITH wt_stg AS (
 -- if the intime for the patient is < the first charted daily weight
 -- then we will have a "gap" at the start of their stay
 -- to prevent this, we look for these gaps and backfill the first weight
--- this adds (153255-149657)=3598 rows, meaning this fix helps for up to 3598 stay_id
+-- this adds (153255-149657)=3598 rows, meaning this fix helps for up
+-- to 3598 stay_id
 , wt_fix AS (
     SELECT ie.stay_id
         -- we add a 2 hour "fuzziness" window