fix: UO rate, vaso pause gaps, line durations, load paths by Chessing234 · Pull Request #2124 · MIT-LCP/mimic-code

Chessing234 · 2026-07-23T09:30:53Z

Summary

urine_output_rate, charlson, SOFA CV, vitalsign temps, vaso pause gaps, line durations
Elixhauser primary/RTRIM (Spaces in codes in elixhauser_ahrq_v37_no_drg.sql #1077); LODS BUN 7.50 removed (lods.sql BUN value #1065)
make_concepts drop via bq CSV; echo charttime null-safe; sqlite/duckdb load paths

Test plan

pytest tests/ (404 passed)
CI: syntax, equivalence, sqlfluff, transpile

Match kdigo_uo so BigQuery truncation and Postgres fractional diffs no longer diverge on the 6/12h rate windows (MIT-LCP#1549). Co-authored-by: Cursor <cursoragent@cursor.com>

Passwords with quotes and unusual user/db names broke the CREATE USER / DATABASE statements. Co-authored-by: Cursor <cursoragent@cursor.com>

Stop pandas DtypeWarning on chartevents/datetimeevents/ inputevents_cv/noteevents during chunked import (MIT-LCP#1237). Co-authored-by: Cursor <cursoragent@cursor.com>

sqlglot rejects 'D/C''d' as adjacent string literals, breaking BigQuery→postgres/duckdb transpile of this concept. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T09:34:13Z

sqlfluff lint step itself passed; the job fail is the annotate action (permissions on fork PRs).

BigQuery rejects timestamp subtraction with interval compares; use DATETIME_DIFF(..., HOUR) like the rest of the concepts. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T09:47:04Z

also folded in the neuroblock DATETIME_DIFF gap check from #2079.

$$1 expands to the shell PID, so the version arg was never validated. Co-authored-by: Cursor <cursoragent@cursor.com>

WHERE ce.rn = 1 dropped charttimes with devices but no flow. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T11:52:37Z

also: vitalsign CCO/Arctic Sun temps (#1358); Charlson age bands; o2_delivery keep device-only rows.

Grouping by linkorderid with min/max start/end treated pauses as continuous infusion (MIT-LCP#1808). Keep per-row intervals and merge only overlapping ones. Co-authored-by: Cursor <cursoragent@cursor.com>

Collapse overlapping procedureevents_mv rows so duration tables no longer emit nested intervals (MIT-LCP#371). Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T12:03:05Z

Also fixed MetaVision pause gaps in vaso durations (#1808) and overlapping arterial/central line intervals (#371).

WHERE seq_num = 1 contradicted the header (and Quan); padded CHAR codes also failed unpadded BETWEEN ranges (MIT-LCP#1077). Co-authored-by: Cursor <cursoragent@cursor.com>

Primary-only filtering skipped secondary codes that DRG exclusions need; RTRIM matches padded ICD-9 storage (MIT-LCP#1077). Co-authored-by: Cursor <cursoragent@cursor.com>

Padded codes break exact and prefix matches the same way as AHRQ (MIT-LCP#1077). Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T12:16:21Z

Also fixed Elixhauser: exclude primary in no_drg, include all diagnoses for DRG version, and RTRIM ICD-9 codes (#1077).

That cutpoint is mmol/L; on MIMIC BUN (mg/dL) it scored normal values as 1 (MIT-LCP#1065). Co-authored-by: Cursor <cursoragent@cursor.com>

Pretty-format column cutting mis-parses table names when rebuilding derived. Co-authored-by: Cursor <cursoragent@cursor.com>

PARSE_DATETIME on a NULL-concatenated string failed rows without a time. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T12:25:23Z

Also fixed LODS BUN 7.50 mg/dL band (#1065), make_concepts drop via bq CSV ls, and null-safe echo charttime parse.

MONTH previously KeyError'd in _SECONDS_PER_UNIT; emit year*12+month. Co-authored-by: Cursor <cursoragent@cursor.com>

Same itemids as IV vitalsign (MIT-LCP#1358): 226329, 227632, 227634. Co-authored-by: Cursor <cursoragent@cursor.com>

Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T12:36:27Z

added: DATETIME_DIFF MONTH transpile, CCO/Arctic Sun temps in III vitals + aline_vitals.

Co-authored-by: Cursor <cursoragent@cursor.com>

SAPS 1984 publishes mmol/L cutpoints; MIMIC labs are mg/dL. Apply PhysioNet Challenge 2012 conversions (glucose x18, BUN x2.8). Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T12:46:54Z

added: echo height PARSE null-guard, aline-aws CCO/Arctic temps, SAPS glucose/BUN mg/dL conversion.

pivoted_oasis reads mimiciii_derived.icustay_hours; make-concepts never created it (or its icustay_times dependency). Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 · 2026-07-23T12:56:13Z

also: make-concepts now builds icustay_times/hours (for pivoted_oasis), arterial/central line durations, and neuroblock_dose.

Chessing234 and others added 4 commits July 23, 2026 12:22

fix: SECOND-based DATETIME_DIFF in urine_output_rate

c06aeec

Match kdigo_uo so BigQuery truncation and Postgres fractional diffs no longer diverge on the 6/12h rate windows (MIT-LCP#1549). Co-authored-by: Cursor <cursoragent@cursor.com>

fix: escape password and quote ids in create_mimic_user

5c49bc4

Passwords with quotes and unusual user/db names broke the CREATE USER / DATABASE statements. Co-authored-by: Cursor <cursoragent@cursor.com>

fix: pin sqlite import dtypes for mixed columns

d4a8305

Stop pandas DtypeWarning on chartevents/datetimeevents/ inputevents_cv/noteevents during chunked import (MIT-LCP#1237). Co-authored-by: Cursor <cursoragent@cursor.com>

fix: avoid escaped quote in neuroblock_dose stopped check

b035858

sqlglot rejects 'D/C''d' as adjacent string literals, breaking BigQuery→postgres/duckdb transpile of this concept. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 mentioned this pull request Jul 23, 2026

fix: emtpy -> empty in mimic-iv postgres load comments #2088

Closed

1 task

fix: use DATETIME_DIFF for neuroblock gap check

24c02b4

BigQuery rejects timestamp subtraction with interval compares; use DATETIME_DIFF(..., HOUR) like the rest of the concepts. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 mentioned this pull request Jul 23, 2026

fix: use DATETIME_DIFF in neuroblock_dose for BigQuery #2079

Closed

1 task

Chessing234 changed the title ~~fix: urine output rate parity, sqlite dtypes, create_user escaping~~ fix: urine output rate parity, sqlite dtypes, create_user, neuroblock Jul 23, 2026

fix: check $1 not PID in copy_concepts script

23f7084

$$1 expands to the shell PID, so the version arg was never validated. Co-authored-by: Cursor <cursoragent@cursor.com>

kotharitaksh451-cyber mentioned this pull request Jul 23, 2026

fix: check $1 not pid in copy_concepts script #2091

Closed

2 tasks

Chessing234 mentioned this pull request Jul 23, 2026

fix: quote paths in mimic-iii make-concepts.sh #2118

Closed

1 task

fix: keep o2-device-only rows after FULL OUTER JOIN

aa06aea

WHERE ce.rn = 1 dropped charttimes with devices but no flow. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 mentioned this pull request Jul 23, 2026

Temperature vital sign not consistently captured by concept #1358

Open

Chessing234 and others added 2 commits July 23, 2026 15:01

fix: exclude MetaVision pause gaps from vaso durations

8f2b9c8

Grouping by linkorderid with min/max start/end treated pauses as continuous infusion (MIT-LCP#1808). Keep per-row intervals and merge only overlapping ones. Co-authored-by: Cursor <cursoragent@cursor.com>

fix: merge overlapping MetaVision arterial/central line intervals

31c72b6

Collapse overlapping procedureevents_mv rows so duration tables no longer emit nested intervals (MIT-LCP#371). Co-authored-by: Cursor <cursoragent@cursor.com>

This was referenced Jul 23, 2026

paused vasopressor durations #1808

Open

Central line/arterial line durations have overlapping rows #371

Open

Chessing234 changed the title ~~fix: UO rate, charlson C4A, sqlite/duckdb load paths, SOFA CV~~ fix: UO rate, vaso pause gaps, line durations, load paths Jul 23, 2026

Chessing234 and others added 3 commits July 23, 2026 15:14

fix: Elixhauser no_drg excludes primary and RTRIMs ICD-9 codes

9e59a04

WHERE seq_num = 1 contradicted the header (and Quan); padded CHAR codes also failed unpadded BETWEEN ranges (MIT-LCP#1077). Co-authored-by: Cursor <cursoragent@cursor.com>

fix: AHRQ Elixhauser with DRG uses all diagnoses, RTRIM codes

15c2f72

Primary-only filtering skipped secondary codes that DRG exclusions need; RTRIM matches padded ICD-9 storage (MIT-LCP#1077). Co-authored-by: Cursor <cursoragent@cursor.com>

fix: RTRIM ICD-9 codes in Quan Elixhauser

afe7707

Padded codes break exact and prefix matches the same way as AHRQ (MIT-LCP#1077). Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 mentioned this pull request Jul 23, 2026

Spaces in codes in elixhauser_ahrq_v37_no_drg.sql #1077

Open

1 task

Chessing234 and others added 3 commits July 23, 2026 15:24

fix: drop LODS BUN >= 7.50 mg/dL score band

70cfd84

That cutpoint is mmol/L; on MIMIC BUN (mg/dL) it scored normal values as 1 (MIT-LCP#1065). Co-authored-by: Cursor <cursoragent@cursor.com>

fix: drop concept tables via bq ls CSV, not cut -f3

5163678

Pretty-format column cutting mis-parses table names when rebuilding derived. Co-authored-by: Cursor <cursoragent@cursor.com>

fix: skip echo charttime parse when time regex misses

6ce72f9

PARSE_DATETIME on a NULL-concatenated string failed rows without a time. Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 mentioned this pull request Jul 23, 2026

lods.sql BUN value #1065

Open

Chessing234 and others added 3 commits July 23, 2026 15:35

fix: transpile DATETIME_DIFF MONTH for Postgres

d7ec3d5

MONTH previously KeyError'd in _SECONDS_PER_UNIT; emit year*12+month. Co-authored-by: Cursor <cursoragent@cursor.com>

fix: include CCO/Arctic Sun temps in III vitals

1fe4366

Same itemids as IV vitalsign (MIT-LCP#1358): 226329, 227632, 227634. Co-authored-by: Cursor <cursoragent@cursor.com>

fix: include CCO/Arctic Sun temps in aline_vitals

0d80d2b

Co-authored-by: Cursor <cursoragent@cursor.com>

Chessing234 and others added 3 commits July 23, 2026 15:46

fix: skip echo height PARSE when time regex misses

fc00594

Co-authored-by: Cursor <cursoragent@cursor.com>

fix: include CCO/Arctic Sun temps in aline-aws vitals

b836c5a

Co-authored-by: Cursor <cursoragent@cursor.com>

fix: convert SAPS glucose/BUN thresholds to mg/dL

1cab27c

SAPS 1984 publishes mmol/L cutpoints; MIMIC labs are mg/dL. Apply PhysioNet Challenge 2012 conversions (glucose x18, BUN x2.8). Co-authored-by: Cursor <cursoragent@cursor.com>

fix: build icustay_times/hours before pivoted_oasis

cb5f9ac

pivoted_oasis reads mimiciii_derived.icustay_hours; make-concepts never created it (or its icustay_times dependency). Co-authored-by: Cursor <cursoragent@cursor.com>

kotharitaksh451-cyber mentioned this pull request Jul 23, 2026

TABLE pivoted_oasis #830

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fix: UO rate, vaso pause gaps, line durations, load paths#2124

fix: UO rate, vaso pause gaps, line durations, load paths#2124
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