fix: load paths, imports, transpile, and CI permissions#2127
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Chessing234 wants to merge 50 commits into
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fix: load paths, imports, transpile, and CI permissions#2127Chessing234 wants to merge 50 commits into
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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>
BigQuery rejects timestamp subtraction with interval compares; use DATETIME_DIFF(..., HOUR) like the rest of the concepts. Co-authored-by: Cursor <cursoragent@cursor.com>
$$1 expands to the shell PID, so the version arg was never validated. Co-authored-by: Cursor <cursoragent@cursor.com>
Lint already ran; fork tokens cannot create check runs. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
check already handles spaces (MIT-LCP#481/MIT-LCP#2068); load still used unquoted datadir and \cd without quoting, so paths with spaces broke at import. Co-authored-by: Cursor <cursoragent@cursor.com>
C4A (Merkel) sits in the C45–C58 string range; Quan 2005 uses WHO ICD-10 and excludes skin malignancy (MIT-LCP#2017). Co-authored-by: Cursor <cursoragent@cursor.com>
Demo loads these tables but validate_demo omitted them, so incomplete demo imports could still pass. Co-authored-by: Cursor <cursoragent@cursor.com>
Paths with apostrophes broke COPY string literals. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
import.sh already accepts both; import.py only globbed *.csv.gz. Co-authored-by: Cursor <cursoragent@cursor.com>
Unquoted case breaks when the parent folder name has spaces. Co-authored-by: Cursor <cursoragent@cursor.com>
echo .. \c prints a literal \c on bash; printf is portable. Co-authored-by: Cursor <cursoragent@cursor.com>
Same path-with-spaces break as MIT-LCP#481; use :'mimic_data_dir'. Co-authored-by: Cursor <cursoragent@cursor.com>
:'var' makes \\cd include literal quotes in the path and breaks CI. Co-authored-by: Cursor <cursoragent@cursor.com>
Same SOFA cardiovascular false-positive as sofa.sql when rates are null. Co-authored-by: Cursor <cursoragent@cursor.com>
Bare GENERATE_SERIES broke icustay_hourly on older DuckDB (MIT-LCP#1736). Co-authored-by: Cursor <cursoragent@cursor.com>
Itemids 226329/227632/227634 were omitted from temperature (MIT-LCP#1358). Co-authored-by: Cursor <cursoragent@cursor.com>
Age 50 was scored 0; CCI awards 1 point starting at 50. 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>
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>
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>
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>
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>
Co-authored-by: Cursor <cursoragent@cursor.com>
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>
pivoted_oasis reads mimiciii_derived.icustay_hours; make-concepts never created it (or its icustay_times dependency). Co-authored-by: Cursor <cursoragent@cursor.com>
SQL existed but make scripts never ran it (MIT-LCP#830). Co-authored-by: Cursor <cursoragent@cursor.com>
Per maintainer feedback on MIT-LCP#2124, keep load-path / transpile / CI fixes here and move concept logic to individual PRs. Co-authored-by: Cursor <cursoragent@cursor.com>
Co-authored-by: Cursor <cursoragent@cursor.com>
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Superseded by #2128 (clean rebase onto main — same infra changes, no stale concept three-dot noise). |
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Replacement for #2124 after dropping concept SQL (now in #2126 / follow-ups).
Made with Cursor