fix: load paths, imports, transpile, and CI permissions - #2124

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Chessing234:fix/uo-rate-sqlite-create-user

Commits on Jul 23, 2026

fix: SECOND-based DATETIME_DIFF in urine_output_rate

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fix: escape password and quote ids in create_mimic_user

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fix: pin sqlite import dtypes for mixed columns

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fix: avoid escaped quote in neuroblock_dose stopped check

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fix: use DATETIME_DIFF for neuroblock gap check

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fix: check $1 not PID in copy_concepts script

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ci: dont fail sqlfluff job when annotate lacks fork perms

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fix: load .csv and .csv.gz in duckdb imports

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fix: require epi/norepi rate > 0 for SOFA CV score 3

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fix: quote datadir for postgres load and wget

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fix: write transpiled sql as utf-8
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fix: exact table name match in validate_concepts.sh
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fix: exclude ICD-10-CM C4A from Charlson malignancy

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fix: include provider/caregiver/ingredientevents in demo validate

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fix: use globs instead of ls in make_concepts.sh
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fix: escape quotes in mimic-iii duckdb COPY paths

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fix: quote sqlite import.sh paths for spaces

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fix: load plain .csv in mimic-iii sqlite import.py

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fix: quote DIRNAME in duckdb import case patterns

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fix: quote paths in mimic-iii make-concepts.sh
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fix: low_memory=False on mimic-iv sqlite read_csv
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fix: use printf for duckdb load progress

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fix: use globs and quote paths in cxr label scripts
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fix: glob + quote paths in chexpert runner too
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fix: quote mimic_data_dir for postgres \\cd in IV/ED/Note

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revert: unquote psql \\cd mimic_data_dir

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fix: require epi/norepi rate > 0 in pivoted_sofa CV score

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fix: keep DuckDB GENERATE_ARRAY as a list for UNNEST

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fix: include CCO and Arctic Sun temps in vitalsign

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fix: Charlson age_score uses half-open decade bands

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

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fix: exclude MetaVision pause gaps from vaso durations

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fix: merge overlapping MetaVision arterial/central line intervals

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

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

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fix: RTRIM ICD-9 codes in Quan Elixhauser

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

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

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fix: skip echo charttime parse when time regex misses

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fix: transpile DATETIME_DIFF MONTH for Postgres

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fix: include CCO/Arctic Sun temps in III vitals

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fix: include CCO/Arctic Sun temps in aline_vitals

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fix: skip echo height PARSE when time regex misses

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

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

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fix: build icustay_times/hours before pivoted_oasis

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Commits on Jul 24, 2026