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

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chessing234 wants to merge 48 commits into

MIT-LCP:mainfrom

chessing234:fix/uo-rate-sqlite-create-user

Closed

fix: load paths, imports, transpile, and CI permissions#2124
chessing234 wants to merge 48 commits into
MIT-LCP:mainfrom
chessing234:fix/uo-rate-sqlite-create-user

Commits on Jul 23, 2026
- fix: SECOND-based DATETIME_DIFF in urine_output_rate
  
  chessing234
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  cursoragent
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  c06aeec
- fix: escape password and quote ids in create_mimic_user
  
  chessing234
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  5c49bc4
- fix: pin sqlite import dtypes for mixed columns
  
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  d4a8305
- fix: avoid escaped quote in neuroblock_dose stopped check
  
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  b035858
- fix: use DATETIME_DIFF for neuroblock gap check
  
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  24c02b4
- fix: check $1 not PID in copy_concepts script
  
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  23f7084
- ci: dont fail sqlfluff job when annotate lacks fork perms
  
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  cb18187
- fix: load .csv and .csv.gz in duckdb imports
  
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  e560823
- fix: require epi/norepi rate > 0 for SOFA CV score 3
  
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  a2d01c4
- fix: quote datadir for postgres load and wget
  
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  1cfb063
- fix: write transpiled sql as utf-8
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  81e4155
- fix: exact table name match in validate_concepts.sh
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  b2711aa
- fix: exclude ICD-10-CM C4A from Charlson malignancy
  
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  8b8833a
- fix: include provider/caregiver/ingredientevents in demo validate
  
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  3327400
- fix: use globs instead of ls in make_concepts.sh
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  475bbda
- fix: escape quotes in mimic-iii duckdb COPY paths
  
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  eafee6f
- fix: quote sqlite import.sh paths for spaces
  
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  51bd9d4
- fix: load plain .csv in mimic-iii sqlite import.py
  
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  88b634f
- fix: quote DIRNAME in duckdb import case patterns
  
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  f7c8a45
- fix: quote paths in mimic-iii make-concepts.sh
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  b3f8c66
- fix: low_memory=False on mimic-iv sqlite read_csv
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  dd56cd3
- fix: use printf for duckdb load progress
  
  chessing234
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  committed
  6f99509
- fix: use globs and quote paths in cxr label scripts
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  f8590e8
- fix: glob + quote paths in chexpert runner too
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  cde84eb
- fix: quote mimic_data_dir for postgres \\cd in IV/ED/Note
  
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  e7d5561
- revert: unquote psql \\cd mimic_data_dir
  
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  6b37856
- fix: require epi/norepi rate > 0 in pivoted_sofa CV score
  
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  committed
  1bb1e33
- fix: keep DuckDB GENERATE_ARRAY as a list for UNNEST
  
  chessing234
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  committed
  2d4f3ae
- fix: include CCO and Arctic Sun temps in vitalsign
  
  chessing234
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  committed
  a229b37
- fix: Charlson age_score uses half-open decade bands
  
  chessing234
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  be93cfa
- fix: keep o2-device-only rows after FULL OUTER JOIN
  
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  committed
  aa06aea
- fix: exclude MetaVision pause gaps from vaso durations
  
  chessing234
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  committed
  8f2b9c8
- fix: merge overlapping MetaVision arterial/central line intervals
  
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  31c72b6
- fix: Elixhauser no_drg excludes primary and RTRIMs ICD-9 codes
  
  chessing234
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  committed
  9e59a04
- fix: AHRQ Elixhauser with DRG uses all diagnoses, RTRIM codes
  
  chessing234
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  15c2f72
- fix: RTRIM ICD-9 codes in Quan Elixhauser
  
  chessing234
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  committed
  afe7707
- fix: drop LODS BUN >= 7.50 mg/dL score band
  
  chessing234
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  committed
  70cfd84
- fix: drop concept tables via bq ls CSV, not cut -f3
  
  chessing234
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  committed
  5163678
- fix: skip echo charttime parse when time regex misses
  
  chessing234
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  committed
  6ce72f9
- fix: transpile DATETIME_DIFF MONTH for Postgres
  
  chessing234
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  cursoragent
  committed
  d7ec3d5
- fix: include CCO/Arctic Sun temps in III vitals
  
  chessing234
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  committed
  1fe4366
- fix: include CCO/Arctic Sun temps in aline_vitals
  
  chessing234
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  committed
  0d80d2b
- fix: skip echo height PARSE when time regex misses
  
  chessing234
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  committed
  fc00594
- fix: include CCO/Arctic Sun temps in aline-aws vitals
  
  chessing234
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  committed
  b836c5a
- fix: convert SAPS glucose/BUN thresholds to mg/dL
  
  chessing234
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  committed
  1cab27c
- fix: build icustay_times/hours before pivoted_oasis
  
  chessing234
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  committed
  cb5f9ac
Commits on Jul 24, 2026
- fix: include pivoted_oasis in postgres/duckdb concept builds
  
  chessing234
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  cursoragent
  committed
  ca766fc
- Merge origin/main into fix branch
  chessing234
  committed
  3a43427

Commits

Commits on Jul 23, 2026

Commits on Jul 24, 2026