fix(mimic-iii): load plain CSV in sqlite import.py (prefer .csv.gz) - #2149
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Co-authored-by: Cursor <cursoragent@cursor.com>
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Use literal suffix stripping so table names are derived from .csv / .csv.gz paths without the historical str.strip class of bugs.
Pin literal suffix stripping and .csv.gz preference so the loader stays aligned with import.sh.
Gives the CSV discovery helpers a cheap, always-on check (requested when this change was reviewed out of a larger infra PR).
Remove the outdated instruction to edit the script when files are uncompressed.
Keep the always-on pytest job discoverable next to the SQLFluff notes.
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Rebased onto main and squashed to the net change after several rounds of trimming; the sqlfluff and sqlite hunks are in MIT-LCP#2148 / MIT-LCP#2149. Covers duckdb load-path quoting for mimic-iii, -ed and -note, the postgres datadir/user quoting and concepts build order, transpile UTF-8 handling with its test, and the validate_demo table lists. The mimic-iv duckdb hunk is dropped: main replaced mimic-iv/buildmimic/duckdb/import_duckdb.sh with build_mimic.sh in MIT-LCP#1757, so that file no longer exists.
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Summary
import.pynow discovers plain.csvas well as.csv.gz, preferring gzip when both exist for the same table (parity withimport.sh).tests/test_mimic_iii_sqlite_import.pyand a PRunit-testsworkflow so CI verifies the behavior.Test plan
pytest tests/test_mimic_iii_sqlite_import.py -q.csvfiles besideimport.pyand confirm tables load without editing the scriptADMISSIONS.csvandADMISSIONS.csv.gzexist, confirm the gzip path is usedMade with Cursor