MIT-LCP/mimic-code: v2.5.0

MIMIC Code v2.5.0

Major changes

• Linting/formatting SQL files with sqlfluff
• Converting BigQuery syntax SQL to postgres/duckdb using sqlglot
• Improvements in concept queries (thanks everyone for contributing!)

What's Changed

• Add linting of SQL files using sqlfluff by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1480
• Postgres shell script update by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1482
• Fixed an error: Line 90, an L is missing, by @lewis738 in https://github.com/MIT-LCP/mimic-code/pull/1503
• fix NULL typo at mysql buildmimic-iv load.sql by @asha-ndf in https://github.com/MIT-LCP/mimic-code/pull/1502
• Fix gh db build by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1504
• fix issue 1279 by @yongfanbeta in https://github.com/MIT-LCP/mimic-code/pull/1497
• Improvements for duckdb by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1489
• fix gh actions by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1506
• Fix norepinephrine in PSQL, tidy vasoactive code by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1505
• Update load.sql by @trostalski in https://github.com/MIT-LCP/mimic-code/pull/1492
• Create view for code_status in MIMIC-IV by @ajb5d in https://github.com/MIT-LCP/mimic-code/pull/1291
• fix typo in extraction of diabetes_without_cc by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1508
• change dir as import_duckdb relies on relative dirs by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1509
• Streamlining and updating Postgres building process for mimic-iv, mimic-iv-notes, mimic-iv-ed by @stefanhgm in https://github.com/MIT-LCP/mimic-code/pull/1537
• fix: MIMIC Note README.md by @aegis301 in https://github.com/MIT-LCP/mimic-code/pull/1592
• remove stale/broken docker scripts, see #684 by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1635
• fixing wrong mimic-iv folder name by @fvillena in https://github.com/MIT-LCP/mimic-code/pull/1639
• Fix constraint.sql for mimic-iv-ed PostgreSQL by @SimonUzL in https://github.com/MIT-LCP/mimic-code/pull/1659
• Add the 'load_7z.sql' script to enable the loading of 'ed' module dat… by @notwarn in https://github.com/MIT-LCP/mimic-code/pull/1656
• Changed column widths to import data without truncating by @KenjiOhtsuka in https://github.com/MIT-LCP/mimic-code/pull/1608
• Update code_status.sql by @SichengH in https://github.com/MIT-LCP/mimic-code/pull/1676
• fix sapsii and oasis score based on issue 1568 by @yongfanbeta in https://github.com/MIT-LCP/mimic-code/pull/1587
• nsaid & acei medication by @Juan-L-Dominguez in https://github.com/MIT-LCP/mimic-code/pull/1680
• Add duckdb build/concepts and use SQLGlot to convert BigQuery SQL into other dialects by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1689
• Add procedures mappings for MIMIC-IV v2.0 - SSSOM format by @a-chahin in https://github.com/MIT-LCP/mimic-code/pull/1419
• Fix GitHub CI by using a Python container by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1783
• Increase admissions language length for postgres schema by @MB-Finski in https://github.com/MIT-LCP/mimic-code/pull/1776
• SQLite python improvements by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1784
• Sqlglot fixes by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1786
• add validate.sql for mimic-iv-note by @Jin-Zhang-Yaoguang in https://github.com/MIT-LCP/mimic-code/pull/1687
• Fix SQLite build using all CSV files by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1788
• ARBs SQL by @Juan-L-Dominguez in https://github.com/MIT-LCP/mimic-code/pull/1690
• Add ARB by @alistairewj in https://github.com/MIT-LCP/mimic-code/pull/1789
• fix #1354 by @rustamzh in https://github.com/MIT-LCP/mimic-code/pull/1785
• Fix bug: Columns dislocation in the 'emar' table. by @Scott1743 in https://github.com/MIT-LCP/mimic-code/pull/1779
• fix: Readme mimic-iv postgres build and concepts links by @chamathpali in https://github.com/MIT-LCP/mimic-code/pull/1685

New Contributors

• @lewis738 made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1503
• @asha-ndf made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1502
• @trostalski made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1492
• @fvillena made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1639
• @SimonUzL made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1659
• @notwarn made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1656
• @KenjiOhtsuka made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1608
• @SichengH made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1676
• @Juan-L-Dominguez made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1680
• @MB-Finski made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1776
• @Jin-Zhang-Yaoguang made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1687
• @rustamzh made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1785
• @Scott1743 made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1779
• @chamathpali made their first contribution in https://github.com/MIT-LCP/mimic-code/pull/1685

Full Changelog: https://github.com/MIT-LCP/mimic-code/compare/v2.4.0...v2.5.0