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MIMIC-IV v2.2 updates #1469

Merged
merged 22 commits into from
Jan 17, 2023
Merged

MIMIC-IV v2.2 updates #1469

merged 22 commits into from
Jan 17, 2023

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alistairewj
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Many updates, mostly for building with MIMIC-IV v2.2

  • psql, mysql, sqlite, bigquery, and duckdb scripts updated
    • changed to mimiciv_* prefix in duckdb for consistency with the rest of the builds
  • GitHub action for duckdb (untested)
  • validation script row counts updated
  • mimic-iv-note build scripts
  • postgres concepts now set search_path

Thanks also to @schu and @DopamineLcy for making PRs off this, made my life easy!

alistairewj and others added 21 commits January 6, 2023 18:30
The `search_path` part of `postgres-make-concepts.sql` was not added in
`convert_bigquery_to_postgres.sh` yet. Add it on order to be able to
re-run the conversion.

Follow-up for 547f623
Re-run `convert_bigquery_to_postgres.sh` to update the Postgres
concepts. In particular, remove an old include..

```
\i measurement/differential_detailed.sql
```

..that leads to the following error:

```
psql:postgres-make-concepts.sql:35: error: measurement/differential_detailed.sql: No such file or directory
```
feat: Add mimic-iv-note (v2.2) loading of postgres
…gres

concepts_postgres: updates (on top of `mimiciv_v2.2_updates`)
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@briangow briangow left a comment

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@alistairewj , there is a lot here. I looked it over but haven't run it.

.github/workflows/duckdb.yml Outdated Show resolved Hide resolved
@alistairewj alistairewj merged commit e1d2dae into main Jan 17, 2023
@alistairewj alistairewj deleted the mimiciv_v2.2_updates branch January 17, 2023 21:30
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4 participants