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concepts_postgres: updates (on top of mimiciv_v2.2_updates) #1468

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schu
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@schu schu commented Jan 12, 2023

A few changes on top of https://github.com/MIT-LCP/mimic-code/tree/mimiciv_v2.2_updates to update the Postgres concepts code. Please see the individual commit messages for details.

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
```
@schu schu mentioned this pull request Jan 12, 2023
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@alistairewj
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Ah thanks for pulling in those updates, though it's interesting your run sorts first_day_bg.sql after first_day_bg_art.sql, as mine doesn't. first_day_bg.sql needs to come before first_day_bg_art.sql so I will manually make the fix, but it might be worth taking a look to see why it's happening in the future.

@alistairewj alistairewj merged commit 5e05342 into MIT-LCP:mimiciv_v2.2_updates Jan 15, 2023
@alistairewj
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Nevermind about the above, I forgot I already made them both rely on the bg view to avoid that above inconsistency :)

@schu schu deleted the schu/update-mimic-iv-concepts-postgres branch January 18, 2023 18:08
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2 participants