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Allow extra options to be passed to psql calls with MIMIC-III #1195

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Dec 8, 2021
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Allow extra options to be passed to psql calls with MIMIC-III #1195

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5 changes: 5 additions & 0 deletions mimic-iii/concepts/README.md
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Expand Up @@ -35,6 +35,11 @@ This can be done as follows:
* e.g. `bash postgres_make_concepts.sh`
* This file runs the scripts after applying a few regular expressions which convert table references and date calculations appropriately.
* This file generates all concepts on the `public` schema.
* Exporting DBCONNEXTRA before calling this script will add this to the
connection string. For example, running:
`DBCONNEXTRA="user=mimic password=mimic" bash postgres_make_concepts.sh`
will add these settings to all of the psql calls. (Note that "dbname"
and "search_path" do not need to be set.)

If you do not have access to a PostgreSQL database with MIMIC, you can read more about building the data within one in the [buildmimic/postgres](https://github.com/MIT-LCP/mimic-code/tree/main/mimic-iii/buildmimic/postgres) folder.

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