The build system for mimic code uses the GNU Makefile system. From a user's point of view this makes the whole process very straightforward. Starting from a fresh system which has both GNU Make installed, PostgreSQL installed, and a local copy of this repository, an instance of the MIMIC database can be imported from PhysioNet by running the following:
make mimic-download
make mimic-gz DATADIR=/path/to/data
Note that if you have already downloaded the data, you can skip the make mimic-download. If you have already decompressed the data into .csv files, then you can run make mimic DATADIR=/path/to/data.
Optionally, additional contributed materialized views can be created afterward by running:
make concepts
Note that you may want to modify parameters at the top of the Makefile - e.g. the username (see below "non-standard username or database name").
In order to avoid the prompts for your database password each time, you may create a file in your home directory called .pgpass containing the following:
localhost:5432:*:mimic:password
Replace mimic with your username and password with your password. Note that this is storage of your database password in the clear and so we would recommend only doing this for installation.
If you need to use a username or database name other than mimic, then you will need to specify this by modifying the top-level Makefile:
DBNAME=mimic
DBUSER=mimic
If you would like to contribute code to create a materialized view to the concepts folder, the existence of this makefile places an additional (and hopefully very minor) burden to ensure that your views are included in this build system. The top-level Makefile (i.e. the one in the root of this repository) is a wrapper that calls concepts/make-concepts.sql: simply add a command which calls the script to this file. The format is fairly straightforward: e.g. adding the \i sepsis/angus.sql line informs the script to call the concepts/sepsis/angus.sql file.