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.
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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:
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`.
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:
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```
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localhost:5432:*:mimic:password
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```
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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.
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###Non-standard username or database name
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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:
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.
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