3  安装eicu至postgresql数据库

注意

说明：来自于github官方账号，非最佳实践，仅留作痕迹。最佳实践参考：https://www.mmphcrc.com/books/phd/eicu.html

4 Create eICU Collaborative Research Database with Postgres

This folder loads the eICU Collaborative Research Database into a local PostgreSQL database system. Before you can create this version, you need to first need to download the CSV tables from PhysioNet.

4.1 Instructions for use

First ensure that Postgres is running on your computer. For installation instructions, see: http://www.postgresql.org/download/

Once Postgres is installed, clone the eicu-code repository into a local directory using the following command:

git clone https://github.com/mit-lcp/eicu-code.git

Change to the postgres/ directory and use make to run the Makefile, which contains instructions for creating eICU in a local Postgres database. For instructions on using the Makefile, run the following command:

make help

4.1.1 Download data

physionetuser=<PHYSIONETUSER> make eicu-download datadir=<DATA_PATH>

4.1.2 Check data exists

Check all of the required files exists. If the files are gzipped check with the following command -

make eicu-check-gz datadir=<DATA_PATH>

If the files are not compressed check with -

make eicu-check datadir=<DATA_PATH>

4.1.3 Create the user/database/schema (optional)

Runs the create_eicu_user.sh script which creates user, database and schema using the environment variables for DBUSER, DBPASS, DBSCHEMA and DBNAME. The default database name, schema, user, password, etc. are defined at the beginning of the Makefile.

make initialize

If you would like to specify a value (e.g. your own user name for the user), you can do so by adding the environment variable set as you would like; e.g.:

make initialize DBUSER=myusername DBPASS=mypassword

Note that you will need to continually pass these settings to the subsequent make commands, otherwise the build will fail.

4.1.4 Build Database

Build the database in 4 phases - 1. Create tables 2. Loads data 3. Add indices 4. Validate

To load gzipped data use -

make eicu-gz datadir=<DATA_PATH>

To load non-compressed data -

make eicu datadir=<DATA_PATH>

4.2 Suggested flow

Assuming postgres is already installed and running

  1. Download data
make eicu-download physionetuser=<PYSIONETUSER> datadir=<DATA_PATH>
  1. Create user, database and schema -
make initialize
  1. Build database -
make eicu-gz datadir=<DATA_PATH>