Docker mimic iv postgres

mimic-iv/buildmimic/postgres/docker/Dockerfile

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+FROM postgres
+COPY ./src/ /docker-entrypoint-initdb.d/
+WORKDIR /app
+EXPOSE 5432

mimic-iv/buildmimic/postgres/docker/README.md

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+# Getting MIMIC-IV up and running with Postgres and Docker
+Use these scripts to quickly get setup with a containerized version of MIMIC-IV
+
+## Steps
+1. Install Docker
+2. Download mimic data from PhysioNet by running the `download_data.sh` script. this will store the files in ./mimic-data/
+3. Edit `POSTGRES_USER` and `POSTGRES_PASSWORD` as needed. Optionally, you can
+   change the host paths for the volume mounts if you would like to change where
+   the data are stored on the host machine.
+4. Build and run the container by running `docker compose up`. This may take awhile. 
+
+Once complete you should have a containerized postgres instance containing MIMIC-IV data in the `mimiciv` database.
+
+## Using the database
+
+```bash
+# spin up a container and detach
+docker compose up -d
+
+# you should now see a running container...e.g docker-mimic-db-1
+docker ps
+
+# if you have psql installed on the host machine you can do...password required
+psql -U <username> -d mimiciv -h localhost
+
+# if you do not have psql installed on host machine you can do...password not
+# required
+docker exec -it docker-mimic-db-1 psql -U <username> -d mimiciv
+
+# psql on host machine...run profile script
+psql -U <username> -d mimiciv -h localhost -f ../validate.sql
+
+# psql not on host machine...need to mv validate into mount director so it can
+# be accessed from container
+cp ../validate.sql ./mimic-data/
+docker exec -it docker-mimic-db-1 psql -U <username> -d mimiciv -f /data/validate.sql
+```

mimic-iv/buildmimic/postgres/docker/docker-compose.yml

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+# Use postgres/example user/password credentials
+version: '3.9'
+services:
+  mimic-db:
+    image: mimiciv
+    build: .
+    restart: always
+    ports:
+      # you may need to change the host port if you have another postgres
+      # instance running on the host machine.
+      - 5432:5432
+    volumes:
+      # this mounts the mimic csv files to the /data/ directory within the
+      # container.
+      - ./mimic-data/:/data/
+      # this maps a directory on the host machine (i.e. ./mimic-db/) to the
+      # container so that the data in the database can persist after container
+      # has been shut down.
+      - /data/mimic-iv-db/:/var/lib/postgresql/data/
+    environment:
+      # this will be the name of the database within Postgres.
+      POSTGRES_DB: physionet-data
+      # set this to the same user that owns the directory storing the .csv data
+      # (hint: check ls -l ./mimic-data/) this should be the user of host
+      # machine. this will also be the user you will use to authenticate with
+      # postgres
+      POSTGRES_USER: mlbernauer
+      # this will be the password for authenticating with postgres...set to
+      # whatever you want
+      POSTGRES_PASSWORD: pass123

mimic-iv/buildmimic/postgres/docker/download_data.sh

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+#!/bin/bash
+read -p "Enter PhysioNet username: " USERNAME
+echo "Downloading MIMIV-IV data to ./mimic-data/"
+wget -P -A gz,txt ./mimic-data/ -r -N -c -nd -np --user ${USERNAME} --ask-password https://physionet.org/files/mimiciv/2.2/