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‎README.md‎

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# ehr_docker
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Docker container building scripts for MIMIC-IV, MIMIC-III, and eICU.
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# ehr_postgres
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Postgres Docker container setup scripts for MIMIC-IV (including ED), MIMIC-III, and eICU datasets.
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## How-to-use
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1. Download EHR data what you want from [physionet](https://physionet.org).
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2. Run `python --mimic_iv {MIMIC_IV_PATH} --mimic_iv_ed {MIMIC_IV_ED_PATH} --mimic_iii {MIMIC_III_PATH} --eicu {EICU_PATH}` to bulid and run docker container.
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* NOTE: You can use each option separately.
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* NOTE: This script automatically removes pre-existing containers and images named `ehr_postgres`.
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3. Run `PGPASSWORD=postgres psql -h localhost -p 5432 -U postgres`, and enjoy!
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* The database names are `mimiciv`, `mimiciii`, `eicu`.
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## NOTE
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- This script has been tested with the following dataset versions: MIMC-IV v2.2, MIMIC-IV-ED v2.2, MIMIC-III v1.4, and eICU v2.0.
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- The whole process takes few hours.
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- Each dataset requires approximately 100GB of storage space.

‎build.py‎

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import argparse
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import os
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import subprocess
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import sys
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start = """FROM postgres:17.2
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ENV POSTGRES_USER=postgres
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ENV POSTGRES_PASSWORD=postgres
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RUN apt update && apt install git make -y
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RUN mkdir /data
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USER postgres
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RUN cd ~
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"""
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mimic_iv = """#!/bin/bash
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set -e
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echo "START BUILDING MIMIC-IV"
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git clone https://github.com/MIT-LCP/mimic-code.git /tmp/mimic-code
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cd /tmp/mimic-code
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if ! psql -U postgres -lqt | cut -d \| -f 1 | grep -wq mimiciv; then
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createdb mimiciv
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fi
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psql -d mimiciv -f mimic-iv/buildmimic/postgres/create.sql
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psql -d mimiciv -v ON_ERROR_STOP=1 -v mimic_data_dir=/tmp/mimic_iv -f mimic-iv/buildmimic/postgres/load{}.sql
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psql -d mimiciv -v ON_ERROR_STOP=1 -v mimic_data_dir=/tmp/mimic_iv -f mimic-iv/buildmimic/postgres/constraint.sql
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psql -d mimiciv -v ON_ERROR_STOP=1 -v mimic_data_dir=/tmp/mimic_iv -f mimic-iv/buildmimic/postgres/index.sql
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psql -d mimiciv -v ON_ERROR_STOP=1 -f mimic-iv/buildmimic/postgres/validate.sql
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cd mimic-iv/concepts_postgres
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psql -d mimiciv -v ON_ERROR_STOP=1 -f postgres-make-concepts.sql
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cd ~
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rm -rf /tmp/mimic-code
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echo "FINISH BUILDING MIMIC-IV"
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"""
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mimic_iv_ed = """#!/bin/bash
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set -e
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echo "START BUILDING MIMIC-IV-ED"
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git clone https://github.com/MIT-LCP/mimic-code.git /tmp/mimic-code
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cd /tmp/mimic-code
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if ! psql -U postgres -lqt | cut -d \| -f 1 | grep -wq mimiciv; then
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createdb mimiciv
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fi
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psql -d mimiciv -f mimic-iv-ed/buildmimic/postgres/create.sql
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psql -d mimiciv -v ON_ERROR_STOP=1 -v mimic_data_dir=/tmp/mimic_iv_ed -f mimic-iv-ed/buildmimic/postgres/load_gz.sql
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psql -d mimiciv -v ON_ERROR_STOP=1 -v mimic_data_dir=/tmp/mimic_iv_ed -f mimic-iv-ed/buildmimic/postgres/validate.sql
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cd ~
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rm -rf /tmp/mimic-code
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echo "FINISH BUILDING MIMIC-IV-ED"
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"""
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mimic_iii = """#!/bin/bash
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set -e
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echo "START BUILDING MIMIC-III"
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git clone https://github.com/MIT-LCP/mimic-code.git /tmp/mimic-code
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cd /tmp/mimic-code/mimic-iii/buildmimic/postgres
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createdb mimiciii
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make mimic{} datadir="/tmp/mimic_iii" DBNAME="mimiciii"
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cd ../../concepts_postgres
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psql -d mimiciii -c "SET search_path TO mimiciii;" -f postgres-functions.sql -f postgres-make-concepts.sql
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cd ~
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rm -rf /tmp/mimic-code
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echo "FINISH BUILDING MIMIC-III"
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"""
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eicu = """
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#!/bin/bash
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set -e
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echo "START BUILDING eICU"
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git clone https://github.com/mit-lcp/eicu-code.git /tmp/eicu-code
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cd /tmp/eicu-code/build-db/postgres
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make initialize
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make eicu{} datadir="/tmp/eicu/"
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cd ~
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rm -rf /tmp/eicu-code
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echo "FINISH BUILDING eICU"
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"""
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script_dict = {
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"mimic_iv": mimic_iv,
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"mimic_iv_ed": mimic_iv_ed,
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"mimic_iii": mimic_iii,
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"eicu": eicu,
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}
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def pares_args():
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parser = argparse.ArgumentParser(description='Build a Dockerfile')
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parser.add_argument("--mimic_iv", type=str, help="MIMIC-IV Path")
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parser.add_argument("--mimic_iv_ed", type=str, help="MIMIC-IV-ED Path")
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parser.add_argument("--mimic_iii", type=str, help="MIMIC-III Path")
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parser.add_argument("--eicu", type=str, help="eicu Path")
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return parser.parse_args()
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def add_dataset(data_path, data_name, check_file, ext):
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if os.path.exists(os.path.join(data_path, check_file + '.csv')):
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ext = ""
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elif os.path.exists(os.path.join(data_path, check_file + ".csv.gz")):
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pass
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else:
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raise ValueError(f"Invalid {data_name} Path")
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with open(f"{data_name}.sh", 'w') as f:
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f.write(script_dict[data_name].format(ext))
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mount_args = ["-v", f"{data_path}:/tmp/{data_name}"]
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write_content = f"COPY {data_name}.sh /docker-entrypoint-initdb.d/{data_name}.sh\n"
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return mount_args, write_content
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def main():
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args = pares_args()
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dockerfile = open("Dockerfile", "w")
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dockerfile.write(start)
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run_args = []
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if args.mimic_iv:
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mount_args, write_content = add_dataset(args.mimic_iv, "mimic_iv", "hosp/admissions", "_gz")
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run_args.extend(mount_args)
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dockerfile.write(write_content)
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if args.mimic_iv_ed:
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mount_args, write_content = add_dataset(args.mimic_iv_ed, "mimic_iv_ed", "edstays", "_gz")
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run_args.extend(mount_args)
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dockerfile.write(write_content)
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if args.mimic_iii:
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mount_args, write_content = add_dataset(args.mimic_iii, "mimic_iii", "ADMISSIONS", "-gz")
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run_args.extend(mount_args)
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dockerfile.write(write_content)
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if args.eicu:
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mount_args, write_content = add_dataset(args.eicu, "eicu", "patient", "-gz")
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run_args.extend(mount_args)
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dockerfile.write(write_content)
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dockerfile.close()
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print("Dockerfile created")
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# Remove container if exists
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subprocess.run(["docker", "stop", "ehr_postgres"], stderr=subprocess.DEVNULL)
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subprocess.run(["docker", "rm", "ehr_postgres"], stderr=subprocess.DEVNULL)
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subprocess.run(["docker", "image", "rm", "ehr_postgres"], stderr=subprocess.DEVNULL)
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subprocess.run(["docker", "build", "-t", "ehr_postgres", "."])
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subprocess.run(["docker", "run", "--name", "ehr_postgres", "-d", "-p", "5432:5432", "-e", "POSTGRES_PASSWORD=postgres", *run_args, "ehr_postgres"])
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print("Docker container created")
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process = subprocess.Popen(
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["docker", "logs", "-f", "ehr_postgres"],
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stdout=subprocess.PIPE,
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stderr=subprocess.STDOUT,
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text=True
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)
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for line in process.stdout:
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sys.stdout.write(line)
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sys.stdout.flush()
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if "PostgreSQL init process complete" in line:
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print("Initialization complete!")
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process.terminate()
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break
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print("EHR_POSTGRES is ready!")
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if __name__ == "__main__":
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main()

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