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Merge pull request #1 from MIT-LCP/main
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‎.github/actions/download-demo/action.yml‎

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name: "Download MIMIC-IV Demo"
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description: "Downloads MIMIC-IV demo data from GCP"
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inputs:
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gcp-project-id:
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required: true
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description: "The Google Cloud Project ID used for billing usage"
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gcp-sa-key:
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required: true
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description: "The service account key used to authenticate with GCP"
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runs:
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using: "composite"
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steps:
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- name: Authenticate with GCP
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uses: 'google-github-actions/auth@v0'
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with:
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project_id: ${{ inputs.gcp-project-id }}
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credentials_json: ${{ inputs.gcp-sa-key }}
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- name: Set up Cloud SDK
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uses: 'google-github-actions/setup-gcloud@v0'
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- name: Download demo data from GCP
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run: |
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echo "Downloading MIMIC-IV demo from GCP."
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gsutil -q -u $PROJECT_ID -m cp -r gs://mimic-iv-archive/v2.0/demo ./
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env:
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PROJECT_ID: ${{ inputs.gcp-project-id }}
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shell: bash

‎.github/workflows/main.yml‎

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create-tables:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- name: Check out repository code
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uses: actions/checkout@v3
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- name: Set up Cloud SDK
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uses: google-github-actions/setup-gcloud@master
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- id: 'auth'
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uses: 'google-github-actions/auth@v0'
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with:
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project_id: ${{ secrets.GCP_PROJECT_ID }}
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service_account_key: ${{ secrets.GCP_SA_KEY }}
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export_default_credentials: true
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project_id: ${{ secrets.GCP_PROJECT_ID }}
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credentials_json: ${{ secrets.GCP_SA_KEY }}
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- name: 'Set up Cloud SDK'
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uses: 'google-github-actions/setup-gcloud@v0'
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- name: Run make_concepts
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run: |

‎.github/workflows/mysql.yml‎

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name: mysql demo db build
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on:
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pull_request_review:
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types: [submitted]
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jobs:
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mimic-iv-mysql:
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# only run if PR is approved
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if: github.event.review.state == 'approved'
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runs-on: ubuntu-22.04
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steps:
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- name: Check out repository code
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uses: actions/checkout@v3
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- name: Download demo data
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uses: ./.github/actions/download-demo
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with:
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gcp-project-id: ${{ secrets.GCP_PROJECT_ID }}
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gcp-sa-key: ${{ secrets.GCP_SA_KEY }}
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- name: Extract demo data to local folder
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run: |
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mv demo/hosp/*.csv.gz ./
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mv demo/icu/*.csv.gz ./
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mv demo/ed/*.csv.gz ./
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gzip -d *.csv.gz
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- name: Start MySQL service
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run: |
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sudo /etc/init.d/mysql start
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mysql -u root -proot -e "SET GLOBAL local_infile=1;"
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mysql -u root -proot -e "SET GLOBAL sql_notes=0;"
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mysql -u root -proot -e "create database mimic"
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- name: Load icu/hosp demo data
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run: |
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echo "Loading data into mysql."
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mysql -u root -proot --local-infile=1 mimic < mimic-iv/buildmimic/mysql/load.sql
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mysql -u root -proot mimic < mimic-iv/buildmimic/mysql/validate_demo.sql > results
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# if we find "FAILED", then we did not pass the build
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if grep -F -q "FAILED" results; then
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echo "Failed the following row counts:"
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head -n 1 results
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grep "FAILED" results
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exit 1
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else
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echo "Built and loaded demo data successfully."
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cat results
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fi
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- name: Load ed demo data
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run: |
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echo "Loading data into mysql."
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mysql -u root -proot --local-infile=1 mimic < mimic-iv-ed/buildmimic/mysql/load.sql
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mysql -u root -proot mimic < mimic-iv-ed/buildmimic/mysql/validate_demo.sql > results
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# if we find "FAILED", then we did not pass the build
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if grep -F -q "FAILED" results; then
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echo "Failed the following row counts:"
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head -n 1 results
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grep "FAILED" results
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exit 1
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else
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echo "Built and loaded demo data successfully."
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cat results
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fi

‎.github/workflows/psql.yml‎

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name: psql demo db build
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on:
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pull_request_review:
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types: [submitted]
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jobs:
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mimic-iv-psql:
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# only run if PR is approved
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if: github.event.review.state == 'approved'
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runs-on: ubuntu-latest
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container: node:latest
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services:
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# Label used to access the service container
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postgres:
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# Docker Hub image
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image: postgres
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env:
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POSTGRES_PASSWORD: postgres
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# Set health checks to wait until postgres has started
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options: >-
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--health-cmd pg_isready
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--health-interval 10s
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--health-timeout 5s
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--health-retries 5
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steps:
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- name: Check out repository code
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uses: actions/checkout@v3
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- name: Download demo data
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uses: ./.github/actions/download-demo
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with:
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gcp-project-id: ${{ secrets.GCP_PROJECT_ID }}
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gcp-sa-key: ${{ secrets.GCP_SA_KEY }}
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- name: Install postgresql-client
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run: |
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apt-get update
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apt-get install --yes --no-install-recommends postgresql-client
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- name: Load icu/hosp data into PostgreSQL
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run: |
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echo "Loading data into psql."
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psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql
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psql -q -h $POSTGRES_HOST -U postgres -v mimic_data_dir=demo -f ${BUILDCODE_PATH}/load_gz.sql
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echo "Validating build."
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psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results
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# if we find "FAILED", then we did not pass the build
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if grep -F -q "FAILED" results; then
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echo "Failed the following row counts:"
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head -n 1 results
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grep "FAILED" results
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exit 1
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else
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echo "Built and loaded demo data successfully."
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cat results
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fi
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env:
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POSTGRES_HOST: postgres
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PGPASSWORD: postgres
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BUILDCODE_PATH: mimic-iv/buildmimic/postgres
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- name: Build mimic-iv concepts
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run: |
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psql -h $POSTGRES_HOST -U postgres -f postgres-functions.sql
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psql -h $POSTGRES_HOST -U postgres -f postgres-make-concepts.sql
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working-directory: ./mimic-iv/concepts_postgres
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env:
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POSTGRES_HOST: postgres
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PGPASSWORD: postgres
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- name: Load ed data into PostgreSQL
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run: |
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echo "Loading data into psql."
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psql -q -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/create.sql
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psql -q -h $POSTGRES_HOST -U postgres -v mimic_data_dir=demo/ed -f ${BUILDCODE_PATH}/load_gz.sql
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echo "Validating build."
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psql -h $POSTGRES_HOST -U postgres -f ${BUILDCODE_PATH}/validate_demo.sql > results
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# if we find "FAILED", then we did not pass the build
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if grep -F -q "FAILED" results; then
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echo "Failed the following row counts:"
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head -n 1 results
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grep "FAILED" results
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exit 1
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else
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echo "Built and loaded demo data successfully."
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cat results
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fi
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env:
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# The hostname used to communicate with the PostgreSQL service container
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POSTGRES_HOST: postgres
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PGPASSWORD: postgres
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# The default PostgreSQL port
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POSTGRES_PORT: 5432
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BUILDCODE_PATH: mimic-iv-ed/buildmimic/postgres

‎README.md‎

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# MIMIC Code Repository [![Build Status](https://travis-ci.org/MIT-LCP/mimic-code.svg?branch=main)](https://travis-ci.org/MIT-LCP/mimic-code) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.821872.svg)](https://doi.org/10.5281/zenodo.821872)
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# MIMIC Code Repository [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6818823.svg)](https://doi.org/10.5281/zenodo.6818823)
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The MIMIC Code Repository is intended to be a central hub for sharing, refining, and reusing code used for analysis of the [MIMIC critical care database](https://mimic.mit.edu). To find out more about MIMIC, please see: https://mimic.mit.edu. Source code for the website is in the [mimic-website GitHub repository](https://github.com/MIT-LCP/mimic-website/).
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If you use code or concepts available in this repository, we would be grateful if you would:
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- cite the dataset(s) you use as described in the PhysioNet project page: [MIMIC-III](https://physionet.org/content/mimiciii/), [MIMIC-IV](https://physionet.org/content/mimiciv/), [MIMIC-IV-ED](https://physionet.org/content/mimic-iv-ed/) , and/or [MIMIC-CXR](https://physionet.org/content/mimic-cxr/)
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- include a DOI for the code rather than a direct link to the GitHub repo, i.e. https://doi.org/10.5281/zenodo.821872
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- cite the Zenodo repository directly as it contains a static copy of the code. Be sure to select the release of MIMIC Code you used from the menu on the right side of the page on Zenodo: https://zenodo.org/record/6818823
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- cite the MIMIC code repository paper: [The MIMIC Code Repository: enabling reproducibility in critical care research](https://doi.org/10.1093/jamia/ocx084)
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```bibtex
@@ -66,7 +66,7 @@ If you use code or concepts available in this repository, we would be grateful i
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## Contributing
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Our team has worked hard to create and share the MIMIC dataset. We encourage you to share the code that you use for data processing and analysis. Sharing code helps to make studies reproducible and promotes collaborative research. To contribute, please:
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Our team has worked hard to create and share the MIMIC datasets. We encourage you to share the code that you use for data processing and analysis. Sharing code helps to make studies reproducible and promotes collaborative research. To contribute, please:
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* Fork the repository using the following link: https://github.com/MIT-LCP/mimic-code/fork. For a background on GitHub forks, see: https://help.github.com/articles/fork-a-repo/
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* Commit your changes to the forked repository.

‎mimic-iii/tests/requirements.txt‎

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numpy==1.18.1
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numpy==1.22.0
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pandas==1.0.3
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psycopg2==2.8.4
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python-dateutil==2.8.1

‎mimic-iv-ed/buildmimic/bigquery/schemas/ed/diagnosis.json‎

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[
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{
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"name": "subject_id",
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"type": "INT64",
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"mode": "REQUIRED"
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},
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{
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"name": "stay_id",
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"type": "INT64",
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"mode": "REQUIRED"
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},
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{
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"name": "seq_num",
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"type": "INT64",
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"mode": "REQUIRED"
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},
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{
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"name": "icd_code",
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"type": "STRING",
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"mode": "REQUIRED"
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},
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{
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"name": "icd_title",
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"type": "STRING",
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"mode": "REQUIRED"
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}
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]

‎mimic-iv-ed/buildmimic/bigquery/schemas/ed/edstays.json‎

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[
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{
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"name": "subject_id",
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"type": "INT64",
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"mode": "REQUIRED"
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},
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{
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"name": "hadm_id",
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"type": "INT64",
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"mode": "NULLABLE"
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},
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{
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"name": "stay_id",
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"type": "INT64",
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"mode": "REQUIRED"
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},
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{
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"name": "intime",
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"type": "DATETIME",
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"mode": "REQUIRED"
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},
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{
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"name": "outtime",
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"type": "DATETIME",
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"mode": "REQUIRED"
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},
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{
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"name": "gender",
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"type": "STRING",
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"mode": "REQUIRED"
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},
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{
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"name": "race",
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"type": "STRING",
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"mode": "NULLABLE"
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},
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{
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"name": "arrival_transport",
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"type": "STRING",
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"mode": "REQUIRED"
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},
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{
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"name": "disposition",
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"type": "STRING",
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"mode": "NULLABLE"
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}
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]

‎mimic-iv-ed/buildmimic/bigquery/schemas/ed/medrecon.json‎

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[
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{
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"name": "subject_id",
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"type": "INT64",
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"mode": "REQUIRED"
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},
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{
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"name": "stay_id",
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"type": "INT64",
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"mode": "REQUIRED"
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},
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{
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"name": "charttime",
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"type": "DATETIME",
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"mode": "NULLABLE"
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},
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{
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"name": "name",
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"type": "STRING",
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"mode": "NULLABLE"
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},
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{
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"name": "gsn",
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"type": "STRING",
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"mode": "NULLABLE"
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},
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{
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"name": "ndc",
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"type": "STRING",
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"mode": "NULLABLE"
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},
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{
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"name": "etc_rn",
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"type": "INT64",
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"mode": "NULLABLE"
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},
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{
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"name": "etccode",
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"type": "STRING",
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"mode": "NULLABLE"
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},
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{
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"name": "etcdescription",
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"type": "STRING",
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"mode": "NULLABLE"
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}
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]

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