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| # Config | |
| PHYSIONETURL=https://physionet.org/works/MIMICIIIClinicalDatabase/files/ | |
| # The following check whether values are passed via environment, set to defaults if not | |
| ifeq ($(DBNAME),) | |
| DBNAME := mimic | |
| endif | |
| ifeq ($(DBUSER),) | |
| DBUSER := postgres | |
| endif | |
| # Specify the password here | |
| # If you don't specify a password, then the role will not require one to login via password authentication | |
| #DBPASS= | |
| # Change "mimiciii" to specify a different schema | |
| DBSCHEMA := mimiciii | |
| # NOTE: you do not need to specify localhost/port | |
| # in fact, this is detrimental if you want to use peer authentication, as "localhost" is not strictly local | |
| #DBHOST := localhost | |
| #DBPORT := 5432 | |
| # when connecting, we use a single variable: DBSTRING | |
| # **do not modify this** | |
| # the create_mimic_user.sh script uses the above variables to create the DB/users | |
| # so it's important to keep this DBSTRING consistent | |
| DBSTRING := dbname=$(DBNAME) user=$(DBUSER) | |
| ifneq ($(DBHOST),) | |
| DBSTRING += host=$(DBHOST) | |
| endif | |
| ifneq ($(DBPORT),) | |
| DBSTRING += port=$(DBPORT) | |
| endif | |
| DBSTRING += options=--search_path=$(DBSCHEMA) | |
| help: | |
| @echo ' ' | |
| @echo '----------------------------------------------------------------------------' | |
| @echo 'Makefile for building MIMIC-III in a local Postgres database ' | |
| @echo ' ' | |
| @echo 'Usage: ' | |
| @echo ' ' | |
| @echo ' Build MIMIC-III using the CSV files in the /path/to/data directory - ' | |
| @echo ' ' | |
| @echo ' make mimic datadir="/path/to/data/" ' | |
| @echo ' ' | |
| @echo ' e.g. make mimic datadir="/data/mimic/v1_3/" ' | |
| @echo ' ' | |
| @echo ' Build MIMIC-III using the .csv.gz files in the /path/to/data directory - ' | |
| @echo ' ' | |
| @echo ' make mimic-gz datadir="/path/to/data/" ' | |
| @echo ' ' | |
| @echo ' e.g. make mimic-gz datadir="/data/mimic/v1_3/" ' | |
| @echo '----------------------------------------------------------------------------' | |
| @echo ' ' | |
| mimic-gz: mimic-check-gz create-user mimic-build-gz | |
| mimic: mimic-check create-user mimic-build | |
| create-user: | |
| @echo '------------------------' | |
| @echo '-- Building MIMIC-III --' | |
| @echo '------------------------' | |
| @echo '' | |
| @sleep 2 | |
| MIMIC_USER="$(DBUSER)" MIMIC_DB="$(DBNAME)" MIMIC_PASSWORD="$(DBPASS)" MIMIC_SCHEMA="$(DBSCHEMA)" ./create_mimic_user.sh | |
| mimic-build-gz: | |
| @echo '------------------------' | |
| @echo '-- Building MIMIC-III --' | |
| @echo '------------------------' | |
| @echo '' | |
| @echo '---------------------' | |
| @echo '-- Creating tables --' | |
| @echo '---------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_create_tables.sql | |
| @echo '' | |
| @echo '------------------' | |
| @echo '-- Loading data --' | |
| @echo '------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_load_data_gz.sql -v mimic_data_dir=${datadir} | |
| @echo '' | |
| @echo '--------------------' | |
| @echo '-- Adding indexes --' | |
| @echo '--------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_add_indexes.sql | |
| @echo '' | |
| @echo '--------------------' | |
| @echo '-- Adding comments --' | |
| @echo '--------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_add_comments.sql | |
| @echo '' | |
| @echo '----------------' | |
| @echo '-- Check data --' | |
| @echo '----------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_checks.sql | |
| mimic-build: | |
| @echo '------------------------' | |
| @echo '-- Building MIMIC-III --' | |
| @echo '------------------------' | |
| @echo '' | |
| @echo '---------------------' | |
| @echo '-- Creating tables --' | |
| @echo '---------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_create_tables.sql | |
| @echo '' | |
| @echo '------------------' | |
| @echo '-- Loading data --' | |
| @echo '------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_load_data.sql -v mimic_data_dir=${datadir} | |
| @echo '' | |
| @echo '--------------------' | |
| @echo '-- Adding indexes --' | |
| @echo '--------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_add_indexes.sql | |
| @echo '' | |
| @echo '--------------------' | |
| @echo '-- Adding comments --' | |
| @echo '--------------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_add_comments.sql | |
| @echo '' | |
| @echo '----------------' | |
| @echo '-- Check data --' | |
| @echo '----------------' | |
| @echo '' | |
| @sleep 2 | |
| psql "$(DBSTRING)" -f postgres_checks.sql | |
| mimic-download: | |
| @echo '------------------------------------------' | |
| @echo '-- Downloading MIMIC-III from PhysioNet --' | |
| @echo '------------------------------------------' | |
| @echo '' | |
| wget --user ${physionetuser} --ask-password -P ${datadir} -A csv.gz -m -p -E -k -K -np -nd "$(PHYSIONETURL)" | |
| #This is fairly inelegant and could be tidied with a for loop and an if to check for gzip, | |
| #but need to maintain compatability with Windows, which baffling lacks these things | |
| mimic-check-gz: | |
| @echo '' | |
| @echo '-----------------------' | |
| @echo '-- Checking for data --' | |
| @echo '-----------------------' | |
| @echo '' | |
| ifeq ("$(wildcard $(datadir)ADMISSIONS.csv.gz)","") | |
| @echo "Unable to find $(datadir)ADMISSIONS.csv.gz - exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CALLOUT.csv.gz)","") | |
| @echo "Unable to find $(datadir)CALLOUT.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CAREGIVERS.csv.gz)","") | |
| @echo "Unable to find $(datadir)CAREGIVERS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CHARTEVENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)CHARTEVENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CPTEVENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)CPTEVENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)DATETIMEEVENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)DATETIMEEVENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_CPT.csv.gz)","") | |
| @echo "Unable to find $(datadir)D_CPT.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)DIAGNOSES_ICD.csv.gz)","") | |
| @echo "Unable to find $(datadir)DIAGNOSES_ICD.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_ICD_DIAGNOSES.csv.gz)","") | |
| @echo "Unable to find $(datadir)D_ICD_DIAGNOSES.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_ICD_PROCEDURES.csv.gz)","") | |
| @echo "Unable to find $(datadir)D_ICD_PROCEDURES.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_ITEMS.csv.gz)","") | |
| @echo "Unable to find $(datadir)D_ITEMS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_LABITEMS.csv.gz)","") | |
| @echo "Unable to find $(datadir)D_LABITEMS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)DRGCODES.csv.gz)","") | |
| @echo "Unable to find $(datadir)DRGCODES.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)ICUSTAYS.csv.gz)","") | |
| @echo "Unable to find $(datadir)ICUSTAYS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)INPUTEVENTS_CV.csv.gz)","") | |
| @echo "Unable to find $(datadir)INPUTEVENTS_CV.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)INPUTEVENTS_MV.csv.gz)","") | |
| @echo "Unable to find $(datadir)INPUTEVENTS_MV.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)LABEVENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)LABEVENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)MICROBIOLOGYEVENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)MICROBIOLOGYEVENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)NOTEEVENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)NOTEEVENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)OUTPUTEVENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)OUTPUTEVENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PATIENTS.csv.gz)","") | |
| @echo "Unable to find $(datadir)PATIENTS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PRESCRIPTIONS.csv.gz)","") | |
| @echo "Unable to find $(datadir)PRESCRIPTIONS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PROCEDUREEVENTS_MV.csv.gz)","") | |
| @echo "Unable to find $(datadir)PROCEDUREEVENTS_MV.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PROCEDURES_ICD.csv.gz)","") | |
| @echo "Unable to find $(datadir)PROCEDURES_ICD.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)SERVICES.csv.gz)","") | |
| @echo "Unable to find $(datadir)SERVICES.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)TRANSFERS.csv.gz)","") | |
| @echo "Unable to find $(datadir)TRANSFERS.csv.gz. Exiting before build."; exit 1 | |
| endif | |
| @echo 'All data present!' | |
| @echo '' | |
| mimic-check: | |
| @echo '' | |
| @echo '-----------------------' | |
| @echo '-- Checking for data --' | |
| @echo '-----------------------' | |
| @echo '' | |
| ifeq ("$(wildcard $(datadir)ADMISSIONS.csv)","") | |
| @echo "Unable to find $(datadir)ADMISSIONS.csv - exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CALLOUT.csv)","") | |
| @echo "Unable to find $(datadir)CALLOUT.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CAREGIVERS.csv)","") | |
| @echo "Unable to find $(datadir)CAREGIVERS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CHARTEVENTS.csv)","") | |
| @echo "Unable to find $(datadir)CHARTEVENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)CPTEVENTS.csv)","") | |
| @echo "Unable to find $(datadir)CPTEVENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)DATETIMEEVENTS.csv)","") | |
| @echo "Unable to find $(datadir)DATETIMEEVENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_CPT.csv)","") | |
| @echo "Unable to find $(datadir)D_CPT.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)DIAGNOSES_ICD.csv)","") | |
| @echo "Unable to find $(datadir)DIAGNOSES_ICD.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_ICD_DIAGNOSES.csv)","") | |
| @echo "Unable to find $(datadir)D_ICD_DIAGNOSES.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_ICD_PROCEDURES.csv)","") | |
| @echo "Unable to find $(datadir)D_ICD_PROCEDURES.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_ITEMS.csv)","") | |
| @echo "Unable to find $(datadir)D_ITEMS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)D_LABITEMS.csv)","") | |
| @echo "Unable to find $(datadir)D_LABITEMS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)DRGCODES.csv)","") | |
| @echo "Unable to find $(datadir)DRGCODES.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)ICUSTAYS.csv)","") | |
| @echo "Unable to find $(datadir)ICUSTAYS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)INPUTEVENTS_CV.csv)","") | |
| @echo "Unable to find $(datadir)INPUTEVENTS_CV.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)INPUTEVENTS_MV.csv)","") | |
| @echo "Unable to find $(datadir)INPUTEVENTS_MV.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)LABEVENTS.csv)","") | |
| @echo "Unable to find $(datadir)LABEVENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)MICROBIOLOGYEVENTS.csv)","") | |
| @echo "Unable to find $(datadir)MICROBIOLOGYEVENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)NOTEEVENTS.csv)","") | |
| @echo "Unable to find $(datadir)NOTEEVENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)OUTPUTEVENTS.csv)","") | |
| @echo "Unable to find $(datadir)OUTPUTEVENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PATIENTS.csv)","") | |
| @echo "Unable to find $(datadir)PATIENTS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PRESCRIPTIONS.csv)","") | |
| @echo "Unable to find $(datadir)PRESCRIPTIONS.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PROCEDUREEVENTS_MV.csv)","") | |
| @echo "Unable to find $(datadir)PROCEDUREEVENTS_MV.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)PROCEDURES_ICD.csv)","") | |
| @echo "Unable to find $(datadir)PROCEDURES_ICD.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)SERVICES.csv)","") | |
| @echo "Unable to find $(datadir)SERVICES.csv. Exiting before build."; exit 1 | |
| endif | |
| ifeq ("$(wildcard $(datadir)TRANSFERS.csv)","") | |
| @echo "Unable to find $(datadir)TRANSFERS.csv. Exiting before build."; exit 1 | |
| endif | |
| @echo 'All data present!' | |
| @echo '' | |
| clean: | |
| @echo | |
| .PHONY: help mimic clean |