diff --git a/mimic-iii/buildmimic/postgres/Makefile b/mimic-iii/buildmimic/postgres/Makefile index a01f97b57..17ea42e20 100644 --- a/mimic-iii/buildmimic/postgres/Makefile +++ b/mimic-iii/buildmimic/postgres/Makefile @@ -2,10 +2,10 @@ PHYSIONETURL=https://physionet.org/works/MIMICIIIClinicalDatabase/files/ PHYSIONETDEMOURL=https://physionet.org/works/MIMICIIIClinicalDatabaseDemo/ -# Ensure that datadir ends in a slash -DATADIR := $(dir $(datadir)) -ifneq ($(datadir),$(DATADIR)) -DATADIR := $(datadir)/ +# Ensure that datadir ends in a slash (avoid $(dir)/wildcard — they break on spaces) +DATADIR := $(datadir) +ifeq ($(filter %/,$(DATADIR)),) +DATADIR := $(DATADIR)/ endif @@ -203,84 +203,32 @@ mimic-check-gz: @echo '-----------------------' @echo '' @echo 'Data path: ' $(DATADIR) -ifeq ("$(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 $(DATADIR)TRANSFERS.csv.gz. Exiting before build."; exit 1 -endif + @test -f "$(DATADIR)ADMISSIONS.csv.gz" || (echo "Unable to find $(DATADIR)ADMISSIONS.csv.gz - exiting before build."; exit 1) + @test -f "$(DATADIR)CALLOUT.csv.gz" || (echo "Unable to find $(DATADIR)CALLOUT.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)CAREGIVERS.csv.gz" || (echo "Unable to find $(DATADIR)CAREGIVERS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)CHARTEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)CHARTEVENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)CPTEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)CPTEVENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)DATETIMEEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)DATETIMEEVENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_CPT.csv.gz" || (echo "Unable to find $(DATADIR)D_CPT.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)DIAGNOSES_ICD.csv.gz" || (echo "Unable to find $(DATADIR)DIAGNOSES_ICD.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_ICD_DIAGNOSES.csv.gz" || (echo "Unable to find $(DATADIR)D_ICD_DIAGNOSES.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_ICD_PROCEDURES.csv.gz" || (echo "Unable to find $(DATADIR)D_ICD_PROCEDURES.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_ITEMS.csv.gz" || (echo "Unable to find $(DATADIR)D_ITEMS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_LABITEMS.csv.gz" || (echo "Unable to find $(DATADIR)D_LABITEMS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)DRGCODES.csv.gz" || (echo "Unable to find $(DATADIR)DRGCODES.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)ICUSTAYS.csv.gz" || (echo "Unable to find $(DATADIR)ICUSTAYS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)INPUTEVENTS_CV.csv.gz" || (echo "Unable to find $(DATADIR)INPUTEVENTS_CV.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)INPUTEVENTS_MV.csv.gz" || (echo "Unable to find $(DATADIR)INPUTEVENTS_MV.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)LABEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)LABEVENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)MICROBIOLOGYEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)MICROBIOLOGYEVENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)NOTEEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)NOTEEVENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)OUTPUTEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)OUTPUTEVENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)PATIENTS.csv.gz" || (echo "Unable to find $(DATADIR)PATIENTS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)PRESCRIPTIONS.csv.gz" || (echo "Unable to find $(DATADIR)PRESCRIPTIONS.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)PROCEDUREEVENTS_MV.csv.gz" || (echo "Unable to find $(DATADIR)PROCEDUREEVENTS_MV.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)PROCEDURES_ICD.csv.gz" || (echo "Unable to find $(DATADIR)PROCEDURES_ICD.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)SERVICES.csv.gz" || (echo "Unable to find $(DATADIR)SERVICES.csv.gz. Exiting before build."; exit 1) + @test -f "$(DATADIR)TRANSFERS.csv.gz" || (echo "Unable to find $(DATADIR)TRANSFERS.csv.gz. Exiting before build."; exit 1) @echo 'All data present!' @echo '' @@ -291,84 +239,32 @@ mimic-check: @echo '-----------------------' @echo '' @echo 'Data path: ' $(DATADIR) -ifeq ("$(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 $(DATADIR)TRANSFERS.csv. Exiting before build."; exit 1 -endif + @test -f "$(DATADIR)ADMISSIONS.csv" || (echo "Unable to find $(DATADIR)ADMISSIONS.csv - exiting before build."; exit 1) + @test -f "$(DATADIR)CALLOUT.csv" || (echo "Unable to find $(DATADIR)CALLOUT.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)CAREGIVERS.csv" || (echo "Unable to find $(DATADIR)CAREGIVERS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)CHARTEVENTS.csv" || (echo "Unable to find $(DATADIR)CHARTEVENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)CPTEVENTS.csv" || (echo "Unable to find $(DATADIR)CPTEVENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)DATETIMEEVENTS.csv" || (echo "Unable to find $(DATADIR)DATETIMEEVENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_CPT.csv" || (echo "Unable to find $(DATADIR)D_CPT.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)DIAGNOSES_ICD.csv" || (echo "Unable to find $(DATADIR)DIAGNOSES_ICD.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_ICD_DIAGNOSES.csv" || (echo "Unable to find $(DATADIR)D_ICD_DIAGNOSES.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_ICD_PROCEDURES.csv" || (echo "Unable to find $(DATADIR)D_ICD_PROCEDURES.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_ITEMS.csv" || (echo "Unable to find $(DATADIR)D_ITEMS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)D_LABITEMS.csv" || (echo "Unable to find $(DATADIR)D_LABITEMS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)DRGCODES.csv" || (echo "Unable to find $(DATADIR)DRGCODES.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)ICUSTAYS.csv" || (echo "Unable to find $(DATADIR)ICUSTAYS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)INPUTEVENTS_CV.csv" || (echo "Unable to find $(DATADIR)INPUTEVENTS_CV.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)INPUTEVENTS_MV.csv" || (echo "Unable to find $(DATADIR)INPUTEVENTS_MV.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)LABEVENTS.csv" || (echo "Unable to find $(DATADIR)LABEVENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)MICROBIOLOGYEVENTS.csv" || (echo "Unable to find $(DATADIR)MICROBIOLOGYEVENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)NOTEEVENTS.csv" || (echo "Unable to find $(DATADIR)NOTEEVENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)OUTPUTEVENTS.csv" || (echo "Unable to find $(DATADIR)OUTPUTEVENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)PATIENTS.csv" || (echo "Unable to find $(DATADIR)PATIENTS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)PRESCRIPTIONS.csv" || (echo "Unable to find $(DATADIR)PRESCRIPTIONS.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)PROCEDUREEVENTS_MV.csv" || (echo "Unable to find $(DATADIR)PROCEDUREEVENTS_MV.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)PROCEDURES_ICD.csv" || (echo "Unable to find $(DATADIR)PROCEDURES_ICD.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)SERVICES.csv" || (echo "Unable to find $(DATADIR)SERVICES.csv. Exiting before build."; exit 1) + @test -f "$(DATADIR)TRANSFERS.csv" || (echo "Unable to find $(DATADIR)TRANSFERS.csv. Exiting before build."; exit 1) @echo 'All data present!' @echo ''