Skip to content

Fix mimic-check for datadir paths with spaces #2068

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Chessing234 wants to merge 1 commit into
base: main
Choose a base branch
from
+56 −160
Open

Fix mimic-check for datadir paths with spaces #2068

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
216 changes: 56 additions & 160 deletions mimic-iii/buildmimic/postgres/Makefile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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


Expand Down Expand Up @@ -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 ''

Expand All @@ -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 ''

Expand Down
Loading