Skip to content

Commit 3443106

Browse files
alistairewjalistairewj
authored
Merge pull request #2068 from Chessing234/fix/481-makefile-datadir-spaces
Fix mimic-check for datadir paths with spaces
2 parents dbadfe8 + 3b55a4e commit 3443106

1 file changed

Lines changed: 56 additions & 160 deletions

File tree

‎mimic-iii/buildmimic/postgres/Makefile‎

Lines changed: 56 additions & 160 deletions
Original file line numberDiff line numberDiff line change
@@ -2,10 +2,10 @@
22
PHYSIONETURL=https://physionet.org/works/MIMICIIIClinicalDatabase/files/
33
PHYSIONETDEMOURL=https://physionet.org/works/MIMICIIIClinicalDatabaseDemo/
44

5-
# Ensure that datadir ends in a slash
6-
DATADIR := $(dir $(datadir))
7-
ifneq ($(datadir),$(DATADIR))
8-
DATADIR := $(datadir)/
5+
# Ensure that datadir ends in a slash (avoid $(dir)/wildcard — they break on spaces)
6+
DATADIR := $(datadir)
7+
ifeq ($(filter %/,$(DATADIR)),)
8+
DATADIR := $(DATADIR)/
99
endif
1010

1111

@@ -203,84 +203,32 @@ mimic-check-gz:
203203
@echo '-----------------------'
204204
@echo ''
205205
@echo 'Data path: ' $(DATADIR)
206-
ifeq ("$(wildcard $(DATADIR)ADMISSIONS.csv.gz)","")
207-
@echo "Unable to find $(DATADIR)ADMISSIONS.csv.gz - exiting before build."; exit 1
208-
endif
209-
ifeq ("$(wildcard $(DATADIR)CALLOUT.csv.gz)","")
210-
@echo "Unable to find $(DATADIR)CALLOUT.csv.gz. Exiting before build."; exit 1
211-
endif
212-
ifeq ("$(wildcard $(DATADIR)CAREGIVERS.csv.gz)","")
213-
@echo "Unable to find $(DATADIR)CAREGIVERS.csv.gz. Exiting before build."; exit 1
214-
endif
215-
ifeq ("$(wildcard $(DATADIR)CHARTEVENTS.csv.gz)","")
216-
@echo "Unable to find $(DATADIR)CHARTEVENTS.csv.gz. Exiting before build."; exit 1
217-
endif
218-
ifeq ("$(wildcard $(DATADIR)CPTEVENTS.csv.gz)","")
219-
@echo "Unable to find $(DATADIR)CPTEVENTS.csv.gz. Exiting before build."; exit 1
220-
endif
221-
ifeq ("$(wildcard $(DATADIR)DATETIMEEVENTS.csv.gz)","")
222-
@echo "Unable to find $(DATADIR)DATETIMEEVENTS.csv.gz. Exiting before build."; exit 1
223-
endif
224-
ifeq ("$(wildcard $(DATADIR)D_CPT.csv.gz)","")
225-
@echo "Unable to find $(DATADIR)D_CPT.csv.gz. Exiting before build."; exit 1
226-
endif
227-
ifeq ("$(wildcard $(DATADIR)DIAGNOSES_ICD.csv.gz)","")
228-
@echo "Unable to find $(DATADIR)DIAGNOSES_ICD.csv.gz. Exiting before build."; exit 1
229-
endif
230-
ifeq ("$(wildcard $(DATADIR)D_ICD_DIAGNOSES.csv.gz)","")
231-
@echo "Unable to find $(DATADIR)D_ICD_DIAGNOSES.csv.gz. Exiting before build."; exit 1
232-
endif
233-
ifeq ("$(wildcard $(DATADIR)D_ICD_PROCEDURES.csv.gz)","")
234-
@echo "Unable to find $(DATADIR)D_ICD_PROCEDURES.csv.gz. Exiting before build."; exit 1
235-
endif
236-
ifeq ("$(wildcard $(DATADIR)D_ITEMS.csv.gz)","")
237-
@echo "Unable to find $(DATADIR)D_ITEMS.csv.gz. Exiting before build."; exit 1
238-
endif
239-
ifeq ("$(wildcard $(DATADIR)D_LABITEMS.csv.gz)","")
240-
@echo "Unable to find $(DATADIR)D_LABITEMS.csv.gz. Exiting before build."; exit 1
241-
endif
242-
ifeq ("$(wildcard $(DATADIR)DRGCODES.csv.gz)","")
243-
@echo "Unable to find $(DATADIR)DRGCODES.csv.gz. Exiting before build."; exit 1
244-
endif
245-
ifeq ("$(wildcard $(DATADIR)ICUSTAYS.csv.gz)","")
246-
@echo "Unable to find $(DATADIR)ICUSTAYS.csv.gz. Exiting before build."; exit 1
247-
endif
248-
ifeq ("$(wildcard $(DATADIR)INPUTEVENTS_CV.csv.gz)","")
249-
@echo "Unable to find $(DATADIR)INPUTEVENTS_CV.csv.gz. Exiting before build."; exit 1
250-
endif
251-
ifeq ("$(wildcard $(DATADIR)INPUTEVENTS_MV.csv.gz)","")
252-
@echo "Unable to find $(DATADIR)INPUTEVENTS_MV.csv.gz. Exiting before build."; exit 1
253-
endif
254-
ifeq ("$(wildcard $(DATADIR)LABEVENTS.csv.gz)","")
255-
@echo "Unable to find $(DATADIR)LABEVENTS.csv.gz. Exiting before build."; exit 1
256-
endif
257-
ifeq ("$(wildcard $(DATADIR)MICROBIOLOGYEVENTS.csv.gz)","")
258-
@echo "Unable to find $(DATADIR)MICROBIOLOGYEVENTS.csv.gz. Exiting before build."; exit 1
259-
endif
260-
ifeq ("$(wildcard $(DATADIR)NOTEEVENTS.csv.gz)","")
261-
@echo "Unable to find $(DATADIR)NOTEEVENTS.csv.gz. Exiting before build."; exit 1
262-
endif
263-
ifeq ("$(wildcard $(DATADIR)OUTPUTEVENTS.csv.gz)","")
264-
@echo "Unable to find $(DATADIR)OUTPUTEVENTS.csv.gz. Exiting before build."; exit 1
265-
endif
266-
ifeq ("$(wildcard $(DATADIR)PATIENTS.csv.gz)","")
267-
@echo "Unable to find $(DATADIR)PATIENTS.csv.gz. Exiting before build."; exit 1
268-
endif
269-
ifeq ("$(wildcard $(DATADIR)PRESCRIPTIONS.csv.gz)","")
270-
@echo "Unable to find $(DATADIR)PRESCRIPTIONS.csv.gz. Exiting before build."; exit 1
271-
endif
272-
ifeq ("$(wildcard $(DATADIR)PROCEDUREEVENTS_MV.csv.gz)","")
273-
@echo "Unable to find $(DATADIR)PROCEDUREEVENTS_MV.csv.gz. Exiting before build."; exit 1
274-
endif
275-
ifeq ("$(wildcard $(DATADIR)PROCEDURES_ICD.csv.gz)","")
276-
@echo "Unable to find $(DATADIR)PROCEDURES_ICD.csv.gz. Exiting before build."; exit 1
277-
endif
278-
ifeq ("$(wildcard $(DATADIR)SERVICES.csv.gz)","")
279-
@echo "Unable to find $(DATADIR)SERVICES.csv.gz. Exiting before build."; exit 1
280-
endif
281-
ifeq ("$(wildcard $(DATADIR)TRANSFERS.csv.gz)","")
282-
@echo "Unable to find $(DATADIR)TRANSFERS.csv.gz. Exiting before build."; exit 1
283-
endif
206+
@test -f "$(DATADIR)ADMISSIONS.csv.gz" || (echo "Unable to find $(DATADIR)ADMISSIONS.csv.gz - exiting before build."; exit 1)
207+
@test -f "$(DATADIR)CALLOUT.csv.gz" || (echo "Unable to find $(DATADIR)CALLOUT.csv.gz. Exiting before build."; exit 1)
208+
@test -f "$(DATADIR)CAREGIVERS.csv.gz" || (echo "Unable to find $(DATADIR)CAREGIVERS.csv.gz. Exiting before build."; exit 1)
209+
@test -f "$(DATADIR)CHARTEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)CHARTEVENTS.csv.gz. Exiting before build."; exit 1)
210+
@test -f "$(DATADIR)CPTEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)CPTEVENTS.csv.gz. Exiting before build."; exit 1)
211+
@test -f "$(DATADIR)DATETIMEEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)DATETIMEEVENTS.csv.gz. Exiting before build."; exit 1)
212+
@test -f "$(DATADIR)D_CPT.csv.gz" || (echo "Unable to find $(DATADIR)D_CPT.csv.gz. Exiting before build."; exit 1)
213+
@test -f "$(DATADIR)DIAGNOSES_ICD.csv.gz" || (echo "Unable to find $(DATADIR)DIAGNOSES_ICD.csv.gz. Exiting before build."; exit 1)
214+
@test -f "$(DATADIR)D_ICD_DIAGNOSES.csv.gz" || (echo "Unable to find $(DATADIR)D_ICD_DIAGNOSES.csv.gz. Exiting before build."; exit 1)
215+
@test -f "$(DATADIR)D_ICD_PROCEDURES.csv.gz" || (echo "Unable to find $(DATADIR)D_ICD_PROCEDURES.csv.gz. Exiting before build."; exit 1)
216+
@test -f "$(DATADIR)D_ITEMS.csv.gz" || (echo "Unable to find $(DATADIR)D_ITEMS.csv.gz. Exiting before build."; exit 1)
217+
@test -f "$(DATADIR)D_LABITEMS.csv.gz" || (echo "Unable to find $(DATADIR)D_LABITEMS.csv.gz. Exiting before build."; exit 1)
218+
@test -f "$(DATADIR)DRGCODES.csv.gz" || (echo "Unable to find $(DATADIR)DRGCODES.csv.gz. Exiting before build."; exit 1)
219+
@test -f "$(DATADIR)ICUSTAYS.csv.gz" || (echo "Unable to find $(DATADIR)ICUSTAYS.csv.gz. Exiting before build."; exit 1)
220+
@test -f "$(DATADIR)INPUTEVENTS_CV.csv.gz" || (echo "Unable to find $(DATADIR)INPUTEVENTS_CV.csv.gz. Exiting before build."; exit 1)
221+
@test -f "$(DATADIR)INPUTEVENTS_MV.csv.gz" || (echo "Unable to find $(DATADIR)INPUTEVENTS_MV.csv.gz. Exiting before build."; exit 1)
222+
@test -f "$(DATADIR)LABEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)LABEVENTS.csv.gz. Exiting before build."; exit 1)
223+
@test -f "$(DATADIR)MICROBIOLOGYEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)MICROBIOLOGYEVENTS.csv.gz. Exiting before build."; exit 1)
224+
@test -f "$(DATADIR)NOTEEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)NOTEEVENTS.csv.gz. Exiting before build."; exit 1)
225+
@test -f "$(DATADIR)OUTPUTEVENTS.csv.gz" || (echo "Unable to find $(DATADIR)OUTPUTEVENTS.csv.gz. Exiting before build."; exit 1)
226+
@test -f "$(DATADIR)PATIENTS.csv.gz" || (echo "Unable to find $(DATADIR)PATIENTS.csv.gz. Exiting before build."; exit 1)
227+
@test -f "$(DATADIR)PRESCRIPTIONS.csv.gz" || (echo "Unable to find $(DATADIR)PRESCRIPTIONS.csv.gz. Exiting before build."; exit 1)
228+
@test -f "$(DATADIR)PROCEDUREEVENTS_MV.csv.gz" || (echo "Unable to find $(DATADIR)PROCEDUREEVENTS_MV.csv.gz. Exiting before build."; exit 1)
229+
@test -f "$(DATADIR)PROCEDURES_ICD.csv.gz" || (echo "Unable to find $(DATADIR)PROCEDURES_ICD.csv.gz. Exiting before build."; exit 1)
230+
@test -f "$(DATADIR)SERVICES.csv.gz" || (echo "Unable to find $(DATADIR)SERVICES.csv.gz. Exiting before build."; exit 1)
231+
@test -f "$(DATADIR)TRANSFERS.csv.gz" || (echo "Unable to find $(DATADIR)TRANSFERS.csv.gz. Exiting before build."; exit 1)
284232
@echo 'All data present!'
285233
@echo ''
286234

@@ -291,84 +239,32 @@ mimic-check:
291239
@echo '-----------------------'
292240
@echo ''
293241
@echo 'Data path: ' $(DATADIR)
294-
ifeq ("$(wildcard $(DATADIR)ADMISSIONS.csv)","")
295-
@echo "Unable to find $(DATADIR)ADMISSIONS.csv - exiting before build."; exit 1
296-
endif
297-
ifeq ("$(wildcard $(DATADIR)CALLOUT.csv)","")
298-
@echo "Unable to find $(DATADIR)CALLOUT.csv. Exiting before build."; exit 1
299-
endif
300-
ifeq ("$(wildcard $(DATADIR)CAREGIVERS.csv)","")
301-
@echo "Unable to find $(DATADIR)CAREGIVERS.csv. Exiting before build."; exit 1
302-
endif
303-
ifeq ("$(wildcard $(DATADIR)CHARTEVENTS.csv)","")
304-
@echo "Unable to find $(DATADIR)CHARTEVENTS.csv. Exiting before build."; exit 1
305-
endif
306-
ifeq ("$(wildcard $(DATADIR)CPTEVENTS.csv)","")
307-
@echo "Unable to find $(DATADIR)CPTEVENTS.csv. Exiting before build."; exit 1
308-
endif
309-
ifeq ("$(wildcard $(DATADIR)DATETIMEEVENTS.csv)","")
310-
@echo "Unable to find $(DATADIR)DATETIMEEVENTS.csv. Exiting before build."; exit 1
311-
endif
312-
ifeq ("$(wildcard $(DATADIR)D_CPT.csv)","")
313-
@echo "Unable to find $(DATADIR)D_CPT.csv. Exiting before build."; exit 1
314-
endif
315-
ifeq ("$(wildcard $(DATADIR)DIAGNOSES_ICD.csv)","")
316-
@echo "Unable to find $(DATADIR)DIAGNOSES_ICD.csv. Exiting before build."; exit 1
317-
endif
318-
ifeq ("$(wildcard $(DATADIR)D_ICD_DIAGNOSES.csv)","")
319-
@echo "Unable to find $(DATADIR)D_ICD_DIAGNOSES.csv. Exiting before build."; exit 1
320-
endif
321-
ifeq ("$(wildcard $(DATADIR)D_ICD_PROCEDURES.csv)","")
322-
@echo "Unable to find $(DATADIR)D_ICD_PROCEDURES.csv. Exiting before build."; exit 1
323-
endif
324-
ifeq ("$(wildcard $(DATADIR)D_ITEMS.csv)","")
325-
@echo "Unable to find $(DATADIR)D_ITEMS.csv. Exiting before build."; exit 1
326-
endif
327-
ifeq ("$(wildcard $(DATADIR)D_LABITEMS.csv)","")
328-
@echo "Unable to find $(DATADIR)D_LABITEMS.csv. Exiting before build."; exit 1
329-
endif
330-
ifeq ("$(wildcard $(DATADIR)DRGCODES.csv)","")
331-
@echo "Unable to find $(DATADIR)DRGCODES.csv. Exiting before build."; exit 1
332-
endif
333-
ifeq ("$(wildcard $(DATADIR)ICUSTAYS.csv)","")
334-
@echo "Unable to find $(DATADIR)ICUSTAYS.csv. Exiting before build."; exit 1
335-
endif
336-
ifeq ("$(wildcard $(DATADIR)INPUTEVENTS_CV.csv)","")
337-
@echo "Unable to find $(DATADIR)INPUTEVENTS_CV.csv. Exiting before build."; exit 1
338-
endif
339-
ifeq ("$(wildcard $(DATADIR)INPUTEVENTS_MV.csv)","")
340-
@echo "Unable to find $(DATADIR)INPUTEVENTS_MV.csv. Exiting before build."; exit 1
341-
endif
342-
ifeq ("$(wildcard $(DATADIR)LABEVENTS.csv)","")
343-
@echo "Unable to find $(DATADIR)LABEVENTS.csv. Exiting before build."; exit 1
344-
endif
345-
ifeq ("$(wildcard $(DATADIR)MICROBIOLOGYEVENTS.csv)","")
346-
@echo "Unable to find $(DATADIR)MICROBIOLOGYEVENTS.csv. Exiting before build."; exit 1
347-
endif
348-
ifeq ("$(wildcard $(DATADIR)NOTEEVENTS.csv)","")
349-
@echo "Unable to find $(DATADIR)NOTEEVENTS.csv. Exiting before build."; exit 1
350-
endif
351-
ifeq ("$(wildcard $(DATADIR)OUTPUTEVENTS.csv)","")
352-
@echo "Unable to find $(DATADIR)OUTPUTEVENTS.csv. Exiting before build."; exit 1
353-
endif
354-
ifeq ("$(wildcard $(DATADIR)PATIENTS.csv)","")
355-
@echo "Unable to find $(DATADIR)PATIENTS.csv. Exiting before build."; exit 1
356-
endif
357-
ifeq ("$(wildcard $(DATADIR)PRESCRIPTIONS.csv)","")
358-
@echo "Unable to find $(DATADIR)PRESCRIPTIONS.csv. Exiting before build."; exit 1
359-
endif
360-
ifeq ("$(wildcard $(DATADIR)PROCEDUREEVENTS_MV.csv)","")
361-
@echo "Unable to find $(DATADIR)PROCEDUREEVENTS_MV.csv. Exiting before build."; exit 1
362-
endif
363-
ifeq ("$(wildcard $(DATADIR)PROCEDURES_ICD.csv)","")
364-
@echo "Unable to find $(DATADIR)PROCEDURES_ICD.csv. Exiting before build."; exit 1
365-
endif
366-
ifeq ("$(wildcard $(DATADIR)SERVICES.csv)","")
367-
@echo "Unable to find $(DATADIR)SERVICES.csv. Exiting before build."; exit 1
368-
endif
369-
ifeq ("$(wildcard $(DATADIR)TRANSFERS.csv)","")
370-
@echo "Unable to find $(DATADIR)TRANSFERS.csv. Exiting before build."; exit 1
371-
endif
242+
@test -f "$(DATADIR)ADMISSIONS.csv" || (echo "Unable to find $(DATADIR)ADMISSIONS.csv - exiting before build."; exit 1)
243+
@test -f "$(DATADIR)CALLOUT.csv" || (echo "Unable to find $(DATADIR)CALLOUT.csv. Exiting before build."; exit 1)
244+
@test -f "$(DATADIR)CAREGIVERS.csv" || (echo "Unable to find $(DATADIR)CAREGIVERS.csv. Exiting before build."; exit 1)
245+
@test -f "$(DATADIR)CHARTEVENTS.csv" || (echo "Unable to find $(DATADIR)CHARTEVENTS.csv. Exiting before build."; exit 1)
246+
@test -f "$(DATADIR)CPTEVENTS.csv" || (echo "Unable to find $(DATADIR)CPTEVENTS.csv. Exiting before build."; exit 1)
247+
@test -f "$(DATADIR)DATETIMEEVENTS.csv" || (echo "Unable to find $(DATADIR)DATETIMEEVENTS.csv. Exiting before build."; exit 1)
248+
@test -f "$(DATADIR)D_CPT.csv" || (echo "Unable to find $(DATADIR)D_CPT.csv. Exiting before build."; exit 1)
249+
@test -f "$(DATADIR)DIAGNOSES_ICD.csv" || (echo "Unable to find $(DATADIR)DIAGNOSES_ICD.csv. Exiting before build."; exit 1)
250+
@test -f "$(DATADIR)D_ICD_DIAGNOSES.csv" || (echo "Unable to find $(DATADIR)D_ICD_DIAGNOSES.csv. Exiting before build."; exit 1)
251+
@test -f "$(DATADIR)D_ICD_PROCEDURES.csv" || (echo "Unable to find $(DATADIR)D_ICD_PROCEDURES.csv. Exiting before build."; exit 1)
252+
@test -f "$(DATADIR)D_ITEMS.csv" || (echo "Unable to find $(DATADIR)D_ITEMS.csv. Exiting before build."; exit 1)
253+
@test -f "$(DATADIR)D_LABITEMS.csv" || (echo "Unable to find $(DATADIR)D_LABITEMS.csv. Exiting before build."; exit 1)
254+
@test -f "$(DATADIR)DRGCODES.csv" || (echo "Unable to find $(DATADIR)DRGCODES.csv. Exiting before build."; exit 1)
255+
@test -f "$(DATADIR)ICUSTAYS.csv" || (echo "Unable to find $(DATADIR)ICUSTAYS.csv. Exiting before build."; exit 1)
256+
@test -f "$(DATADIR)INPUTEVENTS_CV.csv" || (echo "Unable to find $(DATADIR)INPUTEVENTS_CV.csv. Exiting before build."; exit 1)
257+
@test -f "$(DATADIR)INPUTEVENTS_MV.csv" || (echo "Unable to find $(DATADIR)INPUTEVENTS_MV.csv. Exiting before build."; exit 1)
258+
@test -f "$(DATADIR)LABEVENTS.csv" || (echo "Unable to find $(DATADIR)LABEVENTS.csv. Exiting before build."; exit 1)
259+
@test -f "$(DATADIR)MICROBIOLOGYEVENTS.csv" || (echo "Unable to find $(DATADIR)MICROBIOLOGYEVENTS.csv. Exiting before build."; exit 1)
260+
@test -f "$(DATADIR)NOTEEVENTS.csv" || (echo "Unable to find $(DATADIR)NOTEEVENTS.csv. Exiting before build."; exit 1)
261+
@test -f "$(DATADIR)OUTPUTEVENTS.csv" || (echo "Unable to find $(DATADIR)OUTPUTEVENTS.csv. Exiting before build."; exit 1)
262+
@test -f "$(DATADIR)PATIENTS.csv" || (echo "Unable to find $(DATADIR)PATIENTS.csv. Exiting before build."; exit 1)
263+
@test -f "$(DATADIR)PRESCRIPTIONS.csv" || (echo "Unable to find $(DATADIR)PRESCRIPTIONS.csv. Exiting before build."; exit 1)
264+
@test -f "$(DATADIR)PROCEDUREEVENTS_MV.csv" || (echo "Unable to find $(DATADIR)PROCEDUREEVENTS_MV.csv. Exiting before build."; exit 1)
265+
@test -f "$(DATADIR)PROCEDURES_ICD.csv" || (echo "Unable to find $(DATADIR)PROCEDURES_ICD.csv. Exiting before build."; exit 1)
266+
@test -f "$(DATADIR)SERVICES.csv" || (echo "Unable to find $(DATADIR)SERVICES.csv. Exiting before build."; exit 1)
267+
@test -f "$(DATADIR)TRANSFERS.csv" || (echo "Unable to find $(DATADIR)TRANSFERS.csv. Exiting before build."; exit 1)
372268
@echo 'All data present!'
373269
@echo ''
374270

0 commit comments

Comments
 (0)