Project

General

Profile

1 783 aaronmk
##### Configuration
2
3 1921 aaronmk
# Command line
4 1190 aaronmk
log ?= $(if $(test),,1)
5 1257 aaronmk
profile ?=
6 1620 aaronmk
reverify ?= 1
7 1921 aaronmk
debug ?=
8
9
# Makefile
10
tablesSort ?= plots organisms stems specimens
11 1386 aaronmk
exts ?= csv tsv txt xml
12 783 aaronmk
test_n ?= 2
13
14
##### Vars/functions
15
16 640 aaronmk
selfDir_uZPPqC := $(dir $(lastword $(MAKEFILE_LIST)))
17 250 aaronmk
18 1821 aaronmk
# Paths
19
datasrc := $(notdir $(realpath .))
20
root := $(selfDir_uZPPqC)..
21
bin := $(root)/bin
22
mappings := $(root)/mappings
23
24 368 aaronmk
# Make
25 640 aaronmk
SHELL := /bin/bash
26 1509 aaronmk
selfMake = $(MAKE) --makefile=../input.Makefile
27 1821 aaronmk
subMake = $(MAKE) $(@:$(root)/%=%) --directory=$(root)
28 404 aaronmk
+_ = $(+:_%=)
29 368 aaronmk
addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
30
31 1742 aaronmk
# OS
32
os := $(shell uname)
33
forOs = $(patsubst %,%-$(filter Linux Darwin,$(os)),$(1))
34
35
# Formatting
36
SED = sed -$(if $(filter Darwin,$(os)),E,r)
37
38 790 aaronmk
# System
39
date = $(shell date +"%Y-%m-%d-%H-%M-%S")
40
41 640 aaronmk
# Terminal
42 1184 aaronmk
termCols := $(shell tput cols)
43 640 aaronmk
esc := '['
44
reset := $(esc)'0m'
45
emph := $(esc)'7m '
46
endEmph := ' '$(reset)
47
48 368 aaronmk
# Commands
49 1245 aaronmk
MKDIR = mkdir -p
50
mkdir = $(MKDIR) $(@D)
51 395 aaronmk
CP = cp -p
52 1184 aaronmk
diff = diff --unified=2
53
diffVerbose = $(if $(verbose),diff --side-by-side --left-column\
54
--width=$(termCols),$(diff))
55 368 aaronmk
56 1918 aaronmk
# BIEN commands
57 1524 aaronmk
selfMap = $(bin)/cols 0 0
58 1081 aaronmk
psqlOpts := --set ON_ERROR_STOP=1 --quiet
59 1289 aaronmk
psqlAsBien := $(bin)/psql_vegbien $(psqlOpts)
60 353 aaronmk
61 1594 aaronmk
# SVN
62
addDir = $(if $(wildcard $(1)/),svn add --depth=empty $(1),svn mkdir $(1))
63 1771 aaronmk
setSvnIgnore = svn propset svn:ignore $(2) $(1)
64 1594 aaronmk
define addDirWithIgnore
65
$(addDir)
66 1771 aaronmk
$(setSvnIgnore)
67 1594 aaronmk
endef
68
69 783 aaronmk
##### General targets
70 250 aaronmk
71 418 aaronmk
all: _always maps ;
72 247 aaronmk
73 1260 aaronmk
.SUFFIXES: # turn off built-in suffix rules
74
.SECONDARY: # don't automatically delete intermediate files
75 1354 aaronmk
.DELETE_ON_ERROR: # delete target if recipe fails
76 247 aaronmk
77 383 aaronmk
_always:
78
.PHONY: _always
79 250 aaronmk
80 383 aaronmk
clean: _always
81 256 aaronmk
	$(RM) $(all)
82
83 1742 aaronmk
remake: _always clean
84
	+$(selfMake)
85
# re-run make so that cache of existing files is reset
86
87 1627 aaronmk
make_script = ./$< >$@
88 368 aaronmk
89 1604 aaronmk
%/: % _always ;
90
91 1627 aaronmk
# Must come before `%: %.make` to override it
92
src/%: src/%.make _always
93 1663 aaronmk
	(set -x; $(make_script)) 2>>$<.log
94 1627 aaronmk
.PRECIOUS: src/% # save partial outputs of aborted src make scripts
95
96
%: %.make _always
97
	$(make_script)
98
99 783 aaronmk
##### SVN
100 250 aaronmk
101 1594 aaronmk
add: _always
102 1771 aaronmk
	$(call setSvnIgnore,.,$$'')
103 1594 aaronmk
	$(call addDirWithIgnore,src,$$'*')
104
	$(call addDirWithIgnore,maps,$$'.~*')
105
	$(call addDirWithIgnore,import,$$'*')
106
	$(call addDirWithIgnore,test,$$'*.out\n*.xml')
107
	$(call addDirWithIgnore,verify,$$'*.out')
108 766 aaronmk
109 1955 aaronmk
##### Sources
110
111
inputFiles := $(wildcard $(exts:%=src/*.%))
112
ifeq ($(inputFiles),)
113
dbExport := $(firstword $(wildcard src/db.*.sql))
114
endif
115
116
srcs = $(shell $(bin)/sort_filenames $(wildcard $(exts:%=src/*.$*.%)))
117
isCsv = $(if $(srcs),$(if $(filter %.xml,$(srcs)),,1))
118
    # true if $(srcs) non-empty and contains no *.xml
119
catSrcs = $(bin)/cat$(if $(isCsv),_csv) $(srcs)
120
withCatSrcs = $(catSrcs:$(bin)/%=$(bin)/with_%) --
121
122
# Usage: `make {--silent|-s} cat` (removes echoed make commands)
123
cat: $(addprefix cat-,$(tables)) _always ;
124
125
cat-%: _always
126
	$(catSrcs)
127
128 1777 aaronmk
##### Existing maps discovery
129 1776 aaronmk
130 1289 aaronmk
srcMap := maps/src.%.csv
131 1139 aaronmk
fullViaMap := maps/%.full.csv
132 1289 aaronmk
directMap := maps/VegBIEN.%.csv
133
allViaMaps := $(filter-out $(srcMap) $(fullViaMap) $(directMap),\
134 1139 aaronmk
$(wildcard maps/*.csv))
135 728 aaronmk
via := $(firstword $(sort $(basename $(basename $(notdir $(allViaMaps))))))
136 783 aaronmk
137 775 aaronmk
coreMap := $(mappings)/$(via)-VegBIEN.%.csv
138 1524 aaronmk
coreSelfMap := $(mappings)/$(via).self.%.csv
139 783 aaronmk
140 749 aaronmk
viaMaps := $(wildcard $(tablesSort:%=maps/$(via).%.csv))
141 1139 aaronmk
viaMaps += $(filter-out $(viaMaps) $(fullViaMap),$(wildcard maps/$(via).*.csv))
142 783 aaronmk
143 728 aaronmk
autogenMaps := $(subst $(via).,VegBIEN.,$(viaMaps))
144
directMaps := $(autogenMaps) $(filter-out $(autogenMaps),\
145
$(wildcard maps/VegBIEN.*.csv))
146 772 aaronmk
tables := $(directMaps:maps/VegBIEN.%.csv=%)
147 728 aaronmk
148 1921 aaronmk
##### Installation
149
150
install: _always src/install import/install ;
151
152
uninstall: _always import/uninstall src/uninstall ;
153
154
reinstall: _always uninstall install ;
155
156
##### Staging tables
157
158
import/install: _always import/schema $(addprefix import/install-,$(tables)) ;
159
160
import/uninstall: _always import/rm_schema ;
161
# rm_schema will also drop all staging tables
162
163
import/schema: _always
164
	-echo 'CREATE SCHEMA "$(datasrc)";'|$(psqlAsBien)
165
# ignore errors if schema exists
166
167
import/rm_schema: _always
168
	echo 'DROP SCHEMA IF EXISTS "$(datasrc)" CASCADE;'|$(psqlAsBien)
169
170
import/install-%: _always
171 1955 aaronmk
	$(if $(isCsv),$(import_install_))
172
import_install_ = (prefix=; . $(bin)/vegbien_dest; "time" env schema=$(datasrc)\
173 1954 aaronmk
table=$* $(bin)/csv2db $(catSrcs)$(if $(log), &>import/install.log))
174 1921 aaronmk
175 1777 aaronmk
##### Maps building
176
177 1789 aaronmk
# Maps to (try to) build are added to one of these
178 1779 aaronmk
maps :=
179 1789 aaronmk
createOnlyMaps :=
180 1779 aaronmk
181 1775 aaronmk
srcMaps := $(wildcard maps/src.*.csv)
182 1289 aaronmk
183 1931 aaronmk
mkSrcMap = $(catSrcs)|env datasrc=$(datasrc) $(bin)/src_map >$@
184 1779 aaronmk
185
# Autogen src maps with known table names
186
maps/src.%.csv: # no prereqs so only built if doesn't exist
187 1955 aaronmk
	$(if $(isCsv),$(mkSrcMap))
188 1779 aaronmk
# only build if CSV srcs exist for that table name
189
# Try all table names
190 1789 aaronmk
createOnlyMaps += $(tablesSort:%=maps/src.%.csv)
191 1779 aaronmk
192 1273 aaronmk
# Must come before $(root)/% to override it
193 1524 aaronmk
$(coreSelfMap): _always
194 1273 aaronmk
	-+$(subMake)
195 1524 aaronmk
# ignore errors if $(coreSelfMap) does not exist
196 1273 aaronmk
197 1509 aaronmk
# Via maps cleanup
198
ifneq ($(filter maps/.%.last_cleanup,$(MAKECMDGOALS)),)
199 1787 aaronmk
maps/.$(via).%.csv.last_cleanup: maps/$(via).%.csv $(coreMap)
200 1790 aaronmk
	$(bin)/in_place $< env ignore=1 $(bin)/subtract $(word 2,$+) 0 1
201 1509 aaronmk
	touch $@
202
else
203
$(viaMaps): _always
204
	$(selfMake) $(@:maps/%=maps/.%.last_cleanup)
205
endif
206 1273 aaronmk
207 1526 aaronmk
joinSrcMap = $(if $(wildcard maps/src.$*.csv),$(bin)/in_place $@\
208
$(bin)/intersect maps/src.$*.csv 0)
209
210 1273 aaronmk
makeFullCsv = $(if $(shell test -e $(word 2,$+) && echo t),\
211 1817 aaronmk
env ignore=1 $(bin)/union <$+|,<$< )$(bin)/sort_map >$@
212 1524 aaronmk
# can't use $(wildcard) because it won't recheck file after $(coreSelfMap) runs
213 1273 aaronmk
214 1524 aaronmk
maps/$(via).%.full.csv: maps/$(via).%.csv $(coreSelfMap)
215 1273 aaronmk
	$(makeFullCsv)
216 1526 aaronmk
	$(joinSrcMap)
217 1139 aaronmk
maps += $(patsubst maps/%.csv,maps/%.full.csv,$(viaMaps))
218
219 1530 aaronmk
maps/VegBIEN.%.csv: maps/$(via).%.full.csv $(coreMap)
220
	$(bin)/join <$+|$(bin)/sort_map >$@
221
maps += $(autogenMaps)
222
223 1789 aaronmk
maps: $(createOnlyMaps) $(maps) _always ;
224 1139 aaronmk
225
all += $(maps)
226
227 1742 aaronmk
##### Maps validation
228
229
missing_mappings: _always missing_join_mappings missing_input_mappings ;
230
231
missing_%_mappings: _always # stem is one of join|input
232
	@echo $(emph)"Missing $* mappings:"$(endEmph)
233
	@+$(selfMake) remake 2>&1\
234 1800 aaronmk
|$(SED) -n 's/^.*No.* $* mapping for ([0-9A-Za-z_-]+).*$$/\1/p'\
235 1742 aaronmk
$(if $(filter join,$*),|$(bin)/ucase_first 0)|sort|uniq
236
237 1509 aaronmk
##### External dependencies
238
239
$(root)/%: _always
240
	+$(subMake)
241 1628 aaronmk
.PRECIOUS: $(root)/% # let ext. dir's Makefile decide whether to delete on error
242 1509 aaronmk
243 783 aaronmk
##### Mapping
244 368 aaronmk
245 775 aaronmk
+maps = $(filter maps/% $(mappings)/%,$(+_))
246 1451 aaronmk
<in = $(firstword $(filter-out $(+maps),$(+_)))
247
map = $(if $(<in),<$(<in),\
248 1777 aaronmk
$(if $(srcs),$(withCatSrcs),\
249 1451 aaronmk
$(if $(mapEnv),env $(mapEnv),\
250
$(error No input file src/*.$*.{$(exts)}))))\
251
$(root)/map $(+maps)
252 772 aaronmk
map2db = env out_database=vegbien $(map)
253 368 aaronmk
254 783 aaronmk
##### Import to VegBIEN
255 772 aaronmk
256 1378 aaronmk
ifneq ($(dbExport)$(inputFiles),)
257 772 aaronmk
258 1853 aaronmk
profileTest = $(if $(profile),$(if $(test),1))
259
profileOnly = -env profile_to=/dev/fd/3 $(map2db) 3>&1 1>&2|\
260
$(bin)/profile_stats /dev/fd/0
261
262 1594 aaronmk
log_ = import/$*$(if $(n),.n=$(n),).$(date).log
263 1190 aaronmk
trace = $(log_:.log=.trace)
264 1853 aaronmk
import = -$(if $(profileTest),$(profileOnly),(set -x; "time" env commit=1\
265 1190 aaronmk
$(if $(profile),profile_to=$(trace)) $(map2db)) $(if $(log),\
266 1853 aaronmk
$(if $(n),,>>$(log_))) 2>&1$(if $(log),$(if $(n),|tee -a $(log_))))
267 1088 aaronmk
# don't abort on import errors, which often relate to invalid input data
268 624 aaronmk
269 1193 aaronmk
import: $(addprefix import-,$(tables)) _always ;
270 718 aaronmk
271
import-%: maps/VegBIEN.%.csv _always
272
	$(import)
273 772 aaronmk
# default:
274
import-%: _always ;
275 718 aaronmk
276 772 aaronmk
else
277
import: _always ;
278
endif
279
280 790 aaronmk
##### Log files from import
281
282 1594 aaronmk
logs := $(wildcard import/*.log import/*.trace)
283 339 aaronmk
284 383 aaronmk
rm_logs: _always
285 339 aaronmk
	$(RM) $(logs)
286
287 783 aaronmk
##### Verification of import
288 264 aaronmk
289 1194 aaronmk
verify: $(addprefix verify-,$(tables)) _always ;
290
291 1199 aaronmk
verify-%: verify/%.ref verify/%.out _always
292 1184 aaronmk
	-$(diffVerbose) $(+_)
293 1088 aaronmk
# don't abort on verification errors, which are expected during development
294 1194 aaronmk
# default:
295 1199 aaronmk
verify-%: verify/%.out _always
296 1200 aaronmk
	$(if $(shell test -e $< && echo t),cat $<)
297 1199 aaronmk
# don't run if verify/%.out's default do-nothing action was used
298 1200 aaronmk
# can't use $(wildcard) because it won't recheck file after verify/%.out is run
299 368 aaronmk
300 1620 aaronmk
verify = $(if $(reverify),"time" $(psqlAsBien) --set=datasource="'$(datasrc)'"\
301
--no-align --field-separator=$$'\t' --pset=footer=off --pset=null=NULL <$< >$@)
302 514 aaronmk
303 1199 aaronmk
verify/%.out: $(mappings)/verify.%.sql _always
304 1192 aaronmk
	$(verify)
305 1194 aaronmk
# default:
306 1199 aaronmk
verify/%.out: _always ;
307 369 aaronmk
308 1199 aaronmk
all += $(wildcard verify/*.out)
309 1192 aaronmk
310 1378 aaronmk
ifneq ($(dbExport),)
311 1082 aaronmk
%.ref: %.ref.sql
312
	$(dbAsBien) $(db) <$< >$@
313
endif
314
315 1667 aaronmk
##### Editing import
316
317
import/rotate: _always
318 1668 aaronmk
	echo "UPDATE party SET organizationname = organizationname||'.$(date)'\
319 1854 aaronmk
WHERE organizationname = '$(datasrc)';"|$(psqlAsBien)
320 1667 aaronmk
321
import/rm: _always
322 1854 aaronmk
	echo "DELETE FROM party WHERE organizationname = '$(datasrc)';"|\
323
$(psqlAsBien)
324 1667 aaronmk
325 783 aaronmk
##### Testing
326 368 aaronmk
327 723 aaronmk
hasOwnRef = $(filter-out %.2-step.xml,$@)
328 630 aaronmk
testRef = $(1:.2-step.xml=.xml).ref
329
330 897 aaronmk
define runTest
331 776 aaronmk
@echo "Testing $(abspath $@)..."
332 991 aaronmk
>$@ env test=1 n=$(test_n) $(1)
333 1184 aaronmk
@(set -x; $(diff) $(call testRef,$@) $@) 2>&1 || { e=$$?;\
334 780 aaronmk
$(if $(wildcard $(call testRef,$@)),,cat $@;)\
335 777 aaronmk
$(if $(hasOwnRef),\
336
echo $(emph)"To accept new test output:"$(endEmph);\
337
echo "$(MAKE) $@-ok --directory=$(realpath .) --makefile=../input.Makefile";\
338
,\
339
echo $(emph)"Note: The preceding failed test is compared to another test's\
340
output"$(endEmph);\
341
echo $(emph)"When it fails, this always indicates a bug"$(endEmph);\
342
)\
343 652 aaronmk
exit $$e;}
344 628 aaronmk
endef
345
346 897 aaronmk
test2File = $(call runTest,$(map))
347 775 aaronmk
348 876 aaronmk
tests :=
349
350 1139 aaronmk
test/$(via).%.xml: maps/$(via).%.full.csv _always
351 775 aaronmk
	$(test2File)
352 876 aaronmk
tests += test/$(via).%.xml
353 629 aaronmk
354 876 aaronmk
test/VegBIEN.%.xml: maps/VegBIEN.%.csv _always
355 775 aaronmk
	$(test2File)
356 876 aaronmk
tests += test/VegBIEN.%.xml
357 628 aaronmk
358 884 aaronmk
test/VegBIEN.%.2-step.xml: test/$(via).%.xml $(coreMap) _always
359 775 aaronmk
	-$(test2File)
360 722 aaronmk
# Don't abort tester if only 2-step test fails, as it's often finicky
361 876 aaronmk
tests += test/VegBIEN.%.2-step.xml
362 630 aaronmk
363 876 aaronmk
test/import.%.out: maps/VegBIEN.%.csv _always
364 897 aaronmk
	$(call runTest,$(map2db))
365 876 aaronmk
tests += test/import.%.out
366 627 aaronmk
367 876 aaronmk
testOutputs := $(foreach test,$(tests),$(tables:%=$(test)))
368 724 aaronmk
369 1361 aaronmk
.PRECIOUS: $(testOutputs) # save outputs of failed tests so they can be accepted
370
371 876 aaronmk
test: _always $(testOutputs) ;
372
373
all += $(testOutputs)
374
375 634 aaronmk
# Accepts a test output: make <test_output_path>-ok
376 626 aaronmk
%-ok: _always
377 630 aaronmk
	$(CP) $* $(call testRef,$*)
378 502 aaronmk
379 783 aaronmk
##### Input-type-specific
380 368 aaronmk
381 1917 aaronmk
# Each input type needs var $(mapEnv) and targets src/install, src/uninstall
382 624 aaronmk
383 1379 aaronmk
#### DB export
384
385 1378 aaronmk
ifneq ($(dbExport),)
386 256 aaronmk
387 1378 aaronmk
dbEngineExt := $(subst .,,$(suffix $(basename $(notdir $(dbExport)))))
388 1196 aaronmk
db := $(datasrc)
389 622 aaronmk
390 1379 aaronmk
### Installation
391 256 aaronmk
392 1917 aaronmk
src/install: _always db ;
393 339 aaronmk
394 1917 aaronmk
src/uninstall: _always rm_db ;
395 368 aaronmk
396 1379 aaronmk
### DB-engine-specific
397 621 aaronmk
398 624 aaronmk
# Each DB engine needs vars $(dbEngine), $(dbAsBien) and targets db, rm_db
399 256 aaronmk
400 622 aaronmk
ifeq ($(dbEngineExt),my)
401 621 aaronmk
402 622 aaronmk
dbEngine := MySQL
403
404 621 aaronmk
bienPassword := $(shell cat $(root)/config/bien_password)
405
mysqlAs = mysql --user=$(1) --password='$(bienPassword)'
406
mysqlAsRoot := $(call mysqlAs,root)
407
dbAsBien := $(call mysqlAs,bien)
408
409 1097 aaronmk
dbExists = $(shell echo "SHOW DATABASES LIKE '$(db)';"|$(mysqlAsRoot))
410
411
define createDb
412 1098 aaronmk
echo "CREATE DATABASE $(db) DEFAULT CHARACTER SET latin1;"|$(mysqlAsRoot)
413 1097 aaronmk
-$(mysqlAsRoot) --database=$(db) <$<
414
endef
415
# ignore errors in db import so that GRANT will still be run
416
417 1378 aaronmk
db: $(dbExport) _always
418 1097 aaronmk
	$(if $(dbExists),,$(createDb))
419 368 aaronmk
	echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
420 250 aaronmk
421 383 aaronmk
rm_db: _always
422 368 aaronmk
	-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
423
	echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
424 365 aaronmk
# ignore errors if grant not defined
425 250 aaronmk
426 1379 aaronmk
## Unrecognized DB engine
427 368 aaronmk
428
else
429 1378 aaronmk
$(error The DB filename $(dbExport) must be db.my.sql)
430 368 aaronmk
endif
431
432 1379 aaronmk
### Other input types
433 622 aaronmk
434 1379 aaronmk
else
435 624 aaronmk
436 1917 aaronmk
src/install: _always ;
437
src/uninstall: _always ;
438 1379 aaronmk
439 256 aaronmk
endif
440 1379 aaronmk
441
#### DB connection info
442
443
ifneq ($(dbEngine),)
444
# Must come after dbEngine is set
445
mapEnv := in_engine=$(dbEngine) in_database=$(db)
446
endif