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Revision 14817

fix: *Makefile: changed line endings to \n so that `patch` can work with pasted input. use `svn di --extensions --ignore-eol-style` to verify no diff.

View differences:

input.Makefile
1
selfDir_uZPPqC := $(dir $(lastword $(MAKEFILE_LIST)))
2
root := $(selfDir_uZPPqC)..
3
include $(root)/lib/common.Makefile
4

  
5

  
6
##### Configuration
7

  
8
# Command line
9
continue ?=
10
debug ?=
11
full_import ?=
12
import_source ?= 1
13
is_view ?=
14
log ?= $(if $(test),,1)
15
noclobber ?=
16
profile ?=
17
quiet ?=
18
reverify ?= 1
19
schema_only ?=
20
use_staged ?= $(by_col)
21

  
22
# Makefile
23
exts ?= csv tsv tab txt dat dmp
24
test_n ?= 2
25

  
26
##### Vars/functions
27

  
28
# Paths
29
datasrc := $(patsubst .%,%,$(notdir $(realpath .)))
30
bin := $(root)/bin
31
mappings := $(root)/mappings
32

  
33
# Make
34
SHELL := /bin/bash
35
selfMake = $(MAKE) --makefile=../input.Makefile
36
subMake = $(MAKE) "$(@:$(root)/%=%)" --directory=$(root)
37
+_ = $(+:_%=)
38
# used to filter the output of embedded $(shell make ...) invocations
39
filter_make := grep -vF -e lib -e ".Makefile'."
40
addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
41

  
42
# Terminal
43
termCols := $(shell tput cols)
44

  
45
# Commands
46
MKDIR = mkdir -p
47
mkdir = $(MKDIR) $(@D)
48
diff = diff --unified=2
49
diffIgnoreSpace = $(diff) --ignore-space-change
50
diffVerbose = $(if $(verbose),diff --side-by-side --left-column\
51
--width=$(termCols),$(diff))
52

  
53
# BIEN commands
54
sortFilenames = $(shell $(bin)/sort_filenames $(1))
55
selfMap = $(bin)/cols 0 0
56
psqlAsBien := $(bin)/psql_verbose_vegbien
57
psqlNoSearchPath := env no_search_path=1 $(psqlAsBien)
58
# Usage: ($(inDatasrc); cat $(file))|$(psqlCmd)
59
inDatasrc := echo 'SET search_path TO "$(datasrc)";'
60

  
61
# SVN
62
setSvnIgnore = svn propset svn:ignore $(2) $(1)
63
define addDirWithIgnore
64
$(addDir)
65
$(setSvnIgnore)
66
endef
67

  
68
##### Environment
69

  
70
export PATH := $(bin):$(PATH)
71

  
72
##### General targets
73

  
74
all: _always maps ;
75

  
76
clean: _always
77
	$(RM) $(all)
78

  
79
remake: _always clean
80
	+$(selfMake)
81
# re-run make so that cache of existing files is reset
82

  
83
# Only remake if doesn't exist. This prevents unintentional remaking when the
84
# make script is newly checked out from svn (which sets the mod time to now) but
85
# the output is synced externally.
86
# Can't remove prereq to do this, because it determines when the rule applies.
87
make_script = $(if $(wildcard $@),,"time" ./$< >$@)
88

  
89
%/: %/map.csv _always ;
90

  
91
%/: % _always ;
92

  
93
%: %.make
94
	$(make_script)
95
.PRECIOUS: % # save partial outputs of aborted src make scripts
96

  
97
##### Tables discovery
98

  
99
sortFile := import_order.txt
100
noImportFile := _no_import
101

  
102
dontImport = $(wildcard $(noImportFile))$(wildcard $(1)/$(noImportFile))$(if\
103
$(import_source),,$(filter Source,$(1)))
104

  
105
ifeq ($(sort_file_updated),)# keep $(sortFile) up-to-date
106
$(shell sort_file_updated=1 $(selfMake) $(sortFile)|$(filter_make) >&2)
107
export sort_file_updated=1
108
endif
109

  
110
sort_file_tables := $(if $(wildcard $(sortFile)),$(shell cat $(sortFile)))
111
    # $(shell) replaces "\n" with " "
112
tables := $(sort_file_tables)
113
allSubdirs := $(call wildcard/,*/)
114
allTables := $(call sortFilenames,$(filter-out _% verify logs,$(allSubdirs:%/=%)))
115
joinedTables := $(filter-out $(tables),$(allTables))
116
allTables := $(strip $(joinedTables) $(tables))# move joined tables to beginning
117
has_visible_files = $(call wildcard/,$(1)/*)
118
allTables := $(foreach table,$(allTables),$(if\
119
$(call has_visible_files,$(table)),$(table)))
120
ifeq ($(tables),)# none specified in sort file
121
tables := $(allTables)
122
endif
123
importTables := $(foreach table,$(tables),$(if\
124
$(call dontImport,$(table)),,$(table)))
125

  
126
list_tables: _always # use `make -s` to avoid echoing commands
127
	@for table in $(tables); do echo "$$table"; done
128

  
129
$(sortFile): _always
130
	$(if $(filter-out $(sort_file_tables),$(tables)),$(selfMake) -s list_tables >$@)
131
# add any missing tables to $(sortFile)
132

  
133
##### SVN
134

  
135
svnFilesGlob:= */{,{,.}{data,map,VegBIEN}.csv{,.*},*header.*,*.sql,test.xml.ref}
136
svnFilesGlob := {map.csv,*{grants,validations,~}*.sql,{,*/}{*.{log,make},*terms.csv},$(svnFilesGlob)}
137
_svnFilesGlob := {_MySQL/{,*.make},{,*/}{$(noImportFile),*{run,Makefile},*.{md5,url},*README.TXT}}
138
svnFiles = $(filter-out _% logs/% %.data.sql,$(call wildcard/,$(svnFilesGlob)))\
139
$(call wildcard/,$(_svnFilesGlob))
140

  
141
add: _always $(if $(call dontImport,.),,add!) ;
142

  
143
# To update all inputs with these settings: make inputs/add
144
add!: _always Source/add $(allTables:%=%/add)
145
	$(call setSvnIgnore,.,'*')
146
	$(call addDirWithIgnore,logs,$$'*.gz\n*.log.sql\n*.trace')
147
	$(call addDirWithIgnore,verify,$$'*.csv\n*.log\n*.out\n*.tsv\n*.txt\n*.xls\n*.xlsx')
148
	$(call addFile,import_order.txt)
149
	$(if $(wildcard _MySQL/),$(call addDirWithIgnore,_MySQL,'*'))
150
	$(if $(wildcard _src/),$(call addDirWithIgnore,_src,'*'))
151
	$(if $(wildcard _archive/),$(call addDirWithIgnore,_archive,'*'))
152
	# invoke externally to clear $$(wildcard) cache before expanding $$(svnFiles)
153
	$(selfMake) add_files
154

  
155
add_files: _always
156
	$(call add*,$(svnFiles))
157

  
158
# Adds a new table subdir
159
%/add: _always
160
	$(call addDirWithIgnore,$*,'*')
161
	$(call addDirWithIgnore,$*/logs,$$'*.gz\n*.log.sql\n*.trace')
162

  
163
##### Existing maps discovery
164

  
165
anyMap := %/map.csv %/VegBIEN.csv %/unmapped_terms.csv %/new_terms.csv
166

  
167
exts := $(call ci,$(exts))
168
extsFilter := $(addprefix %.,$(exts))
169
dataOnly = $(filter $(extsFilter),$(1))
170

  
171
anyTest = $*/test.%
172
srcsOnly = $(filter-out $(anyMap) $(anyTest) %/logs,$(call dataOnly,$(1)))
173

  
174
srcDict := map.csv
175

  
176
vocab := $(mappings)/VegCore.vocab.csv
177
thesaurus := $(mappings)/VegCore.thesaurus.csv
178
coreMap := $(mappings)/VegCore-VegBIEN.csv
179

  
180
viaMaps := $(tables:%=%/map.csv)
181

  
182
autogenMaps := $(subst map.,VegBIEN.,$(viaMaps))
183
directMaps := $(autogenMaps) $(filter-out $(autogenMaps),\
184
$(wildcard */VegBIEN.csv))
185

  
186
##### Sources
187

  
188
srcs = $(call sortFilenames,$(call srcsOnly,$(wildcard $*/*)))
189
nonHeaderSrcs = $(filter-out %/header.csv %/header.txt,$(srcs))
190
isRef = $(if $(nonHeaderSrcs),,1)
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    # empty subdir, so references an already-installed staging table
192
catSrcs = $(bin)/cat_csv $(nonHeaderSrcs)
193
withCatSrcs = $(catSrcs:$(bin)/%=$(bin)/with_%) --
194

  
195
%/list_srcs: _always # use `make -s` to avoid echoing commands
196
	echo $(nonHeaderSrcs)
197

  
198
# Run with `make -s` to avoid echoing make commands
199
cat: $(importTables:%=%/cat) _always ;
200

  
201
%/cat: _always
202
	$(catSrcs)
203

  
204
##### Input data retrieval
205

  
206
# Must come before `%.sql: _MySQL/%.sql` to override it
207
%.sql: %.sql.make
208
	$(make_script)
209

  
210
# The export must be created with:
211
# `--compatible=postgresql --add-locks=false --set-charset --no-create-info`
212
# Must come before `%.sql: _MySQL/%.sql` to override it
213
%.data.sql: _MySQL/%.data.sql
214
	$(if $(wildcard $@),,$(bin)/my2pg.data <$< >$@)
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216
# The export must be created with:
217
# `--compatible=postgresql --add-locks=false --set-charset`
218
# Add `--no-data` to create a schema-only export.
219
%.sql: _MySQL/%.sql
220
	$(if $(wildcard $@),,$(bin)/my2pg <$< >$@)
221

  
222
##### Staging tables installation
223

  
224
srcTable := %.src
225

  
226
dbExportsWildcard = $(sort $(patsubst _MySQL/%.make,%,$(wildcard\
227
$(1) _MySQL/$(1).make)))
228

  
229
dbExports := $(call dbExportsWildcard,*schema*.sql)# schemas first
230
ifeq ($(schema_only),) # add rest of .sql files
231
dbExports += $(filter-out $(dbExports),$(call dbExportsWildcard,*.sql))
232
endif
233
dbExports := $(filter-out grants.sql,$(dbExports))
234
dbExports := $(strip $(dbExports))# += adds extra whitespace
235
allInstalls := $(if $(dbExports),sql) $(allTables)
236

  
237
datasrc_schema_exists = $(shell schema=$(datasrc)\
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$(root)/lib/runscripts/local.run pg_schema_exists && echo t)
239

  
240
install: _always
241
	$(if $(wildcard ./run),./run install,$(if $(wildcard table.run),$(if\
242
$(datasrc_schema_exists),,+$(selfMake) install_oldstyle)))
243
	+$(selfMake) validate/install
244
# table.run: only run this for datasource dirs
245

  
246
install_oldstyle: _always schema $(allInstalls:%=%/install) ;
247

  
248
uninstall: _always confirm_rm_schema rm_schema ;
249
# rm_schema will also drop all staging tables
250

  
251
reinstall: _always uninstall install ;
252

  
253
confirm_rm_schema: _always
254
	$(if $(filter TNRS,$(datasrc)),$(call confirm,WARNING: This will delete the\
255
TNRS cache!,To save it: make backups/TNRS.backup-remake))
256

  
257
schema: _always
258
	-echo 'CREATE SCHEMA "$(datasrc)";'|$(psqlNoSearchPath)
259
# ignore errors if schema exists
260

  
261
rm_schema: _always
262
	echo 'DROP SCHEMA IF EXISTS "$(datasrc)" CASCADE;'|$(psqlNoSearchPath)
263

  
264
installLog := logs/install.log.sql
265

  
266
log_dir = $(1)logs
267
has_log_dir = $(call and,$(wildcard $(log_dir)),$(call not,$(noclobber)))
268
logInstall = $(if $(has_log_dir),$(if $(quiet),$(2)$(1)$(installLog)\
269
2>&1,2>&1|tee $(3) $(1)$(installLog)))
270
logInstallRoot = $(call logInstall,,>)
271
logInstall* = $(call logInstall,$*/,>)
272
logInstall*Add = $(call logInstall,$*/,>>,-a)# append to log
273

  
274
# Must come before %/install to override it
275
sql/install: $(dbExports)
276
	set -o pipefail; ($(inDatasrc); $(if $(wildcard schema.sql),cat schema.sql;)\
277
cat $(filter-out schema.sql grants.sql,$+)|pg_dump_limit $(if $(wildcard\
278
grants.sql),; cat grants.sql))|"time" env no_search_path=1 \
279
$(bin)/psql_$(if $(debug),verbose,script)_vegbien --set=schema='"$(datasrc)"' \
280
$(logInstallRoot)
281

  
282
# $debug option runs the *.sql import verbosely, to display which statements are
283
# being run. this should only be used for SQL files that use COPY FROM to import
284
# data, to avoid echoing pages of insert statements.
285
cleanup = set -o pipefail; \
286
$(if $(wildcard $*/cleanup.sql),($(inDatasrc); cat $*/cleanup.sql)\
287
|"time" $(psqlNoSearchPath) --echo-all --set=table='"$*"' $(logInstall*Add),\
288
(export schema=$(datasrc) table=$*; . $(bin)/vegbien_dest; unset schemas; \
289
$(bin)/csv2db) $(logInstall*Add))
290

  
291
%/header.csv:
292
	set -o pipefail; \
293
echo 'COPY (SELECT * FROM "$(datasrc)"."$*" LIMIT 0) TO STDOUT CSV HEADER;'|\
294
env no_search_path=1 $(bin)/psql_script_vegbien >$*/header.csv
295

  
296
exportHeader = $(selfMake) "$*/header.csv"
297

  
298
# Don't try to edit a view. Must come before %/install to override it.
299
%_view/install: _always ;
300

  
301
%.sql/run: _always
302
	$(if $(wildcard $(@D)),($(inDatasrc); cat $(@D))|(cd '$(*D)';\
303
"time" env no_search_path=1 ../$(bin)/psql_verbose_vegbien \
304
--set=table='"$(*D)"' --set=table_str=\''"$(*D)"'\'))
305

  
306
%/postprocess.sql: $(thesaurus) _always
307
	$(if $(wildcard $*/run),$(bin)/in_place $@ env text=1 $(bin)/repl $<)
308

  
309
%/postprocess: _always
310
	$(if\
311
$(wildcard $*/run),$*/run postprocess,$(selfMake) "$*/postprocess.sql/run")
312

  
313
%/map_table: _always
314
	$(if $(wildcard $*/run),$*/run map_table)
315

  
316
# For staging tables which are derived by joining together other staging tables.
317
%/install: %/create.sql _always
318
	set -o pipefail; \
319
($(inDatasrc); echo 'CREATE TABLE "$*" AS'; cat $<; echo ';')|"time" \
320
$(psqlNoSearchPath) --echo-all --set=schema='"$(datasrc)"' --set=table='"$*"' \
321
$(logInstall*)
322
	$(exportHeader)
323
	$(selfMake) "$*/postprocess"
324
	$(cleanup)
325

  
326
%/install: _always
327
	$(import_install_)
328
	$(exportHeader)
329
	$(selfMake) "$*/postprocess"
330
	$(cleanup)
331
define import_install_
332
set -o pipefail; (. $(bin)/vegbien_dest; unset schemas; "time" $(nice)\
333
env schema=$(datasrc) table=$* $(bin)/csv2db $(catSrcs) $(logInstall*))
334
$(if $(filter $(srcTable),$*),($(inDatasrc);\
335
echo 'ALTER TABLE "$(datasrc)"."$*" RENAME row_num TO "$*.row_num";')|"time"\
336
$(psqlNoSearchPath) --echo-all --set=table='"$*"' $(logInstall*Add))
337
endef
338
# table-scope src table's row_num col to allow joining it with other tables
339

  
340
%/uninstall: _always
341
	echo 'DROP $(if\
342
$(is_view),VIEW,TABLE) IF EXISTS "$(datasrc)"."$*" CASCADE;'|$(psqlNoSearchPath)
343

  
344
%/reinstall: _always %/uninstall %/install ;
345

  
346
postprocess: _always $(allTables:%=%/postprocess) ;
347

  
348
cleanup: _always $(tables:%=%/cleanup) ;
349

  
350
# WARNING: This removes any index comments, due to a PostgreSQL bug.
351
# This occurs because ALTER TABLE recreates the index but not its comment.
352
%/cleanup: _always
353
	$(cleanup)
354

  
355
##### Maps building
356

  
357
# Maps to (try to) build are added to this
358
maps :=
359

  
360
srcRoot = $(mappings)/root.sh
361
mkSrcMap = (. $(srcRoot); env datasrc=$(datasrc) $(bin)/src_map <$*/header.csv\
362
>$@)
363

  
364
translate = $(if $(wildcard $(1)),$(bin)/in_place $< $(bin)/translate_ci 1 $(1))
365

  
366
$(srcDict):# empty target in case it doesn't exist
367

  
368
# Via maps cleanup
369
ifneq ($(filter %/.map.csv.last_cleanup,$(MAKECMDGOALS)),)
370
%/.map.csv.last_cleanup: %/map.csv $(vocab) $(thesaurus) $(coreMap) $(srcDict)
371
	$(call translate,$(srcDict))
372
	$(bin)/in_place $< $(bin)/canon 1 $(vocab)
373
	$(call translate,$(thesaurus))
374
	$(bin)/in_place $< $(bin)/fix_line_endings
375
	touch $@
376
	+$(selfMake) $(<:%/map.csv=%/unmapped_terms.csv)
377
	+$(selfMake) $(<:%/map.csv=%/new_terms.csv)
378
.PRECIOUS: %/.map.csv.last_cleanup
379
else
380
%/map.csv: _always
381
	$(if $(wildcard $@),,$(mk_map_csv))
382
	+$(selfMake) $(@:%/map.csv=%/.map.csv.last_cleanup)
383
define mk_map_csv
384
+$(selfMake) "$*/header.csv"
385
$(mkSrcMap)
386
endef
387
endif
388

  
389
%/VegBIEN.csv: %/map.csv $(coreMap)
390
	$(if $(wildcard $*/run),-ln -s "../$(coreMap)" "$@"\
391
,<$< $(bin)/cat_cols 1 2|$(bin)/join $(coreMap)|$(bin)/sort_map >$@)
392
# ignore errors if symlink exists
393
maps += $(autogenMaps)
394

  
395
maps: $(maps) _always ;
396

  
397
all += $(maps)
398

  
399
##### Maps validation
400

  
401
# `tail -n +2`: Remove header before running filter_out_ci because filter_out_ci
402
# only removes the header if it matches the vocabulary's header.
403

  
404
%/unmapped_terms.csv: %/map.csv $(coreMap)
405
	tail -n +2 $<|$(bin)/cols 1|$(bin)/filter_out_ci 0 $(coreMap) >$@
406
	$(bin)/autoremove $@
407

  
408
%/new_terms.csv: %/map.csv $(vocab) $(thesaurus) %/unmapped_terms.csv
409
	$(newTerms)
410
	$(bin)/autoremove $@
411
newTerms = tail -n +2 $<|$(bin)/filter_out_ci 0 $(vocab)|$(bin)/filter_out_ci 0\
412
$(thesaurus) $(if $(wildcard $(word 4,$+)),|$(bin)/filter_out_ci 0 $(word 4,$+))\
413
|grep -vE -e '^"?:' -e 'UNUSED' >$@; exit 0 # grep exits nonzero if no match
414

  
415
termsSubdirs := $(tables)
416

  
417
include $(root)/lib/mappings.Makefile
418

  
419
##### External dependencies
420

  
421
$(root)/%: _always
422
	+$(subMake)
423
.PRECIOUS: $(root)/% # let ext. dir's Makefile decide whether to delete on error
424

  
425
##### Mapping
426

  
427
+maps = $(filter %/map.csv %/VegBIEN.csv $(mappings)/%,$(+_))
428
map2db = env in_database=vegbien in_schema=$(datasrc) in_table=$*\
429
out_database=vegbien source=$(datasrc).new $(root)/map $(+maps)
430

  
431
##### Import to VegBIEN
432

  
433
import_temp: $(importTables:%=%/import) _always ;
434

  
435
import: _always import_temp publish validate ; # removes temp suffix when done
436

  
437
rm: _always
438
	echo "SELECT datasource_rm('$(datasrc)');"|"time" $(psqlAsBien)
439

  
440
reimport: _always import ; # import replaces the previous import
441

  
442
profileTest = $(if $(profile),$(if $(test),1))
443
profileOnly = -env profile_to=/dev/fd/3 $(map2db) 3>&1 1>&2|\
444
$(bin)/profile_stats /dev/fd/0
445

  
446
log_ = $*/logs/$(if $(n),n=$(n).,)$(version).log.sql
447

  
448
# Displays the import log file path
449
# Run with `make -s` to avoid echoing make commands
450
%/log_file: _always
451
	echo $$(pwd)/$(log_)
452

  
453
trace = $(log_:.log.sql=.trace)
454
restart_row = $(shell set -x; grep -F Partition: $(log_)|tail -1|$(sed)\
455
's/^.* rows ([[:digit:]]+)-.*$$/\1/')
456
import = $(if $(profileTest),$(profileOnly),(set -x; date; "time" env commit=1\
457
$(if $(profile),profile_to=$(trace)) $(if $(continue),start=$(restart_row))\
458
$(map2db))$(if $(log), >>$(log_) 2>&1))
459

  
460
import? = $(if $(call and,$(full_import),$(call dontImport,.)),,$(import))
461

  
462
%/import_temp: %/VegBIEN.csv _always
463
	$(if $(full_import),-)$(import?)
464
# don't abort on import errors, which often relate to invalid input data
465
# default:
466
%/import_temp: _always ;
467

  
468
%/import: %/import_temp _always ;
469

  
470
#### Taxonomic scrubbing
471

  
472
scrub: _always
473
	$(selfMake) $(root)/scrub & echo $$!
474
# using & (background process) also ignores TNRS errors, so that TNRS bugs do
475
# not prevent the remaining tables from being imported even if TNRS can't be run
476

  
477
# Removes TNRS taxondeterminations
478
unscrub: _always
479
	echo "SELECT delete_scrubbed_taxondeterminations('$(datasrc)');"|\
480
"time" env no_query_results=1 $(psqlAsBien)
481

  
482
rescrub: _always unscrub scrub ;
483

  
484
import_scrub: _always import scrub ;
485

  
486
reimport_scrub: _always reimport scrub ;
487

  
488
%/import_scrub: _always %/import scrub ;
489

  
490
##### Log files from import
491

  
492
logs := $(wildcard */logs/*.log.sql */logs/*.trace)
493

  
494
rm_logs: _always
495
	$(RM) $(logs)
496

  
497
##### Verification of import
498

  
499
### new-style aggregating validations (also work w/ old-style import)
500

  
501
# must be in input.Makefile instead of table.run because some datasources that
502
# we validate still use old-style import
503

  
504
# validations.sql must be in a subdir so it won't get run by sql/install
505
validate/install: _always verify/validations.sql/run ;
506

  
507
validate: _always
508
	echo "SELECT remake_diff_tables('$(datasrc)');"\
509
|$(psqlAsBien)$(if $(log), >>.$(log_) 2>&1)
510

  
511
### old-style aggregating validations (not related to old-style import)
512

  
513
verifyTables := $(patsubst verify/%.ref,%,$(wildcard verify/*.ref))
514

  
515
verify: $(verifyTables:%=%/verify) _always ;
516

  
517
%/verify: verify/%.ref verify/%.out _always
518
	-$(diffVerbose) $(+_)
519
# don't abort on verification errors, which are expected during development
520
# default:
521
%/verify: verify/%.out _always
522
	$(if $(shell test -e $< && echo t),cat $<)
523
# don't run if verify/%.out's default do-nothing action was used
524
# can't use $(wildcard) because it won't recheck file after verify/%.out is run
525

  
526
psqlExport := "time" $(psqlNoSearchPath) --no-align --field-separator=$$'\t'\
527
--pset=footer=off --pset=null=NULL
528
# Note that using $(inDatasrc) will not work with datasources whose tables are
529
# the same name as VegBIEN tables (likely only VegBank), because the datasource
530
# is first in the search_path.
531
verify = $(if $(reverify),($(inDatasrc); cat $<)|$(psqlExport)\
532
--set=datasource="'$(datasrc)'" >$@)
533

  
534
verify/%.out: verify/%.out.sql _always
535
	$(verify)
536
.PRECIOUS: verify/%.out # save partial output in case of error to help debugging
537
# default:
538
verify/%.out: _always ;
539

  
540
all += $(wildcard verify/*.out)
541

  
542
%.ref: %.ref.sql
543
	($(inDatasrc); cat $<)|$(psqlExport) >$@
544
.PRECIOUS: %.ref # there must always be a .ref for the make rules to work
545

  
546
##### Editing import
547

  
548
rename/%: _always
549
	echo "UPDATE source SET shortname = '$*' WHERE shortname = '$(datasrc)';"\
550
|$(psqlAsBien)
551

  
552
%/publish: _always # usage: make inputs/src/src.version/publish
553
	echo "SELECT datasource_publish('$*');"|$(psqlAsBien)
554

  
555
publish: _always $(datasrc).new/publish ; # usage: make inputs/src/publish
556

  
557
##### Testing
558

  
559
testRefOutput = $(subst .by_col,,$(1))
560
testRef = $(testRefOutput).ref
561
hasOwnRef = $(filter $@,$(call testRefOutput,$@))
562
# filter returns non-empty if they are equal
563

  
564
# `rm $@`: Remove outputs of successful tests to reduce clutter
565
# `$(foreach use_staged...)`: Run with use_staged=1
566
define runTest
567
@echo "Testing $(abspath $@)..."
568
>$@ env test=1 n=$(test_n) $(1) $(foreach use_staged,1,$(map2db))
569
$(if $(hasOwnRef),,-)@(set -x; $(diffIgnoreSpace) $(call testRef,$@) $@) 2>&1\
570
&& rm $@ || { e=$$?; $(if $(wildcard $(call testRef,$@)),,cat $@;)\
571
$(if $(hasOwnRef),\
572
{\
573
read -p $(emph)'Accept new test output? (y/n)'$(endEmph) REPLY;\
574
if test "$$REPLY" = y; then\
575
(set -x; $(MAKE) $@-ok --directory=$(realpath .) --makefile=../input.Makefile);\
576
exit 0;\
577
fi;\
578
};,\
579
echo $(emph)"Note: The preceding failed test is compared to another test's\
580
output"$(endEmph);\
581
echo $(emph)"When it fails, this always indicates a bug"$(endEmph);\
582
)\
583
exit $$e;}
584
endef
585

  
586
tests :=
587

  
588
%/test: %/test.xml $(if $(by_col),%/test.by_col.xml) _always ;
589

  
590
# Requires staging tables. To create them, run `make inputs/<datasrc>/install`.
591
# Non-flat-file inputs fall back to mimicking a successful test
592
%/test.xml: %/VegBIEN.csv _always
593
	$(call runTest,by_col=)
594
tests += %/test.xml
595

  
596
%/test.by_col.xml: %/VegBIEN.csv _always
597
	$(call runTest,by_col=1)
598

  
599
# Only run column-based tests if column-based mode enabled, because these tests
600
# are much slower than the row-based tests for small numbers of rows
601
ifneq ($(by_col),)
602
tests += %/test.by_col.xml
603
endif
604

  
605
testOutputs := $(foreach test,$(tests),$(tables:%=$(test)))
606

  
607
.PRECIOUS: $(testOutputs) # save outputs of failed tests so they can be accepted
608

  
609
test: _always $(testOutputs) ;
610

  
611
all += $(wildcard %/test*.xml)
612

  
613
# Accepts a test output: make <test_output_path>-ok
614
%-ok: _always
615
	mv $* $(call testRef,$*)
616

  
617
accept-all: _always
618
	+yes|$(selfMake) test
619

  
620
##### Documentation
621

  
622
steps = $(selfMake) -s $*/import test=1 by_col=1 verbosity=2 n=100\
623
2>&1|$(bin)/debug2redmine >$@
624

  
625
%/logs/steps.by_col.log.sql: _always
626
	+$(steps)
1
selfDir_uZPPqC := $(dir $(lastword $(MAKEFILE_LIST)))
2
root := $(selfDir_uZPPqC)..
3
include $(root)/lib/common.Makefile
4

  
5

  
6
##### Configuration
7

  
8
# Command line
9
continue ?=
10
debug ?=
11
full_import ?=
12
import_source ?= 1
13
is_view ?=
14
log ?= $(if $(test),,1)
15
noclobber ?=
16
profile ?=
17
quiet ?=
18
reverify ?= 1
19
schema_only ?=
20
use_staged ?= $(by_col)
21

  
22
# Makefile
23
exts ?= csv tsv tab txt dat dmp
24
test_n ?= 2
25

  
26
##### Vars/functions
27

  
28
# Paths
29
datasrc := $(patsubst .%,%,$(notdir $(realpath .)))
30
bin := $(root)/bin
31
mappings := $(root)/mappings
32

  
33
# Make
34
SHELL := /bin/bash
35
selfMake = $(MAKE) --makefile=../input.Makefile
36
subMake = $(MAKE) "$(@:$(root)/%=%)" --directory=$(root)
37
+_ = $(+:_%=)
38
# used to filter the output of embedded $(shell make ...) invocations
39
filter_make := grep -vF -e lib -e ".Makefile'."
40
addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
41

  
42
# Terminal
43
termCols := $(shell tput cols)
44

  
45
# Commands
46
MKDIR = mkdir -p
47
mkdir = $(MKDIR) $(@D)
48
diff = diff --unified=2
49
diffIgnoreSpace = $(diff) --ignore-space-change
50
diffVerbose = $(if $(verbose),diff --side-by-side --left-column\
51
--width=$(termCols),$(diff))
52

  
53
# BIEN commands
54
sortFilenames = $(shell $(bin)/sort_filenames $(1))
55
selfMap = $(bin)/cols 0 0
56
psqlAsBien := $(bin)/psql_verbose_vegbien
57
psqlNoSearchPath := env no_search_path=1 $(psqlAsBien)
58
# Usage: ($(inDatasrc); cat $(file))|$(psqlCmd)
59
inDatasrc := echo 'SET search_path TO "$(datasrc)";'
60

  
61
# SVN
62
setSvnIgnore = svn propset svn:ignore $(2) $(1)
63
define addDirWithIgnore
64
$(addDir)
65
$(setSvnIgnore)
66
endef
67

  
68
##### Environment
69

  
70
export PATH := $(bin):$(PATH)
71

  
72
##### General targets
73

  
74
all: _always maps ;
75

  
76
clean: _always
77
	$(RM) $(all)
78

  
79
remake: _always clean
80
	+$(selfMake)
81
# re-run make so that cache of existing files is reset
82

  
83
# Only remake if doesn't exist. This prevents unintentional remaking when the
84
# make script is newly checked out from svn (which sets the mod time to now) but
85
# the output is synced externally.
86
# Can't remove prereq to do this, because it determines when the rule applies.
87
make_script = $(if $(wildcard $@),,"time" ./$< >$@)
88

  
89
%/: %/map.csv _always ;
90

  
91
%/: % _always ;
92

  
93
%: %.make
94
	$(make_script)
95
.PRECIOUS: % # save partial outputs of aborted src make scripts
96

  
97
##### Tables discovery
98

  
99
sortFile := import_order.txt
100
noImportFile := _no_import
101

  
102
dontImport = $(wildcard $(noImportFile))$(wildcard $(1)/$(noImportFile))$(if\
103
$(import_source),,$(filter Source,$(1)))
104

  
105
ifeq ($(sort_file_updated),)# keep $(sortFile) up-to-date
106
$(shell sort_file_updated=1 $(selfMake) $(sortFile)|$(filter_make) >&2)
107
export sort_file_updated=1
108
endif
109

  
110
sort_file_tables := $(if $(wildcard $(sortFile)),$(shell cat $(sortFile)))
111
    # $(shell) replaces "\n" with " "
112
tables := $(sort_file_tables)
113
allSubdirs := $(call wildcard/,*/)
114
allTables := $(call sortFilenames,$(filter-out _% verify logs,$(allSubdirs:%/=%)))
115
joinedTables := $(filter-out $(tables),$(allTables))
116
allTables := $(strip $(joinedTables) $(tables))# move joined tables to beginning
117
has_visible_files = $(call wildcard/,$(1)/*)
118
allTables := $(foreach table,$(allTables),$(if\
119
$(call has_visible_files,$(table)),$(table)))
120
ifeq ($(tables),)# none specified in sort file
121
tables := $(allTables)
122
endif
123
importTables := $(foreach table,$(tables),$(if\
124
$(call dontImport,$(table)),,$(table)))
125

  
126
list_tables: _always # use `make -s` to avoid echoing commands
127
	@for table in $(tables); do echo "$$table"; done
128

  
129
$(sortFile): _always
130
	$(if $(filter-out $(sort_file_tables),$(tables)),$(selfMake) -s list_tables >$@)
131
# add any missing tables to $(sortFile)
132

  
133
##### SVN
134

  
135
svnFilesGlob:= */{,{,.}{data,map,VegBIEN}.csv{,.*},*header.*,*.sql,test.xml.ref}
136
svnFilesGlob := {map.csv,*{grants,validations,~}*.sql,{,*/}{*.{log,make},*terms.csv},$(svnFilesGlob)}
137
_svnFilesGlob := {_MySQL/{,*.make},{,*/}{$(noImportFile),*{run,Makefile},*.{md5,url},*README.TXT}}
138
svnFiles = $(filter-out _% logs/% %.data.sql,$(call wildcard/,$(svnFilesGlob)))\
139
$(call wildcard/,$(_svnFilesGlob))
140

  
141
add: _always $(if $(call dontImport,.),,add!) ;
142

  
143
# To update all inputs with these settings: make inputs/add
144
add!: _always Source/add $(allTables:%=%/add)
145
	$(call setSvnIgnore,.,'*')
146
	$(call addDirWithIgnore,logs,$$'*.gz\n*.log.sql\n*.trace')
147
	$(call addDirWithIgnore,verify,$$'*.csv\n*.log\n*.out\n*.tsv\n*.txt\n*.xls\n*.xlsx')
148
	$(call addFile,import_order.txt)
149
	$(if $(wildcard _MySQL/),$(call addDirWithIgnore,_MySQL,'*'))
150
	$(if $(wildcard _src/),$(call addDirWithIgnore,_src,'*'))
151
	$(if $(wildcard _archive/),$(call addDirWithIgnore,_archive,'*'))
152
	# invoke externally to clear $$(wildcard) cache before expanding $$(svnFiles)
153
	$(selfMake) add_files
154

  
155
add_files: _always
156
	$(call add*,$(svnFiles))
157

  
158
# Adds a new table subdir
159
%/add: _always
160
	$(call addDirWithIgnore,$*,'*')
161
	$(call addDirWithIgnore,$*/logs,$$'*.gz\n*.log.sql\n*.trace')
162

  
163
##### Existing maps discovery
164

  
165
anyMap := %/map.csv %/VegBIEN.csv %/unmapped_terms.csv %/new_terms.csv
166

  
167
exts := $(call ci,$(exts))
168
extsFilter := $(addprefix %.,$(exts))
169
dataOnly = $(filter $(extsFilter),$(1))
170

  
171
anyTest = $*/test.%
172
srcsOnly = $(filter-out $(anyMap) $(anyTest) %/logs,$(call dataOnly,$(1)))
173

  
174
srcDict := map.csv
175

  
176
vocab := $(mappings)/VegCore.vocab.csv
177
thesaurus := $(mappings)/VegCore.thesaurus.csv
178
coreMap := $(mappings)/VegCore-VegBIEN.csv
179

  
180
viaMaps := $(tables:%=%/map.csv)
181

  
182
autogenMaps := $(subst map.,VegBIEN.,$(viaMaps))
183
directMaps := $(autogenMaps) $(filter-out $(autogenMaps),\
184
$(wildcard */VegBIEN.csv))
185

  
186
##### Sources
187

  
188
srcs = $(call sortFilenames,$(call srcsOnly,$(wildcard $*/*)))
189
nonHeaderSrcs = $(filter-out %/header.csv %/header.txt,$(srcs))
190
isRef = $(if $(nonHeaderSrcs),,1)
191
    # empty subdir, so references an already-installed staging table
192
catSrcs = $(bin)/cat_csv $(nonHeaderSrcs)
193
withCatSrcs = $(catSrcs:$(bin)/%=$(bin)/with_%) --
194

  
195
%/list_srcs: _always # use `make -s` to avoid echoing commands
196
	echo $(nonHeaderSrcs)
197

  
198
# Run with `make -s` to avoid echoing make commands
199
cat: $(importTables:%=%/cat) _always ;
200

  
201
%/cat: _always
202
	$(catSrcs)
203

  
204
##### Input data retrieval
205

  
206
# Must come before `%.sql: _MySQL/%.sql` to override it
207
%.sql: %.sql.make
208
	$(make_script)
209

  
210
# The export must be created with:
211
# `--compatible=postgresql --add-locks=false --set-charset --no-create-info`
212
# Must come before `%.sql: _MySQL/%.sql` to override it
213
%.data.sql: _MySQL/%.data.sql
214
	$(if $(wildcard $@),,$(bin)/my2pg.data <$< >$@)
215

  
216
# The export must be created with:
217
# `--compatible=postgresql --add-locks=false --set-charset`
218
# Add `--no-data` to create a schema-only export.
219
%.sql: _MySQL/%.sql
220
	$(if $(wildcard $@),,$(bin)/my2pg <$< >$@)
221

  
222
##### Staging tables installation
223

  
224
srcTable := %.src
225

  
226
dbExportsWildcard = $(sort $(patsubst _MySQL/%.make,%,$(wildcard\
227
$(1) _MySQL/$(1).make)))
228

  
229
dbExports := $(call dbExportsWildcard,*schema*.sql)# schemas first
230
ifeq ($(schema_only),) # add rest of .sql files
231
dbExports += $(filter-out $(dbExports),$(call dbExportsWildcard,*.sql))
232
endif
233
dbExports := $(filter-out grants.sql,$(dbExports))
234
dbExports := $(strip $(dbExports))# += adds extra whitespace
235
allInstalls := $(if $(dbExports),sql) $(allTables)
236

  
237
datasrc_schema_exists = $(shell schema=$(datasrc)\
238
$(root)/lib/runscripts/local.run pg_schema_exists && echo t)
239

  
240
install: _always
241
	$(if $(wildcard ./run),./run install,$(if $(wildcard table.run),$(if\
242
$(datasrc_schema_exists),,+$(selfMake) install_oldstyle)))
243
	+$(selfMake) validate/install
244
# table.run: only run this for datasource dirs
245

  
246
install_oldstyle: _always schema $(allInstalls:%=%/install) ;
247

  
248
uninstall: _always confirm_rm_schema rm_schema ;
249
# rm_schema will also drop all staging tables
250

  
251
reinstall: _always uninstall install ;
252

  
253
confirm_rm_schema: _always
254
	$(if $(filter TNRS,$(datasrc)),$(call confirm,WARNING: This will delete the\
255
TNRS cache!,To save it: make backups/TNRS.backup-remake))
256

  
257
schema: _always
258
	-echo 'CREATE SCHEMA "$(datasrc)";'|$(psqlNoSearchPath)
259
# ignore errors if schema exists
260

  
261
rm_schema: _always
262
	echo 'DROP SCHEMA IF EXISTS "$(datasrc)" CASCADE;'|$(psqlNoSearchPath)
263

  
264
installLog := logs/install.log.sql
265

  
266
log_dir = $(1)logs
267
has_log_dir = $(call and,$(wildcard $(log_dir)),$(call not,$(noclobber)))
268
logInstall = $(if $(has_log_dir),$(if $(quiet),$(2)$(1)$(installLog)\
269
2>&1,2>&1|tee $(3) $(1)$(installLog)))
270
logInstallRoot = $(call logInstall,,>)
271
logInstall* = $(call logInstall,$*/,>)
272
logInstall*Add = $(call logInstall,$*/,>>,-a)# append to log
273

  
274
# Must come before %/install to override it
275
sql/install: $(dbExports)
276
	set -o pipefail; ($(inDatasrc); $(if $(wildcard schema.sql),cat schema.sql;)\
277
cat $(filter-out schema.sql grants.sql,$+)|pg_dump_limit $(if $(wildcard\
278
grants.sql),; cat grants.sql))|"time" env no_search_path=1 \
279
$(bin)/psql_$(if $(debug),verbose,script)_vegbien --set=schema='"$(datasrc)"' \
280
$(logInstallRoot)
281

  
282
# $debug option runs the *.sql import verbosely, to display which statements are
283
# being run. this should only be used for SQL files that use COPY FROM to import
284
# data, to avoid echoing pages of insert statements.
285
cleanup = set -o pipefail; \
286
$(if $(wildcard $*/cleanup.sql),($(inDatasrc); cat $*/cleanup.sql)\
287
|"time" $(psqlNoSearchPath) --echo-all --set=table='"$*"' $(logInstall*Add),\
288
(export schema=$(datasrc) table=$*; . $(bin)/vegbien_dest; unset schemas; \
289
$(bin)/csv2db) $(logInstall*Add))
290

  
291
%/header.csv:
292
	set -o pipefail; \
293
echo 'COPY (SELECT * FROM "$(datasrc)"."$*" LIMIT 0) TO STDOUT CSV HEADER;'|\
294
env no_search_path=1 $(bin)/psql_script_vegbien >$*/header.csv
295

  
296
exportHeader = $(selfMake) "$*/header.csv"
297

  
298
# Don't try to edit a view. Must come before %/install to override it.
299
%_view/install: _always ;
300

  
301
%.sql/run: _always
302
	$(if $(wildcard $(@D)),($(inDatasrc); cat $(@D))|(cd '$(*D)';\
303
"time" env no_search_path=1 ../$(bin)/psql_verbose_vegbien \
304
--set=table='"$(*D)"' --set=table_str=\''"$(*D)"'\'))
305

  
306
%/postprocess.sql: $(thesaurus) _always
307
	$(if $(wildcard $*/run),$(bin)/in_place $@ env text=1 $(bin)/repl $<)
308

  
309
%/postprocess: _always
310
	$(if\
311
$(wildcard $*/run),$*/run postprocess,$(selfMake) "$*/postprocess.sql/run")
312

  
313
%/map_table: _always
314
	$(if $(wildcard $*/run),$*/run map_table)
315

  
316
# For staging tables which are derived by joining together other staging tables.
317
%/install: %/create.sql _always
318
	set -o pipefail; \
319
($(inDatasrc); echo 'CREATE TABLE "$*" AS'; cat $<; echo ';')|"time" \
320
$(psqlNoSearchPath) --echo-all --set=schema='"$(datasrc)"' --set=table='"$*"' \
321
$(logInstall*)
322
	$(exportHeader)
323
	$(selfMake) "$*/postprocess"
324
	$(cleanup)
325

  
326
%/install: _always
327
	$(import_install_)
328
	$(exportHeader)
329
	$(selfMake) "$*/postprocess"
330
	$(cleanup)
331
define import_install_
332
set -o pipefail; (. $(bin)/vegbien_dest; unset schemas; "time" $(nice)\
333
env schema=$(datasrc) table=$* $(bin)/csv2db $(catSrcs) $(logInstall*))
334
$(if $(filter $(srcTable),$*),($(inDatasrc);\
335
echo 'ALTER TABLE "$(datasrc)"."$*" RENAME row_num TO "$*.row_num";')|"time"\
336
$(psqlNoSearchPath) --echo-all --set=table='"$*"' $(logInstall*Add))
337
endef
338
# table-scope src table's row_num col to allow joining it with other tables
339

  
340
%/uninstall: _always
341
	echo 'DROP $(if\
342
$(is_view),VIEW,TABLE) IF EXISTS "$(datasrc)"."$*" CASCADE;'|$(psqlNoSearchPath)
343

  
344
%/reinstall: _always %/uninstall %/install ;
345

  
346
postprocess: _always $(allTables:%=%/postprocess) ;
347

  
348
cleanup: _always $(tables:%=%/cleanup) ;
349

  
350
# WARNING: This removes any index comments, due to a PostgreSQL bug.
351
# This occurs because ALTER TABLE recreates the index but not its comment.
352
%/cleanup: _always
353
	$(cleanup)
354

  
355
##### Maps building
356

  
357
# Maps to (try to) build are added to this
358
maps :=
359

  
360
srcRoot = $(mappings)/root.sh
361
mkSrcMap = (. $(srcRoot); env datasrc=$(datasrc) $(bin)/src_map <$*/header.csv\
362
>$@)
363

  
364
translate = $(if $(wildcard $(1)),$(bin)/in_place $< $(bin)/translate_ci 1 $(1))
365

  
366
$(srcDict):# empty target in case it doesn't exist
367

  
368
# Via maps cleanup
369
ifneq ($(filter %/.map.csv.last_cleanup,$(MAKECMDGOALS)),)
370
%/.map.csv.last_cleanup: %/map.csv $(vocab) $(thesaurus) $(coreMap) $(srcDict)
371
	$(call translate,$(srcDict))
372
	$(bin)/in_place $< $(bin)/canon 1 $(vocab)
373
	$(call translate,$(thesaurus))
374
	$(bin)/in_place $< $(bin)/fix_line_endings
375
	touch $@
376
	+$(selfMake) $(<:%/map.csv=%/unmapped_terms.csv)
377
	+$(selfMake) $(<:%/map.csv=%/new_terms.csv)
378
.PRECIOUS: %/.map.csv.last_cleanup
379
else
380
%/map.csv: _always
381
	$(if $(wildcard $@),,$(mk_map_csv))
382
	+$(selfMake) $(@:%/map.csv=%/.map.csv.last_cleanup)
383
define mk_map_csv
384
+$(selfMake) "$*/header.csv"
385
$(mkSrcMap)
386
endef
387
endif
388

  
389
%/VegBIEN.csv: %/map.csv $(coreMap)
390
	$(if $(wildcard $*/run),-ln -s "../$(coreMap)" "$@"\
391
,<$< $(bin)/cat_cols 1 2|$(bin)/join $(coreMap)|$(bin)/sort_map >$@)
392
# ignore errors if symlink exists
393
maps += $(autogenMaps)
394

  
395
maps: $(maps) _always ;
396

  
397
all += $(maps)
398

  
399
##### Maps validation
400

  
401
# `tail -n +2`: Remove header before running filter_out_ci because filter_out_ci
402
# only removes the header if it matches the vocabulary's header.
403

  
404
%/unmapped_terms.csv: %/map.csv $(coreMap)
405
	tail -n +2 $<|$(bin)/cols 1|$(bin)/filter_out_ci 0 $(coreMap) >$@
406
	$(bin)/autoremove $@
407

  
408
%/new_terms.csv: %/map.csv $(vocab) $(thesaurus) %/unmapped_terms.csv
409
	$(newTerms)
410
	$(bin)/autoremove $@
411
newTerms = tail -n +2 $<|$(bin)/filter_out_ci 0 $(vocab)|$(bin)/filter_out_ci 0\
412
$(thesaurus) $(if $(wildcard $(word 4,$+)),|$(bin)/filter_out_ci 0 $(word 4,$+))\
413
|grep -vE -e '^"?:' -e 'UNUSED' >$@; exit 0 # grep exits nonzero if no match
414

  
415
termsSubdirs := $(tables)
416

  
417
include $(root)/lib/mappings.Makefile
418

  
419
##### External dependencies
420

  
421
$(root)/%: _always
422
	+$(subMake)
423
.PRECIOUS: $(root)/% # let ext. dir's Makefile decide whether to delete on error
424

  
425
##### Mapping
426

  
427
+maps = $(filter %/map.csv %/VegBIEN.csv $(mappings)/%,$(+_))
428
map2db = env in_database=vegbien in_schema=$(datasrc) in_table=$*\
429
out_database=vegbien source=$(datasrc).new $(root)/map $(+maps)
430

  
431
##### Import to VegBIEN
432

  
433
import_temp: $(importTables:%=%/import) _always ;
434

  
435
import: _always import_temp publish validate ; # removes temp suffix when done
436

  
437
rm: _always
438
	echo "SELECT datasource_rm('$(datasrc)');"|"time" $(psqlAsBien)
439

  
440
reimport: _always import ; # import replaces the previous import
441

  
442
profileTest = $(if $(profile),$(if $(test),1))
443
profileOnly = -env profile_to=/dev/fd/3 $(map2db) 3>&1 1>&2|\
444
$(bin)/profile_stats /dev/fd/0
445

  
446
log_ = $*/logs/$(if $(n),n=$(n).,)$(version).log.sql
447

  
448
# Displays the import log file path
449
# Run with `make -s` to avoid echoing make commands
450
%/log_file: _always
451
	echo $$(pwd)/$(log_)
452

  
453
trace = $(log_:.log.sql=.trace)
454
restart_row = $(shell set -x; grep -F Partition: $(log_)|tail -1|$(sed)\
455
's/^.* rows ([[:digit:]]+)-.*$$/\1/')
456
import = $(if $(profileTest),$(profileOnly),(set -x; date; "time" env commit=1\
457
$(if $(profile),profile_to=$(trace)) $(if $(continue),start=$(restart_row))\
458
$(map2db))$(if $(log), >>$(log_) 2>&1))
459

  
460
import? = $(if $(call and,$(full_import),$(call dontImport,.)),,$(import))
461

  
462
%/import_temp: %/VegBIEN.csv _always
463
	$(if $(full_import),-)$(import?)
464
# don't abort on import errors, which often relate to invalid input data
465
# default:
466
%/import_temp: _always ;
467

  
468
%/import: %/import_temp _always ;
469

  
470
#### Taxonomic scrubbing
471

  
472
scrub: _always
473
	$(selfMake) $(root)/scrub & echo $$!
474
# using & (background process) also ignores TNRS errors, so that TNRS bugs do
475
# not prevent the remaining tables from being imported even if TNRS can't be run
476

  
477
# Removes TNRS taxondeterminations
478
unscrub: _always
479
	echo "SELECT delete_scrubbed_taxondeterminations('$(datasrc)');"|\
480
"time" env no_query_results=1 $(psqlAsBien)
481

  
482
rescrub: _always unscrub scrub ;
483

  
484
import_scrub: _always import scrub ;
485

  
486
reimport_scrub: _always reimport scrub ;
487

  
488
%/import_scrub: _always %/import scrub ;
489

  
490
##### Log files from import
491

  
492
logs := $(wildcard */logs/*.log.sql */logs/*.trace)
493

  
494
rm_logs: _always
495
	$(RM) $(logs)
496

  
497
##### Verification of import
498

  
499
### new-style aggregating validations (also work w/ old-style import)
500

  
501
# must be in input.Makefile instead of table.run because some datasources that
502
# we validate still use old-style import
503

  
504
# validations.sql must be in a subdir so it won't get run by sql/install
505
validate/install: _always verify/validations.sql/run ;
506

  
507
validate: _always
508
	echo "SELECT remake_diff_tables('$(datasrc)');"\
509
|$(psqlAsBien)$(if $(log), >>.$(log_) 2>&1)
510

  
511
### old-style aggregating validations (not related to old-style import)
512

  
513
verifyTables := $(patsubst verify/%.ref,%,$(wildcard verify/*.ref))
514

  
515
verify: $(verifyTables:%=%/verify) _always ;
516

  
517
%/verify: verify/%.ref verify/%.out _always
518
	-$(diffVerbose) $(+_)
519
# don't abort on verification errors, which are expected during development
520
# default:
521
%/verify: verify/%.out _always
522
	$(if $(shell test -e $< && echo t),cat $<)
523
# don't run if verify/%.out's default do-nothing action was used
524
# can't use $(wildcard) because it won't recheck file after verify/%.out is run
525

  
526
psqlExport := "time" $(psqlNoSearchPath) --no-align --field-separator=$$'\t'\
527
--pset=footer=off --pset=null=NULL
528
# Note that using $(inDatasrc) will not work with datasources whose tables are
529
# the same name as VegBIEN tables (likely only VegBank), because the datasource
530
# is first in the search_path.
531
verify = $(if $(reverify),($(inDatasrc); cat $<)|$(psqlExport)\
532
--set=datasource="'$(datasrc)'" >$@)
533

  
534
verify/%.out: verify/%.out.sql _always
535
	$(verify)
536
.PRECIOUS: verify/%.out # save partial output in case of error to help debugging
537
# default:
538
verify/%.out: _always ;
539

  
540
all += $(wildcard verify/*.out)
541

  
542
%.ref: %.ref.sql
543
	($(inDatasrc); cat $<)|$(psqlExport) >$@
544
.PRECIOUS: %.ref # there must always be a .ref for the make rules to work
545

  
546
##### Editing import
547

  
548
rename/%: _always
549
	echo "UPDATE source SET shortname = '$*' WHERE shortname = '$(datasrc)';"\
550
|$(psqlAsBien)
551

  
552
%/publish: _always # usage: make inputs/src/src.version/publish
553
	echo "SELECT datasource_publish('$*');"|$(psqlAsBien)
554

  
555
publish: _always $(datasrc).new/publish ; # usage: make inputs/src/publish
556

  
557
##### Testing
558

  
559
testRefOutput = $(subst .by_col,,$(1))
560
testRef = $(testRefOutput).ref
561
hasOwnRef = $(filter $@,$(call testRefOutput,$@))
562
# filter returns non-empty if they are equal
563

  
564
# `rm $@`: Remove outputs of successful tests to reduce clutter
565
# `$(foreach use_staged...)`: Run with use_staged=1
566
define runTest
567
@echo "Testing $(abspath $@)..."
568
>$@ env test=1 n=$(test_n) $(1) $(foreach use_staged,1,$(map2db))
569
$(if $(hasOwnRef),,-)@(set -x; $(diffIgnoreSpace) $(call testRef,$@) $@) 2>&1\
570
&& rm $@ || { e=$$?; $(if $(wildcard $(call testRef,$@)),,cat $@;)\
571
$(if $(hasOwnRef),\
572
{\
573
read -p $(emph)'Accept new test output? (y/n)'$(endEmph) REPLY;\
574
if test "$$REPLY" = y; then\
575
(set -x; $(MAKE) $@-ok --directory=$(realpath .) --makefile=../input.Makefile);\
576
exit 0;\
577
fi;\
578
};,\
579
echo $(emph)"Note: The preceding failed test is compared to another test's\
580
output"$(endEmph);\
581
echo $(emph)"When it fails, this always indicates a bug"$(endEmph);\
582
)\
583
exit $$e;}
584
endef
585

  
586
tests :=
587

  
588
%/test: %/test.xml $(if $(by_col),%/test.by_col.xml) _always ;
589

  
590
# Requires staging tables. To create them, run `make inputs/<datasrc>/install`.
591
# Non-flat-file inputs fall back to mimicking a successful test
592
%/test.xml: %/VegBIEN.csv _always
593
	$(call runTest,by_col=)
594
tests += %/test.xml
595

  
596
%/test.by_col.xml: %/VegBIEN.csv _always
597
	$(call runTest,by_col=1)
598

  
599
# Only run column-based tests if column-based mode enabled, because these tests
600
# are much slower than the row-based tests for small numbers of rows
601
ifneq ($(by_col),)
602
tests += %/test.by_col.xml
603
endif
604

  
605
testOutputs := $(foreach test,$(tests),$(tables:%=$(test)))
606

  
607
.PRECIOUS: $(testOutputs) # save outputs of failed tests so they can be accepted
608

  
609
test: _always $(testOutputs) ;
610

  
611
all += $(wildcard %/test*.xml)
612

  
613
# Accepts a test output: make <test_output_path>-ok
614
%-ok: _always
615
	mv $* $(call testRef,$*)
616

  
617
accept-all: _always
618
	+yes|$(selfMake) test
619

  
620
##### Documentation
621

  
622
steps = $(selfMake) -s $*/import test=1 by_col=1 verbosity=2 n=100\
623
2>&1|$(bin)/debug2redmine >$@
624

  
625
%/logs/steps.by_col.log.sql: _always
626
	+$(steps)

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