| 1 |
783
|
aaronmk
|
##### Configuration
|
| 2 |
|
|
|
| 3 |
|
|
exts ?= csv xml
|
| 4 |
|
|
test_n ?= 2
|
| 5 |
|
|
tablesSort ?= plots organisms stems
|
| 6 |
|
|
mainCoreMapTry ?= organisms specimens
|
| 7 |
|
|
|
| 8 |
|
|
##### Vars/functions
|
| 9 |
|
|
|
| 10 |
640
|
aaronmk
|
selfDir_uZPPqC := $(dir $(lastword $(MAKEFILE_LIST)))
|
| 11 |
250
|
aaronmk
|
|
| 12 |
368
|
aaronmk
|
# Make
|
| 13 |
640
|
aaronmk
|
SHELL := /bin/bash
|
| 14 |
415
|
aaronmk
|
subMake = $(MAKE) $(@F) --directory=$(@D)
|
| 15 |
404
|
aaronmk
|
+_ = $(+:_%=)
|
| 16 |
368
|
aaronmk
|
addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
|
| 17 |
|
|
|
| 18 |
640
|
aaronmk
|
# Terminal
|
| 19 |
|
|
esc := '['
|
| 20 |
|
|
reset := $(esc)'0m'
|
| 21 |
|
|
emph := $(esc)'7m '
|
| 22 |
|
|
endEmph := ' '$(reset)
|
| 23 |
|
|
|
| 24 |
368
|
aaronmk
|
# Commands
|
| 25 |
395
|
aaronmk
|
CP = cp -p
|
| 26 |
|
|
DIFF = diff --unified=2
|
| 27 |
368
|
aaronmk
|
|
| 28 |
783
|
aaronmk
|
# Paths
|
| 29 |
640
|
aaronmk
|
root := $(selfDir_uZPPqC)..
|
| 30 |
775
|
aaronmk
|
mappings := $(root)/mappings
|
| 31 |
368
|
aaronmk
|
psqlAsBien := $(root)/bin/psql_vegbien
|
| 32 |
353
|
aaronmk
|
|
| 33 |
783
|
aaronmk
|
##### General targets
|
| 34 |
250
|
aaronmk
|
|
| 35 |
418
|
aaronmk
|
all: _always maps ;
|
| 36 |
247
|
aaronmk
|
|
| 37 |
|
|
.SUFFIXES:
|
| 38 |
|
|
|
| 39 |
383
|
aaronmk
|
_always:
|
| 40 |
|
|
.PHONY: _always
|
| 41 |
250
|
aaronmk
|
|
| 42 |
383
|
aaronmk
|
clean: _always
|
| 43 |
256
|
aaronmk
|
$(RM) $(all)
|
| 44 |
|
|
|
| 45 |
423
|
aaronmk
|
remake: _always clean all ;
|
| 46 |
|
|
|
| 47 |
515
|
aaronmk
|
%.out: %.make _always
|
| 48 |
368
|
aaronmk
|
./$* >$@
|
| 49 |
|
|
.PRECIOUS: %.out
|
| 50 |
|
|
|
| 51 |
415
|
aaronmk
|
$(root)/%: _always
|
| 52 |
|
|
+$(subMake)
|
| 53 |
|
|
|
| 54 |
783
|
aaronmk
|
##### SVN
|
| 55 |
250
|
aaronmk
|
|
| 56 |
766
|
aaronmk
|
svn_props: _always
|
| 57 |
768
|
aaronmk
|
svn propset svn:ignore $$'.~*\n*.log\n*.out\nsrc*' .
|
| 58 |
766
|
aaronmk
|
$(if $(wildcard test/),svn propset svn:ignore $$'*.out\n*.xml' test)
|
| 59 |
|
|
|
| 60 |
783
|
aaronmk
|
##### Installation
|
| 61 |
766
|
aaronmk
|
|
| 62 |
418
|
aaronmk
|
reinstall: _always uninstall install ;
|
| 63 |
264
|
aaronmk
|
|
| 64 |
783
|
aaronmk
|
##### Maps
|
| 65 |
264
|
aaronmk
|
|
| 66 |
728
|
aaronmk
|
allViaMaps := $(filter-out maps/VegBIEN.%.csv,$(wildcard maps/*.csv))
|
| 67 |
|
|
via := $(firstword $(sort $(basename $(basename $(notdir $(allViaMaps))))))
|
| 68 |
783
|
aaronmk
|
|
| 69 |
775
|
aaronmk
|
coreMap := $(mappings)/$(via)-VegBIEN.%.csv
|
| 70 |
|
|
mainCoreMap := $(firstword $(wildcard $(mainCoreMapTry:%=$(coreMap))))
|
| 71 |
783
|
aaronmk
|
|
| 72 |
749
|
aaronmk
|
viaMaps := $(wildcard $(tablesSort:%=maps/$(via).%.csv))
|
| 73 |
|
|
viaMaps += $(filter-out $(viaMaps),$(wildcard maps/$(via).*.csv))
|
| 74 |
783
|
aaronmk
|
|
| 75 |
728
|
aaronmk
|
autogenMaps := $(subst $(via).,VegBIEN.,$(viaMaps))
|
| 76 |
|
|
directMaps := $(autogenMaps) $(filter-out $(autogenMaps),\
|
| 77 |
|
|
$(wildcard maps/VegBIEN.*.csv))
|
| 78 |
772
|
aaronmk
|
tables := $(directMaps:maps/VegBIEN.%.csv=%)
|
| 79 |
728
|
aaronmk
|
|
| 80 |
724
|
aaronmk
|
maps: $(directMaps) _always ;
|
| 81 |
368
|
aaronmk
|
|
| 82 |
728
|
aaronmk
|
.PRECIOUS: $(allViaMaps) $(directMaps)
|
| 83 |
368
|
aaronmk
|
|
| 84 |
728
|
aaronmk
|
all += $(autogenMaps)
|
| 85 |
|
|
|
| 86 |
775
|
aaronmk
|
maps/VegBIEN.%.csv: maps/$(via).%.csv $(coreMap)
|
| 87 |
415
|
aaronmk
|
$(root)/bin/join_sort <$+ >$@
|
| 88 |
775
|
aaronmk
|
.PRECIOUS: maps/VegBIEN.%.csv $(coreMap)
|
| 89 |
264
|
aaronmk
|
|
| 90 |
783
|
aaronmk
|
##### Mapping
|
| 91 |
368
|
aaronmk
|
|
| 92 |
728
|
aaronmk
|
dbFile := $(firstword $(wildcard src/db.*.sql))
|
| 93 |
772
|
aaronmk
|
inputFiles := $(wildcard src/*.csv src/*.xml)
|
| 94 |
728
|
aaronmk
|
|
| 95 |
775
|
aaronmk
|
+maps = $(filter maps/% $(mappings)/%,$(+_))
|
| 96 |
|
|
<in = $(firstword $(filter-out $(+maps),$(+_)) $(wildcard $(exts:%=src/*.$*.%)))
|
| 97 |
|
|
map = $(if $(<in),<$(<in) ,$(if $(mapEnv),env $(mapEnv) ))$(root)/map $(+maps)
|
| 98 |
772
|
aaronmk
|
map2db = env out_database=vegbien $(map)
|
| 99 |
368
|
aaronmk
|
|
| 100 |
783
|
aaronmk
|
##### Import to VegBIEN
|
| 101 |
772
|
aaronmk
|
|
| 102 |
|
|
ifneq ($(dbFile)$(inputFiles),)
|
| 103 |
|
|
|
| 104 |
718
|
aaronmk
|
import: _always import-all verify ;
|
| 105 |
368
|
aaronmk
|
|
| 106 |
718
|
aaronmk
|
log = $(@:-all=)$(if $(n),.n=$(n),).log
|
| 107 |
772
|
aaronmk
|
import = -(set -x; "time" env commit=1 $(map2db)) \
|
| 108 |
718
|
aaronmk
|
$(if $(n),,>>$(log)) 2>&1$(if $(n),|tee -a $(log))
|
| 109 |
636
|
aaronmk
|
# ignore import errors, which are often benign (e.g. invalid date format)
|
| 110 |
624
|
aaronmk
|
|
| 111 |
772
|
aaronmk
|
ifneq ($(inputFiles),)
|
| 112 |
|
|
import-all: $(addprefix import-,$(tables)) _always ;
|
| 113 |
|
|
else
|
| 114 |
724
|
aaronmk
|
import-all: $(directMaps) _always
|
| 115 |
718
|
aaronmk
|
$(import)
|
| 116 |
772
|
aaronmk
|
endif
|
| 117 |
718
|
aaronmk
|
|
| 118 |
|
|
import-%: maps/VegBIEN.%.csv _always
|
| 119 |
|
|
$(import)
|
| 120 |
772
|
aaronmk
|
# default:
|
| 121 |
|
|
import-%: _always ;
|
| 122 |
718
|
aaronmk
|
|
| 123 |
772
|
aaronmk
|
else
|
| 124 |
|
|
import: _always ;
|
| 125 |
|
|
endif
|
| 126 |
|
|
|
| 127 |
339
|
aaronmk
|
logs := $(wildcard *.log)
|
| 128 |
|
|
|
| 129 |
383
|
aaronmk
|
rm_logs: _always
|
| 130 |
339
|
aaronmk
|
$(RM) $(logs)
|
| 131 |
|
|
|
| 132 |
783
|
aaronmk
|
##### Verification of import
|
| 133 |
264
|
aaronmk
|
|
| 134 |
624
|
aaronmk
|
ifneq ($(wildcard verify.ref*),)
|
| 135 |
|
|
|
| 136 |
514
|
aaronmk
|
verify: verify.ref verify.out _always
|
| 137 |
404
|
aaronmk
|
$(DIFF) $(+_)
|
| 138 |
368
|
aaronmk
|
|
| 139 |
514
|
aaronmk
|
all += verify.out
|
| 140 |
|
|
|
| 141 |
383
|
aaronmk
|
%.out: %.sql _always
|
| 142 |
429
|
aaronmk
|
$(out_cmd)
|
| 143 |
370
|
aaronmk
|
.PRECIOUS: %.out
|
| 144 |
772
|
aaronmk
|
out_cmd = $(psqlAsBien) --no-align --field-separator=' ' --pset=footer=off\
|
| 145 |
429
|
aaronmk
|
--pset=null=NULL <$< >$@
|
| 146 |
369
|
aaronmk
|
|
| 147 |
624
|
aaronmk
|
else
|
| 148 |
|
|
verify: _always ;
|
| 149 |
|
|
endif
|
| 150 |
|
|
|
| 151 |
783
|
aaronmk
|
##### Testing
|
| 152 |
368
|
aaronmk
|
|
| 153 |
624
|
aaronmk
|
ifneq ($(wildcard test/),)
|
| 154 |
|
|
|
| 155 |
724
|
aaronmk
|
tests :=
|
| 156 |
368
|
aaronmk
|
|
| 157 |
723
|
aaronmk
|
hasOwnRef = $(filter-out %.2-step.xml,$@)
|
| 158 |
630
|
aaronmk
|
testRef = $(1:.2-step.xml=.xml).ref
|
| 159 |
|
|
|
| 160 |
629
|
aaronmk
|
define test
|
| 161 |
776
|
aaronmk
|
@echo "Testing $(abspath $@)..."
|
| 162 |
775
|
aaronmk
|
>$@ env test=1 verbose=1 n=$(test_n) $(1)
|
| 163 |
653
|
aaronmk
|
@(set -x; $(DIFF) $(call testRef,$@) $@) 2>&1 || { e=$$?;\
|
| 164 |
780
|
aaronmk
|
$(if $(wildcard $(call testRef,$@)),,cat $@;)\
|
| 165 |
777
|
aaronmk
|
$(if $(hasOwnRef),\
|
| 166 |
|
|
echo $(emph)"To accept new test output:"$(endEmph);\
|
| 167 |
|
|
echo "$(MAKE) $@-ok --directory=$(realpath .) --makefile=../input.Makefile";\
|
| 168 |
|
|
,\
|
| 169 |
|
|
echo $(emph)"Note: The preceding failed test is compared to another test's\
|
| 170 |
|
|
output"$(endEmph);\
|
| 171 |
|
|
echo $(emph)"When it fails, this always indicates a bug"$(endEmph);\
|
| 172 |
|
|
)\
|
| 173 |
652
|
aaronmk
|
exit $$e;}
|
| 174 |
628
|
aaronmk
|
endef
|
| 175 |
|
|
|
| 176 |
775
|
aaronmk
|
test2File = $(call test,$(map))
|
| 177 |
|
|
|
| 178 |
724
|
aaronmk
|
test/$(via).xml: $(viaMaps) _always
|
| 179 |
775
|
aaronmk
|
$(test2File)
|
| 180 |
724
|
aaronmk
|
tests += test/$(via).xml
|
| 181 |
629
|
aaronmk
|
|
| 182 |
724
|
aaronmk
|
test/VegBIEN.xml: $(directMaps) _always
|
| 183 |
775
|
aaronmk
|
$(test2File)
|
| 184 |
724
|
aaronmk
|
tests += test/VegBIEN.xml
|
| 185 |
628
|
aaronmk
|
|
| 186 |
775
|
aaronmk
|
test/VegBIEN.2-step.xml: test/$(via).xml $(mainCoreMap) _always
|
| 187 |
|
|
-$(test2File)
|
| 188 |
722
|
aaronmk
|
# Don't abort tester if only 2-step test fails, as it's often finicky
|
| 189 |
724
|
aaronmk
|
tests += test/VegBIEN.2-step.xml
|
| 190 |
630
|
aaronmk
|
|
| 191 |
724
|
aaronmk
|
test/import.out: $(directMaps) _always
|
| 192 |
718
|
aaronmk
|
$(call test,$(map2db))
|
| 193 |
724
|
aaronmk
|
tests += test/import.out
|
| 194 |
627
|
aaronmk
|
|
| 195 |
724
|
aaronmk
|
test: _always $(tests) ;
|
| 196 |
|
|
|
| 197 |
|
|
.PRECIOUS: $(tests)
|
| 198 |
|
|
|
| 199 |
|
|
all += $(tests)
|
| 200 |
|
|
|
| 201 |
634
|
aaronmk
|
# Accepts a test output: make <test_output_path>-ok
|
| 202 |
626
|
aaronmk
|
%-ok: _always
|
| 203 |
630
|
aaronmk
|
$(CP) $* $(call testRef,$*)
|
| 204 |
502
|
aaronmk
|
|
| 205 |
624
|
aaronmk
|
else
|
| 206 |
|
|
test: _always ;
|
| 207 |
|
|
endif
|
| 208 |
|
|
|
| 209 |
783
|
aaronmk
|
##### Input-type-specific
|
| 210 |
368
|
aaronmk
|
|
| 211 |
624
|
aaronmk
|
# Each input type needs var $(mapEnv) and targets install, uninstall
|
| 212 |
|
|
|
| 213 |
622
|
aaronmk
|
ifneq ($(dbFile),)
|
| 214 |
256
|
aaronmk
|
|
| 215 |
635
|
aaronmk
|
dbEngineExt := $(subst .,,$(suffix $(basename $(notdir $(dbFile)))))
|
| 216 |
|
|
db := $(notdir $(realpath .))
|
| 217 |
622
|
aaronmk
|
|
| 218 |
621
|
aaronmk
|
%.ref: %.ref.sql
|
| 219 |
|
|
$(inputDbAsBien) $(db) <$< >$@
|
| 220 |
|
|
.PRECIOUS: %.ref
|
| 221 |
|
|
|
| 222 |
783
|
aaronmk
|
#### Installation
|
| 223 |
256
|
aaronmk
|
|
| 224 |
621
|
aaronmk
|
install: _always db ;
|
| 225 |
339
|
aaronmk
|
|
| 226 |
621
|
aaronmk
|
uninstall: _always rm_db ;
|
| 227 |
368
|
aaronmk
|
|
| 228 |
783
|
aaronmk
|
#### DB-engine-specific
|
| 229 |
621
|
aaronmk
|
|
| 230 |
624
|
aaronmk
|
# Each DB engine needs vars $(dbEngine), $(dbAsBien) and targets db, rm_db
|
| 231 |
256
|
aaronmk
|
|
| 232 |
622
|
aaronmk
|
ifeq ($(dbEngineExt),my)
|
| 233 |
621
|
aaronmk
|
|
| 234 |
622
|
aaronmk
|
dbEngine := MySQL
|
| 235 |
|
|
|
| 236 |
621
|
aaronmk
|
bienPassword := $(shell cat $(root)/config/bien_password)
|
| 237 |
|
|
mysqlAs = mysql --user=$(1) --password='$(bienPassword)'
|
| 238 |
|
|
mysqlAsRoot := $(call mysqlAs,root)
|
| 239 |
|
|
dbAsBien := $(call mysqlAs,bien)
|
| 240 |
|
|
|
| 241 |
622
|
aaronmk
|
db: $(dbFile) _always
|
| 242 |
635
|
aaronmk
|
echo "CREATE DATABASE $(db) DEFAULT CHARACTER SET latin1;"|$(mysqlAsRoot)
|
| 243 |
|
|
-$(mysqlAsRoot) --database=$(db) <$<
|
| 244 |
368
|
aaronmk
|
echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 245 |
255
|
aaronmk
|
# ignore errors in db import so that GRANT will still be run
|
| 246 |
250
|
aaronmk
|
|
| 247 |
383
|
aaronmk
|
rm_db: _always
|
| 248 |
368
|
aaronmk
|
-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 249 |
|
|
echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
|
| 250 |
365
|
aaronmk
|
# ignore errors if grant not defined
|
| 251 |
250
|
aaronmk
|
|
| 252 |
783
|
aaronmk
|
### Unrecognized DB engine
|
| 253 |
368
|
aaronmk
|
|
| 254 |
|
|
else
|
| 255 |
635
|
aaronmk
|
$(error The DB filename $(dbFile) must have the form db.{my|pg}.sql)
|
| 256 |
368
|
aaronmk
|
endif
|
| 257 |
|
|
|
| 258 |
622
|
aaronmk
|
# Must come after dbEngine is set
|
| 259 |
|
|
mapEnv := in_engine=$(dbEngine) in_database=$(db)
|
| 260 |
|
|
|
| 261 |
783
|
aaronmk
|
#### Unrecognized input type
|
| 262 |
624
|
aaronmk
|
|
| 263 |
256
|
aaronmk
|
else
|
| 264 |
624
|
aaronmk
|
install: _always ;
|
| 265 |
|
|
uninstall: _always ;
|
| 266 |
256
|
aaronmk
|
endif
|
