| 1 |
256
|
aaronmk
|
selfDir_3d1bc249 := $(dir $(lastword $(MAKEFILE_LIST)))
|
| 2 |
250
|
aaronmk
|
|
| 3 |
368
|
aaronmk
|
# Make
|
| 4 |
415
|
aaronmk
|
subMake = $(MAKE) $(@F) --directory=$(@D)
|
| 5 |
404
|
aaronmk
|
+_ = $(+:_%=)
|
| 6 |
368
|
aaronmk
|
addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
|
| 7 |
|
|
|
| 8 |
|
|
# Commands
|
| 9 |
395
|
aaronmk
|
CP = cp -p
|
| 10 |
|
|
DIFF = diff --unified=2
|
| 11 |
368
|
aaronmk
|
|
| 12 |
415
|
aaronmk
|
tablesSort := plots organisms stems
|
| 13 |
502
|
aaronmk
|
vegxMaps := $(wildcard $(tablesSort:%=maps/VegX.%.csv))
|
| 14 |
|
|
vegxMaps += $(filter-out $(vegxMaps),$(wildcard maps/VegX.*.csv))
|
| 15 |
|
|
tables := $(vegxMaps:maps/VegX.%.csv=%)
|
| 16 |
|
|
vegbienMaps := $(subst VegX.,VegBIEN.,$(vegxMaps))
|
| 17 |
247
|
aaronmk
|
|
| 18 |
368
|
aaronmk
|
root := $(selfDir_3d1bc249)..
|
| 19 |
|
|
psqlAsBien := $(root)/bin/psql_vegbien
|
| 20 |
353
|
aaronmk
|
|
| 21 |
401
|
aaronmk
|
# Config
|
| 22 |
|
|
test_n ?= 2
|
| 23 |
|
|
|
| 24 |
250
|
aaronmk
|
#####
|
| 25 |
|
|
|
| 26 |
418
|
aaronmk
|
all: _always maps ;
|
| 27 |
247
|
aaronmk
|
|
| 28 |
|
|
.SUFFIXES:
|
| 29 |
|
|
|
| 30 |
383
|
aaronmk
|
_always:
|
| 31 |
|
|
.PHONY: _always
|
| 32 |
250
|
aaronmk
|
|
| 33 |
383
|
aaronmk
|
clean: _always
|
| 34 |
256
|
aaronmk
|
$(RM) $(all)
|
| 35 |
|
|
|
| 36 |
423
|
aaronmk
|
remake: _always clean all ;
|
| 37 |
|
|
|
| 38 |
515
|
aaronmk
|
%.out: %.make _always
|
| 39 |
368
|
aaronmk
|
./$* >$@
|
| 40 |
|
|
.PRECIOUS: %.out
|
| 41 |
|
|
|
| 42 |
415
|
aaronmk
|
$(root)/%: _always
|
| 43 |
|
|
+$(subMake)
|
| 44 |
|
|
|
| 45 |
250
|
aaronmk
|
#####
|
| 46 |
|
|
|
| 47 |
418
|
aaronmk
|
reinstall: _always uninstall install ;
|
| 48 |
264
|
aaronmk
|
|
| 49 |
|
|
#####
|
| 50 |
|
|
|
| 51 |
418
|
aaronmk
|
maps: $(vegbienMaps) _always ;
|
| 52 |
368
|
aaronmk
|
|
| 53 |
|
|
all += $(vegbienMaps)
|
| 54 |
|
|
|
| 55 |
502
|
aaronmk
|
maps/VegBIEN.%.csv: maps/VegX.%.csv $(root)/mappings/VegX-VegBIEN.%.csv
|
| 56 |
415
|
aaronmk
|
$(root)/bin/join_sort <$+ >$@
|
| 57 |
502
|
aaronmk
|
.PRECIOUS: maps/VegBIEN.%.csv
|
| 58 |
264
|
aaronmk
|
|
| 59 |
368
|
aaronmk
|
#####
|
| 60 |
|
|
|
| 61 |
418
|
aaronmk
|
import: _always $(addprefix import-,$(tables)) verify ;
|
| 62 |
368
|
aaronmk
|
|
| 63 |
|
|
log = $*$(if $(n),.n=$(n),).log
|
| 64 |
|
|
|
| 65 |
624
|
aaronmk
|
import-%: maps/VegBIEN.%.csv _always
|
| 66 |
|
|
-$(import_cmd)
|
| 67 |
628
|
aaronmk
|
import_cmd = (set -x; "time" env commit=1 $(import) $<) \
|
| 68 |
624
|
aaronmk
|
$(if $(n),,>>$(log)) 2>&1$(if $(n),|tee -a $(log))
|
| 69 |
|
|
|
| 70 |
339
|
aaronmk
|
logs := $(wildcard *.log)
|
| 71 |
|
|
|
| 72 |
383
|
aaronmk
|
rm_logs: _always
|
| 73 |
339
|
aaronmk
|
$(RM) $(logs)
|
| 74 |
|
|
|
| 75 |
264
|
aaronmk
|
#####
|
| 76 |
|
|
|
| 77 |
624
|
aaronmk
|
ifneq ($(wildcard verify.ref*),)
|
| 78 |
|
|
|
| 79 |
514
|
aaronmk
|
verify: verify.ref verify.out _always
|
| 80 |
404
|
aaronmk
|
$(DIFF) $(+_)
|
| 81 |
368
|
aaronmk
|
|
| 82 |
514
|
aaronmk
|
all += verify.out
|
| 83 |
|
|
|
| 84 |
383
|
aaronmk
|
%.out: %.sql _always
|
| 85 |
429
|
aaronmk
|
$(out_cmd)
|
| 86 |
370
|
aaronmk
|
.PRECIOUS: %.out
|
| 87 |
429
|
aaronmk
|
out_cmd = $(psqlAsBien) --no-align --field-separator=' ' --pset=footer=off \
|
| 88 |
|
|
--pset=null=NULL <$< >$@
|
| 89 |
369
|
aaronmk
|
|
| 90 |
624
|
aaronmk
|
else
|
| 91 |
|
|
verify: _always ;
|
| 92 |
|
|
endif
|
| 93 |
|
|
|
| 94 |
368
|
aaronmk
|
#####
|
| 95 |
|
|
|
| 96 |
624
|
aaronmk
|
ifneq ($(wildcard test/),)
|
| 97 |
|
|
|
| 98 |
628
|
aaronmk
|
testOutputs := test/VegBIEN.xml test/import.out
|
| 99 |
368
|
aaronmk
|
|
| 100 |
628
|
aaronmk
|
test: _always $(testOutputs) ;
|
| 101 |
395
|
aaronmk
|
|
| 102 |
628
|
aaronmk
|
all += $(testOutputs)
|
| 103 |
|
|
|
| 104 |
|
|
define runTest
|
| 105 |
|
|
env test=1 n=$(test_n) $(1) $(+_)$(if $(2),, >$@) 2>&1$(if $(2), |\
|
| 106 |
|
|
grep -v -E '^$(2)$$' >$@) || { e=$$?; cat $@; exit $$e;}
|
| 107 |
|
|
$(DIFF) $@.ref $@
|
| 108 |
|
|
endef
|
| 109 |
|
|
|
| 110 |
|
|
test/VegBIEN.xml: $(vegbienMaps) _always
|
| 111 |
|
|
$(call runTest,$(map),Processed .* input rows)
|
| 112 |
|
|
.PRECIOUS: test/VegBIEN.xml
|
| 113 |
|
|
|
| 114 |
627
|
aaronmk
|
test/import.out: $(vegbienMaps) _always
|
| 115 |
628
|
aaronmk
|
$(call runTest,$(import))
|
| 116 |
627
|
aaronmk
|
.PRECIOUS: test/import.out
|
| 117 |
|
|
|
| 118 |
626
|
aaronmk
|
%-ok: _always
|
| 119 |
|
|
$(CP) $* $*.ref
|
| 120 |
502
|
aaronmk
|
|
| 121 |
624
|
aaronmk
|
else
|
| 122 |
|
|
test: _always ;
|
| 123 |
|
|
endif
|
| 124 |
|
|
|
| 125 |
368
|
aaronmk
|
#####
|
| 126 |
|
|
|
| 127 |
624
|
aaronmk
|
# Each input type needs var $(mapEnv) and targets install, uninstall
|
| 128 |
|
|
|
| 129 |
622
|
aaronmk
|
dbFile := $(firstword $(wildcard src/*.sql))
|
| 130 |
256
|
aaronmk
|
|
| 131 |
622
|
aaronmk
|
ifneq ($(dbFile),)
|
| 132 |
256
|
aaronmk
|
|
| 133 |
622
|
aaronmk
|
dbFileBasename := $(basename $(notdir $(dbFile)))
|
| 134 |
|
|
dbEngineExt := $(subst .,,$(suffix $(dbFileBasename)))
|
| 135 |
|
|
db := $(basename $(dbFileBasename))
|
| 136 |
|
|
|
| 137 |
621
|
aaronmk
|
%.ref: %.ref.sql
|
| 138 |
|
|
$(inputDbAsBien) $(db) <$< >$@
|
| 139 |
|
|
.PRECIOUS: %.ref
|
| 140 |
|
|
|
| 141 |
368
|
aaronmk
|
####
|
| 142 |
256
|
aaronmk
|
|
| 143 |
621
|
aaronmk
|
install: _always db ;
|
| 144 |
339
|
aaronmk
|
|
| 145 |
621
|
aaronmk
|
uninstall: _always rm_db ;
|
| 146 |
368
|
aaronmk
|
|
| 147 |
621
|
aaronmk
|
####
|
| 148 |
|
|
|
| 149 |
624
|
aaronmk
|
# Each DB engine needs vars $(dbEngine), $(dbAsBien) and targets db, rm_db
|
| 150 |
256
|
aaronmk
|
|
| 151 |
622
|
aaronmk
|
ifeq ($(dbEngineExt),my)
|
| 152 |
621
|
aaronmk
|
|
| 153 |
622
|
aaronmk
|
dbEngine := MySQL
|
| 154 |
|
|
|
| 155 |
621
|
aaronmk
|
bienPassword := $(shell cat $(root)/config/bien_password)
|
| 156 |
|
|
mysqlAs = mysql --user=$(1) --password='$(bienPassword)'
|
| 157 |
|
|
mysqlAsRoot := $(call mysqlAs,root)
|
| 158 |
|
|
dbAsBien := $(call mysqlAs,bien)
|
| 159 |
|
|
|
| 160 |
622
|
aaronmk
|
db: $(dbFile) _always
|
| 161 |
368
|
aaronmk
|
-$(mysqlAsRoot) <$<
|
| 162 |
|
|
echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 163 |
255
|
aaronmk
|
# ignore errors in db import so that GRANT will still be run
|
| 164 |
250
|
aaronmk
|
|
| 165 |
383
|
aaronmk
|
rm_db: _always
|
| 166 |
368
|
aaronmk
|
-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 167 |
|
|
echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
|
| 168 |
365
|
aaronmk
|
# ignore errors if grant not defined
|
| 169 |
250
|
aaronmk
|
|
| 170 |
624
|
aaronmk
|
###
|
| 171 |
368
|
aaronmk
|
|
| 172 |
|
|
else
|
| 173 |
624
|
aaronmk
|
$(error The DB filename $(dbFile) must have the form <db_name>.{my|pg}.sql)
|
| 174 |
368
|
aaronmk
|
endif
|
| 175 |
|
|
|
| 176 |
622
|
aaronmk
|
# Must come after dbEngine is set
|
| 177 |
|
|
mapEnv := in_engine=$(dbEngine) in_database=$(db)
|
| 178 |
|
|
|
| 179 |
624
|
aaronmk
|
####
|
| 180 |
|
|
|
| 181 |
256
|
aaronmk
|
else
|
| 182 |
624
|
aaronmk
|
mapEnv :=
|
| 183 |
|
|
install: _always ;
|
| 184 |
|
|
uninstall: _always ;
|
| 185 |
256
|
aaronmk
|
endif
|
| 186 |
368
|
aaronmk
|
|
| 187 |
|
|
#####
|
| 188 |
|
|
|
| 189 |
|
|
# Must come after mapEnv is set
|
| 190 |
628
|
aaronmk
|
map := $(if $(mapEnv),env $(mapEnv) ,)$(root)/map
|
| 191 |
|
|
import := env out_database=vegbien $(map)
|
