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1
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selfDir_3d1bc249 := $(dir $(lastword $(MAKEFILE_LIST)))
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2
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3
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# Make
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4
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subMake = $(MAKE) $(@F) --directory=$(@D)
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5
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+_ = $(+:_%=)
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6
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addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
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7
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8
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# Commands
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9
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CP = cp -p
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10
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DIFF = diff --unified=2
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11
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12
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tablesSort := plots organisms stems
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13
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vegxMaps := $(wildcard $(tablesSort:%=maps/VegX.%.csv))
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14
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vegxMaps += $(filter-out $(vegxMaps),$(wildcard maps/VegX.*.csv))
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15
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tables := $(vegxMaps:maps/VegX.%.csv=%)
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16
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vegbienMaps := $(subst VegX.,VegBIEN.,$(vegxMaps))
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17
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18
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root := $(selfDir_3d1bc249)..
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19
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psqlAsBien := $(root)/bin/psql_vegbien
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20
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21
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# Config
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22
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test_n ?= 2
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23
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24
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#####
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|
25
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26
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all: _always maps ;
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27
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28
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.SUFFIXES:
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29
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30
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_always:
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31
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.PHONY: _always
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32
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33
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clean: _always
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34
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$(RM) $(all)
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35
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36
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remake: _always clean all ;
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37
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|
38
|
%.out: %.make _always
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|
39
|
./$* >$@
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|
40
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.PRECIOUS: %.out
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|
41
|
|
|
42
|
$(root)/%: _always
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|
43
|
+$(subMake)
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|
44
|
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|
45
|
#####
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|
46
|
|
|
47
|
reinstall: _always uninstall install ;
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|
48
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|
|
49
|
#####
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|
50
|
|
|
51
|
maps: $(vegbienMaps) _always ;
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52
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|
53
|
all += $(vegbienMaps)
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54
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|
|
55
|
maps/VegBIEN.%.csv: maps/VegX.%.csv $(root)/mappings/VegX-VegBIEN.%.csv
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|
56
|
$(root)/bin/join_sort <$+ >$@
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|
57
|
.PRECIOUS: maps/VegBIEN.%.csv
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|
58
|
|
|
59
|
#####
|
|
60
|
|
|
61
|
import: _always $(addprefix import-,$(tables)) verify ;
|
|
62
|
|
|
63
|
log = $*$(if $(n),.n=$(n),).log
|
|
64
|
|
|
65
|
logs := $(wildcard *.log)
|
|
66
|
|
|
67
|
rm_logs: _always
|
|
68
|
$(RM) $(logs)
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|
69
|
|
|
70
|
#####
|
|
71
|
|
|
72
|
verify: verify.ref verify.out _always
|
|
73
|
$(DIFF) $(+_)
|
|
74
|
|
|
75
|
all += verify.out
|
|
76
|
|
|
77
|
%.out: %.sql _always
|
|
78
|
$(out_cmd)
|
|
79
|
.PRECIOUS: %.out
|
|
80
|
out_cmd = $(psqlAsBien) --no-align --field-separator=' ' --pset=footer=off \
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|
81
|
--pset=null=NULL <$< >$@
|
|
82
|
|
|
83
|
#####
|
|
84
|
|
|
85
|
test: test.out _always
|
|
86
|
$(DIFF) $(<:.out=.ref) $<
|
|
87
|
|
|
88
|
all += test.out
|
|
89
|
|
|
90
|
accept: _always
|
|
91
|
$(CP) test.out test.ref
|
|
92
|
|
|
93
|
#####
|
|
94
|
|
|
95
|
ifdef db
|
|
96
|
|
|
97
|
mapEnv := in_engine=$(dbEngine) in_database=$(db)
|
|
98
|
|
|
99
|
####
|
|
100
|
|
|
101
|
ifeq ($(dbEngine),MySQL)
|
|
102
|
|
|
103
|
bienPassword := $(shell cat $(root)/config/bien_password)
|
|
104
|
mysqlAs = mysql --user=$(1) --password='$(bienPassword)'
|
|
105
|
mysqlAsRoot := $(call mysqlAs,root)
|
|
106
|
mysqlAsBien := $(call mysqlAs,bien)
|
|
107
|
|
|
108
|
import-%: maps/VegBIEN.%.csv _always
|
|
109
|
-$(import_cmd)
|
|
110
|
import_cmd = (set -x; "time" env commit=1 $(map) $<) \
|
|
111
|
$(if $(n),,>>$(log)) 2>&1$(if $(n),|tee -a $(log))
|
|
112
|
|
|
113
|
%.ref: %.ref.sql
|
|
114
|
$(mysqlAsBien) $(db) <$< >$@
|
|
115
|
.PRECIOUS: %.ref
|
|
116
|
|
|
117
|
###
|
|
118
|
|
|
119
|
install: _always db ;
|
|
120
|
|
|
121
|
uninstall: _always rm_db ;
|
|
122
|
|
|
123
|
db: src.$(db).sql _always
|
|
124
|
-$(mysqlAsRoot) <$<
|
|
125
|
echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
|
|
126
|
# ignore errors in db import so that GRANT will still be run
|
|
127
|
|
|
128
|
rm_db: _always
|
|
129
|
-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
|
|
130
|
echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
|
|
131
|
# ignore errors if grant not defined
|
|
132
|
|
|
133
|
###
|
|
134
|
|
|
135
|
else
|
|
136
|
$(error dbEngine variable must be one of the following: MySQL, PostgreSQL)
|
|
137
|
endif
|
|
138
|
|
|
139
|
####
|
|
140
|
|
|
141
|
test.out: $(vegbienMaps) _always
|
|
142
|
env test=1 n=$(test_n) $(map) $(+_) >$@ 2>&1 || { e=$$?; cat $@; exit $$e;}
|
|
143
|
.PRECIOUS: test.out
|
|
144
|
|
|
145
|
#####
|
|
146
|
|
|
147
|
else
|
|
148
|
$(error db variable must be set)
|
|
149
|
endif
|
|
150
|
|
|
151
|
#####
|
|
152
|
|
|
153
|
# Must come after mapEnv is set
|
|
154
|
map := env $(mapEnv) out_database=vegbien $(root)/map
|
