1
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selfDir_3d1bc249 := $(dir $(lastword $(MAKEFILE_LIST)))
|
2
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3
|
# Make
|
4
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subMake = $(MAKE) $(@F) --directory=$(@D)
|
5
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+_ = $(+:_%=)
|
6
|
addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
|
7
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|
8
|
# Commands
|
9
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CP = cp -p
|
10
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DIFF = diff --unified=2
|
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))
|
14
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vegxMaps += $(filter-out $(vegxMaps),$(wildcard maps/VegX.*.csv))
|
15
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tables := $(vegxMaps:maps/VegX.%.csv=%)
|
16
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vegbienMaps := $(subst VegX.,VegBIEN.,$(vegxMaps))
|
17
|
|
18
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root := $(selfDir_3d1bc249)..
|
19
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psqlAsBien := $(root)/bin/psql_vegbien
|
20
|
|
21
|
# Config
|
22
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test_n ?= 2
|
23
|
|
24
|
#####
|
25
|
|
26
|
all: _always maps ;
|
27
|
|
28
|
.SUFFIXES:
|
29
|
|
30
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_always:
|
31
|
.PHONY: _always
|
32
|
|
33
|
clean: _always
|
34
|
$(RM) $(all)
|
35
|
|
36
|
remake: _always clean all ;
|
37
|
|
38
|
%.out: %.make _always
|
39
|
./$* >$@
|
40
|
.PRECIOUS: %.out
|
41
|
|
42
|
$(root)/%: _always
|
43
|
+$(subMake)
|
44
|
|
45
|
#####
|
46
|
|
47
|
reinstall: _always uninstall install ;
|
48
|
|
49
|
#####
|
50
|
|
51
|
maps: $(vegbienMaps) _always ;
|
52
|
|
53
|
all += $(vegbienMaps)
|
54
|
|
55
|
maps/VegBIEN.%.csv: maps/VegX.%.csv $(root)/mappings/VegX-VegBIEN.%.csv
|
56
|
$(root)/bin/join_sort <$+ >$@
|
57
|
.PRECIOUS: maps/VegBIEN.%.csv
|
58
|
|
59
|
#####
|
60
|
|
61
|
import: _always $(addprefix import-,$(tables)) verify ;
|
62
|
|
63
|
log = $*$(if $(n),.n=$(n),).log
|
64
|
|
65
|
import-%: maps/VegBIEN.%.csv _always
|
66
|
-$(import_cmd)
|
67
|
import_cmd = (set -x; "time" env commit=1 $(import) $<) \
|
68
|
$(if $(n),,>>$(log)) 2>&1$(if $(n),|tee -a $(log))
|
69
|
|
70
|
logs := $(wildcard *.log)
|
71
|
|
72
|
rm_logs: _always
|
73
|
$(RM) $(logs)
|
74
|
|
75
|
#####
|
76
|
|
77
|
ifneq ($(wildcard verify.ref*),)
|
78
|
|
79
|
verify: verify.ref verify.out _always
|
80
|
$(DIFF) $(+_)
|
81
|
|
82
|
all += verify.out
|
83
|
|
84
|
%.out: %.sql _always
|
85
|
$(out_cmd)
|
86
|
.PRECIOUS: %.out
|
87
|
out_cmd = $(psqlAsBien) --no-align --field-separator=' ' --pset=footer=off \
|
88
|
--pset=null=NULL <$< >$@
|
89
|
|
90
|
else
|
91
|
verify: _always ;
|
92
|
endif
|
93
|
|
94
|
#####
|
95
|
|
96
|
ifneq ($(wildcard test/),)
|
97
|
|
98
|
testOutputs := test/VegX.xml test/VegBIEN.xml test/import.out
|
99
|
|
100
|
test: _always $(testOutputs) ;
|
101
|
|
102
|
.PRECIOUS: $(testOutputs)
|
103
|
|
104
|
all += $(testOutputs)
|
105
|
|
106
|
define test
|
107
|
env test=1 n=$(test_n) $(1) $(+_)$(if $(2),, >$@) 2>&1$(if $(2), |\
|
108
|
grep -v -E '^$(2)$$' >$@) || { e=$$?; cat $@; exit $$e;}
|
109
|
$(DIFF) $@.ref $@
|
110
|
endef
|
111
|
|
112
|
test2File = $(call test,$(map),Processed .* input rows)
|
113
|
test2Db = $(call test,$(import))
|
114
|
|
115
|
test/VegX.xml: $(vegxMaps) _always
|
116
|
$(test2File)
|
117
|
|
118
|
test/VegBIEN.xml: $(vegbienMaps) _always
|
119
|
$(test2File)
|
120
|
|
121
|
test/import.out: $(vegbienMaps) _always
|
122
|
$(test2Db)
|
123
|
|
124
|
%-ok: _always
|
125
|
$(CP) $* $*.ref
|
126
|
|
127
|
else
|
128
|
test: _always ;
|
129
|
endif
|
130
|
|
131
|
#####
|
132
|
|
133
|
# Each input type needs var $(mapEnv) and targets install, uninstall
|
134
|
|
135
|
dbFile := $(firstword $(wildcard src/*.sql))
|
136
|
|
137
|
ifneq ($(dbFile),)
|
138
|
|
139
|
dbFileBasename := $(basename $(notdir $(dbFile)))
|
140
|
dbEngineExt := $(subst .,,$(suffix $(dbFileBasename)))
|
141
|
db := $(basename $(dbFileBasename))
|
142
|
|
143
|
%.ref: %.ref.sql
|
144
|
$(inputDbAsBien) $(db) <$< >$@
|
145
|
.PRECIOUS: %.ref
|
146
|
|
147
|
####
|
148
|
|
149
|
install: _always db ;
|
150
|
|
151
|
uninstall: _always rm_db ;
|
152
|
|
153
|
####
|
154
|
|
155
|
# Each DB engine needs vars $(dbEngine), $(dbAsBien) and targets db, rm_db
|
156
|
|
157
|
ifeq ($(dbEngineExt),my)
|
158
|
|
159
|
dbEngine := MySQL
|
160
|
|
161
|
bienPassword := $(shell cat $(root)/config/bien_password)
|
162
|
mysqlAs = mysql --user=$(1) --password='$(bienPassword)'
|
163
|
mysqlAsRoot := $(call mysqlAs,root)
|
164
|
dbAsBien := $(call mysqlAs,bien)
|
165
|
|
166
|
db: $(dbFile) _always
|
167
|
-$(mysqlAsRoot) <$<
|
168
|
echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
|
169
|
# ignore errors in db import so that GRANT will still be run
|
170
|
|
171
|
rm_db: _always
|
172
|
-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
|
173
|
echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
|
174
|
# ignore errors if grant not defined
|
175
|
|
176
|
###
|
177
|
|
178
|
else
|
179
|
$(error The DB filename $(dbFile) must have the form <db_name>.{my|pg}.sql)
|
180
|
endif
|
181
|
|
182
|
# Must come after dbEngine is set
|
183
|
mapEnv := in_engine=$(dbEngine) in_database=$(db)
|
184
|
|
185
|
####
|
186
|
|
187
|
else
|
188
|
mapEnv :=
|
189
|
install: _always ;
|
190
|
uninstall: _always ;
|
191
|
endif
|
192
|
|
193
|
#####
|
194
|
|
195
|
# Must come after mapEnv is set
|
196
|
map := $(if $(mapEnv),env $(mapEnv) ,)$(root)/map
|
197
|
import := env out_database=vegbien $(map)
|