| 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 |
|
|
vegxMaps := $(wildcard $(tablesSort:%=map.VegX.%.csv))
|
| 14 |
440
|
aaronmk
|
vegxMaps += $(filter-out $(vegxMaps),$(wildcard map.VegX.*.csv))
|
| 15 |
415
|
aaronmk
|
tables := $(vegxMaps:map.VegX.%.csv=%)
|
| 16 |
264
|
aaronmk
|
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) $(all)
|
| 35 |
|
|
|
| 36 |
423
|
aaronmk
|
remake: _always clean all ;
|
| 37 |
|
|
|
| 38 |
383
|
aaronmk
|
%.out: % _always
|
| 39 |
368
|
aaronmk
|
./$* >$@
|
| 40 |
|
|
.PRECIOUS: %.out
|
| 41 |
|
|
|
| 42 |
408
|
aaronmk
|
all += $(wildcard *.out)
|
| 43 |
|
|
|
| 44 |
415
|
aaronmk
|
$(root)/%: _always
|
| 45 |
|
|
+$(subMake)
|
| 46 |
|
|
|
| 47 |
250
|
aaronmk
|
#####
|
| 48 |
|
|
|
| 49 |
418
|
aaronmk
|
reinstall: _always uninstall install ;
|
| 50 |
264
|
aaronmk
|
|
| 51 |
|
|
#####
|
| 52 |
|
|
|
| 53 |
418
|
aaronmk
|
maps: $(vegbienMaps) _always ;
|
| 54 |
368
|
aaronmk
|
|
| 55 |
|
|
all += $(vegbienMaps)
|
| 56 |
|
|
|
| 57 |
415
|
aaronmk
|
map.VegBIEN.%.csv: map.VegX.%.csv $(root)/mappings/VegX-VegBIEN.%.csv
|
| 58 |
|
|
$(root)/bin/join_sort <$+ >$@
|
| 59 |
264
|
aaronmk
|
.PRECIOUS: map.VegBIEN.%.csv
|
| 60 |
|
|
|
| 61 |
368
|
aaronmk
|
#####
|
| 62 |
|
|
|
| 63 |
418
|
aaronmk
|
import: _always $(addprefix import-,$(tables)) verify ;
|
| 64 |
368
|
aaronmk
|
|
| 65 |
|
|
log = $*$(if $(n),.n=$(n),).log
|
| 66 |
|
|
|
| 67 |
339
|
aaronmk
|
logs := $(wildcard *.log)
|
| 68 |
|
|
|
| 69 |
383
|
aaronmk
|
rm_logs: _always
|
| 70 |
339
|
aaronmk
|
$(RM) $(logs)
|
| 71 |
|
|
|
| 72 |
264
|
aaronmk
|
#####
|
| 73 |
|
|
|
| 74 |
418
|
aaronmk
|
verify: _always $(addprefix verify-,$(tables)) ;
|
| 75 |
368
|
aaronmk
|
|
| 76 |
383
|
aaronmk
|
verify-%: verify.%.ref verify.%.out _always
|
| 77 |
404
|
aaronmk
|
$(DIFF) $(+_)
|
| 78 |
368
|
aaronmk
|
|
| 79 |
383
|
aaronmk
|
%.out: %.sql _always
|
| 80 |
429
|
aaronmk
|
$(out_cmd)
|
| 81 |
370
|
aaronmk
|
.PRECIOUS: %.out
|
| 82 |
429
|
aaronmk
|
out_cmd = $(psqlAsBien) --no-align --field-separator=' ' --pset=footer=off \
|
| 83 |
|
|
--pset=null=NULL <$< >$@
|
| 84 |
369
|
aaronmk
|
|
| 85 |
368
|
aaronmk
|
#####
|
| 86 |
|
|
|
| 87 |
418
|
aaronmk
|
test: _always $(addprefix test-,$(tables)) ;
|
| 88 |
368
|
aaronmk
|
|
| 89 |
395
|
aaronmk
|
test-%: test.%.out _always
|
| 90 |
|
|
$(DIFF) $(<:.out=.ref) $<
|
| 91 |
368
|
aaronmk
|
|
| 92 |
395
|
aaronmk
|
accept-%: _always
|
| 93 |
|
|
$(CP) $* $(*:.out=.ref)
|
| 94 |
|
|
|
| 95 |
368
|
aaronmk
|
#####
|
| 96 |
|
|
|
| 97 |
256
|
aaronmk
|
ifdef db
|
| 98 |
|
|
|
| 99 |
264
|
aaronmk
|
mapEnv := in_engine=$(dbEngine) in_database=$(db)
|
| 100 |
256
|
aaronmk
|
|
| 101 |
368
|
aaronmk
|
####
|
| 102 |
256
|
aaronmk
|
|
| 103 |
368
|
aaronmk
|
ifeq ($(dbEngine),MySQL)
|
| 104 |
339
|
aaronmk
|
|
| 105 |
368
|
aaronmk
|
bienPassword := $(shell cat $(root)/config/bien_password)
|
| 106 |
|
|
mysqlAs = mysql --user=$(1) --password='$(bienPassword)'
|
| 107 |
|
|
mysqlAsRoot := $(call mysqlAs,root)
|
| 108 |
|
|
mysqlAsBien := $(call mysqlAs,bien)
|
| 109 |
|
|
|
| 110 |
383
|
aaronmk
|
import-%: map.VegBIEN.%.csv _always
|
| 111 |
385
|
aaronmk
|
-$(import_cmd)
|
| 112 |
383
|
aaronmk
|
import_cmd = (set -x; "time" env commit=1 $(map) $<) \
|
| 113 |
368
|
aaronmk
|
$(if $(n),,>>$(log)) 2>&1$(if $(n),|tee -a $(log))
|
| 114 |
256
|
aaronmk
|
|
| 115 |
369
|
aaronmk
|
%.ref: %.ref.sql
|
| 116 |
371
|
aaronmk
|
$(mysqlAsBien) $(db) <$< >$@
|
| 117 |
369
|
aaronmk
|
.PRECIOUS: %.ref
|
| 118 |
368
|
aaronmk
|
|
| 119 |
|
|
###
|
| 120 |
|
|
|
| 121 |
418
|
aaronmk
|
install: _always db ;
|
| 122 |
256
|
aaronmk
|
|
| 123 |
418
|
aaronmk
|
uninstall: _always rm_db ;
|
| 124 |
256
|
aaronmk
|
|
| 125 |
383
|
aaronmk
|
db: src.$(db).sql _always
|
| 126 |
368
|
aaronmk
|
-$(mysqlAsRoot) <$<
|
| 127 |
|
|
echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 128 |
255
|
aaronmk
|
# ignore errors in db import so that GRANT will still be run
|
| 129 |
250
|
aaronmk
|
|
| 130 |
383
|
aaronmk
|
rm_db: _always
|
| 131 |
368
|
aaronmk
|
-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 132 |
|
|
echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
|
| 133 |
365
|
aaronmk
|
# ignore errors if grant not defined
|
| 134 |
250
|
aaronmk
|
|
| 135 |
368
|
aaronmk
|
###
|
| 136 |
|
|
|
| 137 |
|
|
else
|
| 138 |
|
|
$(error dbEngine variable must be one of the following: MySQL, PostgreSQL)
|
| 139 |
|
|
endif
|
| 140 |
|
|
|
| 141 |
|
|
####
|
| 142 |
|
|
|
| 143 |
383
|
aaronmk
|
test.%.out: map.VegBIEN.%.csv _always
|
| 144 |
401
|
aaronmk
|
env test=1 n=$(test_n) $(map) $< >$@ 2>&1 || { e=$$?; cat $@; exit $$e;}
|
| 145 |
368
|
aaronmk
|
.PRECIOUS: test.%.out
|
| 146 |
|
|
|
| 147 |
256
|
aaronmk
|
#####
|
| 148 |
|
|
|
| 149 |
|
|
else
|
| 150 |
|
|
$(error db variable must be set)
|
| 151 |
|
|
endif
|
| 152 |
368
|
aaronmk
|
|
| 153 |
|
|
#####
|
| 154 |
|
|
|
| 155 |
|
|
# Must come after mapEnv is set
|
| 156 |
|
|
map := env $(mapEnv) out_database=vegbien $(root)/map
|
