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783
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aaronmk
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##### Configuration
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858
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aaronmk
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nolog ?=
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783
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aaronmk
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exts ?= csv xml
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test_n ?= 2
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tablesSort ?= plots organisms stems
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mainCoreMapTry ?= organisms specimens
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##### Vars/functions
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640
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aaronmk
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selfDir_uZPPqC := $(dir $(lastword $(MAKEFILE_LIST)))
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250
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aaronmk
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368
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aaronmk
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# Make
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640
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aaronmk
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SHELL := /bin/bash
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415
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aaronmk
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subMake = $(MAKE) $(@F) --directory=$(@D)
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404
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aaronmk
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+_ = $(+:_%=)
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368
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aaronmk
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addBeforeExt = $(basename $(2))$(1)$(suffix $(2))
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790
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aaronmk
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# System
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date = $(shell date +"%Y-%m-%d-%H-%M-%S")
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640
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aaronmk
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# Terminal
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esc := '['
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reset := $(esc)'0m'
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emph := $(esc)'7m '
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endEmph := ' '$(reset)
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368
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aaronmk
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# Commands
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395
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CP = cp -p
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DIFF = diff --unified=2
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368
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aaronmk
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783
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aaronmk
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# Paths
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640
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aaronmk
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root := $(selfDir_uZPPqC)..
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775
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aaronmk
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mappings := $(root)/mappings
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368
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aaronmk
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psqlAsBien := $(root)/bin/psql_vegbien
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353
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aaronmk
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783
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aaronmk
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##### General targets
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250
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aaronmk
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418
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aaronmk
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all: _always maps ;
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247
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.SUFFIXES:
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383
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_always:
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.PHONY: _always
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250
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aaronmk
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383
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aaronmk
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clean: _always
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256
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aaronmk
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$(RM) $(all)
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423
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aaronmk
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remake: _always clean all ;
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515
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aaronmk
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%.out: %.make _always
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368
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aaronmk
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./$* >$@
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.PRECIOUS: %.out
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415
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aaronmk
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$(root)/%: _always
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+$(subMake)
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783
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aaronmk
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##### SVN
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250
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aaronmk
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766
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aaronmk
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svn_props: _always
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768
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aaronmk
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svn propset svn:ignore $$'.~*\n*.log\n*.out\nsrc*' .
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766
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aaronmk
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$(if $(wildcard test/),svn propset svn:ignore $$'*.out\n*.xml' test)
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783
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aaronmk
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##### Installation
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766
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aaronmk
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418
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reinstall: _always uninstall install ;
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264
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aaronmk
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| 68 |
783
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aaronmk
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##### Maps
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| 69 |
264
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aaronmk
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728
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aaronmk
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allViaMaps := $(filter-out maps/VegBIEN.%.csv,$(wildcard maps/*.csv))
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via := $(firstword $(sort $(basename $(basename $(notdir $(allViaMaps))))))
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| 72 |
783
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aaronmk
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775
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aaronmk
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coreMap := $(mappings)/$(via)-VegBIEN.%.csv
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mainCoreMap := $(firstword $(wildcard $(mainCoreMapTry:%=$(coreMap))))
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783
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aaronmk
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749
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viaMaps := $(wildcard $(tablesSort:%=maps/$(via).%.csv))
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viaMaps += $(filter-out $(viaMaps),$(wildcard maps/$(via).*.csv))
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783
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aaronmk
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| 79 |
728
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aaronmk
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autogenMaps := $(subst $(via).,VegBIEN.,$(viaMaps))
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directMaps := $(autogenMaps) $(filter-out $(autogenMaps),\
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$(wildcard maps/VegBIEN.*.csv))
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772
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aaronmk
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tables := $(directMaps:maps/VegBIEN.%.csv=%)
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| 83 |
728
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aaronmk
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724
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aaronmk
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maps: $(directMaps) _always ;
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| 85 |
368
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aaronmk
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| 86 |
728
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aaronmk
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.PRECIOUS: $(allViaMaps) $(directMaps)
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| 87 |
368
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aaronmk
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| 88 |
728
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aaronmk
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all += $(autogenMaps)
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| 89 |
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775
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aaronmk
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maps/VegBIEN.%.csv: maps/$(via).%.csv $(coreMap)
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| 91 |
415
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aaronmk
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$(root)/bin/join_sort <$+ >$@
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| 92 |
775
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aaronmk
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.PRECIOUS: maps/VegBIEN.%.csv $(coreMap)
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| 93 |
264
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aaronmk
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783
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aaronmk
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##### Mapping
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| 95 |
368
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aaronmk
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| 96 |
728
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aaronmk
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dbFile := $(firstword $(wildcard src/db.*.sql))
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| 97 |
772
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aaronmk
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inputFiles := $(wildcard src/*.csv src/*.xml)
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| 98 |
728
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aaronmk
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| 99 |
775
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aaronmk
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+maps = $(filter maps/% $(mappings)/%,$(+_))
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<in = $(firstword $(filter-out $(+maps),$(+_)) $(wildcard $(exts:%=src/*.$*.%)))
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map = $(if $(<in),<$(<in) ,$(if $(mapEnv),env $(mapEnv) ))$(root)/map $(+maps)
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| 102 |
772
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aaronmk
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map2db = env out_database=vegbien $(map)
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| 103 |
368
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aaronmk
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| 104 |
783
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aaronmk
|
##### Import to VegBIEN
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| 105 |
772
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aaronmk
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| 106 |
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ifneq ($(dbFile)$(inputFiles),)
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718
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aaronmk
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import: _always import-all verify ;
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| 109 |
368
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aaronmk
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| 110 |
790
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aaronmk
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log = $(@:-all=)$(if $(n),.n=$(n),).$(date).log
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| 111 |
772
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aaronmk
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import = -(set -x; "time" env commit=1 $(map2db)) \
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| 112 |
858
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aaronmk
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$(if nolog,,$(if $(n),,>>$(log))) 2>&1$(if nolog,,$(if $(n),|tee -a $(log)))
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| 113 |
636
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aaronmk
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# ignore import errors, which are often benign (e.g. invalid date format)
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624
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aaronmk
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| 115 |
772
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aaronmk
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ifneq ($(inputFiles),)
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import-all: $(addprefix import-,$(tables)) _always ;
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| 117 |
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else
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| 118 |
724
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aaronmk
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import-all: $(directMaps) _always
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| 119 |
718
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aaronmk
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$(import)
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| 120 |
772
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aaronmk
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endif
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| 121 |
718
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aaronmk
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| 122 |
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import-%: maps/VegBIEN.%.csv _always
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| 123 |
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$(import)
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| 124 |
772
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aaronmk
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# default:
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| 125 |
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import-%: _always ;
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| 126 |
718
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aaronmk
|
|
| 127 |
772
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aaronmk
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else
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| 128 |
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import: _always ;
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| 129 |
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endif
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| 130 |
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| 131 |
790
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aaronmk
|
##### Log files from import
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| 132 |
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| 133 |
339
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aaronmk
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logs := $(wildcard *.log)
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| 134 |
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| 135 |
383
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aaronmk
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rm_logs: _always
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| 136 |
339
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aaronmk
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$(RM) $(logs)
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| 137 |
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| 138 |
783
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aaronmk
|
##### Verification of import
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| 139 |
264
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aaronmk
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| 140 |
624
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aaronmk
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ifneq ($(wildcard verify.ref*),)
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| 141 |
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| 142 |
514
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aaronmk
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verify: verify.ref verify.out _always
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| 143 |
404
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aaronmk
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$(DIFF) $(+_)
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| 144 |
368
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aaronmk
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|
| 145 |
514
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aaronmk
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all += verify.out
|
| 146 |
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| 147 |
383
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aaronmk
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%.out: %.sql _always
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| 148 |
429
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aaronmk
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$(out_cmd)
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| 149 |
370
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aaronmk
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.PRECIOUS: %.out
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| 150 |
772
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aaronmk
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out_cmd = $(psqlAsBien) --no-align --field-separator=' ' --pset=footer=off\
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| 151 |
429
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aaronmk
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--pset=null=NULL <$< >$@
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| 152 |
369
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aaronmk
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| 153 |
624
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aaronmk
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else
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| 154 |
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verify: _always ;
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| 155 |
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endif
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| 156 |
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| 157 |
783
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aaronmk
|
##### Testing
|
| 158 |
368
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aaronmk
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|
| 159 |
624
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aaronmk
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ifneq ($(wildcard test/),)
|
| 160 |
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| 161 |
724
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aaronmk
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tests :=
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| 162 |
368
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aaronmk
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| 163 |
723
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aaronmk
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hasOwnRef = $(filter-out %.2-step.xml,$@)
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| 164 |
630
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aaronmk
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testRef = $(1:.2-step.xml=.xml).ref
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| 165 |
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| 166 |
629
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aaronmk
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define test
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| 167 |
776
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aaronmk
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@echo "Testing $(abspath $@)..."
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| 168 |
775
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aaronmk
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>$@ env test=1 verbose=1 n=$(test_n) $(1)
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| 169 |
653
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aaronmk
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@(set -x; $(DIFF) $(call testRef,$@) $@) 2>&1 || { e=$$?;\
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| 170 |
780
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aaronmk
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$(if $(wildcard $(call testRef,$@)),,cat $@;)\
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| 171 |
777
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aaronmk
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$(if $(hasOwnRef),\
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| 172 |
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echo $(emph)"To accept new test output:"$(endEmph);\
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| 173 |
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echo "$(MAKE) $@-ok --directory=$(realpath .) --makefile=../input.Makefile";\
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| 174 |
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,\
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| 175 |
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echo $(emph)"Note: The preceding failed test is compared to another test's\
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| 176 |
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output"$(endEmph);\
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| 177 |
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echo $(emph)"When it fails, this always indicates a bug"$(endEmph);\
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| 178 |
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)\
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| 179 |
652
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aaronmk
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exit $$e;}
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| 180 |
628
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aaronmk
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endef
|
| 181 |
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| 182 |
775
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aaronmk
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test2File = $(call test,$(map))
|
| 183 |
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| 184 |
724
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aaronmk
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test/$(via).xml: $(viaMaps) _always
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| 185 |
775
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aaronmk
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$(test2File)
|
| 186 |
724
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aaronmk
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tests += test/$(via).xml
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| 187 |
629
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aaronmk
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|
| 188 |
724
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aaronmk
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test/VegBIEN.xml: $(directMaps) _always
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| 189 |
775
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aaronmk
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$(test2File)
|
| 190 |
724
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aaronmk
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tests += test/VegBIEN.xml
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| 191 |
628
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aaronmk
|
|
| 192 |
775
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aaronmk
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test/VegBIEN.2-step.xml: test/$(via).xml $(mainCoreMap) _always
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| 193 |
|
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-$(test2File)
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| 194 |
722
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aaronmk
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# Don't abort tester if only 2-step test fails, as it's often finicky
|
| 195 |
724
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aaronmk
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tests += test/VegBIEN.2-step.xml
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| 196 |
630
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aaronmk
|
|
| 197 |
724
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aaronmk
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test/import.out: $(directMaps) _always
|
| 198 |
718
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aaronmk
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$(call test,$(map2db))
|
| 199 |
724
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aaronmk
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tests += test/import.out
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| 200 |
627
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aaronmk
|
|
| 201 |
724
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aaronmk
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test: _always $(tests) ;
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| 202 |
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| 203 |
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.PRECIOUS: $(tests)
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| 204 |
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| 205 |
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all += $(tests)
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| 206 |
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| 207 |
634
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aaronmk
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# Accepts a test output: make <test_output_path>-ok
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| 208 |
626
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aaronmk
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%-ok: _always
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| 209 |
630
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aaronmk
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$(CP) $* $(call testRef,$*)
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| 210 |
502
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aaronmk
|
|
| 211 |
624
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aaronmk
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else
|
| 212 |
|
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test: _always ;
|
| 213 |
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endif
|
| 214 |
|
|
|
| 215 |
783
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aaronmk
|
##### Input-type-specific
|
| 216 |
368
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aaronmk
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|
| 217 |
624
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aaronmk
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# Each input type needs var $(mapEnv) and targets install, uninstall
|
| 218 |
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| 219 |
622
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aaronmk
|
ifneq ($(dbFile),)
|
| 220 |
256
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aaronmk
|
|
| 221 |
635
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aaronmk
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dbEngineExt := $(subst .,,$(suffix $(basename $(notdir $(dbFile)))))
|
| 222 |
|
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db := $(notdir $(realpath .))
|
| 223 |
622
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aaronmk
|
|
| 224 |
621
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aaronmk
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%.ref: %.ref.sql
|
| 225 |
|
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$(inputDbAsBien) $(db) <$< >$@
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| 226 |
|
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.PRECIOUS: %.ref
|
| 227 |
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| 228 |
783
|
aaronmk
|
#### Installation
|
| 229 |
256
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aaronmk
|
|
| 230 |
621
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aaronmk
|
install: _always db ;
|
| 231 |
339
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aaronmk
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| 232 |
621
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aaronmk
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uninstall: _always rm_db ;
|
| 233 |
368
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aaronmk
|
|
| 234 |
783
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aaronmk
|
#### DB-engine-specific
|
| 235 |
621
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aaronmk
|
|
| 236 |
624
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aaronmk
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# Each DB engine needs vars $(dbEngine), $(dbAsBien) and targets db, rm_db
|
| 237 |
256
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aaronmk
|
|
| 238 |
622
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aaronmk
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ifeq ($(dbEngineExt),my)
|
| 239 |
621
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aaronmk
|
|
| 240 |
622
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aaronmk
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dbEngine := MySQL
|
| 241 |
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|
|
| 242 |
621
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aaronmk
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bienPassword := $(shell cat $(root)/config/bien_password)
|
| 243 |
|
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mysqlAs = mysql --user=$(1) --password='$(bienPassword)'
|
| 244 |
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mysqlAsRoot := $(call mysqlAs,root)
|
| 245 |
|
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dbAsBien := $(call mysqlAs,bien)
|
| 246 |
|
|
|
| 247 |
622
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aaronmk
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db: $(dbFile) _always
|
| 248 |
635
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aaronmk
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echo "CREATE DATABASE $(db) DEFAULT CHARACTER SET latin1;"|$(mysqlAsRoot)
|
| 249 |
|
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-$(mysqlAsRoot) --database=$(db) <$<
|
| 250 |
368
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aaronmk
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echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 251 |
255
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aaronmk
|
# ignore errors in db import so that GRANT will still be run
|
| 252 |
250
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aaronmk
|
|
| 253 |
383
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aaronmk
|
rm_db: _always
|
| 254 |
368
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aaronmk
|
-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)
|
| 255 |
|
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echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot)
|
| 256 |
365
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aaronmk
|
# ignore errors if grant not defined
|
| 257 |
250
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aaronmk
|
|
| 258 |
783
|
aaronmk
|
### Unrecognized DB engine
|
| 259 |
368
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aaronmk
|
|
| 260 |
|
|
else
|
| 261 |
635
|
aaronmk
|
$(error The DB filename $(dbFile) must have the form db.{my|pg}.sql)
|
| 262 |
368
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aaronmk
|
endif
|
| 263 |
|
|
|
| 264 |
622
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aaronmk
|
# Must come after dbEngine is set
|
| 265 |
|
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mapEnv := in_engine=$(dbEngine) in_database=$(db)
|
| 266 |
|
|
|
| 267 |
783
|
aaronmk
|
#### Unrecognized input type
|
| 268 |
624
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aaronmk
|
|
| 269 |
256
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aaronmk
|
else
|
| 270 |
624
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aaronmk
|
install: _always ;
|
| 271 |
|
|
uninstall: _always ;
|
| 272 |
256
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aaronmk
|
endif
|
