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include ../lib/common.Makefile
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##### Vars/functions
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# Make
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SHELL := /bin/bash
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# Paths
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bin := ../bin
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inputCoreMaps := DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv\
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VegX-VegBIEN.stems.csv
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# Via formats
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coreMaps := $(wildcard *-VegBIEN.*.csv)
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filenameVia = $(shell echo '$(1)'|grep --only-matching --extended-regexp\
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'^[a-zA-Z]+')
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# can't use --ignore-case because in Mac grep, a bug causes it to break [] exprs
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vias := $(strip $(sort $(foreach coreMap,$(coreMaps),$(call filenameVia,$(coreMap)))))
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# Commands
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review_ = $(bin)/review 1 <$(1) >for_review/$(1)
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review = $(call review_,$@)
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join = env header_num=1 $(bin)/join_union_sort
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selfMap_ = $(bin)/cols 0 0
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mkSelfMap = $(selfMap_) <$<|$(bin)/sort_map >$@
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##### General targets
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all: _always $(inputCoreMaps) dwc_maps vegcsv_maps self_maps ;
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clean: _always
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$(RM) $(all)
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all :=
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##### Core maps cleanup
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ifneq ($(filter .%.last_cleanup,$(MAKECMDGOALS)),)
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.%.last_cleanup: %
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$(bin)/in_place $< $(bin)/simplify_xpath
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$(bin)/in_place $< $(bin)/sort_map
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touch $@
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$(call review_,$<)
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else
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$(inputCoreMaps): _always
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$(MAKE) $(@:%=.%.last_cleanup)
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endif
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##### Self maps
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selfMaps :=
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viaCoreMap = $(via)-VegBIEN.%.csv
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viaSelfMap = $(via).self.%.csv
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viaCoreMaps = $(wildcard $(subst %,*,$(viaCoreMap)))
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define selfMapTargets
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selfMaps += $(viaCoreMaps:$(viaCoreMap)=$(viaSelfMap))
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$(viaSelfMap): $(viaCoreMap)
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$$(mkSelfMap)
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endef
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$(foreach via,$(vias),$(eval $(selfMapTargets)))
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ifneq ($(filter self_maps,$(MAKECMDGOALS)),)
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self_maps: _always $(selfMaps) ;
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else
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self_maps: _always
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$(MAKE) self_maps
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# re-run make so that cache of existing files for $(viaCoreMaps) is reset
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endif
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all += $(selfMaps)
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##### DwC
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dwcMaps :=
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DwC.cs-VegBIEN.specimens.csv: DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv
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$(join) <$+ >$@
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dwcMaps += DwC.cs-VegBIEN.specimens.csv
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DwC-VegBIEN.specimens.csv: DwC.cs-VegBIEN.specimens.csv
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$(bin)/ci_map $< >$@
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dwcMaps += DwC-VegBIEN.specimens.csv
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for_review/VegBIEN-DwC2.specimens.csv: for_review/DwC2-VegBIEN.specimens.csv
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$(bin)/invert <$< >$@
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dwcMaps += for_review/VegBIEN-DwC2.specimens.csv
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# keep comments column(s)
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dwc_maps: _always $(dwcMaps) ;
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all += $(dwcMaps)
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##### VegCSV
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vegcsvMaps :=
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ifneq ($(filter .%.last_cleanup,$(MAKECMDGOALS)),)
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.VegX-VegCSV.stems.csv.last_cleanup: VegX-VegCSV.stems.csv
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$(bin)/in_place $< $(bin)/sort_map
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touch $@
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else
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VegX-VegCSV.stems.csv: _always # initially autogenerated
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$(if $(wildcard $@),,env only_one=1 $(bin)/join \
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<for_review/VegX-VegBIEN.stems.csv for_review/VegBIEN-DwC2.specimens.csv\
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|$(bin)/remove_empty\
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|$(bin)/union VegX.self.stems.csv\
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|$(bin)/union <(echo ',VegCSV[DwC]')\
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|$(bin)/review 1\
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>$@)
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$(MAKE) $(@:%=.%.last_cleanup)
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endif
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VegCSV-VegBIEN.specimens.csv: VegX-VegCSV.stems.csv VegX-VegBIEN.stems.csv\
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DwC2-VegBIEN.specimens.csv
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<$< $(bin)/invert\
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|$(bin)/join $(word 2,$+)\
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|$(bin)/union $(word 3,$+)\
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|$(bin)/sort_map >$@
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vegcsvMaps += VegCSV-VegBIEN.specimens.csv
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vegcsv_maps: _always $(vegcsvMaps) ;
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all += $(vegcsvMaps)
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