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aaronmk
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##### Vars/functions
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aaronmk
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# Paths
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aaronmk
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bin := ../bin
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aaronmk
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coreMaps := DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv\
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VegX-VegBIEN.organisms.csv
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895
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aaronmk
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1272
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aaronmk
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# Commands
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review_ = $(bin)/review <$(1) >for_review/$(1)
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review = $(call review_,$@)
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924
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aaronmk
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1272
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aaronmk
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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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1285
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aaronmk
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removeEmpty = $(bin)/remove_empty
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aaronmk
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aaronmk
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define chRoot
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$(bin)/ch_root <$< >$@
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$(review)
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endef
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785
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aaronmk
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##### General targets
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aaronmk
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all: _always $(coreMaps) join_maps ch_root_maps ;
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aaronmk
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.SUFFIXES: # turn off built-in suffix rules
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.SECONDARY: # don't automatically delete intermediate files
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_always:
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.PHONY: _always
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clean: _always
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aaronmk
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$(RM) $(all)
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all :=
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785
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aaronmk
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##### Core maps cleanup
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ifneq ($(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 $@
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aaronmk
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$(call review_,$<)
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aaronmk
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else
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$(coreMaps): _always
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$(MAKE) $(@:%=.%.last_cleanup)
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endif
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350
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aaronmk
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1272
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aaronmk
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##### DwC
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1115
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aaronmk
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joinMaps :=
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aaronmk
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DwC2.ci-VegBIEN.specimens.csv: DwC2-VegBIEN.specimens.csv
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$(selfMap) <$<|$(bin)/ucase_first 0|$(join) $< >$@
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joinMaps += DwC2.ci-VegBIEN.specimens.csv
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DwC-VegBIEN.specimens.csv: DwC1-DwC2.specimens.csv DwC2.ci-VegBIEN.specimens.csv
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$(join) <$+ >$@
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joinMaps += DwC-VegBIEN.specimens.csv
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1140
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aaronmk
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DwC.self.specimens.csv: DwC-VegBIEN.specimens.csv
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1270
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aaronmk
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$(selfMap) <$< >$@
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joinMaps += DwC.self.specimens.csv
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aaronmk
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DwC-VegBIEN.specimens.no_empty.csv: DwC-VegBIEN.specimens.csv
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$(removeEmpty) <$< >$@
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joinMaps += DwC-VegBIEN.specimens.no_empty.csv
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join_maps: $(joinMaps) ;
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all += $(joinMaps)
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1272
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aaronmk
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##### VegX
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aaronmk
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924
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aaronmk
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chRootMaps :=
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aaronmk
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VegX-VegBIEN.plots.csv: VegX-VegBIEN.organisms.csv
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env \
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left_in_root='/*s/individualOrganismObservation/*ID->/*s/plotObservation' \
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left_out_root='/*s/plotObservation' \
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aaronmk
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right_in_root='/taxonoccurrence/*_id/locationevent' \
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right_out_root='/locationevent' \
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439
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aaronmk
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$(chRoot)
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chRootMaps += VegX-VegBIEN.plots.csv
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439
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aaronmk
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VegX-VegBIEN.stems.csv: VegX-VegBIEN.organisms.csv
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env \
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aaronmk
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left_in_root='/*s/individualOrganismObservation->/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]' \
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left_out_root='/*s/individualOrganismObservation[relatedItem[relationshipType=stemParent]/relatedItemID]' \
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right_in_root='/taxonoccurrence/aggregateoccurrence/*_id/plantobservation/stemobservation' \
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right_out_root='/stemobservation' \
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439
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aaronmk
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$(chRoot)
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aaronmk
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chRootMaps += VegX-VegBIEN.plots.csv
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ch_root_maps: $(chRootMaps) ;
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all += $(chRootMaps)
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