| 1 |
785
|
aaronmk
|
##### Vars/functions
|
| 2 |
|
|
|
| 3 |
1272
|
aaronmk
|
# Paths
|
| 4 |
895
|
aaronmk
|
bin := ../bin
|
| 5 |
1824
|
aaronmk
|
inputCoreMaps := DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv\
|
| 6 |
1843
|
aaronmk
|
VegX-VegBIEN.stems.csv
|
| 7 |
895
|
aaronmk
|
|
| 8 |
1824
|
aaronmk
|
# Via formats
|
| 9 |
|
|
coreMaps := $(wildcard *-VegBIEN.*.csv)
|
| 10 |
|
|
filenameVia = $(shell echo '$(1)'|grep --only-matching --extended-regexp\
|
| 11 |
|
|
'^[a-zA-Z]+')
|
| 12 |
|
|
# can't use --ignore-case because in Mac grep, a bug causes it to break [] exprs
|
| 13 |
|
|
vias := $(strip $(sort $(foreach coreMap,$(coreMaps),$(call filenameVia,$(coreMap)))))
|
| 14 |
|
|
|
| 15 |
1272
|
aaronmk
|
# Commands
|
| 16 |
|
|
|
| 17 |
1115
|
aaronmk
|
review_ = $(bin)/review <$(1) >for_review/$(1)
|
| 18 |
|
|
review = $(call review_,$@)
|
| 19 |
924
|
aaronmk
|
|
| 20 |
1272
|
aaronmk
|
join = env header_num=1 $(bin)/join_union_sort
|
| 21 |
1824
|
aaronmk
|
selfMap_ = $(bin)/cols 0 0
|
| 22 |
|
|
mkSelfMap = $(selfMap_) <$<|$(bin)/sort_map >$@
|
| 23 |
744
|
aaronmk
|
|
| 24 |
1272
|
aaronmk
|
define chRoot
|
| 25 |
|
|
$(bin)/ch_root <$< >$@
|
| 26 |
|
|
$(review)
|
| 27 |
|
|
endef
|
| 28 |
|
|
|
| 29 |
785
|
aaronmk
|
##### General targets
|
| 30 |
|
|
|
| 31 |
1824
|
aaronmk
|
all: _always $(inputCoreMaps) dwc_maps vegx_maps self_maps ;
|
| 32 |
150
|
aaronmk
|
|
| 33 |
1260
|
aaronmk
|
.SUFFIXES: # turn off built-in suffix rules
|
| 34 |
|
|
.SECONDARY: # don't automatically delete intermediate files
|
| 35 |
1354
|
aaronmk
|
.DELETE_ON_ERROR: # delete target if recipe fails
|
| 36 |
223
|
aaronmk
|
|
| 37 |
383
|
aaronmk
|
_always:
|
| 38 |
|
|
.PHONY: _always
|
| 39 |
188
|
aaronmk
|
|
| 40 |
383
|
aaronmk
|
clean: _always
|
| 41 |
196
|
aaronmk
|
$(RM) $(all)
|
| 42 |
188
|
aaronmk
|
|
| 43 |
924
|
aaronmk
|
all :=
|
| 44 |
|
|
|
| 45 |
785
|
aaronmk
|
##### Core maps cleanup
|
| 46 |
198
|
aaronmk
|
|
| 47 |
895
|
aaronmk
|
ifneq ($(filter .%.last_cleanup,$(MAKECMDGOALS)),)
|
| 48 |
|
|
.%.last_cleanup: %
|
| 49 |
|
|
$(bin)/in_place $< $(bin)/simplify_xpath
|
| 50 |
1132
|
aaronmk
|
$(bin)/in_place $< $(bin)/sort_map
|
| 51 |
895
|
aaronmk
|
touch $@
|
| 52 |
1115
|
aaronmk
|
$(call review_,$<)
|
| 53 |
895
|
aaronmk
|
else
|
| 54 |
1824
|
aaronmk
|
$(inputCoreMaps): _always
|
| 55 |
895
|
aaronmk
|
$(MAKE) $(@:%=.%.last_cleanup)
|
| 56 |
|
|
endif
|
| 57 |
350
|
aaronmk
|
|
| 58 |
1824
|
aaronmk
|
##### Self maps
|
| 59 |
|
|
|
| 60 |
|
|
selfMaps :=
|
| 61 |
|
|
|
| 62 |
|
|
viaCoreMap = $(via)-VegBIEN.%.csv
|
| 63 |
|
|
viaSelfMap = $(via).self.%.csv
|
| 64 |
|
|
viaCoreMaps = $(wildcard $(subst %,*,$(viaCoreMap)))
|
| 65 |
|
|
|
| 66 |
|
|
define selfMapTargets
|
| 67 |
|
|
selfMaps += $(viaCoreMaps:$(viaCoreMap)=$(viaSelfMap))
|
| 68 |
|
|
|
| 69 |
|
|
$(viaSelfMap): $(viaCoreMap)
|
| 70 |
|
|
$$(mkSelfMap)
|
| 71 |
|
|
endef
|
| 72 |
|
|
$(foreach via,$(vias),$(eval $(selfMapTargets)))
|
| 73 |
|
|
|
| 74 |
|
|
ifneq ($(filter self_maps,$(MAKECMDGOALS)),)
|
| 75 |
|
|
self_maps: _always $(selfMaps) ;
|
| 76 |
|
|
else
|
| 77 |
|
|
self_maps: _always
|
| 78 |
|
|
$(MAKE) self_maps
|
| 79 |
|
|
# re-run make so that cache of existing files for $(viaCoreMaps) is reset
|
| 80 |
|
|
endif
|
| 81 |
|
|
|
| 82 |
|
|
all += $(selfMaps)
|
| 83 |
|
|
|
| 84 |
1272
|
aaronmk
|
##### DwC
|
| 85 |
1115
|
aaronmk
|
|
| 86 |
1812
|
aaronmk
|
dwcMaps :=
|
| 87 |
1115
|
aaronmk
|
|
| 88 |
1452
|
aaronmk
|
DwC.cs-VegBIEN.specimens.csv: DwC1-DwC2.specimens.csv DwC2-VegBIEN.specimens.csv
|
| 89 |
|
|
$(join) <$+ >$@
|
| 90 |
1812
|
aaronmk
|
dwcMaps += DwC.cs-VegBIEN.specimens.csv
|
| 91 |
1452
|
aaronmk
|
|
| 92 |
1802
|
aaronmk
|
DwC-VegBIEN.specimens.csv: DwC.cs-VegBIEN.specimens.csv
|
| 93 |
1457
|
aaronmk
|
$(bin)/ci_map $< >$@
|
| 94 |
1812
|
aaronmk
|
dwcMaps += DwC-VegBIEN.specimens.csv
|
| 95 |
1118
|
aaronmk
|
|
| 96 |
1824
|
aaronmk
|
dwc_maps: _always $(dwcMaps) ;
|
| 97 |
1140
|
aaronmk
|
|
| 98 |
1812
|
aaronmk
|
all += $(dwcMaps)
|
| 99 |
1115
|
aaronmk
|
|
| 100 |
1272
|
aaronmk
|
##### VegX
|
| 101 |
212
|
aaronmk
|
|
| 102 |
1812
|
aaronmk
|
vegxMaps :=
|
| 103 |
924
|
aaronmk
|
|
| 104 |
1818
|
aaronmk
|
rootAttrs := :[@xmlns:tcs="http://www.tdwg.org/schemas/tcs/1.01"]
|
| 105 |
1816
|
aaronmk
|
|
| 106 |
1843
|
aaronmk
|
VegX-VegBIEN.organisms.csv: VegX-VegBIEN.stems.csv
|
| 107 |
|
|
env \
|
| 108 |
|
|
left_in_root='$(rootAttrs)/*s/individualOrganismObservation[relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID]/relatedIndividual/relatedItem[itemRelationship=stemParent]/relatedItemID->/*s/individualOrganismObservation' \
|
| 109 |
|
|
left_out_root='$(rootAttrs)/*s/individualOrganismObservation' \
|
| 110 |
|
|
right_in_root='/stemobservation/*_id/plantobservation' \
|
| 111 |
|
|
right_out_root='/plantobservation' \
|
| 112 |
|
|
$(chRoot)
|
| 113 |
|
|
vegxMaps += VegX-VegBIEN.organisms.csv
|
| 114 |
|
|
|
| 115 |
438
|
aaronmk
|
VegX-VegBIEN.plots.csv: VegX-VegBIEN.organisms.csv
|
| 116 |
188
|
aaronmk
|
env \
|
| 117 |
1816
|
aaronmk
|
left_in_root='$(rootAttrs)/*s/individualOrganismObservation/*ID->/*s/plotObservation' \
|
| 118 |
439
|
aaronmk
|
left_out_root='/*s/plotObservation' \
|
| 119 |
1843
|
aaronmk
|
right_in_root='/plantobservation/aggregateoccurrence/*_id/taxonoccurrence/*_id/locationevent' \
|
| 120 |
525
|
aaronmk
|
right_out_root='/locationevent' \
|
| 121 |
439
|
aaronmk
|
$(chRoot)
|
| 122 |
1812
|
aaronmk
|
vegxMaps += VegX-VegBIEN.plots.csv
|
| 123 |
439
|
aaronmk
|
|
| 124 |
1824
|
aaronmk
|
vegx_maps: _always $(vegxMaps) ;
|
| 125 |
924
|
aaronmk
|
|
| 126 |
1812
|
aaronmk
|
all += $(vegxMaps)
|
