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1
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SED = sed -$(if $(filter Darwin,$(shell uname)),E,r)
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2
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3
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repl = ../scripts/util/repl
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4
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sort = ../scripts/util/sort 1 0
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5
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chRoot = ../scripts/util/ch_root <$< >$@
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6
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empty = $(SED) -n \
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7
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's/^CREATE TABLE ([0-9A-Za-z_]+) \($$/TRUNCATE \1 CASCADE;/p' <$< >$@
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8
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9
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misc = schemas/vegbien.sql schemas/vegbien_empty.sql VegX-VegBIEN.organisms.csv
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10
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11
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12
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all: FORCE $(misc)
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13
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$(MAKE) plots
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14
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./join VegX VegBank
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15
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./join VegX VegBIEN
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16
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./review
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17
|
.PRECIOUS: $(misc)
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18
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19
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.SUFFIXES:
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20
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21
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FORCE:
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22
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.PHONY: FORCE
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23
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24
|
all =\
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25
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$(wildcard for_review/*.csv) \
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26
|
$(filter-out VegX-% VegBank-%,$(wildcard *-VegBank.*.csv)) \
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27
|
VegX-*.plots.csv $(misc)
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28
|
|
|
29
|
clean: FORCE
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30
|
$(RM) $(all)
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31
|
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32
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33
|
schemas/vegbien.sql: schemas/vegbank.sql
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34
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$(repl) <$< VegBank-VegBIEN.schema.csv|$(repl) VegBank-VegBIEN.csv >$@
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35
|
|
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36
|
schemas/vegbien_empty.sql: schemas/vegbien.sql
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37
|
$(empty)
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|
38
|
|
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39
|
VegX-VegBIEN.organisms.csv: VegX-VegBank.organisms.csv
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|
40
|
$(repl) <$< VegBank-VegBIEN.csv 1|$(sort) >$@
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41
|
|
|
42
|
|
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43
|
plots: FORCE $(subst .organisms.,.plots.,$(wildcard VegX-*.organisms.csv))
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44
|
|
|
45
|
chRoot2PlotsLeftVegx =\
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|
46
|
env \
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|
47
|
left_in_root='/*s/individualOrganismObservation/*ID->/*s/plotObservation' \
|
|
48
|
left_out_root='/*s/plotObservation' \
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|
49
|
$(chRoot)
|
|
50
|
|
|
51
|
VegX-VegBank.plots.csv: VegX-VegBank.organisms.csv
|
|
52
|
$(chRoot2PlotsVegxVegbank)
|
|
53
|
chRoot2PlotsVegxVegbank =\
|
|
54
|
env \
|
|
55
|
right_in_root='/taxonObservation/*_ID/observation' \
|
|
56
|
right_out_root='/observation' \
|
|
57
|
$(chRoot2PlotsLeftVegx)
|
|
58
|
|
|
59
|
VegX-VegBIEN.plots.csv: VegX-VegBIEN.organisms.csv
|
|
60
|
$(chRoot2PlotsVegxVegbien)
|
|
61
|
chRoot2PlotsVegxVegbien =\
|
|
62
|
env \
|
|
63
|
right_in_root='/taxonoccurrence/*_ID/plotevent' \
|
|
64
|
right_out_root='/plotevent' \
|
|
65
|
$(chRoot2PlotsLeftVegx)
|
