| 1 |
235
|
aaronmk
|
os = $(shell uname)
|
| 2 |
224
|
aaronmk
|
|
| 3 |
235
|
aaronmk
|
SED = sed -$(if $(filter Darwin,$(os)),E,r)
|
| 4 |
|
|
|
| 5 |
240
|
aaronmk
|
#####
|
| 6 |
224
|
aaronmk
|
|
| 7 |
240
|
aaronmk
|
all: _not_file misc
|
| 8 |
197
|
aaronmk
|
$(MAKE) plots
|
| 9 |
198
|
aaronmk
|
./join VegX VegBank
|
| 10 |
|
|
./join VegX VegBIEN
|
| 11 |
199
|
aaronmk
|
./review
|
| 12 |
150
|
aaronmk
|
|
| 13 |
223
|
aaronmk
|
.SUFFIXES:
|
| 14 |
|
|
|
| 15 |
235
|
aaronmk
|
_not_file:
|
| 16 |
|
|
.PHONY: _not_file
|
| 17 |
188
|
aaronmk
|
|
| 18 |
240
|
aaronmk
|
misc = schemas/vegbien.sql schemas/vegbien_empty.sql VegX-VegBIEN.organisms.csv
|
| 19 |
|
|
|
| 20 |
199
|
aaronmk
|
all =\
|
| 21 |
|
|
$(wildcard for_review/*.csv) \
|
| 22 |
|
|
$(filter-out VegX-% VegBank-%,$(wildcard *-VegBank.*.csv)) \
|
| 23 |
223
|
aaronmk
|
VegX-*.plots.csv $(misc)
|
| 24 |
196
|
aaronmk
|
|
| 25 |
235
|
aaronmk
|
clean: _not_file
|
| 26 |
196
|
aaronmk
|
$(RM) $(all)
|
| 27 |
188
|
aaronmk
|
|
| 28 |
240
|
aaronmk
|
#####
|
| 29 |
198
|
aaronmk
|
|
| 30 |
240
|
aaronmk
|
misc: $(misc)
|
| 31 |
|
|
.PRECIOUS: $(misc)
|
| 32 |
|
|
|
| 33 |
350
|
aaronmk
|
bin = ../bin
|
| 34 |
|
|
in_place = $(bin)/in_place
|
| 35 |
356
|
aaronmk
|
cat_csv = $(bin)/cat_csv
|
| 36 |
350
|
aaronmk
|
repl = $(bin)/repl
|
| 37 |
|
|
sort = $(bin)/sort 1 0
|
| 38 |
|
|
chRoot = $(bin)/ch_root <$< >$@
|
| 39 |
240
|
aaronmk
|
empty = $(SED) -n \
|
| 40 |
|
|
's/^CREATE TABLE ([0-9A-Za-z_]+) \($$/TRUNCATE \1 CASCADE;/p' <$< >$@
|
| 41 |
|
|
|
| 42 |
356
|
aaronmk
|
VegBank-VegBIEN.%.csv: VegBank-VegBIEN.csv VegBank-VegBIEN.%_only.csv
|
| 43 |
|
|
$(bin)/cat_csv <$+ >$@
|
| 44 |
|
|
.PRECIOUS: VegBank-VegBIEN.%.csv
|
| 45 |
|
|
|
| 46 |
212
|
aaronmk
|
schemas/vegbien.sql: schemas/vegbank.sql
|
| 47 |
356
|
aaronmk
|
$(repl) <$< VegBank-VegBIEN.schema.csv >$@
|
| 48 |
212
|
aaronmk
|
|
| 49 |
223
|
aaronmk
|
schemas/vegbien_empty.sql: schemas/vegbien.sql
|
| 50 |
|
|
$(empty)
|
| 51 |
|
|
|
| 52 |
350
|
aaronmk
|
VegX-VegBank.organisms.csv: _not_file
|
| 53 |
|
|
$(in_place) $@ $(sort)
|
| 54 |
|
|
|
| 55 |
212
|
aaronmk
|
VegX-VegBIEN.organisms.csv: VegX-VegBank.organisms.csv
|
| 56 |
221
|
aaronmk
|
$(repl) <$< VegBank-VegBIEN.csv 1|$(sort) >$@
|
| 57 |
212
|
aaronmk
|
|
| 58 |
240
|
aaronmk
|
#####
|
| 59 |
212
|
aaronmk
|
|
| 60 |
235
|
aaronmk
|
plots: _not_file $(subst .organisms.,.plots.,$(wildcard VegX-*.organisms.csv))
|
| 61 |
197
|
aaronmk
|
|
| 62 |
188
|
aaronmk
|
chRoot2PlotsLeftVegx =\
|
| 63 |
|
|
env \
|
| 64 |
|
|
left_in_root='/*s/individualOrganismObservation/*ID->/*s/plotObservation' \
|
| 65 |
|
|
left_out_root='/*s/plotObservation' \
|
| 66 |
|
|
$(chRoot)
|
| 67 |
|
|
|
| 68 |
|
|
VegX-VegBank.plots.csv: VegX-VegBank.organisms.csv
|
| 69 |
|
|
$(chRoot2PlotsVegxVegbank)
|
| 70 |
|
|
chRoot2PlotsVegxVegbank =\
|
| 71 |
|
|
env \
|
| 72 |
|
|
right_in_root='/taxonObservation/*_ID/observation' \
|
| 73 |
|
|
right_out_root='/observation' \
|
| 74 |
|
|
$(chRoot2PlotsLeftVegx)
|
| 75 |
|
|
|
| 76 |
|
|
VegX-VegBIEN.plots.csv: VegX-VegBIEN.organisms.csv
|
| 77 |
|
|
$(chRoot2PlotsVegxVegbien)
|
| 78 |
|
|
chRoot2PlotsVegxVegbien =\
|
| 79 |
|
|
env \
|
| 80 |
200
|
aaronmk
|
right_in_root='/taxonoccurrence/*_ID/plotevent' \
|
| 81 |
188
|
aaronmk
|
right_out_root='/plotevent' \
|
| 82 |
|
|
$(chRoot2PlotsLeftVegx)
|
