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