log ?= $(if $(test),,1)

profile ?=

reverify ?= 1

exts ?= csv tsv txt xml

test_n ?= 2

tablesSort ?= plots organisms stems specimens

selfDir_uZPPqC := $(dir $(lastword $(MAKEFILE_LIST)))

# Paths

# Make

SHELL := /bin/bash

selfMake = $(MAKE) --makefile=../input.Makefile

subMake = $(MAKE) $(@:$(root)/%=%) --directory=$(root)

+_ = $(+:_%=)

addBeforeExt = $(basename $(2))$(1)$(suffix $(2))

# OS

# System

# Terminal

termCols := $(shell tput cols)

esc := '['

# Commands

MKDIR = mkdir -p

CP = cp -p

diff = diff --unified=2

# Commands

selfMap = $(bin)/cols 0 0

psqlOpts := --set ON_ERROR_STOP=1 --quiet

psqlAsBien := $(bin)/psql_vegbien $(psqlOpts)

# SVN

setSvnIgnore = svn propset svn:ignore $(2) $(1)

define addDirWithIgnore

$(setSvnIgnore)

endef

##### General targets

all: _always maps ;

.SUFFIXES: # turn off built-in suffix rules

.DELETE_ON_ERROR: # delete target if recipe fails

_always:

clean: _always

	$(RM) $(all)

remake: _always clean

make_script = ./$< >$@

%/: % _always ;

# Must come before `%: %.make` to override it

	(set -x; $(make_script)) 2>>$<.log

.PRECIOUS: src/% # save partial outputs of aborted src make scripts

##### SVN

add: _always

	$(call setSvnIgnore,.,$$'')

	$(call addDirWithIgnore,src,$$'*')

##### Installation

reinstall: _always uninstall install ;

##### Existing maps discovery

srcMap := maps/src.%.csv

fullViaMap := maps/%.full.csv

directMap := maps/VegBIEN.%.csv

$(wildcard maps/*.csv))

via := $(firstword $(sort $(basename $(basename $(notdir $(allViaMaps))))))

coreMap := $(mappings)/$(via)-VegBIEN.%.csv

coreSelfMap := $(mappings)/$(via).self.%.csv

viaMaps := $(wildcard $(tablesSort:%=maps/$(via).%.csv))

viaMaps += $(filter-out $(viaMaps) $(fullViaMap),$(wildcard maps/$(via).*.csv))

autogenMaps := $(subst $(via).,VegBIEN.,$(viaMaps))

tables := $(directMaps:maps/VegBIEN.%.csv=%)

##### Sources

withCatSrcs = $(catSrcs:$(bin)/%=$(bin)/with_%) --

# Maps to (try to) build are added to one of these

maps :=

createOnlyMaps :=

srcMaps := $(wildcard maps/src.*.csv)

mkSrcMap = env datasrc=$(datasrc) $(withCatSrcs) $(bin)/src_map >$@

createOnlyMaps += $(tablesSort:%=maps/src.%.csv)

# Must come before $(root)/% to override it

$(coreSelfMap): _always

	-+$(subMake)

# ignore errors if $(coreSelfMap) does not exist

# Via maps cleanup

maps/.$(via).%.csv.last_cleanup: maps/$(via).%.csv $(coreMap)

	$(bin)/in_place $< env ignore=1 $(bin)/subtract $(word 2,$+) 0 1

	touch $@

joinSrcMap = $(if $(wildcard maps/src.$*.csv),$(bin)/in_place $@\

makeFullCsv = $(if $(shell test -e $(word 2,$+) && echo t),\

env ignore=1 $(bin)/union <$+|,<$< )$(bin)/sort_map >$@

# can't use $(wildcard) because it won't recheck file after $(coreSelfMap) runs

maps/$(via).%.full.csv: maps/$(via).%.csv $(coreSelfMap)

	$(makeFullCsv)

	$(joinSrcMap)

maps += $(patsubst maps/%.csv,maps/%.full.csv,$(viaMaps))

maps/VegBIEN.%.csv: maps/$(via).%.full.csv $(coreMap)

maps: $(createOnlyMaps) $(maps) _always ;

##### Maps validation

|$(SED) -n 's/^.*No.* $* mapping for ([0-9A-Za-z_-]+).*$$/\1/p'\

$(if $(filter join,$*),|$(bin)/ucase_first 0)|sort|uniq

##### External dependencies

.PRECIOUS: $(root)/% # let ext. dir's Makefile decide whether to delete on error

##### Mapping

dbExport := $(firstword $(wildcard src/db.*.sql))

inputFiles := $(wildcard $(exts:%=src/*.%))

+maps = $(filter maps/% $(mappings)/%,$(+_))

<in = $(firstword $(filter-out $(+maps),$(+_)))

$(if $(srcs),$(withCatSrcs),\

$(if $(mapEnv),env $(mapEnv),\

map2db = env out_database=vegbien $(map)

##### Import to VegBIEN

ifneq ($(dbExport)$(inputFiles),)

profileTest = $(if $(profile),$(if $(test),1))

log_ = import/$*$(if $(n),.n=$(n),).$(date).log

trace = $(log_:.log=.trace)

import = -$(if $(profileTest),$(profileOnly),(set -x; "time" env commit=1\

$(if $(profile),profile_to=$(trace)) $(map2db)) $(if $(log),\

$(if $(n),,>>$(log_))) 2>&1$(if $(log),$(if $(n),|tee -a $(log_))))

# don't abort on import errors, which often relate to invalid input data

import: $(addprefix import-,$(tables)) _always ;

# default:

else

##### Log files from import

logs := $(wildcard import/*.log import/*.trace)

rm_logs: _always

	$(RM) $(logs)

##### Verification of import

verify: $(addprefix verify-,$(tables)) _always ;

verify-%: verify/%.ref verify/%.out _always

	-$(diffVerbose) $(+_)

# don't abort on verification errors, which are expected during development

# default:

verify-%: verify/%.out _always

	$(if $(shell test -e $< && echo t),cat $<)

# don't run if verify/%.out's default do-nothing action was used

# can't use $(wildcard) because it won't recheck file after verify/%.out is run

verify = $(if $(reverify),"time" $(psqlAsBien) --set=datasource="'$(datasrc)'"\

verify/%.out: $(mappings)/verify.%.sql _always

	$(verify)

# default:

verify/%.out: _always ;

all += $(wildcard verify/*.out)

ifneq ($(dbExport),)

%.ref: %.ref.sql

##### Editing import

	echo "UPDATE party SET organizationname = organizationname||'.$(date)'\

WHERE organizationname = '$(datasrc)';"|$(psqlAsBien)

	echo "DELETE FROM party WHERE organizationname = '$(datasrc)';"|\

##### Testing

hasOwnRef = $(filter-out %.2-step.xml,$@)

testRef = $(1:.2-step.xml=.xml).ref

define runTest

@echo "Testing $(abspath $@)..."

>$@ env test=1 n=$(test_n) $(1)

@(set -x; $(diff) $(call testRef,$@) $@) 2>&1 || { e=$$?;\

$(if $(wildcard $(call testRef,$@)),,cat $@;)\

$(if $(hasOwnRef),\

exit $$e;}

endef

test2File = $(call runTest,$(map))

tests :=

test/$(via).%.xml: maps/$(via).%.full.csv _always

	$(test2File)

tests += test/$(via).%.xml

test/VegBIEN.%.xml: maps/VegBIEN.%.csv _always

	$(test2File)

tests += test/VegBIEN.%.xml

test/VegBIEN.%.2-step.xml: test/$(via).%.xml $(coreMap) _always

	-$(test2File)

# Don't abort tester if only 2-step test fails, as it's often finicky

tests += test/VegBIEN.%.2-step.xml

test/import.%.out: maps/VegBIEN.%.csv _always

	$(call runTest,$(map2db))

tests += test/import.%.out

testOutputs := $(foreach test,$(tests),$(tables:%=$(test)))

.PRECIOUS: $(testOutputs) # save outputs of failed tests so they can be accepted

test: _always $(testOutputs) ;

# Accepts a test output: make <test_output_path>-ok

%-ok: _always

	$(CP) $* $(call testRef,$*)

##### Input-type-specific

# Each input type needs var $(mapEnv) and targets install, uninstall

#### DB export

ifneq ($(dbExport),)

dbEngineExt := $(subst .,,$(suffix $(basename $(notdir $(dbExport)))))

db := $(datasrc)

### Installation

install: _always db ;

uninstall: _always rm_db ;

### DB-engine-specific

# Each DB engine needs vars $(dbEngine), $(dbAsBien) and targets db, rm_db

ifeq ($(dbEngineExt),my)

dbEngine := MySQL

bienPassword := $(shell cat $(root)/config/bien_password)

dbExists = $(shell echo "SHOW DATABASES LIKE '$(db)';"|$(mysqlAsRoot))

echo "CREATE DATABASE $(db) DEFAULT CHARACTER SET latin1;"|$(mysqlAsRoot)

-$(mysqlAsRoot) --database=$(db) <$<

db: $(dbExport) _always

	$(if $(dbExists),,$(createDb))

	echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot)

rm_db: _always

	-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot)

# ignore errors if grant not defined

## Unrecognized DB engine

$(error The DB filename $(dbExport) must be db.my.sql)

endif

### Other input types

else

endif