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root := .
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include lib/common.Makefile
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##### Vars/functions
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# Make
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SHELL := /bin/bash
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# Paths
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bin := bin
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##### Environment
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export PGOPTIONS = --client-min-messages=WARNING
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##### General targets
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remake: _always clean
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	$(MAKE)
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# re-run make so that cache of existing files is reset
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%/remake: _always
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	$(MAKE) $(@D)/clean
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	$(MAKE) $(@D)/
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# re-run make so that cache of existing files is reset
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%-remake: _always
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	rm -f $*
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	$(MAKE) $*
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# re-run make so that cache of existing files is reset
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%/reinstall: _always %/uninstall %/install ;
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##### Installation
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# public must be installed *after* inputs because some views depend on inputs
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install: _always core mysql inputs/download inputs/install schemas/install test
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	@$(done)
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uninstall: _always rm_mysql rm_core ;
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reinstall: _always uninstall install ;
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##### Core: VegBIEN DB and dependencies
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core: _always $(call forOs,python php postgres misc) db
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	@$(done)
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rm_core: _always rm_db ;
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reinstall_core: _always rm_core core ;
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##### Python
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python-Linux: _always
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	-sudo apt-get --yes install python
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	-sudo apt-get --yes install python3
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	-sudo apt-get --yes install python-dev
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	-sudo apt-get --yes install python-dateutil
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	-sudo apt-get --yes install python-parallel
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	-sudo apt-get --yes install python-profiler
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	-sudo apt-get --yes install python-pip
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	-sudo apt-get --yes install pymetrics
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	-sudo pip install ordereddict
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	-sudo pip install pp
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python-Darwin: _always
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	@# Python 2 comes preinstalled
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	@echo $(emph)'Installing Python 3.2 on Mac OS X:'$(endEmph)
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	@echo 'Download it: http://www.python.org/ftp/python/3.2.3/python-3.2.3-macosx10.6.dmg'
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	@echo 'Open the disk image'
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	@echo 'Run the installer in it'
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	@$(wait)
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	@echo $(emph)'Installing python-dateutil on Mac OS X:'$(endEmph)
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	@echo 'Download it for Python 2: http://labix.org/download/python-dateutil/python-dateutil-1.5.tar.gz'
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	@echo 'Extract the archive'
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	@echo 'Change to the directory of the extracted files'
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	@echo 'Run python setup.py build'
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	@echo 'Run sudo python setup.py install'
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	@echo "Run python -c 'import dateutil'"
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	@echo 'Download it for Python 3: http://labix.org/download/python-dateutil/python-dateutil-2.0.tar.gz'
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	@echo 'Extract the archive'
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	@echo 'Change to the directory of the extracted files'
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	@echo 'Run python3 setup.py build'
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	@echo 'Run sudo python3 setup.py install'
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	@echo "Run python3 -c 'import dateutil'"
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	@$(wait)
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	@echo $(emph)'Installing pip on Mac OS X:'$(endEmph)
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	@echo 'Follow the instructions at http://www.pip-installer.org/en/latest/installing.html'
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	@$(wait)
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##### PHP
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php-Linux: _always
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	-sudo apt-get --yes install php-http-request
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php-Darwin: _always
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	@echo $(emph)'Installing PHP PEAR and HTTP_Request on Mac OS X:'$(endEmph)
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	@echo 'Download http://pear.php.net/go-pear.phar'
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	@echo 'Change to the directory of the downloaded file'
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	@echo 'Run php -d detect_unicode=0 go-pear.phar'
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	@echo 'Whenever prompted, press Enter to select default options'
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	@echo 'Add $$HOME/pear/bin to your $$PATH'
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	@echo 'Add $(HOME)/pear/share/pear to your php.ini include_path'
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	@echo 'If needed, set $$PHPRC to your php.ini'
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	@echo "Run pear install HTTP_Request"
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	@echo 'To run a php command: php -c <php.ini-path> ...'
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	@$(wait)
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##### PostgreSQL
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define editPhppgadmin
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-sudo patch /etc/phppgadmin/config.inc.php lib/phpPgAdmin.config.inc.php.diff
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sudo cp -n /usr/share/phppgadmin/login.php /usr/share/phppgadmin/login.php.old
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-sudo patch /usr/share/phppgadmin/login.php lib/phpPgAdmin.login.php.diff
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endef
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# ignore errors if patch has already been applied
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editPhppgadminApacheConf = echo $$'1\n,s/deny from all/allow from all/\nwq'|\
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sudo ed --loose-exit-status --verbose /etc/phppgadmin/apache.conf
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apacheConf := /etc/apache2/apache2.conf
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apacheConfPhppgadminLine := Include /etc/phppgadmin/apache.conf
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editApacheConfForPhppgadmin =\
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$(if $(shell grep -F "$(apacheConfPhppgadminLine)" $(apacheConf)),,\
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$(call sudoAppend,$(apacheConf),\n$(apacheConfPhppgadminLine)))
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nonApacheOnPort80 = $(shell sudo lsof -i :80|tail -n +2|grep -v -F apache2)
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editApachePortsConf = echo $$'1\n,s/\\b80\\b/8080/g\nwq'|\
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sudo ed --loose-exit-status --verbose /etc/apache2/ports.conf
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asAdmin := sudo -E -u postgres
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asBien := sudo -E -u bien
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pgVersion = "$$(env minor=1 bin/pg_version)"
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linuxPostgresDir := /etc/postgresql/9.1/main
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define pg_ctl-Linux
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$(asAdmin) /etc/init.d/postgresql $(1)
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sleep 2
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endef
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macPostgresDir := /Library/PostgreSQL/9.1
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define macUsePostgresLib
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sudo mv $(libDest) $(libDest).old||sudo rm -f $(libDest)
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sudo ln -s $(macPostgresDir)/lib/$(1) $(libDest)
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endef
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libDest = /usr/lib/$(1)
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macPostgresLibs := libcrypto libssl
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macPostgresLibs := $(macPostgresLibs) $(macPostgresLibs:%=%.1.0.0)
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macPostgresLibs := $(macPostgresLibs:%=%.dylib)
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define pg_ctl-Darwin
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$(asAdmin) pg_ctl -D $(macPostgresDir)/data -l $(macPostgresDir)/postgres.log $(1)
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sleep 2
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endef
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confirmPostgresReload = $(call confirm,Modifying postgresql.conf and pg_hba.conf)
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define postgresReload-Linux
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@$(confirmPostgresReload)
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@echo $(emph)'kernel.shmmax must be set to at least 4GB minus 1 byte:'$(endEmph)
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@echo 'Append the following to /etc/sysctl.conf:'
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@echo 'kernel.shmmax=4294967295'
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@$(wait)
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chmod a+r schemas/*.conf || $(asBien) chmod a+r schemas/*.conf
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-$(asAdmin) mv -n $(linuxPostgresDir)/postgresql.conf $(linuxPostgresDir)/postgresql.conf.old
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$(asAdmin) cp --preserve=timestamps schemas/postgresql.conf $(linuxPostgresDir)/postgresql.conf
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-$(asAdmin) mv -n $(linuxPostgresDir)/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf.old
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$(asAdmin) cp --preserve=timestamps schemas/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf
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$(call pg_ctl-Linux,restart)
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endef
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define postgresReload-Darwin
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@$(confirmPostgresReload)
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chmod a+r schemas/*.conf
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-$(asAdmin) mv -n $(macPostgresDir)/data/postgresql.conf $(macPostgresDir)/data/postgresql.conf.old
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$(asAdmin) cp schemas/postgresql.Mac.conf $(macPostgresDir)/data/postgresql.conf
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-$(asAdmin) mv -n $(macPostgresDir)/data/pg_hba.conf $(macPostgresDir)/data/pg_hba.conf.old
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$(asAdmin) cp schemas/pg_hba.Mac.conf $(macPostgresDir)/data/pg_hba.conf
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$(call pg_ctl-Darwin,restart)
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endef
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postgres_reload: _always
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	$($(call forOs,postgresReload))
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postgres-Linux: _always
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	-sudo apt-get --yes install postgresql
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	-sudo apt-get --yes install postgresql-contrib
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	-sudo apt-get --yes install postgresql-plpython3-$(pgVersion)
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	-sudo apt-get --yes install libpq-dev
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	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis
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	-sudo apt-get --yes install phppgadmin
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	$(editPhppgadmin)
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	$(editPhppgadminApacheConf)
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	$(editApacheConfForPhppgadmin)
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	$(if $(nonApacheOnPort80),$(editApachePortsConf))
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	-sudo apache2ctl restart
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	-sudo pip install psycopg2
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	-$(MAKE) $(postgresReload-Linux)
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# run pg_version inline because it needs postgresql to be installed first
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# ignore errors if conf files already edited
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postgres-Darwin: _always
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	@echo $(emph)'Installing PostgreSQL on Mac OS X:'$(endEmph)
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	@echo 'Download it using the topmost "Mac OS X" link at http://http://www.enterprisedb.com/products-services-training/pgdownload'
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	@echo 'Open the disk image'
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	@echo 'Run the installer in it'
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	@$(wait)
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	$(foreach lib,$(macPostgresLibs),$(call macUsePostgresLib,$(lib)))
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	-$(MAKE) $(postgresReload-Darwin)
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postgres-: _always ; # other OSes
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psqlOpts := --set ON_ERROR_STOP=1 --quiet
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psqlAsAdmin := $(asAdmin) psql $(psqlOpts)
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    # -E preserves env vars so PGOPTIONS is passed to psql
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psqlAsAdminVegbien := $(psqlAsAdmin) vegbien
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bienPassword := $(shell cat config/bien_password)
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bienReadPassword := $(shell cat config/bien_read_password)
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##### Misc.
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misc-Linux: _always
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	cp -p "$(shell which dotlockfile)" bin/
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misc-Darwin: _always ;
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##### VegBIEN DB
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#### DB and users
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confirmRmDb = $(call confirm,WARNING: This will delete your entire VegBIEN\
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DB!,This includes all archived imports and staging tables.)
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confirmRmPublicSchema = $(call confirm,WARNING: This will delete the current\
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public schema of your VegBIEN DB!,To save it: make schemas/rotate)
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rmPublicSchema := $(call rmSchemaCmd,public)
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db: mk_db rm_initial_public _always ;
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mk_db: _always
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	-echo "CREATE USER public_;"|$(psqlAsAdmin)
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	-echo "CREATE USER bien PASSWORD '$(bienPassword)';"|$(psqlAsAdmin)
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	-echo "CREATE USER bien_read PASSWORD '$(bienReadPassword)' IN ROLE bien \
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NOINHERIT;"|$(psqlAsAdmin)
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	-echo "CREATE DATABASE vegbien WITH OWNER bien TEMPLATE template1 \
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ENCODING 'UTF8' LC_COLLATE 'en_US.UTF-8' LC_CTYPE 'en_US.UTF-8';"|$(psqlAsAdmin)
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	-echo "CREATE EXTENSION hstore SCHEMA pg_catalog;"|$(psqlAsAdminVegbien)
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	-$(asAdmin) createlang plpython3u vegbien
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	-cat config/users.sql|$(psqlAsAdmin)
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# ignore errors if user/database/etc. exists
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rm_initial_public: _always
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	@$(confirmRmPublicSchema)
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	echo $(rmPublicSchema)|$(psqlAsAdminVegbien)
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# drop public schema *as admin* because it starts out owned by postgres
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rm_db: _always
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	@$(confirmRmDb)
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	echo "DROP DATABASE IF EXISTS vegbien;"|$(psqlAsAdmin)
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	echo "DROP USER IF EXISTS bien_read;"|$(psqlAsAdmin)
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	echo "DROP USER IF EXISTS bien;"|$(psqlAsAdmin)
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	echo "DROP USER IF EXISTS public_;"|$(psqlAsAdmin)
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reinstall_db: _always rm_db db ;
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##### MySQL
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mysql: _always $(call forOs,mysql) mysql_users
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	@$(done)
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rm_mysql: _always rm_mysql_users ;
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mysql-Linux: _always
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	@echo $(emph)"If asked for MySQL root password, enter $(bienPassword)"$(endEmph)
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	@$(wait)
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	-sudo apt-get --yes install mysql-server
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	-sudo apt-get --yes install mysql-client
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	-sudo apt-get --yes install python-mysqldb
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	-sudo apt-get --yes install phpmyadmin
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mysql-Darwin: _always
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	@echo $(emph)'Installing MySQLdb Python driver on Mac OS X 10.7 (may work on other versions):'$(endEmph)
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	@echo 'Download it using "latest version" link at http://sourceforge.net/projects/mysql-python/files/'
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	@echo 'Extract the archive'
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	@echo '(From http://www.rustyrazorblade.com/2011/11/installing-mysqldb-on-macos-lion/:)'
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	@echo 'Run ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib'
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	@echo 'Run ln -s /usr/local/mysql/lib /usr/local/mysql/lib/mysql'
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	@echo '(From http://blog.infoentropy.com/MySQL-python_EnvironmentError_mysql_config_not_found:)'
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	@echo 'Edit site.cfg and change the line like "mysql_config = " to "mysql_config = /usr/local/mysql/bin/mysql_config"'
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	@echo '(From http://www.mangoorange.com/2008/08/01/installing-python-mysqldb-122-on-mac-os-x/:)'
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	@echo 'Change to the directory of the extracted files'
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	@echo 'Run python setup.py clean'
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	@echo 'Run python setup.py build'
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	@echo 'Run sudo python setup.py install'
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	@echo "Run python -c 'import MySQLdb'"
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	@$(wait)
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mysql-: _always # other OSes
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mysqlAsRoot := mysql --user=root --password='$(bienPassword)'
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mysql_users: _always
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	-echo "CREATE USER 'bien'@'localhost' IDENTIFIED BY '$(bienPassword)';"\
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|$(mysqlAsRoot)
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	-echo "CREATE USER 'bien_read'@'%' IDENTIFIED BY '$(bienReadPassword)';"\
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|$(mysqlAsRoot)
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# ignore errors if user exists
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rm_mysql_users: _always
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	-echo "DROP USER 'bien_read'@'localhost';"|$(mysqlAsRoot)
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	-echo "DROP USER 'bien'@'%';"|$(mysqlAsRoot)
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# ignore errors if user exists
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##### Datasources
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inputs: _always inputs/all ;
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inputs/install: _always
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	echo '. bin/reinstall_all; wait'|bash -s
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import: _always import-msg inputs/import_scrub ;
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import-msg: _always
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	@echo $(emph)"To import all inputs at once:"$(endEmph) . bin/import_all
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	@echo
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scrub: _always inputs/.TNRS/tnrs/tnrs-remake\
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inputs/.TNRS/public.unscrubbed_taxondetermination_view/scrub-remake ;
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verify: _always inputs/verify
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	@$(done)
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test: _always inputs/test
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	@$(done)
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##### Testing
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test-all: _always remake test missing_mappings
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	@$(done)
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##### Subdir forwarding
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# Must come last so overridden targets are not forwarded
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define subdirTargets
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$(subdir): _always
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	+$$(subMake)
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$(subdir)%: _always
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	+$$(subMake)
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.PRECIOUS: $(subdir)% # let subdir's Makefile decide whether to delete on error
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$(subdir)reinstall: _always $(subdir)uninstall $(subdir)install ;
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endef
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$(foreach subdir,$(wildcard */),$(eval $(subdirTargets)))
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Makefile: ;
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%: $(addsuffix %,$(dir $(shell echo */Makefile))) _always ;
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#### Maps validation
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termsSubdirs := $(call no/,$(call wildcard/,inputs/*/))
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include lib/mappings.Makefile