root := .

include lib/common.Makefile

##### Vars/functions

# Make

SHELL := /bin/bash

# Paths

bin := bin

##### Environment

export PGOPTIONS = --client-min-messages=WARNING

##### General targets

remake: _always clean

	$(MAKE)

# re-run make so that cache of existing files is reset

%/remake: _always

	$(MAKE) $(@D)/clean

	$(MAKE) $(@D)/

# re-run make so that cache of existing files is reset

%-remake: _always

	rm -f $*

	$(MAKE) $*

# re-run make so that cache of existing files is reset

%/reinstall: _always %/uninstall %/install ;

##### Installation

# public must be installed *after* inputs because some views depend on inputs

install: _always core mysql inputs/download inputs/install schemas/install test

	@$(done)

uninstall: _always rm_mysql rm_core ;

reinstall: _always uninstall install ;

##### Core: VegBIEN DB and dependencies

core: _always $(call forOs,python php postgres) db

	@$(done)

rm_core: _always rm_db ;

reinstall_core: _always rm_core core ;

##### Python

python-Linux: _always

	-sudo apt-get --yes install python

	-sudo apt-get --yes install python3

	-sudo apt-get --yes install python-dev

	-sudo apt-get --yes install python-dateutil

	-sudo apt-get --yes install python-parallel

	-sudo apt-get --yes install python-profiler

	-sudo apt-get --yes install python-pip

	-sudo apt-get --yes install pymetrics

	-sudo pip install ordereddict

	-sudo pip install pp

python-Darwin: _always

	@# Python 2 comes preinstalled

	@echo $(emph)'Installing Python 3.2 on Mac OS X:'$(endEmph)

	@echo 'Download it: http://www.python.org/ftp/python/3.2.3/python-3.2.3-macosx10.6.dmg'

	@echo 'Open the disk image'

	@echo 'Run the installer in it'

	@$(wait)

	@echo $(emph)'Installing python-dateutil on Mac OS X:'$(endEmph)

	@echo 'Download it for Python 2: http://labix.org/download/python-dateutil/python-dateutil-1.5.tar.gz'

	@echo 'Extract the archive'

	@echo 'Change to the directory of the extracted files'

	@echo 'Run python setup.py build'

	@echo 'Run sudo python setup.py install'

	@echo "Run python -c 'import dateutil'"

	@echo 'Download it for Python 3: http://labix.org/download/python-dateutil/python-dateutil-2.0.tar.gz'

	@echo 'Extract the archive'

	@echo 'Change to the directory of the extracted files'

	@echo 'Run python3 setup.py build'

	@echo 'Run sudo python3 setup.py install'

	@echo "Run python3 -c 'import dateutil'"

	@$(wait)

	@echo $(emph)'Installing pip on Mac OS X:'$(endEmph)

	@echo 'Follow the instructions at http://www.pip-installer.org/en/latest/installing.html'

	@$(wait)

##### PHP

php-Linux: _always

	-sudo apt-get --yes install php-http-request

php-Darwin: _always

	@echo $(emph)'Installing PHP PEAR and HTTP_Request on Mac OS X:'$(endEmph)

	@echo 'Download http://pear.php.net/go-pear.phar'

	@echo 'Change to the directory of the downloaded file'

	@echo 'Run php -d detect_unicode=0 go-pear.phar'

	@echo 'Whenever prompted, press Enter to select default options'

	@echo 'Add $$HOME/pear/bin to your $$PATH'

	@echo 'Add $(HOME)/pear/share/pear to your php.ini include_path'

	@echo 'If needed, set $$PHPRC to your php.ini'

	@echo "Run pear install HTTP_Request"

	@echo 'To run a php command: php -c <php.ini-path> ...'

	@$(wait)

##### PostgreSQL

define editPhppgadmin

-sudo patch /etc/phppgadmin/config.inc.php lib/phpPgAdmin.config.inc.php.diff

sudo cp -n /usr/share/phppgadmin/login.php /usr/share/phppgadmin/login.php.old

-sudo patch /usr/share/phppgadmin/login.php lib/phpPgAdmin.login.php.diff

endef

# ignore errors if patch has already been applied

editPhppgadminApacheConf = echo $$'1\n,s/deny from all/allow from all/\nwq'|\

sudo ed --loose-exit-status --verbose /etc/phppgadmin/apache.conf

apacheConf := /etc/apache2/apache2.conf

apacheConfPhppgadminLine := Include /etc/phppgadmin/apache.conf

editApacheConfForPhppgadmin =\

$(if $(shell grep -F "$(apacheConfPhppgadminLine)" $(apacheConf)),,\

$(call sudoAppend,$(apacheConf),\n$(apacheConfPhppgadminLine)))

nonApacheOnPort80 = $(shell sudo lsof -i :80|tail -n +2|grep -v -F apache2)

editApachePortsConf = echo $$'1\n,s/\\b80\\b/8080/g\nwq'|\

sudo ed --loose-exit-status --verbose /etc/apache2/ports.conf

asAdmin := sudo -E -u postgres

asBien := sudo -E -u bien

pgVersion = "$$(env minor=1 bin/pg_version)"

linuxPostgresDir := /etc/postgresql/9.1/main

define pg_ctl-Linux

$(asAdmin) /etc/init.d/postgresql $(1)

sleep 2

endef

macPostgresDir := /Library/PostgreSQL/9.1

define macUsePostgresLib

sudo mv $(libDest) $(libDest).old||sudo rm -f $(libDest)

sudo ln -s $(macPostgresDir)/lib/$(1) $(libDest)

endef

libDest = /usr/lib/$(1)

macPostgresLibs := libcrypto libssl

macPostgresLibs := $(macPostgresLibs) $(macPostgresLibs:%=%.1.0.0)

macPostgresLibs := $(macPostgresLibs:%=%.dylib)

define pg_ctl-Darwin

$(asAdmin) pg_ctl -D $(macPostgresDir)/data -l $(macPostgresDir)/postgres.log $(1)

sleep 2

endef

confirmPostgresReload = $(call confirm,Modifying postgresql.conf and pg_hba.conf)

define postgresReload-Linux

@$(confirmPostgresReload)

@echo $(emph)'kernel.shmmax must be set to at least 4GB minus 1 byte:'$(endEmph)

@echo 'Append the following to /etc/sysctl.conf:'

@echo 'kernel.shmmax=4294967295'

@$(wait)

chmod a+r schemas/*.conf || $(asBien) chmod a+r schemas/*.conf

-$(asAdmin) mv -n $(linuxPostgresDir)/postgresql.conf $(linuxPostgresDir)/postgresql.conf.old

$(asAdmin) cp --preserve=timestamps schemas/postgresql.conf $(linuxPostgresDir)/postgresql.conf

-$(asAdmin) mv -n $(linuxPostgresDir)/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf.old

$(asAdmin) cp --preserve=timestamps schemas/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf

$(call pg_ctl-Linux,restart)

endef

define postgresReload-Darwin

@$(confirmPostgresReload)

chmod a+r schemas/*.conf

-$(asAdmin) mv -n $(macPostgresDir)/data/postgresql.conf $(macPostgresDir)/data/postgresql.conf.old

$(asAdmin) cp schemas/postgresql.Mac.conf $(macPostgresDir)/data/postgresql.conf

-$(asAdmin) mv -n $(macPostgresDir)/data/pg_hba.conf $(macPostgresDir)/data/pg_hba.conf.old

$(asAdmin) cp schemas/pg_hba.Mac.conf $(macPostgresDir)/data/pg_hba.conf

$(call pg_ctl-Darwin,restart)

endef

postgres_reload: _always

	$($(call forOs,postgresReload))

postgres-Linux: _always

	-sudo apt-get --yes install postgresql

	-sudo apt-get --yes install postgresql-contrib

	-sudo apt-get --yes install postgresql-plpython3-$(pgVersion)

	-sudo apt-get --yes install libpq-dev

	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis

	-sudo apt-get --yes install phppgadmin

	$(editPhppgadmin)

	$(editPhppgadminApacheConf)

	$(editApacheConfForPhppgadmin)

	$(if $(nonApacheOnPort80),$(editApachePortsConf))

	-sudo apache2ctl restart

	-sudo pip install psycopg2

	-$(MAKE) $(postgresReload-Linux)

# run pg_version inline because it needs postgresql to be installed first

# ignore errors if conf files already edited

postgres-Darwin: _always

	@echo $(emph)'Installing PostgreSQL on Mac OS X:'$(endEmph)

	@echo 'Download it using the topmost "Mac OS X" link at http://http://www.enterprisedb.com/products-services-training/pgdownload'

	@echo 'Open the disk image'

	@echo 'Run the installer in it'

	@$(wait)

	$(foreach lib,$(macPostgresLibs),$(call macUsePostgresLib,$(lib)))

	-$(MAKE) $(postgresReload-Darwin)

postgres-: _always ; # other OSes

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

psqlAsAdmin := $(asAdmin) psql $(psqlOpts)

    # -E preserves env vars so PGOPTIONS is passed to psql

psqlAsAdminVegbien := $(psqlAsAdmin) vegbien

bienPassword := $(shell cat config/bien_password)

bienReadPassword := $(shell cat config/bien_read_password)

##### VegBIEN DB

#### DB and users

confirmRmDb = $(call confirm,WARNING: This will delete your entire VegBIEN\

DB!,This includes all archived imports and staging tables.)

confirmRmPublicSchema = $(call confirm,WARNING: This will delete the current\

public schema of your VegBIEN DB!,To save it: make schemas/rotate)

rmPublicSchema := $(call rmSchemaCmd,public)

db: mk_db rm_initial_public _always ;

mk_db: _always

	-echo "CREATE USER public_;"|$(psqlAsAdmin)

	-echo "CREATE USER bien PASSWORD '$(bienPassword)';"|$(psqlAsAdmin)

	-echo "CREATE USER bien_read PASSWORD '$(bienReadPassword)' IN ROLE bien \

NOINHERIT;"|$(psqlAsAdmin)

	-echo "CREATE DATABASE vegbien WITH OWNER bien TEMPLATE template1 \

ENCODING 'UTF8' LC_COLLATE 'en_US.UTF-8' LC_CTYPE 'en_US.UTF-8';"|$(psqlAsAdmin)

	-echo "CREATE EXTENSION hstore SCHEMA pg_catalog;"|$(psqlAsAdminVegbien)

	-$(asAdmin) createlang plpython3u vegbien

# ignore errors if user/database/etc. exists

rm_initial_public: _always

	@$(confirmRmPublicSchema)

	echo $(rmPublicSchema)|$(psqlAsAdminVegbien)

# drop public schema *as admin* because it starts out owned by postgres

rm_db: _always

	@$(confirmRmDb)

	echo "DROP DATABASE IF EXISTS vegbien;"|$(psqlAsAdmin)

	echo "DROP USER IF EXISTS bien_read;"|$(psqlAsAdmin)

	echo "DROP USER IF EXISTS bien;"|$(psqlAsAdmin)

	echo "DROP USER IF EXISTS public_;"|$(psqlAsAdmin)

reinstall_db: _always rm_db db ;

##### MySQL

mysql: _always $(call forOs,mysql) mysql_user

	@$(done)

rm_mysql: _always rm_mysql_user ;

mysql-Linux: _always

	@echo $(emph)"If asked for MySQL root password, enter $(bienPassword)"$(endEmph)

	@$(wait)

	-sudo apt-get --yes install mysql-server mysql-client python-mysqldb

mysql-Darwin: _always

	@echo $(emph)'Installing MySQLdb Python driver on Mac OS X 10.7 (may work on other versions):'$(endEmph)

	@echo 'Download it using "latest version" link at http://sourceforge.net/projects/mysql-python/files/'

	@echo 'Extract the archive'

	@echo '(From http://www.rustyrazorblade.com/2011/11/installing-mysqldb-on-macos-lion/:)'

	@echo 'Run ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib'

	@echo 'Run ln -s /usr/local/mysql/lib /usr/local/mysql/lib/mysql'

	@echo '(From http://blog.infoentropy.com/MySQL-python_EnvironmentError_mysql_config_not_found:)'

	@echo 'Edit site.cfg and change the line like "mysql_config = " to "mysql_config = /usr/local/mysql/bin/mysql_config"'

	@echo '(From http://www.mangoorange.com/2008/08/01/installing-python-mysqldb-122-on-mac-os-x/:)'

	@echo 'Change to the directory of the extracted files'

	@echo 'Run python setup.py clean'

	@echo 'Run python setup.py build'

	@echo 'Run sudo python setup.py install'

	@echo "Run python -c 'import MySQLdb'"

	@$(wait)

mysql-: _always # other OSes

mysqlAsRoot := mysql --user=root --password='$(bienPassword)'

mysql_user: _always

	-$($@_cmd)

# ignore errors if user exists

mysql_user_cmd = echo "CREATE USER 'bien'@'localhost' IDENTIFIED BY \

'$(bienPassword)';"|$(mysqlAsRoot)

rm_mysql_user: _always

	-echo "DROP USER 'bien'@'localhost';"|$(mysqlAsRoot)

# ignore errors if user exists

##### Datasources

inputs: _always inputs/all ;

inputs/install: _always

	echo '. bin/reinstall_all; wait'|bash -s

import: _always import-msg inputs/import_scrub ;

import-msg: _always

	@echo $(emph)"To import all inputs at once:"$(endEmph) . bin/import_all

	@echo

scrub: _always inputs/.TNRS/tnrs/tnrs-remake\

inputs/.TNRS/public.unscrubbed_taxondetermination_view/scrub-remake ;

verify: _always inputs/verify

	@$(done)

test: _always inputs/test

	@$(done)

##### Testing

test-all: _always remake test missing_mappings

	@$(done)

##### Subdir forwarding

# Must come last so overridden targets are not forwarded

define subdirTargets

$(subdir): _always

	+$$(subMake)

$(subdir)%: _always

	+$$(subMake)

.PRECIOUS: $(subdir)% # let subdir's Makefile decide whether to delete on error

$(subdir)reinstall: _always $(subdir)uninstall $(subdir)install ;

endef

$(foreach subdir,$(wildcard */),$(eval $(subdirTargets)))

Makefile: ;

%: $(addsuffix %,$(dir $(shell echo */Makefile))) _always ;

#### Maps validation

termsSubdirs := $(call no/,$(call wildcard/,inputs/*/))

include lib/mappings.Makefile