Project

General

Profile

1 5459 aaronmk
root := .
2 3762 aaronmk
include lib/common.Makefile
3
4
5 784 aaronmk
##### Vars/functions
6
7 244 aaronmk
# Make
8 247 aaronmk
SHELL := /bin/bash
9 244 aaronmk
10 4607 aaronmk
# Paths
11
bin := bin
12
13 784 aaronmk
##### Environment
14
15 225 aaronmk
export PGOPTIONS = --client-min-messages=WARNING
16
17 784 aaronmk
##### General targets
18 225 aaronmk
19 1274 aaronmk
remake: _always clean
20
	$(MAKE)
21
# re-run make so that cache of existing files is reset
22
23 784 aaronmk
##### Installation
24 241 aaronmk
25 6102 aaronmk
# public must be installed *after* inputs because some views depend on inputs
26 13359 aaronmk
# schemas/public/install also tests that a clean public schema will be
27
# installable by full-database import
28 14739 aaronmk
install: _always bin/install config/download/live core mysql \
29
inputs/download/live inputs/install schemas/public/reinstall
30 241 aaronmk
	@$(done)
31 13419 aaronmk
# schemas/public/install would errexit if the public schema already exists
32 202 aaronmk
33 6200 aaronmk
uninstall: _always rm_mysql rm_core ;
34 241 aaronmk
35 418 aaronmk
reinstall: _always uninstall install ;
36 225 aaronmk
37 14700 aaronmk
##### bin/install: live and test environments
38 9742 aaronmk
39 14741 aaronmk
define uutils_install
40
(mkdir -p ~/software/uutils/; cd ~/software/uutils/; \
41
svn co http://uutils.googlecode.com/svn/trunk/ .; make install)
42
@echo $(emph)'reload PATH:'$(endEmph)
43
@echo 'press Enter'
44
@echo 'press Ctrl-D'
45
@echo 'reopen the terminal window'
46
@echo 'rerun `make install`'
47
@$(wait)
48 14744 aaronmk
@false
49 14741 aaronmk
50
endef
51
uutils_install? = $(if $(wildcard ~/software/uutils/),,$(uutils_install))
52
53 14700 aaronmk
bin/install: _always
54 14741 aaronmk
	$(uutils_install?)
55 9742 aaronmk
	mkdir -p ~/bin
56 11844 aaronmk
	-ln -s $(realpath bin/make) ~/bin
57
# ignore errors if file exists
58 9742 aaronmk
59 784 aaronmk
##### Core: VegBIEN DB and dependencies
60 202 aaronmk
61 8817 aaronmk
core: _always $(call forOs,apache python php postgres misc) db
62 241 aaronmk
	@$(done)
63 235 aaronmk
64 1746 aaronmk
rm_core: _always rm_db ;
65 241 aaronmk
66 418 aaronmk
reinstall_core: _always rm_core core ;
67 241 aaronmk
68 8817 aaronmk
##### Apache
69
70
apache-Linux: _always
71 13360 aaronmk
	# Apache 2.4, which comes with Ubuntu 14.04
72 8818 aaronmk
	-sudo apt-get --yes install apache2
73 13360 aaronmk
	#-sudo apt-get --yes install libapache2-mod-php5
74 8817 aaronmk
75
apache-Darwin: _always ;
76
77 784 aaronmk
##### Python
78
79 383 aaronmk
python-Linux: _always
80 6544 aaronmk
	-sudo apt-get --yes install python
81
	-sudo apt-get --yes install python3
82
	-sudo apt-get --yes install python-dev
83
	-sudo apt-get --yes install python-dateutil
84
	-sudo apt-get --yes install python-parallel
85
	-sudo apt-get --yes install python-profiler
86
	-sudo apt-get --yes install python-pip
87
	-sudo apt-get --yes install pymetrics
88 284 aaronmk
89 383 aaronmk
python-Darwin: _always
90 7230 aaronmk
	@# Python 2 comes preinstalled
91 6190 aaronmk
	@echo $(emph)'Installing Python 3.2 on Mac OS X:'$(endEmph)
92
	@echo 'Download it: http://www.python.org/ftp/python/3.2.3/python-3.2.3-macosx10.6.dmg'
93
	@echo 'Open the disk image'
94
	@echo 'Run the installer in it'
95
	@$(wait)
96 284 aaronmk
	@echo $(emph)'Installing python-dateutil on Mac OS X:'$(endEmph)
97 7231 aaronmk
	@echo 'Download it for Python 2: http://labix.org/download/python-dateutil/python-dateutil-1.5.tar.gz'
98 284 aaronmk
	@echo 'Extract the archive'
99
	@echo 'Change to the directory of the extracted files'
100
	@echo 'Run python setup.py build'
101
	@echo 'Run sudo python setup.py install'
102
	@echo "Run python -c 'import dateutil'"
103 7231 aaronmk
	@echo 'Download it for Python 3: http://labix.org/download/python-dateutil/python-dateutil-2.0.tar.gz'
104
	@echo 'Extract the archive'
105
	@echo 'Change to the directory of the extracted files'
106
	@echo 'Run python3 setup.py build'
107
	@echo 'Run sudo python3 setup.py install'
108
	@echo "Run python3 -c 'import dateutil'"
109 284 aaronmk
	@$(wait)
110 3156 aaronmk
	@echo $(emph)'Installing pip on Mac OS X:'$(endEmph)
111
	@echo 'Follow the instructions at http://www.pip-installer.org/en/latest/installing.html'
112
	@$(wait)
113 284 aaronmk
114 1599 aaronmk
##### PHP
115
116
php-Linux: _always
117 6544 aaronmk
	-sudo apt-get --yes install php-http-request
118 1599 aaronmk
119
php-Darwin: _always
120 1600 aaronmk
	@echo $(emph)'Installing PHP PEAR and HTTP_Request on Mac OS X:'$(endEmph)
121
	@echo 'Download http://pear.php.net/go-pear.phar'
122
	@echo 'Change to the directory of the downloaded file'
123
	@echo 'Run php -d detect_unicode=0 go-pear.phar'
124
	@echo 'Whenever prompted, press Enter to select default options'
125
	@echo 'Add $$HOME/pear/bin to your $$PATH'
126
	@echo 'Add $(HOME)/pear/share/pear to your php.ini include_path'
127 1665 aaronmk
	@echo 'If needed, set $$PHPRC to your php.ini'
128 1600 aaronmk
	@echo "Run pear install HTTP_Request"
129
	@echo 'To run a php command: php -c <php.ini-path> ...'
130 1599 aaronmk
	@$(wait)
131
132 784 aaronmk
##### PostgreSQL
133
134 6824 aaronmk
define editPhppgadmin
135 6853 aaronmk
-sudo patch /etc/phppgadmin/config.inc.php lib/phpPgAdmin.config.inc.php.diff
136 6824 aaronmk
sudo cp -n /usr/share/phppgadmin/login.php /usr/share/phppgadmin/login.php.old
137 6853 aaronmk
-sudo patch /usr/share/phppgadmin/login.php lib/phpPgAdmin.login.php.diff
138 6824 aaronmk
endef
139 6853 aaronmk
# ignore errors if patch has already been applied
140 6824 aaronmk
141 1970 aaronmk
editPhppgadminApacheConf = echo $$'1\n,s/deny from all/allow from all/\nwq'|\
142 336 aaronmk
sudo ed --loose-exit-status --verbose /etc/phppgadmin/apache.conf
143 334 aaronmk
144
apacheConf := /etc/apache2/apache2.conf
145
apacheConfPhppgadminLine := Include /etc/phppgadmin/apache.conf
146
editApacheConfForPhppgadmin =\
147
$(if $(shell grep -F "$(apacheConfPhppgadminLine)" $(apacheConf)),,\
148
$(call sudoAppend,$(apacheConf),\n$(apacheConfPhppgadminLine)))
149
150 6337 aaronmk
asBien := sudo -E -u bien
151 4752 aaronmk
pgVersion = "$$(env minor=1 bin/pg_version)"
152
153 11662 aaronmk
linuxPostgresDir := /etc/postgresql/9.3/main
154 6201 aaronmk
define pg_ctl-Linux
155 14067 aaronmk
$(asAdmin) /etc/init.d/postgresql $(1)\
156 14068 aaronmk
# if doesn'\''t work, run `rm $(linuxPostgresDir)/postmaster.pid` and retry
157 6201 aaronmk
endef
158 6198 aaronmk
159 13797 aaronmk
macPostgresDir := /usr/local/var/postgres
160 6201 aaronmk
define pg_ctl-Darwin
161 14067 aaronmk
brew services $(1) postgresql\
162 14068 aaronmk
# if doesn'\''t work, run `rm $(macPostgresDir)/postmaster.pid` and retry
163 14067 aaronmk
endef
164 14066 aaronmk
#pg_ctl -D $(macPostgresDir) $(1)
165 6197 aaronmk
166 13012 aaronmk
postgres_restart: postgres_restart-$(os) _always ;
167
postgres_restart-Linux: _always
168 13015 aaronmk
	@# for some reason, pg_ctl does not work when run inside make
169 13012 aaronmk
	@echo $(emph)'restart PostgreSQL manually:'$(endEmph)
170 14068 aaronmk
	@echo '$(call pg_ctl-$(os),restart)'
171 13014 aaronmk
	@$(wait)
172 13012 aaronmk
postgres_restart-Darwin: _always
173 13990 aaronmk
	@# for some reason, pg_ctl does not work when run inside make
174
	@echo $(emph)'restart PostgreSQL manually:'$(endEmph)
175 14068 aaronmk
	@echo '$(call pg_ctl-$(os),restart)'
176 13990 aaronmk
	@$(wait)
177 13011 aaronmk
178 6503 aaronmk
confirmPostgresReload = $(call confirm,Modifying postgresql.conf and pg_hba.conf)
179
180 6333 aaronmk
define postgresReload-Linux
181 6503 aaronmk
@$(confirmPostgresReload)
182
@echo $(emph)'kernel.shmmax must be set to at least 4GB minus 1 byte:'$(endEmph)
183
@echo 'Append the following to /etc/sysctl.conf:'
184
@echo 'kernel.shmmax=4294967295'
185
@$(wait)
186 6447 aaronmk
chmod a+r schemas/*.conf || $(asBien) chmod a+r schemas/*.conf
187 6823 aaronmk
-$(asAdmin) mv -n $(linuxPostgresDir)/postgresql.conf $(linuxPostgresDir)/postgresql.conf.old
188 6333 aaronmk
$(asAdmin) cp --preserve=timestamps schemas/postgresql.conf $(linuxPostgresDir)/postgresql.conf
189 6823 aaronmk
-$(asAdmin) mv -n $(linuxPostgresDir)/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf.old
190 6335 aaronmk
$(asAdmin) cp --preserve=timestamps schemas/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf
191 13013 aaronmk
$(MAKE) postgres_restart-$(os)
192 6333 aaronmk
193
endef
194
195
define postgresReload-Darwin
196 6503 aaronmk
@$(confirmPostgresReload)
197 6336 aaronmk
chmod a+r schemas/*.conf
198 13797 aaronmk
-$(asAdmin) mv -n $(macPostgresDir)/postgresql.conf $(macPostgresDir)/postgresql.conf.old
199
$(asAdmin) cp schemas/postgresql.Mac.conf $(macPostgresDir)/postgresql.conf
200
-$(asAdmin) mv -n $(macPostgresDir)/pg_hba.conf $(macPostgresDir)/pg_hba.conf.old
201
$(asAdmin) cp schemas/pg_hba.Mac.conf $(macPostgresDir)/pg_hba.conf
202
-$(asAdmin) mv -n $(macPostgresDir)/pg_ident.conf $(macPostgresDir)/pg_ident.conf.old
203
$(asAdmin) cp schemas/pg_ident.Mac.conf $(macPostgresDir)/pg_ident.conf
204 13013 aaronmk
$(MAKE) postgres_restart-$(os)
205 6333 aaronmk
206
endef
207
208 6334 aaronmk
postgres_reload: _always
209
	$($(call forOs,postgresReload))
210
211 12548 aaronmk
phppgadmin-Linux: _always
212
	-sudo apt-get --yes install phppgadmin
213
	$(editPhppgadmin)
214
	$(editPhppgadminApacheConf)
215
	-sudo ln -s ../conf.d/phppgadmin /etc/apache2/conf-available/phppgadmin.conf
216
	sudo a2enconf phppgadmin
217
	$(editApacheConfForPhppgadmin)
218
	-sudo apache2ctl restart
219
220 6333 aaronmk
postgres-Linux: _always
221 11661 aaronmk
	-sudo apt-get --yes install postgresql-9.3
222
	-sudo apt-get --yes install postgresql-contrib-$(pgVersion)
223 6544 aaronmk
	-sudo apt-get --yes install postgresql-plpython3-$(pgVersion)
224
	-sudo apt-get --yes install libpq-dev
225 13788 aaronmk
	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis-2.1-scripts
226
	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis-2.1
227 14751 aaronmk
	-sudo apt-get --yes install pgadmin3
228 12548 aaronmk
	-$(MAKE) phppgadmin-Linux
229 6333 aaronmk
	-sudo pip install psycopg2
230 14750 aaronmk
	$(postgresReload-Linux)
231 6333 aaronmk
# run pg_version inline because it needs postgresql to be installed first
232
# ignore errors if conf files already edited
233
234 383 aaronmk
postgres-Darwin: _always
235 13797 aaronmk
	ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
236
	brew doctor
237
	brew install postgis # also installs PostgreSQL
238
	-$(postgresReload-Darwin)
239 11674 aaronmk
	-sudo easy_install psycopg2
240 14750 aaronmk
	$(postgresReload-Darwin)
241 235 aaronmk
242 418 aaronmk
postgres-: _always ; # other OSes
243 241 aaronmk
244 2624 aaronmk
psqlAsAdminVegbien := $(psqlAsAdmin) vegbien
245 14749 aaronmk
# **IMPORTANT**: must use = instead of := because these files are not available
246
#  until config/download/live has run
247
bienPassword = $(shell cat config/bien_password)
248
bienReadPassword = $(shell cat config/bien_read_password)
249 241 aaronmk
250 7422 aaronmk
##### Misc.
251
252 7423 aaronmk
misc-Linux: _always
253
	cp -p "$(shell which dotlockfile)" bin/
254 7422 aaronmk
255
misc-Darwin: _always ;
256
257 784 aaronmk
##### VegBIEN DB
258 241 aaronmk
259 6331 aaronmk
#### DB and users
260 1967 aaronmk
261 2090 aaronmk
confirmRmDb = $(call confirm,WARNING: This will delete your entire VegBIEN\
262 3374 aaronmk
DB!,This includes all archived imports and staging tables.)
263 2089 aaronmk
264 2633 aaronmk
confirmRmPublicSchema = $(call confirm,WARNING: This will delete the current\
265
public schema of your VegBIEN DB!,To save it: make schemas/rotate)
266 2089 aaronmk
267 2091 aaronmk
rmPublicSchema := $(call rmSchemaCmd,public)
268 1967 aaronmk
269 14031 aaronmk
db: mk_db rm_initial_public schemas/reinstall _always ;
270 1967 aaronmk
271
mk_db: _always
272 13848 aaronmk
	-echo "CREATE USER public_ PASSWORD 'password';"|$(psqlAsAdmin)
273 1745 aaronmk
	-echo "CREATE USER bien PASSWORD '$(bienPassword)';"|$(psqlAsAdmin)
274 6331 aaronmk
	-echo "CREATE USER bien_read PASSWORD '$(bienReadPassword)' IN ROLE bien \
275
NOINHERIT;"|$(psqlAsAdmin)
276 2037 aaronmk
	-echo "CREATE DATABASE vegbien WITH OWNER bien TEMPLATE template1 \
277 1940 aaronmk
ENCODING 'UTF8' LC_COLLATE 'en_US.UTF-8' LC_CTYPE 'en_US.UTF-8';"|$(psqlAsAdmin)
278 6221 aaronmk
	-echo "CREATE EXTENSION hstore SCHEMA pg_catalog;"|$(psqlAsAdminVegbien)
279 13806 aaronmk
	-echo "CREATE EXTENSION plpython3u;"|$(psqlAsAdminVegbien)
280 13789 aaronmk
	-echo 'CREATE SCHEMA postgis;'|$(psqlAsAdminVegbien)
281 13798 aaronmk
	-echo 'GRANT USAGE ON SCHEMA postgis TO public;'|$(psqlAsAdminVegbien)
282 13789 aaronmk
	-echo 'CREATE EXTENSION postgis SCHEMA postgis;'\
283
|$(psqlAsAdminVegbien)
284 11150 aaronmk
	# unset ON_ERROR_STOP so user-exists errors don't prevent further user-adds
285
	-cat config/users.sql|$(psqlAsAdmin) --set ON_ERROR_STOP
286 2627 aaronmk
# ignore errors if user/database/etc. exists
287 2091 aaronmk
288
rm_initial_public: _always
289 2089 aaronmk
	@$(confirmRmPublicSchema)
290 2624 aaronmk
	echo $(rmPublicSchema)|$(psqlAsAdminVegbien)
291 1967 aaronmk
# drop public schema *as admin* because it starts out owned by postgres
292 241 aaronmk
293 383 aaronmk
rm_db: _always
294 1748 aaronmk
	@$(confirmRmDb)
295
	echo "DROP DATABASE IF EXISTS vegbien;"|$(psqlAsAdmin)
296 6331 aaronmk
	echo "DROP USER IF EXISTS bien_read;"|$(psqlAsAdmin)
297 1748 aaronmk
	echo "DROP USER IF EXISTS bien;"|$(psqlAsAdmin)
298 6822 aaronmk
	echo "DROP USER IF EXISTS public_;"|$(psqlAsAdmin)
299 241 aaronmk
300 418 aaronmk
reinstall_db: _always rm_db db ;
301 241 aaronmk
302 784 aaronmk
##### MySQL
303 241 aaronmk
304 7572 aaronmk
mysql: _always $(call forOs,mysql) mysql_users
305 241 aaronmk
	@$(done)
306
307 7572 aaronmk
rm_mysql: _always rm_mysql_users ;
308 241 aaronmk
309 383 aaronmk
mysql-Linux: _always
310 244 aaronmk
	@echo $(emph)"If asked for MySQL root password, enter $(bienPassword)"$(endEmph)
311 238 aaronmk
	@$(wait)
312 7574 aaronmk
	-sudo apt-get --yes install mysql-server
313
	-sudo apt-get --yes install mysql-client
314 10223 aaronmk
	-sudo apt-get --yes install mysql-workbench
315 7574 aaronmk
	-sudo apt-get --yes install python-mysqldb
316 7575 aaronmk
	-sudo apt-get --yes install phpmyadmin
317 235 aaronmk
318 383 aaronmk
mysql-Darwin: _always
319 244 aaronmk
	@echo $(emph)'Installing MySQLdb Python driver on Mac OS X 10.7 (may work on other versions):'$(endEmph)
320 235 aaronmk
	@echo 'Download it using "latest version" link at http://sourceforge.net/projects/mysql-python/files/'
321
	@echo 'Extract the archive'
322
	@echo '(From http://www.rustyrazorblade.com/2011/11/installing-mysqldb-on-macos-lion/:)'
323 284 aaronmk
	@echo 'Run ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib'
324
	@echo 'Run ln -s /usr/local/mysql/lib /usr/local/mysql/lib/mysql'
325 235 aaronmk
	@echo '(From http://blog.infoentropy.com/MySQL-python_EnvironmentError_mysql_config_not_found:)'
326
	@echo 'Edit site.cfg and change the line like "mysql_config = " to "mysql_config = /usr/local/mysql/bin/mysql_config"'
327
	@echo '(From http://www.mangoorange.com/2008/08/01/installing-python-mysqldb-122-on-mac-os-x/:)'
328
	@echo 'Change to the directory of the extracted files'
329 284 aaronmk
	@echo 'Run python setup.py clean'
330
	@echo 'Run python setup.py build'
331 235 aaronmk
	@echo 'Run sudo python setup.py install'
332
	@echo "Run python -c 'import MySQLdb'"
333 238 aaronmk
	@$(wait)
334 235 aaronmk
335 383 aaronmk
mysql-: _always # other OSes
336 235 aaronmk
337 247 aaronmk
mysqlAsRoot := mysql --user=root --password='$(bienPassword)'
338 235 aaronmk
339 7572 aaronmk
mysql_users: _always
340 7573 aaronmk
	-echo "CREATE USER 'bien'@'localhost' IDENTIFIED BY '$(bienPassword)';"\
341
|$(mysqlAsRoot)
342
	-echo "CREATE USER 'bien_read'@'%' IDENTIFIED BY '$(bienReadPassword)';"\
343
|$(mysqlAsRoot)
344 364 aaronmk
# ignore errors if user exists
345 202 aaronmk
346 7572 aaronmk
rm_mysql_users: _always
347 7573 aaronmk
	-echo "DROP USER 'bien_read'@'localhost';"|$(mysqlAsRoot)
348
	-echo "DROP USER 'bien'@'%';"|$(mysqlAsRoot)
349 364 aaronmk
# ignore errors if user exists
350 202 aaronmk
351 784 aaronmk
##### Datasources
352 202 aaronmk
353 418 aaronmk
inputs: _always inputs/all ;
354 245 aaronmk
355 7268 aaronmk
import: _always import-msg inputs/import_scrub ;
356 1542 aaronmk
import-msg: _always
357 1550 aaronmk
	@echo $(emph)"To import all inputs at once:"$(endEmph) . bin/import_all
358 1542 aaronmk
	@echo
359 250 aaronmk
360 7836 aaronmk
scrub: _always inputs/.TNRS/tnrs/tnrs-remake ;
361 7264 aaronmk
362 1458 aaronmk
verify: _always inputs/verify
363 1241 aaronmk
	@$(done)
364 386 aaronmk
365 1458 aaronmk
test: _always inputs/test
366 397 aaronmk
	@$(done)
367 1458 aaronmk
368
##### Testing
369
370 1743 aaronmk
test-all: _always remake test missing_mappings
371 1458 aaronmk
	@$(done)
372 1967 aaronmk
373
##### Subdir forwarding
374
375
# Must come last so overridden targets are not forwarded
376
377
define subdirTargets
378
$(subdir): _always
379
	+$$(subMake)
380
381
$(subdir)%: _always
382
	+$$(subMake)
383
.PRECIOUS: $(subdir)% # let subdir's Makefile decide whether to delete on error
384
385
$(subdir)reinstall: _always $(subdir)uninstall $(subdir)install ;
386
endef
387
$(foreach subdir,$(wildcard */),$(eval $(subdirTargets)))
388
389
Makefile: ;
390
391
%: $(addsuffix %,$(dir $(shell echo */Makefile))) _always ;
392 1999 aaronmk
393 11848 aaronmk
#### Overrides of forwarded commands
394
395 11862 aaronmk
# commented out to avoid a cascade of "overriding commands for target" warnings
396
#inputs/reinstall: _always
397
#	echo '. bin/reinstall_all; wait'|bash -s
398 11848 aaronmk
399 1999 aaronmk
#### Maps validation
400
401 4607 aaronmk
termsSubdirs := $(call no/,$(call wildcard/,inputs/*/))
402
403 3764 aaronmk
include lib/mappings.Makefile