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 12548 aaronmk
	-$(MAKE) phppgadmin-Linux
228 6333 aaronmk
	-sudo pip install psycopg2
229 6503 aaronmk
	-$(MAKE) $(postgresReload-Linux)
230 6333 aaronmk
# run pg_version inline because it needs postgresql to be installed first
231
# ignore errors if conf files already edited
232
233 383 aaronmk
postgres-Darwin: _always
234 13797 aaronmk
	ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
235
	brew doctor
236
	brew install postgis # also installs PostgreSQL
237
	-$(postgresReload-Darwin)
238 11674 aaronmk
	-sudo easy_install psycopg2
239 11845 aaronmk
	-$(postgresReload-Darwin)
240 235 aaronmk
241 418 aaronmk
postgres-: _always ; # other OSes
242 241 aaronmk
243 2624 aaronmk
psqlAsAdminVegbien := $(psqlAsAdmin) vegbien
244 272 aaronmk
bienPassword := $(shell cat config/bien_password)
245 6331 aaronmk
bienReadPassword := $(shell cat config/bien_read_password)
246 241 aaronmk
247 7422 aaronmk
##### Misc.
248
249 7423 aaronmk
misc-Linux: _always
250
	cp -p "$(shell which dotlockfile)" bin/
251 7422 aaronmk
252
misc-Darwin: _always ;
253
254 784 aaronmk
##### VegBIEN DB
255 241 aaronmk
256 6331 aaronmk
#### DB and users
257 1967 aaronmk
258 2090 aaronmk
confirmRmDb = $(call confirm,WARNING: This will delete your entire VegBIEN\
259 3374 aaronmk
DB!,This includes all archived imports and staging tables.)
260 2089 aaronmk
261 2633 aaronmk
confirmRmPublicSchema = $(call confirm,WARNING: This will delete the current\
262
public schema of your VegBIEN DB!,To save it: make schemas/rotate)
263 2089 aaronmk
264 2091 aaronmk
rmPublicSchema := $(call rmSchemaCmd,public)
265 1967 aaronmk
266 14031 aaronmk
db: mk_db rm_initial_public schemas/reinstall _always ;
267 1967 aaronmk
268
mk_db: _always
269 13848 aaronmk
	-echo "CREATE USER public_ PASSWORD 'password';"|$(psqlAsAdmin)
270 1745 aaronmk
	-echo "CREATE USER bien PASSWORD '$(bienPassword)';"|$(psqlAsAdmin)
271 6331 aaronmk
	-echo "CREATE USER bien_read PASSWORD '$(bienReadPassword)' IN ROLE bien \
272
NOINHERIT;"|$(psqlAsAdmin)
273 2037 aaronmk
	-echo "CREATE DATABASE vegbien WITH OWNER bien TEMPLATE template1 \
274 1940 aaronmk
ENCODING 'UTF8' LC_COLLATE 'en_US.UTF-8' LC_CTYPE 'en_US.UTF-8';"|$(psqlAsAdmin)
275 6221 aaronmk
	-echo "CREATE EXTENSION hstore SCHEMA pg_catalog;"|$(psqlAsAdminVegbien)
276 13806 aaronmk
	-echo "CREATE EXTENSION plpython3u;"|$(psqlAsAdminVegbien)
277 13789 aaronmk
	-echo 'CREATE SCHEMA postgis;'|$(psqlAsAdminVegbien)
278 13798 aaronmk
	-echo 'GRANT USAGE ON SCHEMA postgis TO public;'|$(psqlAsAdminVegbien)
279 13789 aaronmk
	-echo 'CREATE EXTENSION postgis SCHEMA postgis;'\
280
|$(psqlAsAdminVegbien)
281 11150 aaronmk
	# unset ON_ERROR_STOP so user-exists errors don't prevent further user-adds
282
	-cat config/users.sql|$(psqlAsAdmin) --set ON_ERROR_STOP
283 2627 aaronmk
# ignore errors if user/database/etc. exists
284 2091 aaronmk
285
rm_initial_public: _always
286 2089 aaronmk
	@$(confirmRmPublicSchema)
287 2624 aaronmk
	echo $(rmPublicSchema)|$(psqlAsAdminVegbien)
288 1967 aaronmk
# drop public schema *as admin* because it starts out owned by postgres
289 241 aaronmk
290 383 aaronmk
rm_db: _always
291 1748 aaronmk
	@$(confirmRmDb)
292
	echo "DROP DATABASE IF EXISTS vegbien;"|$(psqlAsAdmin)
293 6331 aaronmk
	echo "DROP USER IF EXISTS bien_read;"|$(psqlAsAdmin)
294 1748 aaronmk
	echo "DROP USER IF EXISTS bien;"|$(psqlAsAdmin)
295 6822 aaronmk
	echo "DROP USER IF EXISTS public_;"|$(psqlAsAdmin)
296 241 aaronmk
297 418 aaronmk
reinstall_db: _always rm_db db ;
298 241 aaronmk
299 784 aaronmk
##### MySQL
300 241 aaronmk
301 7572 aaronmk
mysql: _always $(call forOs,mysql) mysql_users
302 241 aaronmk
	@$(done)
303
304 7572 aaronmk
rm_mysql: _always rm_mysql_users ;
305 241 aaronmk
306 383 aaronmk
mysql-Linux: _always
307 244 aaronmk
	@echo $(emph)"If asked for MySQL root password, enter $(bienPassword)"$(endEmph)
308 238 aaronmk
	@$(wait)
309 7574 aaronmk
	-sudo apt-get --yes install mysql-server
310
	-sudo apt-get --yes install mysql-client
311 10223 aaronmk
	-sudo apt-get --yes install mysql-workbench
312 7574 aaronmk
	-sudo apt-get --yes install python-mysqldb
313 7575 aaronmk
	-sudo apt-get --yes install phpmyadmin
314 235 aaronmk
315 383 aaronmk
mysql-Darwin: _always
316 244 aaronmk
	@echo $(emph)'Installing MySQLdb Python driver on Mac OS X 10.7 (may work on other versions):'$(endEmph)
317 235 aaronmk
	@echo 'Download it using "latest version" link at http://sourceforge.net/projects/mysql-python/files/'
318
	@echo 'Extract the archive'
319
	@echo '(From http://www.rustyrazorblade.com/2011/11/installing-mysqldb-on-macos-lion/:)'
320 284 aaronmk
	@echo 'Run ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib'
321
	@echo 'Run ln -s /usr/local/mysql/lib /usr/local/mysql/lib/mysql'
322 235 aaronmk
	@echo '(From http://blog.infoentropy.com/MySQL-python_EnvironmentError_mysql_config_not_found:)'
323
	@echo 'Edit site.cfg and change the line like "mysql_config = " to "mysql_config = /usr/local/mysql/bin/mysql_config"'
324
	@echo '(From http://www.mangoorange.com/2008/08/01/installing-python-mysqldb-122-on-mac-os-x/:)'
325
	@echo 'Change to the directory of the extracted files'
326 284 aaronmk
	@echo 'Run python setup.py clean'
327
	@echo 'Run python setup.py build'
328 235 aaronmk
	@echo 'Run sudo python setup.py install'
329
	@echo "Run python -c 'import MySQLdb'"
330 238 aaronmk
	@$(wait)
331 235 aaronmk
332 383 aaronmk
mysql-: _always # other OSes
333 235 aaronmk
334 247 aaronmk
mysqlAsRoot := mysql --user=root --password='$(bienPassword)'
335 235 aaronmk
336 7572 aaronmk
mysql_users: _always
337 7573 aaronmk
	-echo "CREATE USER 'bien'@'localhost' IDENTIFIED BY '$(bienPassword)';"\
338
|$(mysqlAsRoot)
339
	-echo "CREATE USER 'bien_read'@'%' IDENTIFIED BY '$(bienReadPassword)';"\
340
|$(mysqlAsRoot)
341 364 aaronmk
# ignore errors if user exists
342 202 aaronmk
343 7572 aaronmk
rm_mysql_users: _always
344 7573 aaronmk
	-echo "DROP USER 'bien_read'@'localhost';"|$(mysqlAsRoot)
345
	-echo "DROP USER 'bien'@'%';"|$(mysqlAsRoot)
346 364 aaronmk
# ignore errors if user exists
347 202 aaronmk
348 784 aaronmk
##### Datasources
349 202 aaronmk
350 418 aaronmk
inputs: _always inputs/all ;
351 245 aaronmk
352 7268 aaronmk
import: _always import-msg inputs/import_scrub ;
353 1542 aaronmk
import-msg: _always
354 1550 aaronmk
	@echo $(emph)"To import all inputs at once:"$(endEmph) . bin/import_all
355 1542 aaronmk
	@echo
356 250 aaronmk
357 7836 aaronmk
scrub: _always inputs/.TNRS/tnrs/tnrs-remake ;
358 7264 aaronmk
359 1458 aaronmk
verify: _always inputs/verify
360 1241 aaronmk
	@$(done)
361 386 aaronmk
362 1458 aaronmk
test: _always inputs/test
363 397 aaronmk
	@$(done)
364 1458 aaronmk
365
##### Testing
366
367 1743 aaronmk
test-all: _always remake test missing_mappings
368 1458 aaronmk
	@$(done)
369 1967 aaronmk
370
##### Subdir forwarding
371
372
# Must come last so overridden targets are not forwarded
373
374
define subdirTargets
375
$(subdir): _always
376
	+$$(subMake)
377
378
$(subdir)%: _always
379
	+$$(subMake)
380
.PRECIOUS: $(subdir)% # let subdir's Makefile decide whether to delete on error
381
382
$(subdir)reinstall: _always $(subdir)uninstall $(subdir)install ;
383
endef
384
$(foreach subdir,$(wildcard */),$(eval $(subdirTargets)))
385
386
Makefile: ;
387
388
%: $(addsuffix %,$(dir $(shell echo */Makefile))) _always ;
389 1999 aaronmk
390 11848 aaronmk
#### Overrides of forwarded commands
391
392 11862 aaronmk
# commented out to avoid a cascade of "overriding commands for target" warnings
393
#inputs/reinstall: _always
394
#	echo '. bin/reinstall_all; wait'|bash -s
395 11848 aaronmk
396 1999 aaronmk
#### Maps validation
397
398 4607 aaronmk
termsSubdirs := $(call no/,$(call wildcard/,inputs/*/))
399
400 3764 aaronmk
include lib/mappings.Makefile