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
	$(MAKE)
21
# re-run make so that cache of existing files is reset
22
23 784 aaronmk
##### Installation
24 241 aaronmk
25 6102 aaronmk
# public must be installed *after* inputs because some views depend on inputs
26 13359 aaronmk
# schemas/public/install also tests that a clean public schema will be
27
# installable by full-database import
28 11896 aaronmk
install: _always config core mysql inputs/download/live inputs/install \
29 13419 aaronmk
schemas/public/reinstall
30 241 aaronmk
	@$(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 9742 aaronmk
##### config: live and test environments
38
39
config: _always
40
	mkdir -p ~/bin
41 11844 aaronmk
	-ln -s $(realpath bin/make) ~/bin
42
# ignore errors if file exists
43 9742 aaronmk
44 784 aaronmk
##### Core: VegBIEN DB and dependencies
45 202 aaronmk
46 8817 aaronmk
core: _always $(call forOs,apache python php postgres misc) db
47 241 aaronmk
	@$(done)
48 235 aaronmk
49 1746 aaronmk
rm_core: _always rm_db ;
50 241 aaronmk
51 418 aaronmk
reinstall_core: _always rm_core core ;
52 241 aaronmk
53 8817 aaronmk
##### Apache
54
55
apache-Linux: _always
56 13360 aaronmk
	# Apache 2.4, which comes with Ubuntu 14.04
57 8818 aaronmk
	-sudo apt-get --yes install apache2
58 13360 aaronmk
	#-sudo apt-get --yes install libapache2-mod-php5
59 8817 aaronmk
60
apache-Darwin: _always ;
61
62 784 aaronmk
##### Python
63
64 383 aaronmk
python-Linux: _always
65 6544 aaronmk
	-sudo apt-get --yes install python
66
	-sudo apt-get --yes install python3
67
	-sudo apt-get --yes install python-dev
68
	-sudo apt-get --yes install python-dateutil
69
	-sudo apt-get --yes install python-parallel
70
	-sudo apt-get --yes install python-profiler
71
	-sudo apt-get --yes install python-pip
72
	-sudo apt-get --yes install pymetrics
73 1845 aaronmk
	-sudo pip install pp
74 284 aaronmk
75 383 aaronmk
python-Darwin: _always
76 7230 aaronmk
	@# Python 2 comes preinstalled
77 6190 aaronmk
	@echo $(emph)'Installing Python 3.2 on Mac OS X:'$(endEmph)
78
	@echo 'Download it: http://www.python.org/ftp/python/3.2.3/python-3.2.3-macosx10.6.dmg'
79
	@echo 'Open the disk image'
80
	@echo 'Run the installer in it'
81
	@$(wait)
82 284 aaronmk
	@echo $(emph)'Installing python-dateutil on Mac OS X:'$(endEmph)
83 7231 aaronmk
	@echo 'Download it for Python 2: http://labix.org/download/python-dateutil/python-dateutil-1.5.tar.gz'
84 284 aaronmk
	@echo 'Extract the archive'
85
	@echo 'Change to the directory of the extracted files'
86
	@echo 'Run python setup.py build'
87
	@echo 'Run sudo python setup.py install'
88
	@echo "Run python -c 'import dateutil'"
89 7231 aaronmk
	@echo 'Download it for Python 3: http://labix.org/download/python-dateutil/python-dateutil-2.0.tar.gz'
90
	@echo 'Extract the archive'
91
	@echo 'Change to the directory of the extracted files'
92
	@echo 'Run python3 setup.py build'
93
	@echo 'Run sudo python3 setup.py install'
94
	@echo "Run python3 -c 'import dateutil'"
95 284 aaronmk
	@$(wait)
96 3156 aaronmk
	@echo $(emph)'Installing pip on Mac OS X:'$(endEmph)
97
	@echo 'Follow the instructions at http://www.pip-installer.org/en/latest/installing.html'
98
	@$(wait)
99 284 aaronmk
100 1599 aaronmk
##### PHP
101
102
php-Linux: _always
103 6544 aaronmk
	-sudo apt-get --yes install php-http-request
104 1599 aaronmk
105
php-Darwin: _always
106 1600 aaronmk
	@echo $(emph)'Installing PHP PEAR and HTTP_Request on Mac OS X:'$(endEmph)
107
	@echo 'Download http://pear.php.net/go-pear.phar'
108
	@echo 'Change to the directory of the downloaded file'
109
	@echo 'Run php -d detect_unicode=0 go-pear.phar'
110
	@echo 'Whenever prompted, press Enter to select default options'
111
	@echo 'Add $$HOME/pear/bin to your $$PATH'
112
	@echo 'Add $(HOME)/pear/share/pear to your php.ini include_path'
113 1665 aaronmk
	@echo 'If needed, set $$PHPRC to your php.ini'
114 1600 aaronmk
	@echo "Run pear install HTTP_Request"
115
	@echo 'To run a php command: php -c <php.ini-path> ...'
116 1599 aaronmk
	@$(wait)
117
118 784 aaronmk
##### PostgreSQL
119
120 6824 aaronmk
define editPhppgadmin
121 6853 aaronmk
-sudo patch /etc/phppgadmin/config.inc.php lib/phpPgAdmin.config.inc.php.diff
122 6824 aaronmk
sudo cp -n /usr/share/phppgadmin/login.php /usr/share/phppgadmin/login.php.old
123 6853 aaronmk
-sudo patch /usr/share/phppgadmin/login.php lib/phpPgAdmin.login.php.diff
124 6824 aaronmk
endef
125 6853 aaronmk
# ignore errors if patch has already been applied
126 6824 aaronmk
127 1970 aaronmk
editPhppgadminApacheConf = echo $$'1\n,s/deny from all/allow from all/\nwq'|\
128 336 aaronmk
sudo ed --loose-exit-status --verbose /etc/phppgadmin/apache.conf
129 334 aaronmk
130
apacheConf := /etc/apache2/apache2.conf
131
apacheConfPhppgadminLine := Include /etc/phppgadmin/apache.conf
132
editApacheConfForPhppgadmin =\
133
$(if $(shell grep -F "$(apacheConfPhppgadminLine)" $(apacheConf)),,\
134
$(call sudoAppend,$(apacheConf),\n$(apacheConfPhppgadminLine)))
135
136 6337 aaronmk
asBien := sudo -E -u bien
137 4752 aaronmk
pgVersion = "$$(env minor=1 bin/pg_version)"
138
139 11662 aaronmk
linuxPostgresDir := /etc/postgresql/9.3/main
140 6201 aaronmk
define pg_ctl-Linux
141
$(asAdmin) /etc/init.d/postgresql $(1)
142
endef
143 6198 aaronmk
144 11662 aaronmk
macPostgresDir := /Library/PostgreSQL/9.3
145 6187 aaronmk
define macUsePostgresLib
146
sudo mv $(libDest) $(libDest).old||sudo rm -f $(libDest)
147 6196 aaronmk
sudo ln -s $(macPostgresDir)/lib/$(1) $(libDest)
148 6187 aaronmk
149
endef
150
libDest = /usr/lib/$(1)
151
152 11675 aaronmk
macPostgresLibs := libcrypto libcrypto.1.0.0 libssl libssl.1.0.0 libpq.5
153 6187 aaronmk
macPostgresLibs := $(macPostgresLibs:%=%.dylib)
154
155 6201 aaronmk
define pg_ctl-Darwin
156 13314 aaronmk
(cd /; $(asAdmin) pg_ctl -D $(macPostgresDir)/data -l $(macPostgresDir)/data/postgres.log $(1))
157
	# cd: due to pg_ctl bug, current directory must be accessible by it
158 6201 aaronmk
sleep 2
159
endef
160 6197 aaronmk
161 13012 aaronmk
postgres_restart: postgres_restart-$(os) _always ;
162
postgres_restart-Linux: _always
163 13015 aaronmk
	@# for some reason, pg_ctl does not work when run inside make
164 13012 aaronmk
	@echo $(emph)'restart PostgreSQL manually:'$(endEmph)
165
	@echo $(call pg_ctl-$(os),restart)
166 13014 aaronmk
	@$(wait)
167 13012 aaronmk
postgres_restart-Darwin: _always
168 13315 aaronmk
	$(call pg_ctl-$(os),restart)
169 13011 aaronmk
170 6503 aaronmk
confirmPostgresReload = $(call confirm,Modifying postgresql.conf and pg_hba.conf)
171
172 6333 aaronmk
define postgresReload-Linux
173 6503 aaronmk
@$(confirmPostgresReload)
174
@echo $(emph)'kernel.shmmax must be set to at least 4GB minus 1 byte:'$(endEmph)
175
@echo 'Append the following to /etc/sysctl.conf:'
176
@echo 'kernel.shmmax=4294967295'
177
@$(wait)
178 6447 aaronmk
chmod a+r schemas/*.conf || $(asBien) chmod a+r schemas/*.conf
179 6823 aaronmk
-$(asAdmin) mv -n $(linuxPostgresDir)/postgresql.conf $(linuxPostgresDir)/postgresql.conf.old
180 6333 aaronmk
$(asAdmin) cp --preserve=timestamps schemas/postgresql.conf $(linuxPostgresDir)/postgresql.conf
181 6823 aaronmk
-$(asAdmin) mv -n $(linuxPostgresDir)/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf.old
182 6335 aaronmk
$(asAdmin) cp --preserve=timestamps schemas/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf
183 13013 aaronmk
$(MAKE) postgres_restart-$(os)
184 6333 aaronmk
185
endef
186
187
define postgresReload-Darwin
188 6503 aaronmk
@$(confirmPostgresReload)
189 6336 aaronmk
chmod a+r schemas/*.conf
190 6823 aaronmk
-$(asAdmin) mv -n $(macPostgresDir)/data/postgresql.conf $(macPostgresDir)/data/postgresql.conf.old
191 6333 aaronmk
$(asAdmin) cp schemas/postgresql.Mac.conf $(macPostgresDir)/data/postgresql.conf
192 6823 aaronmk
-$(asAdmin) mv -n $(macPostgresDir)/data/pg_hba.conf $(macPostgresDir)/data/pg_hba.conf.old
193 6335 aaronmk
$(asAdmin) cp schemas/pg_hba.Mac.conf $(macPostgresDir)/data/pg_hba.conf
194 10121 aaronmk
-$(asAdmin) mv -n $(macPostgresDir)/data/pg_ident.conf $(macPostgresDir)/data/pg_ident.conf.old
195
$(asAdmin) cp schemas/pg_ident.Mac.conf $(macPostgresDir)/data/pg_ident.conf
196 13013 aaronmk
$(MAKE) postgres_restart-$(os)
197 6333 aaronmk
198
endef
199
200 6334 aaronmk
postgres_reload: _always
201
	$($(call forOs,postgresReload))
202
203 12548 aaronmk
phppgadmin-Linux: _always
204
	-sudo apt-get --yes install phppgadmin
205
	$(editPhppgadmin)
206
	$(editPhppgadminApacheConf)
207
	-sudo ln -s ../conf.d/phppgadmin /etc/apache2/conf-available/phppgadmin.conf
208
	sudo a2enconf phppgadmin
209
	$(editApacheConfForPhppgadmin)
210
	-sudo apache2ctl restart
211
212 6333 aaronmk
postgres-Linux: _always
213 11661 aaronmk
	-sudo apt-get --yes install postgresql-9.3
214
	-sudo apt-get --yes install postgresql-contrib-$(pgVersion)
215 6544 aaronmk
	-sudo apt-get --yes install postgresql-plpython3-$(pgVersion)
216
	-sudo apt-get --yes install libpq-dev
217 13788 aaronmk
	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis-2.1-scripts
218
	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis-2.1
219 12548 aaronmk
	-$(MAKE) phppgadmin-Linux
220 6333 aaronmk
	-sudo pip install psycopg2
221 6503 aaronmk
	-$(MAKE) $(postgresReload-Linux)
222 6333 aaronmk
# run pg_version inline because it needs postgresql to be installed first
223
# ignore errors if conf files already edited
224
225 383 aaronmk
postgres-Darwin: _always
226 254 aaronmk
	@echo $(emph)'Installing PostgreSQL on Mac OS X:'$(endEmph)
227
	@echo 'Download it using the topmost "Mac OS X" link at http://http://www.enterprisedb.com/products-services-training/pgdownload'
228
	@echo 'Open the disk image'
229
	@echo 'Run the installer in it'
230
	@$(wait)
231 6187 aaronmk
	$(foreach lib,$(macPostgresLibs),$(call macUsePostgresLib,$(lib)))
232 11674 aaronmk
	-sudo easy_install psycopg2
233 11845 aaronmk
	-$(postgresReload-Darwin)
234 235 aaronmk
235 418 aaronmk
postgres-: _always ; # other OSes
236 241 aaronmk
237 2624 aaronmk
psqlAsAdminVegbien := $(psqlAsAdmin) vegbien
238 272 aaronmk
bienPassword := $(shell cat config/bien_password)
239 6331 aaronmk
bienReadPassword := $(shell cat config/bien_read_password)
240 241 aaronmk
241 7422 aaronmk
##### Misc.
242
243 7423 aaronmk
misc-Linux: _always
244
	cp -p "$(shell which dotlockfile)" bin/
245 7422 aaronmk
246
misc-Darwin: _always ;
247
248 784 aaronmk
##### VegBIEN DB
249 241 aaronmk
250 6331 aaronmk
#### DB and users
251 1967 aaronmk
252 2090 aaronmk
confirmRmDb = $(call confirm,WARNING: This will delete your entire VegBIEN\
253 3374 aaronmk
DB!,This includes all archived imports and staging tables.)
254 2089 aaronmk
255 2633 aaronmk
confirmRmPublicSchema = $(call confirm,WARNING: This will delete the current\
256
public schema of your VegBIEN DB!,To save it: make schemas/rotate)
257 2089 aaronmk
258 2091 aaronmk
rmPublicSchema := $(call rmSchemaCmd,public)
259 1967 aaronmk
260 8844 aaronmk
db: mk_db rm_initial_public schemas/install _always ;
261 1967 aaronmk
262
mk_db: _always
263 6822 aaronmk
	-echo "CREATE USER public_;"|$(psqlAsAdmin)
264 1745 aaronmk
	-echo "CREATE USER bien PASSWORD '$(bienPassword)';"|$(psqlAsAdmin)
265 6331 aaronmk
	-echo "CREATE USER bien_read PASSWORD '$(bienReadPassword)' IN ROLE bien \
266
NOINHERIT;"|$(psqlAsAdmin)
267 2037 aaronmk
	-echo "CREATE DATABASE vegbien WITH OWNER bien TEMPLATE template1 \
268 1940 aaronmk
ENCODING 'UTF8' LC_COLLATE 'en_US.UTF-8' LC_CTYPE 'en_US.UTF-8';"|$(psqlAsAdmin)
269 6221 aaronmk
	-echo "CREATE EXTENSION hstore SCHEMA pg_catalog;"|$(psqlAsAdminVegbien)
270 10126 aaronmk
	-$(asAdmin) createlang -U postgres plpython3u vegbien
271 13789 aaronmk
	-echo 'CREATE SCHEMA postgis;'|$(psqlAsAdminVegbien)
272
	-echo 'CREATE EXTENSION postgis SCHEMA postgis;'\
273
|$(psqlAsAdminVegbien)
274 11150 aaronmk
	# unset ON_ERROR_STOP so user-exists errors don't prevent further user-adds
275
	-cat config/users.sql|$(psqlAsAdmin) --set ON_ERROR_STOP
276 2627 aaronmk
# ignore errors if user/database/etc. exists
277 2091 aaronmk
278
rm_initial_public: _always
279 2089 aaronmk
	@$(confirmRmPublicSchema)
280 2624 aaronmk
	echo $(rmPublicSchema)|$(psqlAsAdminVegbien)
281 1967 aaronmk
# drop public schema *as admin* because it starts out owned by postgres
282 241 aaronmk
283 383 aaronmk
rm_db: _always
284 1748 aaronmk
	@$(confirmRmDb)
285
	echo "DROP DATABASE IF EXISTS vegbien;"|$(psqlAsAdmin)
286 6331 aaronmk
	echo "DROP USER IF EXISTS bien_read;"|$(psqlAsAdmin)
287 1748 aaronmk
	echo "DROP USER IF EXISTS bien;"|$(psqlAsAdmin)
288 6822 aaronmk
	echo "DROP USER IF EXISTS public_;"|$(psqlAsAdmin)
289 241 aaronmk
290 418 aaronmk
reinstall_db: _always rm_db db ;
291 241 aaronmk
292 784 aaronmk
##### MySQL
293 241 aaronmk
294 7572 aaronmk
mysql: _always $(call forOs,mysql) mysql_users
295 241 aaronmk
	@$(done)
296
297 7572 aaronmk
rm_mysql: _always rm_mysql_users ;
298 241 aaronmk
299 383 aaronmk
mysql-Linux: _always
300 244 aaronmk
	@echo $(emph)"If asked for MySQL root password, enter $(bienPassword)"$(endEmph)
301 238 aaronmk
	@$(wait)
302 7574 aaronmk
	-sudo apt-get --yes install mysql-server
303
	-sudo apt-get --yes install mysql-client
304 10223 aaronmk
	-sudo apt-get --yes install mysql-workbench
305 7574 aaronmk
	-sudo apt-get --yes install python-mysqldb
306 7575 aaronmk
	-sudo apt-get --yes install phpmyadmin
307 235 aaronmk
308 383 aaronmk
mysql-Darwin: _always
309 244 aaronmk
	@echo $(emph)'Installing MySQLdb Python driver on Mac OS X 10.7 (may work on other versions):'$(endEmph)
310 235 aaronmk
	@echo 'Download it using "latest version" link at http://sourceforge.net/projects/mysql-python/files/'
311
	@echo 'Extract the archive'
312
	@echo '(From http://www.rustyrazorblade.com/2011/11/installing-mysqldb-on-macos-lion/:)'
313 284 aaronmk
	@echo 'Run ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib'
314
	@echo 'Run ln -s /usr/local/mysql/lib /usr/local/mysql/lib/mysql'
315 235 aaronmk
	@echo '(From http://blog.infoentropy.com/MySQL-python_EnvironmentError_mysql_config_not_found:)'
316
	@echo 'Edit site.cfg and change the line like "mysql_config = " to "mysql_config = /usr/local/mysql/bin/mysql_config"'
317
	@echo '(From http://www.mangoorange.com/2008/08/01/installing-python-mysqldb-122-on-mac-os-x/:)'
318
	@echo 'Change to the directory of the extracted files'
319 284 aaronmk
	@echo 'Run python setup.py clean'
320
	@echo 'Run python setup.py build'
321 235 aaronmk
	@echo 'Run sudo python setup.py install'
322
	@echo "Run python -c 'import MySQLdb'"
323 238 aaronmk
	@$(wait)
324 235 aaronmk
325 383 aaronmk
mysql-: _always # other OSes
326 235 aaronmk
327 247 aaronmk
mysqlAsRoot := mysql --user=root --password='$(bienPassword)'
328 235 aaronmk
329 7572 aaronmk
mysql_users: _always
330 7573 aaronmk
	-echo "CREATE USER 'bien'@'localhost' IDENTIFIED BY '$(bienPassword)';"\
331
|$(mysqlAsRoot)
332
	-echo "CREATE USER 'bien_read'@'%' IDENTIFIED BY '$(bienReadPassword)';"\
333
|$(mysqlAsRoot)
334 364 aaronmk
# ignore errors if user exists
335 202 aaronmk
336 7572 aaronmk
rm_mysql_users: _always
337 7573 aaronmk
	-echo "DROP USER 'bien_read'@'localhost';"|$(mysqlAsRoot)
338
	-echo "DROP USER 'bien'@'%';"|$(mysqlAsRoot)
339 364 aaronmk
# ignore errors if user exists
340 202 aaronmk
341 784 aaronmk
##### Datasources
342 202 aaronmk
343 418 aaronmk
inputs: _always inputs/all ;
344 245 aaronmk
345 7268 aaronmk
import: _always import-msg inputs/import_scrub ;
346 1542 aaronmk
import-msg: _always
347 1550 aaronmk
	@echo $(emph)"To import all inputs at once:"$(endEmph) . bin/import_all
348 1542 aaronmk
	@echo
349 250 aaronmk
350 7836 aaronmk
scrub: _always inputs/.TNRS/tnrs/tnrs-remake ;
351 7264 aaronmk
352 1458 aaronmk
verify: _always inputs/verify
353 1241 aaronmk
	@$(done)
354 386 aaronmk
355 1458 aaronmk
test: _always inputs/test
356 397 aaronmk
	@$(done)
357 1458 aaronmk
358
##### Testing
359
360 1743 aaronmk
test-all: _always remake test missing_mappings
361 1458 aaronmk
	@$(done)
362 1967 aaronmk
363
##### Subdir forwarding
364
365
# Must come last so overridden targets are not forwarded
366
367
define subdirTargets
368
$(subdir): _always
369
	+$$(subMake)
370
371
$(subdir)%: _always
372
	+$$(subMake)
373
.PRECIOUS: $(subdir)% # let subdir's Makefile decide whether to delete on error
374
375
$(subdir)reinstall: _always $(subdir)uninstall $(subdir)install ;
376
endef
377
$(foreach subdir,$(wildcard */),$(eval $(subdirTargets)))
378
379
Makefile: ;
380
381
%: $(addsuffix %,$(dir $(shell echo */Makefile))) _always ;
382 1999 aaronmk
383 11848 aaronmk
#### Overrides of forwarded commands
384
385 11862 aaronmk
# commented out to avoid a cascade of "overriding commands for target" warnings
386
#inputs/reinstall: _always
387
#	echo '. bin/reinstall_all; wait'|bash -s
388 11848 aaronmk
389 1999 aaronmk
#### Maps validation
390
391 4607 aaronmk
termsSubdirs := $(call no/,$(call wildcard/,inputs/*/))
392
393 3764 aaronmk
include lib/mappings.Makefile