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 13797 aaronmk
macPostgresDir := /usr/local/var/postgres
145 6201 aaronmk
define pg_ctl-Darwin
146 13989 aaronmk
brew services $(1) postgresql
147 14066 aaronmk
#pg_ctl -D $(macPostgresDir) $(1)
148 6201 aaronmk
endef
149 6197 aaronmk
150 13012 aaronmk
postgres_restart: postgres_restart-$(os) _always ;
151
postgres_restart-Linux: _always
152 13015 aaronmk
	@# for some reason, pg_ctl does not work when run inside make
153 13012 aaronmk
	@echo $(emph)'restart PostgreSQL manually:'$(endEmph)
154
	@echo $(call pg_ctl-$(os),restart)
155 13014 aaronmk
	@$(wait)
156 13012 aaronmk
postgres_restart-Darwin: _always
157 13990 aaronmk
	@# for some reason, pg_ctl does not work when run inside make
158
	@echo $(emph)'restart PostgreSQL manually:'$(endEmph)
159 13989 aaronmk
	@echo $(call pg_ctl-$(os),restart)
160 13990 aaronmk
	@$(wait)
161 13011 aaronmk
162 6503 aaronmk
confirmPostgresReload = $(call confirm,Modifying postgresql.conf and pg_hba.conf)
163
164 6333 aaronmk
define postgresReload-Linux
165 6503 aaronmk
@$(confirmPostgresReload)
166
@echo $(emph)'kernel.shmmax must be set to at least 4GB minus 1 byte:'$(endEmph)
167
@echo 'Append the following to /etc/sysctl.conf:'
168
@echo 'kernel.shmmax=4294967295'
169
@$(wait)
170 6447 aaronmk
chmod a+r schemas/*.conf || $(asBien) chmod a+r schemas/*.conf
171 6823 aaronmk
-$(asAdmin) mv -n $(linuxPostgresDir)/postgresql.conf $(linuxPostgresDir)/postgresql.conf.old
172 6333 aaronmk
$(asAdmin) cp --preserve=timestamps schemas/postgresql.conf $(linuxPostgresDir)/postgresql.conf
173 6823 aaronmk
-$(asAdmin) mv -n $(linuxPostgresDir)/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf.old
174 6335 aaronmk
$(asAdmin) cp --preserve=timestamps schemas/pg_hba.conf $(linuxPostgresDir)/pg_hba.conf
175 13013 aaronmk
$(MAKE) postgres_restart-$(os)
176 6333 aaronmk
177
endef
178
179
define postgresReload-Darwin
180 6503 aaronmk
@$(confirmPostgresReload)
181 6336 aaronmk
chmod a+r schemas/*.conf
182 13797 aaronmk
-$(asAdmin) mv -n $(macPostgresDir)/postgresql.conf $(macPostgresDir)/postgresql.conf.old
183
$(asAdmin) cp schemas/postgresql.Mac.conf $(macPostgresDir)/postgresql.conf
184
-$(asAdmin) mv -n $(macPostgresDir)/pg_hba.conf $(macPostgresDir)/pg_hba.conf.old
185
$(asAdmin) cp schemas/pg_hba.Mac.conf $(macPostgresDir)/pg_hba.conf
186
-$(asAdmin) mv -n $(macPostgresDir)/pg_ident.conf $(macPostgresDir)/pg_ident.conf.old
187
$(asAdmin) cp schemas/pg_ident.Mac.conf $(macPostgresDir)/pg_ident.conf
188 13013 aaronmk
$(MAKE) postgres_restart-$(os)
189 6333 aaronmk
190
endef
191
192 6334 aaronmk
postgres_reload: _always
193
	$($(call forOs,postgresReload))
194
195 12548 aaronmk
phppgadmin-Linux: _always
196
	-sudo apt-get --yes install phppgadmin
197
	$(editPhppgadmin)
198
	$(editPhppgadminApacheConf)
199
	-sudo ln -s ../conf.d/phppgadmin /etc/apache2/conf-available/phppgadmin.conf
200
	sudo a2enconf phppgadmin
201
	$(editApacheConfForPhppgadmin)
202
	-sudo apache2ctl restart
203
204 6333 aaronmk
postgres-Linux: _always
205 11661 aaronmk
	-sudo apt-get --yes install postgresql-9.3
206
	-sudo apt-get --yes install postgresql-contrib-$(pgVersion)
207 6544 aaronmk
	-sudo apt-get --yes install postgresql-plpython3-$(pgVersion)
208
	-sudo apt-get --yes install libpq-dev
209 13788 aaronmk
	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis-2.1-scripts
210
	-sudo apt-get --yes install postgresql-$(pgVersion)-postgis-2.1
211 12548 aaronmk
	-$(MAKE) phppgadmin-Linux
212 6333 aaronmk
	-sudo pip install psycopg2
213 6503 aaronmk
	-$(MAKE) $(postgresReload-Linux)
214 6333 aaronmk
# run pg_version inline because it needs postgresql to be installed first
215
# ignore errors if conf files already edited
216
217 383 aaronmk
postgres-Darwin: _always
218 13797 aaronmk
	ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
219
	brew doctor
220
	brew install postgis # also installs PostgreSQL
221
	-$(postgresReload-Darwin)
222 11674 aaronmk
	-sudo easy_install psycopg2
223 11845 aaronmk
	-$(postgresReload-Darwin)
224 235 aaronmk
225 418 aaronmk
postgres-: _always ; # other OSes
226 241 aaronmk
227 2624 aaronmk
psqlAsAdminVegbien := $(psqlAsAdmin) vegbien
228 272 aaronmk
bienPassword := $(shell cat config/bien_password)
229 6331 aaronmk
bienReadPassword := $(shell cat config/bien_read_password)
230 241 aaronmk
231 7422 aaronmk
##### Misc.
232
233 7423 aaronmk
misc-Linux: _always
234
	cp -p "$(shell which dotlockfile)" bin/
235 7422 aaronmk
236
misc-Darwin: _always ;
237
238 784 aaronmk
##### VegBIEN DB
239 241 aaronmk
240 6331 aaronmk
#### DB and users
241 1967 aaronmk
242 2090 aaronmk
confirmRmDb = $(call confirm,WARNING: This will delete your entire VegBIEN\
243 3374 aaronmk
DB!,This includes all archived imports and staging tables.)
244 2089 aaronmk
245 2633 aaronmk
confirmRmPublicSchema = $(call confirm,WARNING: This will delete the current\
246
public schema of your VegBIEN DB!,To save it: make schemas/rotate)
247 2089 aaronmk
248 2091 aaronmk
rmPublicSchema := $(call rmSchemaCmd,public)
249 1967 aaronmk
250 14031 aaronmk
db: mk_db rm_initial_public schemas/reinstall _always ;
251 1967 aaronmk
252
mk_db: _always
253 13848 aaronmk
	-echo "CREATE USER public_ PASSWORD 'password';"|$(psqlAsAdmin)
254 1745 aaronmk
	-echo "CREATE USER bien PASSWORD '$(bienPassword)';"|$(psqlAsAdmin)
255 6331 aaronmk
	-echo "CREATE USER bien_read PASSWORD '$(bienReadPassword)' IN ROLE bien \
256
NOINHERIT;"|$(psqlAsAdmin)
257 2037 aaronmk
	-echo "CREATE DATABASE vegbien WITH OWNER bien TEMPLATE template1 \
258 1940 aaronmk
ENCODING 'UTF8' LC_COLLATE 'en_US.UTF-8' LC_CTYPE 'en_US.UTF-8';"|$(psqlAsAdmin)
259 6221 aaronmk
	-echo "CREATE EXTENSION hstore SCHEMA pg_catalog;"|$(psqlAsAdminVegbien)
260 13806 aaronmk
	-echo "CREATE EXTENSION plpython3u;"|$(psqlAsAdminVegbien)
261 13789 aaronmk
	-echo 'CREATE SCHEMA postgis;'|$(psqlAsAdminVegbien)
262 13798 aaronmk
	-echo 'GRANT USAGE ON SCHEMA postgis TO public;'|$(psqlAsAdminVegbien)
263 13789 aaronmk
	-echo 'CREATE EXTENSION postgis SCHEMA postgis;'\
264
|$(psqlAsAdminVegbien)
265 11150 aaronmk
	# unset ON_ERROR_STOP so user-exists errors don't prevent further user-adds
266
	-cat config/users.sql|$(psqlAsAdmin) --set ON_ERROR_STOP
267 2627 aaronmk
# ignore errors if user/database/etc. exists
268 2091 aaronmk
269
rm_initial_public: _always
270 2089 aaronmk
	@$(confirmRmPublicSchema)
271 2624 aaronmk
	echo $(rmPublicSchema)|$(psqlAsAdminVegbien)
272 1967 aaronmk
# drop public schema *as admin* because it starts out owned by postgres
273 241 aaronmk
274 383 aaronmk
rm_db: _always
275 1748 aaronmk
	@$(confirmRmDb)
276
	echo "DROP DATABASE IF EXISTS vegbien;"|$(psqlAsAdmin)
277 6331 aaronmk
	echo "DROP USER IF EXISTS bien_read;"|$(psqlAsAdmin)
278 1748 aaronmk
	echo "DROP USER IF EXISTS bien;"|$(psqlAsAdmin)
279 6822 aaronmk
	echo "DROP USER IF EXISTS public_;"|$(psqlAsAdmin)
280 241 aaronmk
281 418 aaronmk
reinstall_db: _always rm_db db ;
282 241 aaronmk
283 784 aaronmk
##### MySQL
284 241 aaronmk
285 7572 aaronmk
mysql: _always $(call forOs,mysql) mysql_users
286 241 aaronmk
	@$(done)
287
288 7572 aaronmk
rm_mysql: _always rm_mysql_users ;
289 241 aaronmk
290 383 aaronmk
mysql-Linux: _always
291 244 aaronmk
	@echo $(emph)"If asked for MySQL root password, enter $(bienPassword)"$(endEmph)
292 238 aaronmk
	@$(wait)
293 7574 aaronmk
	-sudo apt-get --yes install mysql-server
294
	-sudo apt-get --yes install mysql-client
295 10223 aaronmk
	-sudo apt-get --yes install mysql-workbench
296 7574 aaronmk
	-sudo apt-get --yes install python-mysqldb
297 7575 aaronmk
	-sudo apt-get --yes install phpmyadmin
298 235 aaronmk
299 383 aaronmk
mysql-Darwin: _always
300 244 aaronmk
	@echo $(emph)'Installing MySQLdb Python driver on Mac OS X 10.7 (may work on other versions):'$(endEmph)
301 235 aaronmk
	@echo 'Download it using "latest version" link at http://sourceforge.net/projects/mysql-python/files/'
302
	@echo 'Extract the archive'
303
	@echo '(From http://www.rustyrazorblade.com/2011/11/installing-mysqldb-on-macos-lion/:)'
304 284 aaronmk
	@echo 'Run ln -s /usr/local/mysql/lib/libmysqlclient.18.dylib /usr/lib/libmysqlclient.18.dylib'
305
	@echo 'Run ln -s /usr/local/mysql/lib /usr/local/mysql/lib/mysql'
306 235 aaronmk
	@echo '(From http://blog.infoentropy.com/MySQL-python_EnvironmentError_mysql_config_not_found:)'
307
	@echo 'Edit site.cfg and change the line like "mysql_config = " to "mysql_config = /usr/local/mysql/bin/mysql_config"'
308
	@echo '(From http://www.mangoorange.com/2008/08/01/installing-python-mysqldb-122-on-mac-os-x/:)'
309
	@echo 'Change to the directory of the extracted files'
310 284 aaronmk
	@echo 'Run python setup.py clean'
311
	@echo 'Run python setup.py build'
312 235 aaronmk
	@echo 'Run sudo python setup.py install'
313
	@echo "Run python -c 'import MySQLdb'"
314 238 aaronmk
	@$(wait)
315 235 aaronmk
316 383 aaronmk
mysql-: _always # other OSes
317 235 aaronmk
318 247 aaronmk
mysqlAsRoot := mysql --user=root --password='$(bienPassword)'
319 235 aaronmk
320 7572 aaronmk
mysql_users: _always
321 7573 aaronmk
	-echo "CREATE USER 'bien'@'localhost' IDENTIFIED BY '$(bienPassword)';"\
322
|$(mysqlAsRoot)
323
	-echo "CREATE USER 'bien_read'@'%' IDENTIFIED BY '$(bienReadPassword)';"\
324
|$(mysqlAsRoot)
325 364 aaronmk
# ignore errors if user exists
326 202 aaronmk
327 7572 aaronmk
rm_mysql_users: _always
328 7573 aaronmk
	-echo "DROP USER 'bien_read'@'localhost';"|$(mysqlAsRoot)
329
	-echo "DROP USER 'bien'@'%';"|$(mysqlAsRoot)
330 364 aaronmk
# ignore errors if user exists
331 202 aaronmk
332 784 aaronmk
##### Datasources
333 202 aaronmk
334 418 aaronmk
inputs: _always inputs/all ;
335 245 aaronmk
336 7268 aaronmk
import: _always import-msg inputs/import_scrub ;
337 1542 aaronmk
import-msg: _always
338 1550 aaronmk
	@echo $(emph)"To import all inputs at once:"$(endEmph) . bin/import_all
339 1542 aaronmk
	@echo
340 250 aaronmk
341 7836 aaronmk
scrub: _always inputs/.TNRS/tnrs/tnrs-remake ;
342 7264 aaronmk
343 1458 aaronmk
verify: _always inputs/verify
344 1241 aaronmk
	@$(done)
345 386 aaronmk
346 1458 aaronmk
test: _always inputs/test
347 397 aaronmk
	@$(done)
348 1458 aaronmk
349
##### Testing
350
351 1743 aaronmk
test-all: _always remake test missing_mappings
352 1458 aaronmk
	@$(done)
353 1967 aaronmk
354
##### Subdir forwarding
355
356
# Must come last so overridden targets are not forwarded
357
358
define subdirTargets
359
$(subdir): _always
360
	+$$(subMake)
361
362
$(subdir)%: _always
363
	+$$(subMake)
364
.PRECIOUS: $(subdir)% # let subdir's Makefile decide whether to delete on error
365
366
$(subdir)reinstall: _always $(subdir)uninstall $(subdir)install ;
367
endef
368
$(foreach subdir,$(wildcard */),$(eval $(subdirTargets)))
369
370
Makefile: ;
371
372
%: $(addsuffix %,$(dir $(shell echo */Makefile))) _always ;
373 1999 aaronmk
374 11848 aaronmk
#### Overrides of forwarded commands
375
376 11862 aaronmk
# commented out to avoid a cascade of "overriding commands for target" warnings
377
#inputs/reinstall: _always
378
#	echo '. bin/reinstall_all; wait'|bash -s
379 11848 aaronmk
380 1999 aaronmk
#### Maps validation
381
382 4607 aaronmk
termsSubdirs := $(call no/,$(call wildcard/,inputs/*/))
383
384 3764 aaronmk
include lib/mappings.Makefile