Revision 383
Added by Aaron Marcuse-Kubitza over 12 years ago
| inputs/input.Makefile | ||
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##### |
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all: _not_file maps import verify
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all: _always maps import verify
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.SUFFIXES: |
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_not_file:
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.PHONY: _not_file
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_always:
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.PHONY: _always
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clean: _not_file
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clean: _always
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$(RM) $(all) |
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rm-%: _not_file
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rm-%: _always
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$(RM) $* |
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%.out: % _not_file
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%.out: % _always
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./$* >$@ |
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.PRECIOUS: %.out |
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##### |
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reinstall: _not_file uninstall install
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reinstall: _always uninstall install
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##### |
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maps: $(vegbienMaps) _not_file
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maps: $(vegbienMaps) _always
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all += $(vegbienMaps) |
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|
| ... | ... | |
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##### |
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import: _not_file $(addprefix import-,$(tables))
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import: _always $(addprefix import-,$(tables))
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log = $*$(if $(n),.n=$(n),).log |
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logs := $(wildcard *.log) |
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rm_logs: _not_file
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rm_logs: _always
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$(RM) $(logs) |
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##### |
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verify: _not_file $(addprefix verify-,$(tables))
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verify: _always $(addprefix verify-,$(tables))
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verify-%: verify.%.ref verify.%.out _not_file
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verify-%: verify.%.ref verify.%.out _always
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$(DIFF) |
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%.out: %.sql _not_file
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%.out: %.sql _always
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$(psqlAsBien) --no-align --field-separator=' ' --pset=footer=off <$< >$@ |
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.PRECIOUS: %.out |
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|
| ... | ... | |
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##### |
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test: _not_file $(addprefix test-,$(tables))
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test: _always $(addprefix test-,$(tables))
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test-%: test.%.ref test.%.out _not_file
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test-%: test.%.ref test.%.out _always
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$(DIFF) |
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all += $(filter-out %.ref,$(wildcard test.*.out)) |
| ... | ... | |
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mysqlAsRoot := $(call mysqlAs,root) |
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mysqlAsBien := $(call mysqlAs,bien) |
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import-%: map.VegBIEN.%.csv _not_file
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$(importCmd)
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importCmd = (set -x; "time" env commit=1 $(map) $<) \
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import-%: map.VegBIEN.%.csv _always
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-$($@_cmd)
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import_cmd = (set -x; "time" env commit=1 $(map) $<) \
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$(if $(n),,>>$(log)) 2>&1$(if $(n),|tee -a $(log)) |
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%.ref: %.ref.sql |
| ... | ... | |
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### |
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install: _not_file db
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install: _always db
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uninstall: _not_file rm_db
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uninstall: _always rm_db
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db: src.$(db).sql _not_file
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db: src.$(db).sql _always
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-$(mysqlAsRoot) <$< |
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echo "GRANT SELECT ON $(db).* TO 'bien'@'localhost';"|$(mysqlAsRoot) |
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# ignore errors in db import so that GRANT will still be run |
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rm_db: _not_file
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rm_db: _always
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-echo "REVOKE ALL ON $(db).* FROM 'bien'@'localhost';"|$(mysqlAsRoot) |
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echo "DROP DATABASE IF EXISTS $(db);"|$(mysqlAsRoot) |
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# ignore errors if grant not defined |
| ... | ... | |
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#### |
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test.%.out: map.VegBIEN.%.csv _not_file
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test.%.out: map.VegBIEN.%.csv _always
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env n=2 $(map) $< >$@ 2>&1 |
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.PRECIOUS: test.%.out |
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|
| Makefile | ||
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##### |
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all: _not_file install
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all: _always install
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.SUFFIXES: |
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_not_file:
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.PHONY: _not_file
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_always:
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.PHONY: _always
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##### |
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install: _not_file core mysql inputs test
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install: _always core mysql inputs test
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@$(done) |
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uninstall: _not_file rm_inputs rm_mysql rm_core
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uninstall: _always rm_inputs rm_mysql rm_core
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reinstall: _not_file uninstall install
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reinstall: _always uninstall install
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##### |
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core: _not_file $(call forOs,python postgres) postgres_user db
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core: _always $(call forOs,python postgres) postgres_user db
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@$(done) |
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rm_core: _not_file rm_db rm_postgres_user
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rm_core: _always rm_db rm_postgres_user
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reinstall_core: _not_file rm_core core
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reinstall_core: _always rm_core core
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python-Linux: _not_file
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python-Linux: _always
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-sudo apt-get install python python-dev python-dateutil python-pip |
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python-Darwin: _not_file
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python-Darwin: _always
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@echo $(emph)'Installing python-dateutil on Mac OS X:'$(endEmph) |
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@echo 'Download it: http://labix.org/download/python-dateutil/python-dateutil-1.5.tar.gz' |
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@echo 'Extract the archive' |
| ... | ... | |
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editApachePortsConf = echo $$'1\n,s/\\b80\\b/8080/g\nwq'|\ |
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sudo ed --loose-exit-status --verbose /etc/apache2/ports.conf |
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postgres-Linux: _not_file
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postgres-Linux: _always
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-sudo apt-get install postgresql libpq-dev phppgadmin |
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$(editPhppgadminApacheConf) |
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$(editApacheConfForPhppgadmin) |
| ... | ... | |
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-sudo pip install psycopg2 |
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# ignore errors if conf files already edited |
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postgres-Darwin: _not_file
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postgres-Darwin: _always
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@echo $(emph)'Installing PostgreSQL on Mac OS X:'$(endEmph) |
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@echo 'Download it using the topmost "Mac OS X" link at http://http://www.enterprisedb.com/products-services-training/pgdownload' |
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@echo 'Open the disk image' |
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@echo 'Run the installer in it' |
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@$(wait) |
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postgres-: _not_file # other OSes
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postgres-: _always # other OSes
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psqlOpts := --set ON_ERROR_STOP=1 --quiet |
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psqlAsAdmin := sudo -u postgres psql $(psqlOpts) |
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psqlAsBien := ./bin/psql_vegbien $(psqlOpts) |
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bienPassword := $(shell cat config/bien_password) |
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postgres_user: _not_file
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postgres_user: _always
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-echo "CREATE USER bien PASSWORD '$(bienPassword)';"|$(psqlAsAdmin) |
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# ignore errors if user exists |
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rm_postgres_user: _not_file
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rm_postgres_user: _always
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echo "DROP USER IF EXISTS bien;"|$(psqlAsAdmin) |
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##### |
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db: _not_file
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-$(dbCreateCmd)
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db: _always
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-$($@_create_cmd)
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$(psqlAsBien) <mappings/schemas/vegbien.sql |
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# ignore errors if database exists |
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dbCreateCmd = echo "CREATE DATABASE vegbien OWNER bien ENCODING 'UTF8' \
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db_create_cmd = echo "CREATE DATABASE vegbien OWNER bien ENCODING 'UTF8' \
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TEMPLATE template1;"|$(psqlAsAdmin) |
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rm_db: _not_file
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rm_db: _always
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echo "DROP DATABASE IF EXISTS vegbien;"|$(psqlAsAdmin) |
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reinstall_db: _not_file rm_db db
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reinstall_db: _always rm_db db
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empty_db: _not_file
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empty_db: _always
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$(psqlAsBien) <mappings/schemas/vegbien_empty.sql |
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##### |
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mysql: _not_file $(call forOs,mysql) mysql_user
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mysql: _always $(call forOs,mysql) mysql_user
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@$(done) |
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rm_mysql: _not_file rm_mysql_user
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rm_mysql: _always rm_mysql_user
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mysql-Linux: _not_file
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mysql-Linux: _always
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@echo $(emph)"If asked for MySQL root password, enter $(bienPassword)"$(endEmph) |
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@$(wait) |
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-sudo apt-get install mysql-server mysql-client python-mysqldb |
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mysql-Darwin: _not_file
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mysql-Darwin: _always
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@echo $(emph)'Installing MySQLdb Python driver on Mac OS X 10.7 (may work on other versions):'$(endEmph) |
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@echo 'Download it using "latest version" link at http://sourceforge.net/projects/mysql-python/files/' |
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@echo 'Extract the archive' |
| ... | ... | |
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@echo "Run python -c 'import MySQLdb'" |
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@$(wait) |
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mysql-: _not_file # other OSes
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mysql-: _always # other OSes
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mysqlAsRoot := mysql --user=root --password='$(bienPassword)' |
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mysql_user: _not_file
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mysql_user: _always
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-$($@_cmd) |
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# ignore errors if user exists |
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mysql_user_cmd = echo "CREATE USER 'bien'@'localhost' IDENTIFIED BY \ |
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'$(bienPassword)';"|$(mysqlAsRoot) |
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rm_mysql_user: _not_file
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rm_mysql_user: _always
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-echo "DROP USER 'bien'@'localhost';"|$(mysqlAsRoot) |
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# ignore errors if user exists |
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|
| ... | ... | |
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inputs := $(wildcard inputs/*/) |
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inputs: _not_file $(addsuffix install,$(inputs))
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inputs: _always $(addsuffix install,$(inputs))
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rm_inputs: _not_file $(addsuffix uninstall,$(inputs))
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rm_inputs: _always $(addsuffix uninstall,$(inputs))
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verify: _not_file $(addsuffix verify,$(inputs))
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verify: _always $(addsuffix verify,$(inputs))
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test2: _not_file $(addsuffix test,$(inputs))
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test2: _always $(addsuffix test,$(inputs))
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inputs/%: _not_file
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inputs/%: _always
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+$(subMake) |
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# ignore errors in sub-makes |
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##### |
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test: _not_file test-map
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test: _always test-map
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@$(done) |
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test-%: _not_file
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test-%: _always
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./test/$(*F) |
| mappings/Makefile | ||
|---|---|---|
| 4 | 4 |
|
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##### |
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all: _not_file misc
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all: _always misc
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$(MAKE) plots |
| 9 | 9 |
./join VegX VegBIEN |
| 10 | 10 |
./review |
| 11 | 11 |
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.SUFFIXES: |
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_not_file:
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.PHONY: _not_file
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_always:
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.PHONY: _always
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|
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misc := schemas/vegbien.sql schemas/vegbien_empty.sql |
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all = $(wildcard for_review/*.csv) \ |
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$(filter-out VegX-%,$(wildcard *-VegBIEN.*.csv)) VegX-*.plots.csv $(misc) |
| 21 | 21 |
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clean: _not_file
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clean: _always
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$(RM) $(all) |
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|
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%:: %.make |
| ... | ... | |
| 41 | 41 |
schemas/vegbien_empty.sql: schemas/vegbien.sql |
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$(empty) |
| 43 | 43 |
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VegX-VegBIEN.organisms.csv: _not_file
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VegX-VegBIEN.organisms.csv: _always
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$(bin)/in_place $@ $(sort) |
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##### |
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plots: _not_file $(subst .organisms.,.plots.,$(wildcard VegX-*.organisms.csv))
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plots: _always $(subst .organisms.,.plots.,$(wildcard VegX-*.organisms.csv))
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chRoot2PlotsLeftVegx =\ |
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env \ |
Also available in: Unified diff
Makefiles: Changed _not_file to _always because _not_file is sometimes used to force a file to always be remade