mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-10-24 02:04:04 +08:00
Nate Coraor
d294af4866
Database and tool migrations won't work if you use galaxy.ini.sample. Perhaps it should automatically try appending .sample? Or we should really be encouraging people to use the config file properly.
49 lines
1.6 KiB
Python
49 lines
1.6 KiB
Python
import sys
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import os.path
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import logging
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] ) # remove scripts/ from the path
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sys.path = new_path
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from galaxy import eggs
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import pkg_resources
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pkg_resources.require( "SQLAlchemy" )
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pkg_resources.require( "decorator" )
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pkg_resources.require( "Tempita " )
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pkg_resources.require( "sqlalchemy-migrate" )
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from migrate.versioning.shell import main
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from ConfigParser import SafeConfigParser
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from galaxy.model.orm.scripts import require_dialect_egg
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from galaxy.model.orm.scripts import read_config_file_arg
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log = logging.getLogger( __name__ )
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config_file = read_config_file_arg( sys.argv, 'config/galaxy.ini', 'universe_wsgi.ini' )
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if not os.path.exists( config_file ):
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print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file
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sys.exit( 1 )
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repo = 'lib/tool_shed/galaxy_install/migrate'
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cp = SafeConfigParser()
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cp.read( config_file )
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if config_file == 'config/galaxy.ini.sample' and 'GALAXY_TEST_DBURI' in os.environ:
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# Running functional tests.
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db_url = os.environ[ 'GALAXY_TEST_DBURI' ]
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elif cp.has_option( "app:main", "install_database_connection" ):
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db_url = cp.get( "app:main", "install_database_connection" )
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elif cp.has_option( "app:main", "database_connection" ):
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db_url = cp.get( "app:main", "database_connection" )
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elif cp.has_option( "app:main", "database_file" ):
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db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" )
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else:
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db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
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require_dialect_egg( db_url )
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main( repository=repo, url=db_url )
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