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87 lines
3.0 KiB
Python
87 lines
3.0 KiB
Python
# This script allows easy access to Galaxy's database layer via the
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# Galaxy models. For example:
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# % python -i scripts/db_shell.py
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# >>> new_user = User("admin@gmail.com")
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# >>> new_user.set_password
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# >>> sa_session.add(new_user)
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# >>> sa_session.commit()
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# >>> sa_session.query(User).all()
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#
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# You can also use this script as a library, for instance see https://gist.github.com/1979583
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# TODO: This script overlaps a lot with manage_db.py and create_db.py,
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# these should maybe be refactored to remove duplication.
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import sys, os.path, 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( "decorator" )
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pkg_resources.require( "sqlalchemy-migrate" )
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pkg_resources.require( "SQLAlchemy" )
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from ConfigParser import SafeConfigParser
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log = logging.getLogger( __name__ )
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if sys.argv[-1] in [ 'tool_shed' ]:
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# Need to pop the last arg so the command line args will be correct
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# for sqlalchemy-migrate
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webapp = sys.argv.pop()
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config_file = 'tool_shed_wsgi.ini'
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repo = 'lib/galaxy/webapps/tool_shed/model/migrate'
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else:
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# Poor man's optparse
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config_file = 'universe_wsgi.ini'
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if '-c' in sys.argv:
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pos = sys.argv.index( '-c' )
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sys.argv.pop(pos)
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config_file = sys.argv.pop( pos )
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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/galaxy/model/migrate'
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cp = SafeConfigParser()
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cp.read( config_file )
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if 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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dialect_to_egg = {
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"sqlite" : "pysqlite>=2",
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"postgres" : "psycopg2",
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"mysql" : "MySQL_python"
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}
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dialect = ( db_url.split( ':', 1 ) )[0]
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try:
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egg = dialect_to_egg[dialect]
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try:
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pkg_resources.require( egg )
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log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
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except:
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# If the module is in the path elsewhere (i.e. non-egg), it'll still load.
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log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
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except KeyError:
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# Let this go, it could possibly work with db's we don't support
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log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
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# Setup DB scripting environment
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from sqlalchemy import *
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from sqlalchemy.orm import *
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from sqlalchemy.exc import *
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engine = create_engine(db_url, echo=True)
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db_session = scoped_session( sessionmaker( bind = engine ) )
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from galaxy.model.mapping import context as sa_session
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sa_session.bind = engine
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from galaxy.model import *
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