https://github.com/galaxyproject/galaxy
Tip revision: 7fd8dfca2da167789c2afa83e02cf2bc302fdb06 authored by Nate Coraor on 08 February 2013, 16:21:50 UTC
merge changes from next-stable branch
merge changes from next-stable branch
Tip revision: 7fd8dfc
db_shell.py
# This script allows easy access to Galaxy's database layer via the
# Galaxy models. For example:
# % python -i scripts/db_shell.py
# >>> new_user = User("admin@gmail.com")
# >>> new_user.set_password
# >>> sa_session.add(new_user)
# >>> sa_session.commit()
# >>> sa_session.query(User).all()
#
# You can also use this script as a library, for instance see https://gist.github.com/1979583
# TODO: This script overlaps a lot with manage_db.py and create_db.py,
# these should maybe be refactored to remove duplication.
import sys, os.path, logging
new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
sys.path = new_path
from galaxy import eggs
import pkg_resources
pkg_resources.require( "sqlalchemy-migrate" )
pkg_resources.require( "SQLAlchemy" )
from ConfigParser import SafeConfigParser
log = logging.getLogger( __name__ )
if sys.argv[-1] in [ 'community' ]:
# Need to pop the last arg so the command line args will be correct
# for sqlalchemy-migrate
webapp = sys.argv.pop()
config_file = 'community_wsgi.ini'
repo = 'lib/galaxy/webapps/community/model/migrate'
else:
# Poor man's optparse
config_file = 'universe_wsgi.ini'
if '-c' in sys.argv:
pos = sys.argv.index( '-c' )
sys.argv.pop(pos)
config_file = sys.argv.pop( pos )
if not os.path.exists( config_file ):
print "Galaxy config file does not exist (hint: use '-c config.ini' for non-standard locations): %s" % config_file
sys.exit( 1 )
repo = 'lib/galaxy/model/migrate'
cp = SafeConfigParser()
cp.read( config_file )
if cp.has_option( "app:main", "database_connection" ):
db_url = cp.get( "app:main", "database_connection" )
elif cp.has_option( "app:main", "database_file" ):
db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % cp.get( "app:main", "database_file" )
else:
db_url = "sqlite:///./database/universe.sqlite?isolation_level=IMMEDIATE"
dialect_to_egg = {
"sqlite" : "pysqlite>=2",
"postgres" : "psycopg2",
"mysql" : "MySQL_python"
}
dialect = ( db_url.split( ':', 1 ) )[0]
try:
egg = dialect_to_egg[dialect]
try:
pkg_resources.require( egg )
log.debug( "%s egg successfully loaded for %s dialect" % ( egg, dialect ) )
except:
# If the module is in the path elsewhere (i.e. non-egg), it'll still load.
log.warning( "%s egg not found, but an attempt will be made to use %s anyway" % ( egg, dialect ) )
except KeyError:
# Let this go, it could possibly work with db's we don't support
log.error( "database_connection contains an unknown SQLAlchemy database dialect: %s" % dialect )
# Setup DB scripting environment
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.exc import *
engine = create_engine(db_url, echo=True)
db_session = scoped_session( sessionmaker( bind = engine ) )
from galaxy.model.mapping import context as sa_session
sa_session.bind = engine
from galaxy.model import *