importer.py

import os, sys, cPickle, ConfigParser, logging, traceback
assert sys.version_info[:2] >= ( 2, 4 )

new_path = [ os.path.join( os.getcwd(), "lib" ) ]
new_path.extend( sys.path[1:] ) # remove scripts/ from the path
new_path.append( os.path.join( os.getcwd(), "importer" )) #add own importer package
new_path.append("/usr/lib64/python2.5/site-packages") #add our locally installed packages
sys.path = new_path


from galaxy import eggs
import pkg_resources
import galaxy.model.mapping
import galaxy.util

pkg_resources.require( "SQLAlchemy >= 0.4" )
import sqlalchemy as sa
from sqlalchemy.orm.session import Session

from galaxy.model.orm import and_, eagerload
import sha


assert sys.version_info[:2] >= ( 2, 4 )

log = logging.getLogger(__name__)


def __main__():
    app = parseConfig()
    username = "name" + "1"
    session = app.model.session
    transaction = session.begin()
    try:
       createUser(app, username, "123456")
       raise Exception('test for rollback', 'test for rollback')
       transaction.commit()
    except Exception:
       transaction.rollback()
       print("error: rollback")
    user = app.model.User.filter_by(email=username).first()
    if not user:
       print "user not created"
    else:
       print "user created: " + user.email + " " + " ".join(map(lambda r: r.name, user.all_roles()))

       
def createUser(app, username, password):
    """creates a user and his private role ("r" + username) and associates them in the database""" 
    password = sha.new( password ).hexdigest()
    user = app.model.User(username, password)
    user.flush()
    role = app.model.Role( name="r" + username, description="private role of " + username, type=app.model.Role.types.PRIVATE )
    role.flush()
    userRoleAssociation = app.model.UserRoleAssociation(user, role)
    userRoleAssociation.flush()


class ImportData(object):
    """Encapsulates the state of a Universe application"""
    def __init__( self, database_connection=None, file_path=None ):
        if database_connection is None:
            raise Exception( "ImportData requires a database_connection value" )
        if file_path is None:
            raise Exception( "ImportData requires a file_path value" )
        self.database_connection = database_connection
        self.file_path = file_path
        # Setup the database engine and ORM
        self.model = galaxy.model.mapping.init( self.file_path, self.database_connection, engine_options={}, create_tables=False )


def parseConfig():
    """Parses the config and inits the Application object"""
    conf_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} )
    ini_file = sys.argv[1]
    conf_parser.read( ini_file )
    configuration = {}
    for key, value in conf_parser.items( "app:main" ):
        configuration[key] = value
    
    if 'database_connection' in configuration:
        database_connection = configuration['database_connection']
    else:
        database_connection = "sqlite:///%s?isolation_level=Immediate" % configuration["database_file"]
    file_path = configuration['file_path']
    app = ImportData( database_connection=database_connection, file_path=file_path )
    return app


if __name__ == "__main__":
   __main__()

importer.sh

#!/bin/sh

cd `dirname $0`
python -ES ./importer/importer.py universe_wsgi.ini $@