# 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 import os.path db_shell_path = __file__ new_path = [ os.path.join( os.path.dirname( db_shell_path ), os.path.pardir, "lib" ) ] new_path.extend( sys.path[1:] ) # remove scripts/ from the path sys.path = new_path from galaxy.model.orm.scripts import get_config from galaxy import eggs eggs.require( "decorator" ) eggs.require( "Tempita" ) eggs.require( "SQLAlchemy" ) db_url = get_config( sys.argv )['db_url'] # Setup DB scripting environment from sqlalchemy import * from sqlalchemy.orm import * from sqlalchemy.exc import * from galaxy.model.mapping import init sa_session = init( '/tmp/', db_url ).context from galaxy.model import * # Helper function for debugging sqlalchemy queries... # http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query import decimal import datetime def printquery(statement, bind=None): """ print a query, with values filled in for debugging purposes *only* for security, you should always separate queries from their values please also note that this function is quite slow """ import sqlalchemy.orm if isinstance(statement, sqlalchemy.orm.Query): if bind is None: bind = statement.session.get_bind( statement._mapper_zero_or_none() ) statement = statement.statement elif bind is None: bind = statement.bind dialect = bind.dialect compiler = statement._compiler(dialect) class LiteralCompiler(compiler.__class__): def visit_bindparam( self, bindparam, within_columns_clause=False, literal_binds=False, **kwargs ): return super(LiteralCompiler, self).render_literal_bindparam( bindparam, within_columns_clause=within_columns_clause, literal_binds=literal_binds, **kwargs ) def render_literal_value(self, value, type_): """Render the value of a bind parameter as a quoted literal. This is used for statement sections that do not accept bind paramters on the target driver/database. This should be implemented by subclasses using the quoting services of the DBAPI. """ if isinstance(value, basestring): value = value.replace("'", "''") return "'%s'" % value elif value is None: return "NULL" elif isinstance(value, (float, int, long)): return repr(value) elif isinstance(value, decimal.Decimal): return str(value) elif isinstance(value, datetime.datetime): return "TO_DATE('%s','YYYY-MM-DD HH24:MI:SS')" % value.strftime("%Y-%m-%d %H:%M:%S") else: raise NotImplementedError( "Don't know how to literal-quote value %r" % value ) compiler = LiteralCompiler(dialect, statement) print compiler.process(statement)