galaxy.model.orm package¶

galaxy.model.orm - ORM-related functionality

Submodules¶

galaxy.model.orm.engine_factory module¶

galaxy.model.orm.engine_factory.build_engine(url, engine_options, database_query_profiling_proxy=False, trace_logger=None, slow_query_log_threshold=0, thread_local_log=None)[source]¶

galaxy.model.orm.logging_connection_proxy module¶

galaxy.model.orm.logging_connection_proxy.stripwd(s)[source]¶

galaxy.model.orm.logging_connection_proxy.pretty_stack()[source]¶

class galaxy.model.orm.logging_connection_proxy.LoggingProxy[source]¶

Bases: sqlalchemy.interfaces.ConnectionProxy

Logs SQL statements using standard logging module

begin(conn, begin)[source]¶

commit(conn, commit)[source]¶

rollback(conn, rollback)[source]¶

cursor_execute(execute, cursor, statement, parameters, context, executemany)[source]¶

class galaxy.model.orm.logging_connection_proxy.TraceLoggerProxy(trace_logger)[source]¶

Bases: sqlalchemy.interfaces.ConnectionProxy

Logs SQL statements using a metlog client

__init__(trace_logger)[source]¶

cursor_execute(execute, cursor, statement, parameters, context, executemany)[source]¶

galaxy.model.orm.now module¶

galaxy.model.orm.now.now()¶: Return a new datetime representing UTC day and time.

galaxy.model.orm.scripts module¶

Code to support database helper scripts (create_db.py, manage_db.py, etc…).

galaxy.model.orm.scripts.get_config(argv, use_argparse=True, cwd=None)[source]¶

Read sys.argv and parse out repository of migrations and database url.

>>> import os
>>> from six.moves.configparser import SafeConfigParser
>>> from shutil import rmtree
>>> from tempfile import mkdtemp
>>> config_dir = mkdtemp()
>>> os.makedirs(os.path.join(config_dir, 'config'))
>>> def write_ini(path, property, value):
...     p = SafeConfigParser()
...     p.add_section('app:main')
...     p.set('app:main', property, value)
...     with open(os.path.join(config_dir, 'config', path), 'w') as f: p.write(f)
>>> write_ini('tool_shed.ini', 'database_connection', 'sqlite:///pg/testdb1')
>>> config = get_config(['manage_db.py', 'tool_shed'], cwd=config_dir)
>>> config['repo'].endswith('galaxy/webapps/tool_shed/model/migrate')
True
>>> config['db_url']
'sqlite:///pg/testdb1'
>>> write_ini('galaxy.ini', 'data_dir', '/moo')
>>> config = get_config(['manage_db.py'], cwd=config_dir)
>>> uri_with_env = os.getenv("GALAXY_TEST_DBURI", "sqlite:////moo/universe.sqlite?isolation_level=IMMEDIATE")
>>> config['db_url'] == uri_with_env
True
>>> config['repo'].endswith('galaxy/model/migrate')
True
>>> rmtree(config_dir)

galaxy.model.orm.scripts.manage_db()[source]¶