https://github.com/galaxyproject/galaxy
Tip revision: ef2dfb9f4aa09b7fae9700916ac29207675c409d authored by mvdbeek on 16 March 2021, 18:27:14 UTC
Update version to 21.01
Update version to 21.01
Tip revision: ef2dfb9
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 -c config/galaxy.ini
# >>> new_user = User("admin@gmail.com")
# >>> new_user.set_password
# >>> sa_session.add(new_user)
# >>> sa_session.commit()
# >>> sa_session.query(User).all()
#
# If you use ipython use:
# % ipython -i scripts/db_shell.py -- -c config/galaxy.ini
#
# 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 datetime
import decimal
import os.path
import sys
# Setup DB scripting environment
from sqlalchemy import * # noqa
from sqlalchemy.orm import * # noqa
from sqlalchemy.exc import * # noqa
from sqlalchemy.sql import label # noqa
sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, 'lib')))
from galaxy.datatypes.registry import Registry
from galaxy.model import * # noqa
from galaxy.model import set_datatypes_registry # More explicit than `*` import
from galaxy.model.mapping import init
from galaxy.model.orm.scripts import get_config
registry = Registry()
registry.load_datatypes()
set_datatypes_registry(registry)
db_url = get_config(sys.argv)['db_url']
sa_session = init('/tmp/', db_url).context
# Helper function for debugging sqlalchemy queries...
# http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query
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 = 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().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, str):
value = value.replace("'", "''")
return "'%s'" % value
elif value is None:
return "NULL"
elif isinstance(value, (float, int)):
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))