mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-19 10:51:34 +08:00
John Davis
5d376fdacc
For ToolShed, we have create_toolshed_db.sh. For galaxy and toolshed install databases (gxy and tsi branches under alembic), we use the `init` subcommand of the `db.sh` script (`./db.sh init`), which has exactly the same functionality as these deleted scripts. To the best of my knowledge, these are not used anywhere else (unlike, for example, scripts/manage_db.py, which is called from the ansible-galaxy role).
97 lines
3.4 KiB
Python
97 lines
3.4 KiB
Python
# This script allows easy access to Galaxy's database layer via the
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# Galaxy models. For example:
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# % python -i scripts/db_shell.py -c config/galaxy.ini
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# >>> new_user = User("admin@gmail.com")
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# >>> new_user.set_password
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# >>> sa_session.add(new_user)
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# >>> sa_session.commit()
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# >>> sa_session.query(User).all()
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#
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# If you use ipython use:
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# % ipython -i scripts/db_shell.py -- -c config/galaxy.ini
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#
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# You can also use this script as a library, for instance see https://gist.github.com/1979583
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# these should maybe be refactored to remove duplication.
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import datetime
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import decimal
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import os.path
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import sys
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# Setup DB scripting environment
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from sqlalchemy import * # noqa
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from sqlalchemy.exc import * # noqa
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from sqlalchemy.orm import * # noqa
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from sqlalchemy.sql import label # noqa
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sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pardir, "lib")))
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from galaxy.datatypes.registry import Registry
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from galaxy.model import * # noqa
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from galaxy.model import set_datatypes_registry # More explicit than `*` import
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from galaxy.model.mapping import init
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from galaxy.model.orm.scripts import get_config
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registry = Registry()
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registry.load_datatypes()
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set_datatypes_registry(registry)
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config = get_config(sys.argv)
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db_url = config["db_url"]
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sa_session = init("/tmp/", db_url).context
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# Helper function for debugging sqlalchemy queries...
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# http://stackoverflow.com/questions/5631078/sqlalchemy-print-the-actual-query
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def printquery(statement, bind=None):
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"""
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Print a query, with values filled in
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for debugging purposes *only*
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for security, you should always separate queries from their values
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please also note that this function is quite slow
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"""
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import sqlalchemy.orm
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if isinstance(statement, sqlalchemy.orm.Query):
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if bind is None:
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bind = statement.session.get_bind()
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statement = statement.statement
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elif bind is None:
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bind = statement.bind
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dialect = bind.dialect
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compiler = statement._compiler(dialect)
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class LiteralCompiler(compiler.__class__):
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def visit_bindparam(self, bindparam, within_columns_clause=False, literal_binds=False, **kwargs):
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return super().render_literal_bindparam(
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bindparam, within_columns_clause=within_columns_clause, literal_binds=literal_binds, **kwargs
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)
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def render_literal_value(self, value, type_):
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"""Render the value of a bind parameter as a quoted literal.
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This is used for statement sections that do not accept bind paramters
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on the target driver/database.
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This should be implemented by subclasses using the quoting services
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of the DBAPI.
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"""
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if isinstance(value, str):
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value = value.replace("'", "''")
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return "'%s'" % value
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elif value is None:
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return "NULL"
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elif isinstance(value, (float, int)):
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return repr(value)
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elif isinstance(value, decimal.Decimal):
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return str(value)
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elif isinstance(value, datetime.datetime):
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return "TO_DATE('%s','YYYY-MM-DD HH24:MI:SS')" % value.strftime("%Y-%m-%d %H:%M:%S")
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else:
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raise NotImplementedError("Don't know how to literal-quote value %r" % value)
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compiler = LiteralCompiler(dialect, statement)
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print(compiler.process(statement))
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