mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
bd0cefa020
They are expressions that get uselessly evaluated. These were reported as B018 errors by flake8-bugbear 21.11.28 , but B018 for strings has then been disabled in 21.11.29 since these strings can also be used as inline attribute doc strings or module variable docstrings (not our case though).
60 lines
2.6 KiB
Python
60 lines
2.6 KiB
Python
import argparse
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import os
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import sys
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from configparser import ConfigParser
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from sqlalchemy import create_engine, MetaData
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from sqlalchemy.orm import scoped_session, sessionmaker
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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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import galaxy.model.tool_shed_install.mapping as mapping
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def main(opts, session, model):
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'''
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Find all tool shed repositories with the bad path and update with the correct path.
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'''
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for row in session.query(model.ToolShedRepository).all():
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if 'shed_config_filename' in row.metadata_:
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if row.metadata_['shed_config_filename'] == opts.bad_filename:
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row.metadata_['shed_config_filename'] = opts.good_filename
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session.add(row)
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session.flush()
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return 0
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def create_database(config_file):
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parser = ConfigParser()
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parser.read(config_file)
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# Determine which database connection to use.
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database_connection = parser.get('app:main', 'install_database_connection')
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if database_connection is None:
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database_connection = parser.get('app:main', 'database_connection')
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if database_connection is None:
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database_connection = 'sqlite:///%s' % parser.get('app:main', 'database_file')
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if database_connection is None:
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print('Unable to determine correct database connection.')
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exit(1)
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# Initialize the database connection.
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engine = create_engine(database_connection)
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MetaData(bind=engine)
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install_session = scoped_session(sessionmaker(bind=engine, autoflush=False, autocommit=True))
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model = mapping.init(database_connection)
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return install_session, model
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if __name__ == '__main__':
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parser = argparse.ArgumentParser()
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parser.add_argument('--config_file', dest='config_file', required=True, help="The path to your Galaxy configuration .ini file.")
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parser.add_argument('--from', dest='bad_filename', required=True, help="The old, invalid path to the shed_tool_conf.xml or migrated_tools_conf.xml file.")
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parser.add_argument('--to', dest='good_filename', required=True, help="The updated path to the shed_tool_conf.xml or migrated_tools_conf.xml file.")
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parser.add_argument('--force', dest='force', action='store_true', help="Use this flag to set the new path even if the file does not (yet) exist there.")
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opts = parser.parse_args()
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if not os.path.exists(opts.good_filename) and not opts.force:
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print('The file %s does not exist, use the --force option to proceed.' % opts.good_filename)
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exit(1)
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session, model = create_database(opts.config_file)
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exit(main(opts, session, model))
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