mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-21 13:50:20 +08:00
Nicola Soranzo
21b44bf348
using the following command: ``` autopep8 -i -r --exclude $(sed -e 's|^|./|' -e 's|/$||' .ci/flake8_blacklist.txt | paste -sd,) --select E201,E202 . ```
61 lines
2.6 KiB
Python
61 lines
2.6 KiB
Python
import argparse
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import ConfigParser
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import os
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import sys
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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.SafeConfigParser()
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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 file.'''
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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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