mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-08-31 01:02:04 +08:00
John Davis
83 lines
2.7 KiB
Python
83 lines
2.7 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 (
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create_engine,
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MetaData,
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)
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from sqlalchemy.orm import (
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scoped_session,
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sessionmaker,
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)
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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.commit()
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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:///{}".format(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))
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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(
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"--config_file", dest="config_file", required=True, help="The path to your Galaxy configuration .ini file."
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)
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parser.add_argument(
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"--from",
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dest="bad_filename",
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required=True,
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help="The old, invalid path to the shed_tool_conf.xml or migrated_tools_conf.xml file.",
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)
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parser.add_argument(
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"--to",
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dest="good_filename",
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required=True,
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help="The updated path to the shed_tool_conf.xml or migrated_tools_conf.xml file.",
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)
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parser.add_argument(
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"--force",
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dest="force",
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action="store_true",
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help="Use this flag to set the new path even if the file does not (yet) exist there.",
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)
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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(f"The file {opts.good_filename} does not exist, use the --force option to proceed.")
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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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