mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +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 . ```
131 lines
4.5 KiB
Python
Executable File
131 lines
4.5 KiB
Python
Executable File
#!/usr/bin/python
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import optparse
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import ConfigParser
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import os
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import sys
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sys.path.insert(1, os.path.join(os.path.dirname(__file__), os.pardir, os.pardir, os.pardir, 'lib'))
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from sqlalchemy.exc import OperationalError, ProgrammingError
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import galaxy.webapps.tool_shed.model.mapping as tool_shed_model
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from tool_shed.util import xml_util
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def check_db(config_parser):
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dburi = None
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if config_parser.has_option('app:main', 'database_connection'):
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dburi = config_parser.get('app:main', 'database_connection')
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elif config_parser.has_option('app:main', 'database_file'):
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db_file = config_parser.get('app:main', 'database_file')
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dburi = "sqlite:///%s?isolation_level=IMMEDIATE" % db_file
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else:
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sys.exit('The database configuration setting is missing from the tool_shed.ini file. Add this setting before attempting to bootstrap.')
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sa_session = None
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database_exists_message = 'The database configured for this Tool Shed is not new, so bootstrapping is not allowed. '
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database_exists_message += 'Create a new database that has not been migrated before attempting to bootstrap.'
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try:
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model = tool_shed_model.init(config_parser.get('app:main', 'file_path'), dburi, engine_options={}, create_tables=False)
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sa_session = model.context.current
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sys.exit(database_exists_message)
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except ProgrammingError:
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pass
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except OperationalError:
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pass
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try:
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if sa_session is not None:
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result = sa_session.execute('SELECT version FROM migrate_version').first()
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if result[0] >= 2:
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sys.exit(database_exists_message)
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else:
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pass
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except ProgrammingError:
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pass
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if config_parser.has_option('app:main', 'hgweb_config_dir'):
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hgweb_config_parser = ConfigParser.ConfigParser()
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hgweb_dir = config_parser.get('app:main', 'hgweb_config_dir')
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hgweb_config_file = os.path.join(hgweb_dir, 'hgweb.config')
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if not os.path.exists(hgweb_config_file):
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sys.exit(0)
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hgweb_config_parser.read(hgweb_config_file)
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configured_repos = hgweb_config_parser.items('paths')
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if len(configured_repos) >= 1:
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message = "This Tool Shed's hgweb.config file contains entries, so bootstrapping is not allowed. Delete"
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message += " the current hgweb.config file along with all associated repositories in the configured "
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message += "location before attempting to boostrap."
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sys.exit(message)
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else:
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sys.exit(0)
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else:
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sys.exit(0)
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sys.exit(0)
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def admin_user_info():
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user_info_config = os.path.abspath(os.path.join(os.getcwd(), 'scripts/tool_shed/bootstrap_tool_shed', 'user_info.xml'))
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tree, error_message = xml_util.parse_xml(user_info_config)
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username = None
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email = None
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password = None
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if tree is None:
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print "The XML file ", user_info_config, " seems to be invalid, using defaults."
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email = 'admin@test.org'
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password = 'testuser'
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username = 'admin'
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else:
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root = tree.getroot()
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for elem in root:
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if elem.tag == 'email':
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email = elem.text
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elif elem.tag == 'password':
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password = elem.text
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elif elem.tag == 'username':
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username = elem.text
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return (username, email, password)
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def get_local_tool_shed_url(config_parser):
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port = '9009'
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if config_parser.has_section('server:main'):
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if config_parser.has_option('server:main', 'port'):
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port = config_parser.get('server:main', 'port')
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host = '127.0.0.1'
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print 'http://%s:%s' % (host, port)
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return 0
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def main(args):
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config_parser = ConfigParser.ConfigParser()
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if os.path.exists(args.config):
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config_parser.read(args.config)
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else:
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return 1
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if args.method == 'check_db':
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return check_db(config_parser)
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elif args.method == 'admin_user_info':
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(username, email, password) = admin_user_info()
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print '%s__SEP__%s__SEP__%s' % (username, email, password)
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return 0
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elif args.method == 'get_url':
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return get_local_tool_shed_url(config_parser)
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else:
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return 1
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parser = optparse.OptionParser()
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parser.add_option('-c', '--config_file', dest='config', action='store', default='config/tool_shed.ini.sample')
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parser.add_option('-e', '--execute', dest='method', action='store', default='check_db')
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(args, options) = parser.parse_args()
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if __name__ == '__main__':
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sys.exit(main(args))
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