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https://github.com/galaxyproject/galaxy.git
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131 lines
4.6 KiB
Python
Executable File
131 lines
4.6 KiB
Python
Executable File
#!/usr/bin/python
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import argparse
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import ConfigParser
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import os
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import sys
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new_path = [ os.path.join( os.getcwd(), "lib" ) ]
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new_path.extend( sys.path[1:] )
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sys.path = new_path
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from galaxy import eggs
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eggs.require( "SQLAlchemy >= 0.4" )
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import galaxy.webapps.tool_shed.model.mapping as tool_shed_model
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from sqlalchemy.exc import ProgrammingError
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from sqlalchemy.exc import OperationalError
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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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print 'The database configuration setting is missing from the tool_shed.ini file. Add this setting before attempting to bootstrap.'
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exit(1)
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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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print database_exists_message
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exit(1)
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except ProgrammingError, e:
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pass
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except OperationalError, e:
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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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print database_exists_message
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exit(1)
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else:
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pass
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except ProgrammingError, e:
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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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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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print
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exit(1)
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else:
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exit(0)
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else:
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exit(0)
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exit(0)
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def admin_user_info( config_parser ):
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user_info_config = os.path.abspath( os.path.join( os.getcwd(), 'lib/tool_shed/scripts/bootstrap_tool_shed', 'user_info.xml' ) )
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tree, error_message = xml_util.parse_xml( user_info_config )
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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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print '%s__SEP__%s__SEP__%s' % ( username, email, password )
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return 0
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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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return admin_user_info( config_parser )
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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 = argparse.ArgumentParser()
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parser.add_argument( '-c', '--config_file', dest='config', action='store', default='config/tool_shed.ini.sample' )
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parser.add_argument( '-e', '--execute', dest='method', action='store', default='check_db' )
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args = parser.parse_args()
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if __name__ == '__main__':
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exit( main( args ) )
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