""" Universe configuration builder. """ import sys, os import logging, logging.config from optparse import OptionParser import ConfigParser from galaxy.util import string_as_bool from galaxy import eggs import pkg_resources log = logging.getLogger( __name__ ) def resolve_path( path, root ): """If 'path' is relative make absolute by prepending 'root'""" if not( os.path.isabs( path ) ): path = os.path.join( root, path ) return path class ConfigurationError( Exception ): pass class Configuration( object ): def __init__( self, **kwargs ): self.config_dict = kwargs self.root = kwargs.get( 'root_dir', '.' ) # Collect the umask and primary gid from the environment self.umask = os.umask( 077 ) # get the current umask os.umask( self.umask ) # can't get w/o set, so set it back self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster # Database related configuration self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) self.database_connection = kwargs.get( "database_connection", False ) self.database_engine_options = get_database_engine_options( kwargs ) self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) ) # Where dataset files are stored self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) self.admin_users = kwargs.get( "admin_users", "" ) self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.smtp_server = kwargs.get( 'smtp_server', None ) self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) self.brand = kwargs.get( 'brand', None ) self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' ) self.bugs_email = kwargs.get( 'bugs_email', None ) self.blog_url = kwargs.get( 'blog_url', None ) self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False self.cloud_controller_instance = False self.datatypes_config = kwargs.get( 'datatypes_config_file', 'community_datatypes_conf.xml' ) # Proxy features self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) # Parse global_conf and save the parser global_conf = kwargs.get( 'global_conf', None ) global_conf_parser = ConfigParser.ConfigParser() self.global_conf_parser = global_conf_parser if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) def get( self, key, default ): return self.config_dict.get( key, default ) def get_bool( self, key, default ): if key in self.config_dict: return string_as_bool( self.config_dict[key] ) else: return default def check( self ): # Check that required directories exist for path in self.root, self.file_path, self.template_path: if not os.path.isdir( path ): raise ConfigurationError("Directory does not exist: %s" % path ) def is_admin_user( self, user ): """ Determine if the provided user is listed in `admin_users`. """ admin_users = self.get( "admin_users", "" ).split( "," ) return user is not None and user.email in admin_users def get_database_engine_options( kwargs ): """ Allow options for the SQLAlchemy database engine to be passed by using the prefix "database_engine_option_". """ conversions = { 'convert_unicode': string_as_bool, 'pool_timeout': int, 'echo': string_as_bool, 'echo_pool': string_as_bool, 'pool_recycle': int, 'pool_size': int, 'max_overflow': int, 'pool_threadlocal': string_as_bool, 'server_side_cursors': string_as_bool } prefix = "database_engine_option_" prefix_len = len( prefix ) rval = {} for key, value in kwargs.iteritems(): if key.startswith( prefix ): key = key[prefix_len:] if key in conversions: value = conversions[key](value) rval[ key ] = value return rval def configure_logging( config ): """ Allow some basic logging configuration to be read from the cherrpy config. """ # PasteScript will have already configured the logger if the appropriate # sections were found in the config file, so we do nothing if the # config has a loggers section, otherwise we do some simple setup # using the 'log_*' values from the config. if config.global_conf_parser.has_section( "loggers" ): return format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] destination = config.get( "log_destination", "stdout" ) log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) # Get root logger root = logging.getLogger() # Set level root.setLevel( level ) # Turn down paste httpserver logging if level <= logging.DEBUG: logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) # Remove old handlers for h in root.handlers[:]: root.removeHandler(h) # Create handler if destination == "stdout": handler = logging.StreamHandler( sys.stdout ) else: handler = logging.FileHandler( destination ) # Create formatter formatter = logging.Formatter( format ) # Hook everything up handler.setFormatter( formatter ) root.addHandler( handler )