/lib/galaxy/webapps/reports/config.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 118 lines · 115 code · 2 blank · 1 comment · 0 complexity · 2d69c5b6305f82b3957080e6d5edc762 MD5 · raw file
- """Universe configuration builder."""
- import sys, os, logging, logging.config, ConfigParser
- from optparse import OptionParser
- from galaxy.util import string_as_bool
- 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', '.' )
- # 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 )
- # 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.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.require_login = string_as_bool( kwargs.get( "require_login", "False" ) )
- 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/reports" ), self.root )
- self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail")
- self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
- self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
- self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
- self.brand = kwargs.get( 'brand', None )
- # Configuration for the message box directly below the masthead.
- self.message_box_visible = kwargs.get( 'message_box_visible', False )
- self.message_box_content = kwargs.get( 'message_box_content', None )
- self.message_box_class = kwargs.get( 'message_box_class', 'info' )
- self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
- self.blog_url = kwargs.get( 'blog_url', None )
- self.screencasts_url = kwargs.get( 'screencasts_url', None )
- self.log_events = False
- self.cookie_path = kwargs.get( "cookie_path", "/" )
- # Error logging with sentry
- self.sentry_dsn = kwargs.get( 'sentry_dsn', None )
- #Parse global_conf
- global_conf = kwargs.get( 'global_conf', None )
- global_conf_parser = ConfigParser.ConfigParser()
- 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 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 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
- }
- 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.
- """
- 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 )