[2] | 1 | """ |
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| 2 | Universe configuration builder. |
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| 3 | """ |
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| 4 | |
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| 5 | import sys, os |
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| 6 | import logging, logging.config |
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| 7 | from optparse import OptionParser |
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| 8 | import ConfigParser |
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| 9 | from galaxy.util import string_as_bool |
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| 10 | |
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| 11 | from galaxy import eggs |
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| 12 | import pkg_resources |
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| 13 | |
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| 14 | log = logging.getLogger( __name__ ) |
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| 15 | |
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| 16 | def resolve_path( path, root ): |
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| 17 | """If 'path' is relative make absolute by prepending 'root'""" |
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| 18 | if not( os.path.isabs( path ) ): |
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| 19 | path = os.path.join( root, path ) |
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| 20 | return path |
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| 21 | |
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| 22 | class ConfigurationError( Exception ): |
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| 23 | pass |
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| 24 | |
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| 25 | class Configuration( object ): |
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| 26 | def __init__( self, **kwargs ): |
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| 27 | self.config_dict = kwargs |
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| 28 | self.root = kwargs.get( 'root_dir', '.' ) |
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| 29 | # Collect the umask and primary gid from the environment |
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| 30 | self.umask = os.umask( 077 ) # get the current umask |
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| 31 | os.umask( self.umask ) # can't get w/o set, so set it back |
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| 32 | self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster |
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| 33 | # Database related configuration |
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| 34 | self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root ) |
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| 35 | self.database_connection = kwargs.get( "database_connection", False ) |
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| 36 | self.database_engine_options = get_database_engine_options( kwargs ) |
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| 37 | self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) ) |
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| 38 | # Where dataset files are stored |
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| 39 | self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root ) |
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| 40 | self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root ) |
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| 41 | self.cookie_path = kwargs.get( "cookie_path", "/" ) |
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| 42 | self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) |
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| 43 | self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) |
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| 44 | self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) ) |
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| 45 | self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None ) |
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| 46 | self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None ) |
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| 47 | self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) ) |
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| 48 | self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) ) |
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| 49 | self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root ) |
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| 50 | self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root ) |
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| 51 | self.admin_users = kwargs.get( "admin_users", "" ) |
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| 52 | self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail") |
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| 53 | self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu") |
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| 54 | self.error_email_to = kwargs.get( 'error_email_to', None ) |
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| 55 | self.smtp_server = kwargs.get( 'smtp_server', None ) |
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| 56 | self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) ) |
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| 57 | self.brand = kwargs.get( 'brand', None ) |
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| 58 | self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' ) |
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| 59 | self.bugs_email = kwargs.get( 'bugs_email', None ) |
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| 60 | self.blog_url = kwargs.get( 'blog_url', None ) |
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| 61 | self.screencasts_url = kwargs.get( 'screencasts_url', None ) |
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| 62 | self.log_events = False |
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| 63 | self.cloud_controller_instance = False |
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| 64 | self.datatypes_config = kwargs.get( 'datatypes_config_file', 'community_datatypes_conf.xml' ) |
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| 65 | # Proxy features |
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| 66 | self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) |
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| 67 | self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False ) |
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| 68 | # Parse global_conf and save the parser |
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| 69 | global_conf = kwargs.get( 'global_conf', None ) |
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| 70 | global_conf_parser = ConfigParser.ConfigParser() |
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| 71 | self.global_conf_parser = global_conf_parser |
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| 72 | if global_conf and "__file__" in global_conf: |
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| 73 | global_conf_parser.read(global_conf['__file__']) |
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| 74 | def get( self, key, default ): |
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| 75 | return self.config_dict.get( key, default ) |
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| 76 | def get_bool( self, key, default ): |
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| 77 | if key in self.config_dict: |
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| 78 | return string_as_bool( self.config_dict[key] ) |
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| 79 | else: |
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| 80 | return default |
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| 81 | def check( self ): |
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| 82 | # Check that required directories exist |
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| 83 | for path in self.root, self.file_path, self.template_path: |
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| 84 | if not os.path.isdir( path ): |
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| 85 | raise ConfigurationError("Directory does not exist: %s" % path ) |
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| 86 | def is_admin_user( self, user ): |
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| 87 | """ |
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| 88 | Determine if the provided user is listed in `admin_users`. |
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| 89 | """ |
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| 90 | admin_users = self.get( "admin_users", "" ).split( "," ) |
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| 91 | return user is not None and user.email in admin_users |
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| 92 | |
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| 93 | def get_database_engine_options( kwargs ): |
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| 94 | """ |
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| 95 | Allow options for the SQLAlchemy database engine to be passed by using |
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| 96 | the prefix "database_engine_option_". |
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| 97 | """ |
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| 98 | conversions = { |
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| 99 | 'convert_unicode': string_as_bool, |
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| 100 | 'pool_timeout': int, |
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| 101 | 'echo': string_as_bool, |
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| 102 | 'echo_pool': string_as_bool, |
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| 103 | 'pool_recycle': int, |
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| 104 | 'pool_size': int, |
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| 105 | 'max_overflow': int, |
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| 106 | 'pool_threadlocal': string_as_bool, |
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| 107 | 'server_side_cursors': string_as_bool |
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| 108 | } |
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| 109 | prefix = "database_engine_option_" |
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| 110 | prefix_len = len( prefix ) |
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| 111 | rval = {} |
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| 112 | for key, value in kwargs.iteritems(): |
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| 113 | if key.startswith( prefix ): |
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| 114 | key = key[prefix_len:] |
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| 115 | if key in conversions: |
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| 116 | value = conversions[key](value) |
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| 117 | rval[ key ] = value |
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| 118 | return rval |
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| 119 | |
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| 120 | def configure_logging( config ): |
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| 121 | """ |
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| 122 | Allow some basic logging configuration to be read from the cherrpy |
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| 123 | config. |
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| 124 | """ |
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| 125 | # PasteScript will have already configured the logger if the appropriate |
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| 126 | # sections were found in the config file, so we do nothing if the |
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| 127 | # config has a loggers section, otherwise we do some simple setup |
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| 128 | # using the 'log_*' values from the config. |
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| 129 | if config.global_conf_parser.has_section( "loggers" ): |
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| 130 | return |
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| 131 | format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" ) |
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| 132 | level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ] |
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| 133 | destination = config.get( "log_destination", "stdout" ) |
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| 134 | log.info( "Logging at '%s' level to '%s'" % ( level, destination ) ) |
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| 135 | # Get root logger |
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| 136 | root = logging.getLogger() |
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| 137 | # Set level |
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| 138 | root.setLevel( level ) |
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| 139 | # Turn down paste httpserver logging |
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| 140 | if level <= logging.DEBUG: |
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| 141 | logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN ) |
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| 142 | # Remove old handlers |
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| 143 | for h in root.handlers[:]: |
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| 144 | root.removeHandler(h) |
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| 145 | # Create handler |
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| 146 | if destination == "stdout": |
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| 147 | handler = logging.StreamHandler( sys.stdout ) |
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| 148 | else: |
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| 149 | handler = logging.FileHandler( destination ) |
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| 150 | # Create formatter |
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| 151 | formatter = logging.Formatter( format ) |
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| 152 | # Hook everything up |
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| 153 | handler.setFormatter( formatter ) |
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| 154 | root.addHandler( handler ) |
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