/lib/galaxy/webapps/community/config.py
Python | 174 lines | 164 code | 4 blank | 6 comment | 0 complexity | cc1db2bb9c452fa8414aea7ce824adc8 MD5 | raw file
1"""
2Universe configuration builder.
3"""
4
5import sys, os
6import logging, logging.config
7from optparse import OptionParser
8import ConfigParser
9from galaxy.util import string_as_bool
10
11from galaxy import eggs
12import pkg_resources
13
14log = logging.getLogger( __name__ )
15
16def resolve_path( path, root ):
17 """If 'path' is relative make absolute by prepending 'root'"""
18 if not( os.path.isabs( path ) ):
19 path = os.path.join( root, path )
20 return path
21
22class ConfigurationError( Exception ):
23 pass
24
25class Configuration( object ):
26 def __init__( self, **kwargs ):
27 self.config_dict = kwargs
28 self.root = kwargs.get( 'root_dir', '.' )
29 # Collect the umask and primary gid from the environment
30 self.umask = os.umask( 077 ) # get the current umask
31 os.umask( self.umask ) # can't get w/o set, so set it back
32 self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
33 # Database related configuration
34 self.database = resolve_path( kwargs.get( "database_file", "database/universe.d" ), self.root )
35 self.database_connection = kwargs.get( "database_connection", False )
36 self.database_engine_options = get_database_engine_options( kwargs )
37 self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) )
38 # Where dataset files are stored
39 self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
40 self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
41 self.cookie_path = kwargs.get( "cookie_path", "/" )
42 # web API
43 self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) )
44 self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
45 self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
46 self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
47 # Tool stuff
48 self.tool_secret = kwargs.get( "tool_secret", "" )
49 self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
50 self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
51 self.ftp_upload_dir = kwargs.get( 'ftp_upload_dir', None )
52 # Location for dependencies
53 if 'tool_dependency_dir' in kwargs:
54 self.tool_dependency_dir = resolve_path( kwargs.get( "tool_dependency_dir" ), self.root )
55 self.use_tool_dependencies = True
56 else:
57 self.tool_dependency_dir = None
58 self.use_tool_dependencies = False
59 self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
60 self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
61 self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )
62 self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) )
63 self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
64 self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) )
65 self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
66 self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates/community" ), self.root )
67 self.admin_users = kwargs.get( "admin_users", "" )
68 self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail")
69 self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu")
70 self.error_email_to = kwargs.get( 'error_email_to', None )
71 self.smtp_server = kwargs.get( 'smtp_server', None )
72 self.smtp_username = kwargs.get( 'smtp_username', None )
73 self.smtp_password = kwargs.get( 'smtp_password', None )
74 self.start_job_runners = kwargs.get( 'start_job_runners', None )
75 self.email_from = kwargs.get( 'email_from', None )
76 self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
77 self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
78 self.brand = kwargs.get( 'brand', None )
79 self.support_url = kwargs.get( 'support_url', 'http://wiki.g2.bx.psu.edu/Support' )
80 self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
81 self.blog_url = kwargs.get( 'blog_url', None )
82 self.screencasts_url = kwargs.get( 'screencasts_url', None )
83 self.log_events = False
84 self.cloud_controller_instance = False
85 # Proxy features
86 self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False )
87 self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
88 # Parse global_conf and save the parser
89 global_conf = kwargs.get( 'global_conf', None )
90 global_conf_parser = ConfigParser.ConfigParser()
91 self.global_conf_parser = global_conf_parser
92 if global_conf and "__file__" in global_conf:
93 global_conf_parser.read(global_conf['__file__'])
94 def get( self, key, default ):
95 return self.config_dict.get( key, default )
96 def get_bool( self, key, default ):
97 if key in self.config_dict:
98 return string_as_bool( self.config_dict[key] )
99 else:
100 return default
101 def check( self ):
102 # Check that required directories exist
103 for path in self.root, self.file_path, self.template_path:
104 if not os.path.isdir( path ):
105 raise ConfigurationError("Directory does not exist: %s" % path )
106 def is_admin_user( self, user ):
107 """
108 Determine if the provided user is listed in `admin_users`.
109 """
110 admin_users = self.get( "admin_users", "" ).split( "," )
111 return user is not None and user.email in admin_users
112
113def get_database_engine_options( kwargs ):
114 """
115 Allow options for the SQLAlchemy database engine to be passed by using
116 the prefix "database_engine_option_".
117 """
118 conversions = {
119 'convert_unicode': string_as_bool,
120 'pool_timeout': int,
121 'echo': string_as_bool,
122 'echo_pool': string_as_bool,
123 'pool_recycle': int,
124 'pool_size': int,
125 'max_overflow': int,
126 'pool_threadlocal': string_as_bool,
127 'server_side_cursors': string_as_bool
128 }
129 prefix = "database_engine_option_"
130 prefix_len = len( prefix )
131 rval = {}
132 for key, value in kwargs.iteritems():
133 if key.startswith( prefix ):
134 key = key[prefix_len:]
135 if key in conversions:
136 value = conversions[key](value)
137 rval[ key ] = value
138 return rval
139
140def configure_logging( config ):
141 """
142 Allow some basic logging configuration to be read from the cherrpy
143 config.
144 """
145 # PasteScript will have already configured the logger if the appropriate
146 # sections were found in the config file, so we do nothing if the
147 # config has a loggers section, otherwise we do some simple setup
148 # using the 'log_*' values from the config.
149 if config.global_conf_parser.has_section( "loggers" ):
150 return
151 format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" )
152 level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ]
153 destination = config.get( "log_destination", "stdout" )
154 log.info( "Logging at '%s' level to '%s'" % ( level, destination ) )
155 # Get root logger
156 root = logging.getLogger()
157 # Set level
158 root.setLevel( level )
159 # Turn down paste httpserver logging
160 if level <= logging.DEBUG:
161 logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN )
162 # Remove old handlers
163 for h in root.handlers[:]:
164 root.removeHandler(h)
165 # Create handler
166 if destination == "stdout":
167 handler = logging.StreamHandler( sys.stdout )
168 else:
169 handler = logging.FileHandler( destination )
170 # Create formatter
171 formatter = logging.Formatter( format )
172 # Hook everything up
173 handler.setFormatter( formatter )
174 root.addHandler( handler )