root/galaxy-central/lib/galaxy/config.py

リビジョン 2, 14.1 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
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    deprecated_options = ( 'database_file', )
27    def __init__( self, **kwargs ):
28        self.config_dict = kwargs
29        self.root = kwargs.get( 'root_dir', '.' )
30        # Collect the umask and primary gid from the environment
31        self.umask = os.umask( 077 ) # get the current umask
32        os.umask( self.umask ) # can't get w/o set, so set it back
33        self.gid = os.getgid() # if running under newgrp(1) we'll need to fix the group of data created on the cluster
34        # Database related configuration
35        self.database = resolve_path( kwargs.get( "database_file", "database/universe.sqlite" ), self.root )
36        self.database_connection =  kwargs.get( "database_connection", False )
37        self.database_engine_options = get_database_engine_options( kwargs )                       
38        self.database_create_tables = string_as_bool( kwargs.get( "database_create_tables", "True" ) )
39        self.database_query_profiling_proxy = string_as_bool( kwargs.get( "database_query_profiling_proxy", "False" ) )
40        # Where dataset files are stored
41        self.file_path = resolve_path( kwargs.get( "file_path", "database/files" ), self.root )
42        self.new_file_path = resolve_path( kwargs.get( "new_file_path", "database/tmp" ), self.root )
43        self.cookie_path = kwargs.get( "cookie_path", "/" )
44        # web API
45        self.enable_api = string_as_bool( kwargs.get( 'enable_api', False ) )
46        # dataset Track files
47        self.track_store_path = kwargs.get( "track_store_path", "${extra_files_path}/tracks")
48        self.tool_path = resolve_path( kwargs.get( "tool_path", "tools" ), self.root )
49        self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() )
50        self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
51        self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root )
52        self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root )
53        self.tool_secret = kwargs.get( "tool_secret", "" )
54        self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" )
55        self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) )
56        self.retry_metadata_internally = string_as_bool( kwargs.get( "retry_metadata_internally", "True" ) )
57        self.use_remote_user = string_as_bool( kwargs.get( "use_remote_user", "False" ) )
58        self.remote_user_maildomain = kwargs.get( "remote_user_maildomain", None )
59        self.remote_user_logout_href = kwargs.get( "remote_user_logout_href", None )
60        self.require_login = string_as_bool( kwargs.get( "require_login", "False" ) )
61        self.allow_user_creation = string_as_bool( kwargs.get( "allow_user_creation", "True" ) )
62        self.allow_user_deletion = string_as_bool( kwargs.get( "allow_user_deletion", "False" ) )
63        self.new_user_dataset_access_role_default_private = string_as_bool( kwargs.get( "new_user_dataset_access_role_default_private", "False" ) )
64        self.template_path = resolve_path( kwargs.get( "template_path", "templates" ), self.root )
65        self.template_cache = resolve_path( kwargs.get( "template_cache_path", "database/compiled_templates" ), self.root )
66        self.local_job_queue_workers = int( kwargs.get( "local_job_queue_workers", "5" ) )
67        self.cluster_job_queue_workers = int( kwargs.get( "cluster_job_queue_workers", "3" ) )
68        self.job_queue_cleanup_interval = int( kwargs.get("job_queue_cleanup_interval", "5") )
69        self.cluster_files_directory = os.path.abspath( kwargs.get( "cluster_files_directory", "database/pbs" ) )
70        self.job_working_directory = resolve_path( kwargs.get( "job_working_directory", "database/job_working_directory" ), self.root )
71        self.outputs_to_working_directory = string_as_bool( kwargs.get( 'outputs_to_working_directory', False ) )
72        self.output_size_limit = int( kwargs.get( 'output_size_limit', 0 ) )
73        self.job_walltime = kwargs.get( 'job_walltime', None )
74        self.admin_users = kwargs.get( "admin_users", "" )
75        self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-user-join@bx.psu.edu")
76        self.error_email_to = kwargs.get( 'error_email_to', None )
77        self.smtp_server = kwargs.get( 'smtp_server', None )
78        self.start_job_runners = kwargs.get( 'start_job_runners', None )
79        self.default_cluster_job_runner = kwargs.get( 'default_cluster_job_runner', 'local:///' )
80        self.pbs_application_server = kwargs.get('pbs_application_server', "" )
81        self.pbs_dataset_server = kwargs.get('pbs_dataset_server', "" )
82        self.pbs_dataset_path = kwargs.get('pbs_dataset_path', "" )
83        self.pbs_stage_path = kwargs.get('pbs_stage_path', "" )
84        self.use_heartbeat = string_as_bool( kwargs.get( 'use_heartbeat', 'False' ) )
85        self.use_memdump = string_as_bool( kwargs.get( 'use_memdump', 'False' ) )
86        self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
87        self.log_events = string_as_bool( kwargs.get( 'log_events', 'False' ) )
88        self.ucsc_display_sites = kwargs.get( 'ucsc_display_sites', "main,test,archaea,ucla" ).lower().split(",")
89        self.gbrowse_display_sites = kwargs.get( 'gbrowse_display_sites', "wormbase,tair,modencode_worm,modencode_fly" ).lower().split(",")
90        self.genetrack_display_sites = kwargs.get( 'genetrack_display_sites', "main,test" ).lower().split(",")
91        self.brand = kwargs.get( 'brand', None )
92        self.wiki_url = kwargs.get( 'wiki_url', 'http://g2.trac.bx.psu.edu/' )
93        self.bugs_email = kwargs.get( 'bugs_email', None )
94        self.blog_url = kwargs.get( 'blog_url', None )
95        self.screencasts_url = kwargs.get( 'screencasts_url', None )
96        self.library_import_dir = kwargs.get( 'library_import_dir', None )
97        if self.library_import_dir is not None and not os.path.exists( self.library_import_dir ):
98            raise ConfigurationError( "library_import_dir specified in config (%s) does not exist" % self.library_import_dir )
99        self.user_library_import_dir = kwargs.get( 'user_library_import_dir', None )
100        if self.user_library_import_dir is not None and not os.path.exists( self.user_library_import_dir ):
101            raise ConfigurationError( "user_library_import_dir specified in config (%s) does not exist" % self.user_library_import_dir )
102        self.allow_library_path_paste = kwargs.get( 'allow_library_path_paste', False )
103        self.disable_library_comptypes = kwargs.get( 'disable_library_comptypes', '' ).lower().split( ',' )
104        # Location for dependencies
105        if 'tool_dependency_dir' in kwargs:
106            self.tool_dependency_dir = resolve_path( kwargs.get( "tool_dependency_dir" ), self.root )
107            self.use_tool_dependencies = True
108        else:
109            self.tool_dependency_dir = None
110            self.use_tool_dependencies = False
111        # Configuration options for taking advantage of nginx features
112        self.upstream_gzip = string_as_bool( kwargs.get( 'upstream_gzip', False ) )
113        self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False )
114        self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
115        self.nginx_x_archive_files_base = kwargs.get( 'nginx_x_archive_files_base', False )
116        self.nginx_upload_store = kwargs.get( 'nginx_upload_store', False )
117        self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
118        if self.nginx_upload_store:
119            self.nginx_upload_store = os.path.abspath( self.nginx_upload_store )
120        # Parse global_conf and save the parser
121        global_conf = kwargs.get( 'global_conf', None )
122        global_conf_parser = ConfigParser.ConfigParser()
123        self.global_conf_parser = global_conf_parser
124        if global_conf and "__file__" in global_conf:
125            global_conf_parser.read(global_conf['__file__'])
126        # Heartbeat log file name override
127        if global_conf is not None:
128            self.heartbeat_log = global_conf.get( 'heartbeat_log', 'heartbeat.log' )
129        #Store per-tool runner config
130        try:
131            self.tool_runners = global_conf_parser.items("galaxy:tool_runners")
132        except ConfigParser.NoSectionError:
133            self.tool_runners = []
134        self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
135        # Cloud configuration options
136        self.cloud_controller_instance = string_as_bool( kwargs.get( 'cloud_controller_instance', 'False' ) )
137        if self.cloud_controller_instance == True:
138            self.enable_cloud_execution = string_as_bool( kwargs.get( 'enable_cloud_execution', 'True' ) )
139        else:
140            self.enable_cloud_execution = string_as_bool( kwargs.get( 'enable_cloud_execution', 'False' ) )
141        # Galaxy messaging (AMQP) configuration options
142        self.amqp = {}
143        try:
144            amqp_config = global_conf_parser.items("galaxy_amqp")
145        except ConfigParser.NoSectionError:
146            amqp_config = {}
147        for k, v in amqp_config:
148            self.amqp[k] = v
149    def get( self, key, default ):
150        return self.config_dict.get( key, default )
151    def get_bool( self, key, default ):
152        if key in self.config_dict:
153            return string_as_bool( self.config_dict[key] )
154        else:
155            return default
156    def check( self ):
157        # Check that required directories exist
158        for path in self.root, self.file_path, self.tool_path, self.tool_data_path, self.template_path, self.job_working_directory, self.cluster_files_directory:
159            if not os.path.isdir( path ):
160                raise ConfigurationError("Directory does not exist: %s" % path )
161        # Check that required files exist
162        for path in self.tool_config, self.datatypes_config:
163            if not os.path.isfile(path):
164                raise ConfigurationError("File not found: %s" % path )
165        # Check job runners so the admin can scramble dependent egg.
166        if self.start_job_runners is not None:
167            runner_to_egg = dict( pbs = 'pbs_python', sge = 'DRMAA_python', drmaa = 'drmaa' )
168            for runner in self.start_job_runners.split( ',' ):
169                try:
170                    pkg_resources.require( runner_to_egg[runner] )
171                except eggs.EggNotFetchable, e:
172                    raise eggs.EggNotFetchable( 'You must scramble the %s egg to use the %s job runner.  Instructions are available at:\n  http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster' % ( runner_to_egg[runner], runner ) )
173                except KeyError:
174                    raise Exception( 'No such job runner: %s.  Please double-check the value of start_job_runners in universe_wsgi.ini' % runner )
175        # Check for deprecated options.
176        for key in self.config_dict.keys():
177            if key in self.deprecated_options:
178                log.warning( "Config option '%s' is deprecated and will be removed in a future release.  Please consult the latest version of the sample configuration file." % key )
179               
180    def is_admin_user( self,user ):
181        """
182        Determine if the provided user is listed in `admin_users`.
183       
184        NOTE: This is temporary, admin users will likely be specified in the
185              database in the future.
186        """
187        admin_users = self.get( "admin_users", "" ).split( "," )
188        return ( user is not None and user.email in admin_users )
189
190def get_database_engine_options( kwargs ):
191    """
192    Allow options for the SQLAlchemy database engine to be passed by using
193    the prefix "database_engine_option_".
194    """
195    conversions =  {
196        'convert_unicode': string_as_bool,
197        'pool_timeout': int,
198        'echo': string_as_bool,
199        'echo_pool': string_as_bool,
200        'pool_recycle': int,
201        'pool_size': int,
202        'max_overflow': int,
203        'pool_threadlocal': string_as_bool,
204        'server_side_cursors': string_as_bool
205    }
206    prefix = "database_engine_option_"
207    prefix_len = len( prefix )
208    rval = {}
209    for key, value in kwargs.iteritems():
210        if key.startswith( prefix ):
211            key = key[prefix_len:]
212            if key in conversions:
213                value = conversions[key](value)
214            rval[ key  ] = value
215    return rval
216
217def configure_logging( config ):
218    """
219    Allow some basic logging configuration to be read from the cherrpy
220    config.
221    """
222    # PasteScript will have already configured the logger if the appropriate
223    # sections were found in the config file, so we do nothing if the
224    # config has a loggers section, otherwise we do some simple setup
225    # using the 'log_*' values from the config.
226    if config.global_conf_parser.has_section( "loggers" ):
227        return
228    format = config.get( "log_format", "%(name)s %(levelname)s %(asctime)s %(message)s" )
229    level = logging._levelNames[ config.get( "log_level", "DEBUG" ) ]
230    destination = config.get( "log_destination", "stdout" )
231    log.info( "Logging at '%s' level to '%s'" % ( level, destination ) )
232    # Get root logger
233    root = logging.getLogger()
234    # Set level
235    root.setLevel( level )
236    # Turn down paste httpserver logging
237    if level <= logging.DEBUG:
238        logging.getLogger( "paste.httpserver.ThreadPool" ).setLevel( logging.WARN )
239    # Remove old handlers
240    for h in root.handlers[:]:
241        root.removeHandler(h)
242    # Create handler
243    if destination == "stdout":
244        handler = logging.StreamHandler( sys.stdout )
245    else:
246        handler = logging.FileHandler( destination )
247    # Create formatter
248    formatter = logging.Formatter( format )   
249    # Hook everything up
250    handler.setFormatter( formatter )
251    root.addHandler( handler )
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