def __init__(self, root=None, **kwd): Bunch.__init__(self, **kwd) if not root: root = tempfile.mkdtemp() self._remove_root = True else: self._remove_root = False self.root = root self.data_dir = os.path.join(root, 'database') self.security = IdEncodingHelper(id_secret=GALAXY_TEST_UNITTEST_SECRET) self.database_connection = kwd.get( 'database_connection', GALAXY_TEST_IN_MEMORY_DB_CONNECTION) # objectstore config values... self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.object_store_cache_path = '/tmp/cache' self.object_store_store_by = "uuid" self.umask = os.umask(0o77) self.gid = os.getgid() # objectstore config directories... self.jobs_directory = os.path.join(self.data_dir, 'jobs_directory') self.new_file_path = os.path.join(self.data_dir, 'tmp') self.file_path = os.path.join(self.data_dir, 'files') self.server_name = "main"
def __init__(self, root=None, **kwargs): Bunch.__init__(self, **kwargs) root = root or '/tmp' self.security = security.SecurityHelper(id_secret='bler') self.use_remote_user = kwargs.get('use_remote_user', False) self.file_path = '/tmp' self.jobs_directory = '/tmp' self.new_file_path = '/tmp' self.tool_data_path = '/tmp' self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.user_activation_on = False self.new_user_dataset_access_role_default_private = False self.expose_dataset_path = True self.allow_user_dataset_purge = True self.enable_old_display_applications = True self.umask = 0o77 # Follow two required by GenomeBuilds self.len_file_path = os.path.join('tool-data', 'shared', 'ucsc', 'chrom') self.builds_file_path = os.path.join('tool-data', 'shared', 'ucsc', 'builds.txt.sample') self.migrated_tools_config = "/tmp/migrated_tools_conf.xml" self.preserve_python_environment = "always" # set by MockDir self.root = root
def __init__(self, root=None, **kwargs): Bunch.__init__(self, **kwargs) if not root: root = tempfile.mkdtemp() self._remove_root = True else: self._remove_root = False self.security = idencoding.IdEncodingHelper( id_secret='6e46ed6483a833c100e68cc3f1d0dd76') self.database_connection = kwargs.get('database_connection', "sqlite:///:memory:") self.use_remote_user = kwargs.get('use_remote_user', False) self.data_dir = os.path.join(root, 'database') self.file_path = os.path.join(self.data_dir, 'files') self.jobs_directory = os.path.join(self.data_dir, 'jobs_directory') self.new_file_path = os.path.join(self.data_dir, 'tmp') self.tool_data_path = os.path.join(root, 'tool-data') self.tool_dependency_dir = None self.metadata_strategy = 'legacy' self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.object_store_cache_path = '/tmp/cache' self.umask = os.umask(0o77) self.gid = os.getgid() self.user_activation_on = False self.new_user_dataset_access_role_default_private = False self.expose_dataset_path = True self.allow_user_dataset_purge = True self.enable_old_display_applications = True self.redact_username_in_logs = False self.auth_config_file = "config/auth_conf.xml.sample" self.error_email_to = "*****@*****.**" self.password_expiration_period = 0 self.umask = 0o77 # Compliance related config self.redact_email_in_job_name = False # Follow two required by GenomeBuilds self.len_file_path = os.path.join('tool-data', 'shared', 'ucsc', 'chrom') self.builds_file_path = os.path.join('tool-data', 'shared', 'ucsc', 'builds.txt.sample') self.preserve_python_environment = "always" self.enable_beta_gdpr = False self.legacy_eager_objectstore_initialization = True self.version_major = "19.09" # set by MockDir self.root = root self.config_file = None
def __init__( self, **kwd ): Bunch.__init__( self, **kwd ) self.primary_file = None self.composite_files = odict() self.dbkey = None self.warnings = [] self._temp_filenames = [] #store all created filenames here, delete on cleanup
def __init__(self, **kwargs): Bunch.__init__(self, **kwargs) self.security = security.SecurityHelper(id_secret='bler') self.file_path = '/tmp' self.job_working_directory = '/tmp' self.new_file_path = '/tmp' self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.user_activation_on = False self.new_user_dataset_access_role_default_private = False self.allow_user_dataset_purge = True
def __init__( self, **kwargs ): Bunch.__init__( self, **kwargs ) self.security = security.SecurityHelper( id_secret='bler' ) self.file_path = '/tmp' self.job_working_directory = '/tmp' self.new_file_path = '/tmp' self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.user_activation_on = False self.new_user_dataset_access_role_default_private = False self.expose_dataset_path = True self.allow_user_dataset_purge = True self.enable_old_display_applications = True
def __init__( self, root=None, **kwargs ): Bunch.__init__( self, **kwargs ) self.security = security.SecurityHelper( id_secret='bler' ) self.file_path = '/tmp' self.job_working_directory = '/tmp' self.new_file_path = '/tmp' self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.user_activation_on = False self.new_user_dataset_access_role_default_private = False self.expose_dataset_path = True self.allow_user_dataset_purge = True self.enable_old_display_applications = True # set by MockDir self.root = root
def __init__( self, root=None, **kwargs ): Bunch.__init__( self, **kwargs ) self.security = security.SecurityHelper( id_secret='bler' ) self.use_remote_user = kwargs.get( 'use_remote_user', False ) self.file_path = '/tmp' self.jobs_directory = '/tmp' self.new_file_path = '/tmp' self.object_store_config_file = '' self.object_store = 'disk' self.object_store_check_old_style = False self.user_activation_on = False self.new_user_dataset_access_role_default_private = False self.expose_dataset_path = True self.allow_user_dataset_purge = True self.enable_old_display_applications = True self.umask = 0o77 # set by MockDir self.root = root