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)
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
