galaxy.files package¶

class galaxy.files.FileSourcePath(file_source, path)¶

Bases: tuple

property file_source¶: Alias for field number 0

property path¶: Alias for field number 1

class galaxy.files.FileSourceScore(file_source, score)¶

Bases: tuple

property file_source¶: Alias for field number 0

property score¶: Alias for field number 1

exception galaxy.files.NoMatchingFileSource[source]¶: Bases: Exception

class galaxy.files.ConfiguredFileSources(file_sources_config: ConfiguredFileSourcesConfig, conf_file=None, conf_dict=None, load_stock_plugins=False)[source]¶

Bases: object

Load plugins and resolve Galaxy URIs to FileSource objects.

__init__(file_sources_config: ConfiguredFileSourcesConfig, conf_file=None, conf_dict=None, load_stock_plugins=False)[source]¶

find_best_match(url: str)[source]¶: Returns the best matching file source for handling a particular url. Each filesource scores its own ability to match a particular url, and the highest scorer with a score > 0 is selected.

get_file_source_path(uri)[source]¶: Parse uri into a FileSource object and a path relative to its base.

validate_uri_root(uri, user_context)[source]¶

looks_like_uri(path_or_uri)[source]¶

plugins_to_dict(for_serialization: bool = False, user_context: Optional[FileSourceDictifiable] = None, browsable_only: Optional[bool] = False) → List[Dict[str, Any]][source]¶

to_dict(for_serialization: bool = False, user_context: Optional[FileSourceDictifiable] = None) → Dict[str, Any][source]¶

static from_app_config(config)[source]¶

static from_dict(as_dict, load_stock_plugins=False)[source]¶

class galaxy.files.NullConfiguredFileSources[source]¶

Bases: ConfiguredFileSources

__init__()[source]¶

class galaxy.files.ConfiguredFileSourcesConfig(symlink_allowlist=None, fetch_url_allowlist=None, library_import_dir=None, user_library_import_dir=None, ftp_upload_dir=None, ftp_upload_purge=True)[source]¶

Bases: object

__init__(symlink_allowlist=None, fetch_url_allowlist=None, library_import_dir=None, user_library_import_dir=None, ftp_upload_dir=None, ftp_upload_purge=True)[source]¶

static from_app_config(config)[source]¶

to_dict()[source]¶

static from_dict(as_dict)[source]¶

class galaxy.files.FileSourceDictifiable[source]¶

Bases: Dictifiable

dict_collection_visible_keys = ('email', 'username', 'ftp_dir', 'preferences', 'is_admin')¶

to_dict(view='collection', value_mapper=None)[source]¶: Return item dictionary.

property role_names: Set[str]¶

property group_names: Set[str]¶

property file_sources¶: Return other filesources available in the system, for chained filesource resolution

class galaxy.files.ProvidesUserFileSourcesUserContext(trans, **kwargs)[source]¶

Bases: FileSourceDictifiable

Implement a FileSourcesUserContext from a Galaxy ProvidesUserContext (e.g. trans).

__init__(trans, **kwargs)[source]¶

property email¶

property username¶

property ftp_dir¶

property preferences¶

property role_names: Set[str]¶: The set of role names of this user.

property group_names: Set[str]¶: The set of group names to which this user belongs.

property is_admin¶: Whether this user is an administrator.

property user_vault¶: User vault namespace

property app_vault¶: App vault namespace

property file_sources¶: Return other filesources available in the system, for chained filesource resolution

class galaxy.files.DictFileSourcesUserContext(**kwd)[source]¶

Bases: FileSourceDictifiable

__init__(**kwd)[source]¶

property email¶

property username¶

property ftp_dir¶

property preferences¶

property role_names¶

property group_names¶

property is_admin¶

property user_vault¶

property app_vault¶

property file_sources¶: Return other filesources available in the system, for chained filesource resolution

Subpackages¶

Submodules¶

galaxy.files.uris module¶

galaxy.files.uris.stream_url_to_str(path: str, file_sources: Optional[ConfiguredFileSources] = None, prefix: str = 'gx_file_stream') → str[source]¶

galaxy.files.uris.stream_url_to_file(url: str, file_sources: Optional[ConfiguredFileSources] = None, prefix: str = 'gx_file_stream', dir: Optional[str] = None, user_context=None, target_path: Optional[str] = None, file_source_opts: Optional[FilesSourceOptions] = None) → str[source]¶

galaxy.files.uris.stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd)[source]¶: Writes a stream to a temporary file, returns the temporary file’s name

galaxy.files.uris.validate_uri_access(uri: str, is_admin: bool, ip_allowlist: List[Union[IPv4Address, IPv6Address, IPv4Network, IPv6Network]]) → None[source]¶

Perform uniform checks on supplied URIs.

Prevent access to local IPs not found in ip_allowlist.
Don’t allow non-admins to access file:// URIs.

galaxy.files.uris.validate_non_local(uri: str, ip_allowlist: List[Union[IPv4Address, IPv6Address, IPv4Network, IPv6Network]]) → str[source]¶