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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

Bases: Exception

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

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)

find_best_match(url: str)

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)

Parse uri into a FileSource object and a path relative to its base.

validate_uri_root(uri, user_context)

looks_like_uri(path_or_uri)

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

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

static from_app_config(config)

static from_dict(as_dict, load_stock_plugins=False)

class galaxy.files.NullConfiguredFileSources

Bases: ConfiguredFileSources

__init__()

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)

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)

static from_app_config(config)

to_dict()

static from_dict(as_dict)

class galaxy.files.FileSourceDictifiable

Bases: Dictifiable

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

to_dict(view='collection', value_mapper=None)

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)

Bases: FileSourceDictifiable

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

__init__(trans, **kwargs)

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)

Bases: FileSourceDictifiable

__init__(**kwd)

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

• galaxy.files.sources package
  • FilesSourceProperties
    • FilesSourceProperties.file_sources_config
    • FilesSourceProperties.id
    • FilesSourceProperties.label
    • FilesSourceProperties.doc
    • FilesSourceProperties.scheme
    • FilesSourceProperties.writable
    • FilesSourceProperties.requires_roles
    • FilesSourceProperties.requires_groups
    • FilesSourceProperties.uri_root
    • FilesSourceProperties.type
    • FilesSourceProperties.browsable
  • FilesSourceOptions
    • FilesSourceOptions.writeable
    • FilesSourceOptions.extra_props
    • FilesSourceOptions.__init__()
  • SingleFileSource
    • SingleFileSource.get_writable()
    • SingleFileSource.user_has_access()
    • SingleFileSource.realize_to()
    • SingleFileSource.write_from()
    • SingleFileSource.score_url_match()
    • SingleFileSource.to_relative_path()
    • SingleFileSource.to_dict()
  • SupportsBrowsing
    • SupportsBrowsing.get_uri_root()
    • SupportsBrowsing.list()
  • FilesSource
    • FilesSource.get_browsable()
  • BaseFilesSource
    • BaseFilesSource.plugin_type
    • BaseFilesSource.get_browsable()
    • BaseFilesSource.get_prefix()
    • BaseFilesSource.get_scheme()
    • BaseFilesSource.get_writable()
    • BaseFilesSource.user_has_access()
    • BaseFilesSource.user_context_required
    • BaseFilesSource.get_uri_root()
    • BaseFilesSource.to_relative_path()
    • BaseFilesSource.score_url_match()
    • BaseFilesSource.uri_from_path()
    • BaseFilesSource.to_dict()
    • BaseFilesSource.to_dict_time()
    • BaseFilesSource.list()
    • BaseFilesSource.write_from()
    • BaseFilesSource.realize_to()
  • uri_join()
  • slash_join()
  • Submodules
  • galaxy.files.sources.anvil module
  • galaxy.files.sources.basespace module
  • galaxy.files.sources.dropbox module
  • galaxy.files.sources.ftp module
  • galaxy.files.sources.galaxy module
  • galaxy.files.sources.googlecloudstorage module
  • galaxy.files.sources.googledrive module
  • galaxy.files.sources.onedata module
  • galaxy.files.sources.posix module
  • galaxy.files.sources.s3 module
  • galaxy.files.sources.s3fs module
  • galaxy.files.sources.ssh module
  • galaxy.files.sources.webdav module
• galaxy.files.unittest_utils package
  • TestConfiguredFileSources
    • TestConfiguredFileSources.__init__()
  • TestPosixConfiguredFileSources
    • TestPosixConfiguredFileSources.__init__()
  • setup_root()
  • write_file_fixtures()

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

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

galaxy.files.uris.stream_to_file(stream, suffix='', prefix='', dir=None, text=False, **kwd)

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

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