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galaxy.files.sources package¶

class galaxy.files.sources.FilesSource[source]¶

Bases: object

abstract get_uri_root() → str[source]¶: Return a prefix for the root (e.g. gxfiles://prefix/).

abstract get_scheme() → str[source]¶: Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

abstract get_writable()[source]¶: Return a boolean indicating if this target is writable.

abstract user_has_access(user_context) → bool[source]¶: Return a boolean indicating if the user can access the FileSource.

abstract list(source_path='/', recursive=False, user_context=None)[source]¶: Return dictionary of ‘Directory’s and ‘File’s.

abstract realize_to(source_path, native_path, user_context=None)[source]¶: Realize source path (relative to uri root) to local file system path.

abstract write_from(target_path, native_path, user_context=None)[source]¶: Write file at native path to target_path (relative to uri root).

abstract to_dict(for_serialization=False, user_context=None)[source]¶

Return a dictified representation of this FileSource instance.

If user_context is supplied, properties should be written so user context doesn’t need to be present after the plugin is re-hydrated.

class galaxy.files.sources.BaseFilesSource[source]¶

Bases: FilesSource

plugin_type: ClassVar[str]¶

get_prefix()[source]¶

get_scheme()[source]¶: Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

get_writable()[source]¶: Return a boolean indicating if this target is writable.

user_has_access(user_context) → bool[source]¶: Return a boolean indicating if the user can access the FileSource.

property user_context_required: bool¶

get_uri_root()[source]¶: Return a prefix for the root (e.g. gxfiles://prefix/).

uri_from_path(path)[source]¶

to_dict(for_serialization=False, user_context=None)[source]¶

Return a dictified representation of this FileSource instance.

If user_context is supplied, properties should be written so user context doesn’t need to be present after the plugin is re-hydrated.

to_dict_time(ctime)[source]¶

list(path='/', recursive=False, user_context=None)[source]¶: Return dictionary of ‘Directory’s and ‘File’s.

write_from(target_path, native_path, user_context=None)[source]¶: Write file at native path to target_path (relative to uri root).

realize_to(source_path, native_path, user_context=None)[source]¶: Realize source path (relative to uri root) to local file system path.

galaxy.files.sources.uri_join(*args)[source]¶

galaxy.files.sources.slash_join(*args)[source]¶

Submodules¶

galaxy.files.sources.anvil module¶

class galaxy.files.sources.anvil.AnVILFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'anvil'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs.anvilfs'¶

galaxy.files.sources.basespace module¶

class galaxy.files.sources.basespace.BaseSpaceFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'basespace'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs-basespace'¶

galaxy.files.sources.dropbox module¶

class galaxy.files.sources.dropbox.DropboxFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'dropbox'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs.dropboxfs'¶

galaxy.files.sources.ftp module¶

class galaxy.files.sources.ftp.FtpFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'ftp'¶

required_module¶: alias of FTPFS

required_package: ClassVar[str] = 'fs.ftpfs'¶

galaxy.files.sources.galaxy module¶

Static Galaxy file sources - ftp and libraries.

class galaxy.files.sources.galaxy.UserFtpFilesSource(label='FTP Directory', doc="Galaxy User's FTP Directory", root='${user.ftp_dir}', **kwd)[source]¶

Bases: PosixFilesSource

plugin_type: ClassVar[str] = 'gxftp'¶

__init__(label='FTP Directory', doc="Galaxy User's FTP Directory", root='${user.ftp_dir}', **kwd)[source]¶

get_prefix()[source]¶

get_scheme()[source]¶: Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

class galaxy.files.sources.galaxy.LibraryImportFilesSource(label='Library Import Directory', doc="Galaxy's library import directory", root='${config.library_import_dir}', **kwd)[source]¶

Bases: PosixFilesSource

plugin_type: ClassVar[str] = 'gximport'¶

__init__(label='Library Import Directory', doc="Galaxy's library import directory", root='${config.library_import_dir}', **kwd)[source]¶

get_prefix()[source]¶

get_scheme()[source]¶: Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

class galaxy.files.sources.galaxy.UserLibraryImportFilesSource(label='Library User Import Directory', doc="Galaxy's user library import directory", root='${config.user_library_import_dir}/${user.email}', **kwd)[source]¶

Bases: PosixFilesSource

plugin_type: ClassVar[str] = 'gxuserimport'¶

__init__(label='Library User Import Directory', doc="Galaxy's user library import directory", root='${config.user_library_import_dir}/${user.email}', **kwd)[source]¶

get_prefix()[source]¶

get_scheme()[source]¶: Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

galaxy.files.sources.googlecloudstorage module¶

class galaxy.files.sources.googlecloudstorage.GoogleCloudStorageFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'googlecloudstorage'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs-gcsfs'¶

galaxy.files.sources.googledrive module¶

class galaxy.files.sources.googledrive.GoogleDriveFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'googledrive'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs.googledrivefs'¶

galaxy.files.sources.onedata module¶

class galaxy.files.sources.onedata.OneDataFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'onedata'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs-onedatafs'¶

galaxy.files.sources.posix module¶

class galaxy.files.sources.posix.PosixFilesSource(**kwd)[source]¶

Bases: BaseFilesSource

plugin_type: ClassVar[str] = 'posix'¶

__init__(**kwd)[source]¶

galaxy.files.sources.s3 module¶

class galaxy.files.sources.s3.S3FilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 's3'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs-s3fs'¶

galaxy.files.sources.s3fs module¶

class galaxy.files.sources.s3fs.S3FsFilesSource(**kwd)[source]¶

Bases: BaseFilesSource

plugin_type: ClassVar[str] = 's3fs'¶

__init__(**kwd)[source]¶

galaxy.files.sources.ssh module¶

class galaxy.files.sources.ssh.SshFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'ssh'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs.sshfs'¶

galaxy.files.sources.webdav module¶

class galaxy.files.sources.webdav.WebDavFilesSource(**kwd)[source]¶

Bases: PyFilesystem2FilesSource

plugin_type: ClassVar[str] = 'webdav'¶

required_module: ClassVar[Optional[Type[FS]]] = None¶

required_package: ClassVar[str] = 'fs.webdavfs'¶