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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.

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'