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galaxy.files.sources package

class galaxy.files.sources.FilesSource

Bases: object

abstract get_uri_root()

Return a prefix for the root (e.g. gxfiles://prefix/).

abstract get_scheme()

Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

abstract get_writable()

Return a boolean indicating if this target is writable.

abstract list(source_path='/', recursive=False, user_context=None)

Return dictionary of ‘Directory’s and ‘File’s.

abstract realize_to(source_path, native_path, user_context=None)

Realize source path (relative to uri root) to local file system path.

write_from(target_path, native_path, user_context=None)

Write file at native path to target_path (relative to uri root).

abstract to_dict(for_serialization=False, user_context=None)

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

Bases: galaxy.files.sources.FilesSource

get_prefix()

get_scheme()

Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

get_writable()

Return a boolean indicating if this target is writable.

get_uri_root()

Return a prefix for the root (e.g. gxfiles://prefix/).

uri_from_path(path)

to_dict(for_serialization=False, user_context=None)

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)

write_from(target_path, native_path, user_context=None)

Write file at native path to target_path (relative to uri root).

galaxy.files.sources.uri_join(*args)

galaxy.files.sources.slash_join(*args)

Submodules

galaxy.files.sources.dropbox module

class galaxy.files.sources.dropbox.DropboxFilesSource(**kwd)

Bases: galaxy.files.sources._pyfilesystem2.PyFilesystem2FilesSource

plugin_type = 'dropbox'

required_module = None

required_package = 'fs.dropboxfs'

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)

Bases: galaxy.files.sources.posix.PosixFilesSource

plugin_type = 'gxftp'

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

Initialize self. See help(type(self)) for accurate signature.

get_prefix()

get_scheme()

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)

Bases: galaxy.files.sources.posix.PosixFilesSource

plugin_type = 'gximport'

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

Initialize self. See help(type(self)) for accurate signature.

get_prefix()

get_scheme()

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)

Bases: galaxy.files.sources.posix.PosixFilesSource

plugin_type = 'gxuserimport'

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

Initialize self. See help(type(self)) for accurate signature.

get_prefix()

get_scheme()

Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path).

galaxy.files.sources.posix module

class galaxy.files.sources.posix.PosixFilesSource(**kwd)

Bases: galaxy.files.sources.BaseFilesSource

plugin_type = 'posix'

__init__(**kwd)

Initialize self. See help(type(self)) for accurate signature.

list(path='/', recursive=True, user_context=None)

Return dictionary of ‘Directory’s and ‘File’s.

realize_to(source_path, native_path, user_context=None)

Realize source path (relative to uri root) to local file system path.

galaxy.files.sources.s3 module

class galaxy.files.sources.s3.S3FilesSource(**kwd)

Bases: galaxy.files.sources._pyfilesystem2.PyFilesystem2FilesSource

plugin_type = 's3'

required_module = None

required_package = 'fs-s3fs'

galaxy.files.sources.webdav module

class galaxy.files.sources.webdav.WebDavFilesSource(**kwd)

Bases: galaxy.files.sources._pyfilesystem2.PyFilesystem2FilesSource

plugin_type = 'webdav'

required_module = None

required_package = 'fs.webdavfs'