Warning

This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

galaxy.files.sources package

class galaxy.files.sources.FilesSource[source]

Bases: object

abstract get_uri_root()[source]

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

abstract get_scheme()[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 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: galaxy.files.sources.FilesSource

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.

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]
write_from(target_path, native_path, user_context=None)[source]

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

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

Submodules

galaxy.files.sources.dropbox module

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

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)[source]

Bases: galaxy.files.sources.posix.PosixFilesSource

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

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

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: 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)[source]

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

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: 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)[source]

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

get_prefix()[source]
get_scheme()[source]

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)[source]

Bases: galaxy.files.sources.BaseFilesSource

plugin_type = 'posix'
__init__(**kwd)[source]

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

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

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

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.s3 module

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

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)[source]

Bases: galaxy.files.sources._pyfilesystem2.PyFilesystem2FilesSource

plugin_type = 'webdav'
required_module = None
required_package = 'fs.webdavfs'