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 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: 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.

user_has_access(user_context)bool[source]

Return a boolean indicating if the user can access the FileSource.

property user_context_required
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.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.

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'