iRODS paths

iRODS paths follow a certain pattern just like the local paths of different operating systems. To allow for similar path operations on iRODS paths, rather than using strings, iBridges offers an class with similar pathlib-like functionality.

Why prefer `pathlib.path` and `IrodsPath` over strings?

Note

• To work with pathlib and IrodsPath is safer since it takes care of the correct concatenation of parts of the path according to the operating system and their specific setup.

• To work with pathlib and IrodsPath is more convenient since you can easily determine certain parts of a path, like parent, name and parts and easily check whether a path exists.

A complete tutorial on iRODS paths can be followed here.

IrodsPath

In iRODS the / is used as separator and all paths on an iRODS server start with /<zone_name>. Users usually have a personal home collection in iRODS: /<zone_name>/home/<user name>. Group-based iRODS instances like Yoda will give you access to a group home collection: /<zone_name>/home/<group name>

iBridges implements a selection of functions which are comparable to their counterparts in pathlib.

In the Installation we showed you how to set a default home, which we can address by ~ in IrodsPath.

from ibridges import IrodsPath
home = IrodsPath(session, '~')
print(home)

This will give you the value which you set in the irods_environment.json. If you did not set any irods_home the home will default to /<zone_name>/home/<user name>.

Note, that we still need to verify whether the path exists on the iRODS server.

home.collection_exists()

Below we present a selection of possible iRODS path manipulations:

irods_path = IrodsPath(session, session.home)
print(f'Extend {irods_path}:', irods_path.joinpath('new_collection'))
print(f'{irods_path} exists:', irods_path.exists())
print(f'{irods_path} is collection:', irods_path.collection_exists())
print(f'{irods_path} is data object:', irods_path.dataobject_exists())
print(f'{irods_path} has parts: {irods_path.parts}')

Concatenating iRODS paths and local paths

In data transfers often iRODS collections that correspond to a local folder have to be created. Below we show how you can create an iRODS collection with the same name as an arbitrary local folder.

We create the local path that points to a folder:

from pathlib import Path
path  = Path.home().joinpath('new_dir')
print(path)

We will create new_dir in our iRODS home collection:

from ibridges import IrodsPath

name = path.name
irods_home = IrodsPath(session, '~')
new_irods_coll_path = irods_home.joinpath(name)
print(new_irods_coll_path)

coll = IrodsPath.create_collection(session, new_irods_coll_path)