iRODS Search

iBridges offers an easy way to search for data. You can pass a combination of path, metadata keys and values and checksum. The output will be a list of dictionaries, one dictionary for each found item, which contain information where to find the item on the iRODS server.

Search data by Path

In the example below we search for a data object by its path. The path can be an IrodsPath or a string:

from ibridges import search_data
    search_data(session, path=IrodsPath(session, "dataobj_name"))

The result is a list of dictionaries.

[{'COLL_NAME': '/you/irods/home',
'DATA_NAME': 'dataobj_name',
'D_DATA_CHECKSUM': 'sha2:XGiECYZOtUfP9lnCGyZaBBkBGLaJJw1p6eoc0GxLeKU='}]

For collections the dictionary only contains the entry COLL_NAME.

To find all subcollections and dataobjects in a collection use the % as wildcard:

search_data(session, path=IrodsPath(session, "subcoll/%"))

Search data by metadata

We can also use the metadata we generated above to search for data. We need to create a python dictionary which contains the metadata keys ad their values. The values are again optional.

key_vals = {'key': 'value'}
search_data(session, key_vals = key_vals)
key_vals = {'key': ''}
search_data(session, key_vals = key_vals)

Use the % as a wild card again to match any combination of characters.

Search data by checksum

The search by checksum is handy to find duplicate data. in iBridges we always create checksums when data is uploaded. The checksum is unique for the file we uploaded and can be used to identify the files. E.g. when you uploaded the same file twice, once as file.txt and once as file1.txt you can find the two duplicates by their checksum:

obj = IrodsPath(session, "~", "dataobj_name").dataobject
search_data(session, checksum = obj.checksum)