Metadata

iRODS offers metadata as key, value, units triplets. The type is always string. Below we show how to create an ibridges.Metadata object from a dataobject or collection.

The Metadata object

    from ibridges.interactive import interactive_auth
    from ibridges import Metadata
    from ibridges import IrodsPath

session = interactive_auth()
    obj = IrodsPath(session, "~", "dataobj_name").dataobject
    meta = Metadata(obj)

With the object meta we can now access and manipulate the metadata of the data object.

Add, set and delete metadata

Add metadata to a collection or data object:
meta.add('NewKey', 'NewValue', 'NewUnit') print(meta)
- You always need to provide a key and a value, the unit is optional and can be left out.
- You can have several metadata entries with the same key but different values and units, i.e. metadata keys are not unique in iRODS but the combination of key, value and unit must be unique.
Set metadata:
meta.set('ExistingKey', 'Value', 'Unit')
The set function is a special function. It sets all metadata items with the key ExistingKey to the value and unit. It is the implementation of the icommands imeta set.

Delete metadata of a collection or data object:

meta.delete('NewKey', 'NewValue', 'NewUnit')

Export Metadata

The function Metadata.to_dict will provide you with a python dictionary containing the user-defined metadata:

meta.to_dict()

{
'name': '<obj_name>',
'irods_id': 24490075,
'checksum': 'sha2:XGiECYZOtUfP9lnCGyZaBBkBGLaJJw1p6eoc0GxLeKU=',
'metadata': [('Key', 'Value', 'Unit'), ('Key', 'Value', 'Unit1')]
}

The dictionary contains the name of the data object or collection and its iRODS identifier. For data objects the checksum is also listed under the key checksum. The checksum is not calculated, but extracted from the iRODS database.

The user-defined metadata can be accessed with the key metadata.

Export metadata of all member of a collection

Above we showed how to export the metadata of one collection or data object. In case you want to export metadata of all memebers of a collection you can use:

from ibridges.export_metadata import export_metadata_to_dict

coll = IrodsPath(session, <coll_path>).collection
meta = Metadata(coll)
export_metadata_to_dict(meta, session)

The resulting dictionary is built like above and contains two additional keys subcollections and dataobjects.

Under subcollections we will find the extracted metadata of all subcollection and under dataobjects the extracted metadata for all data objects. Those extracted metadata are also represented by dictionaries as shown above, they only contain one extra key rel_path which denotes the path relative to the collection which we gave as input to the function.

{
'ibridges_metadata_version': 1.0,
'name': 'Demo',
'irods_id': 24484787,
'metadata': [('Key', 'very_important', None)],
'subcollections': [
    {
        'name': 'subDemo',
        'irods_id': 24490064,
        'rel_path': 'Demo',
        'metadata': []
        },
    {
        'name': 'my_books',
        'irods_id': 24502538,
        'rel_path': 'my_books',
        'metadata': []}
    ],
'dataobjects': [
    {
        'name': 'AliceInWonderland.txt',
        'irods_id': 24484789,
        'checksum': 'sha2:TQzOrHuw1qRQ6zh8xm5GEuVKGjs22STdgQCdezv8LY4=',
        'rel_path': 'my_books/AliceInWonderland.txt',
        'metadata': [('author', 'Lewis Carroll', None)]
        }
    ]
}