Convert_json_to_baton_objs doesn't convert correctly, as replicas are not within the output

[irinaColgiu]

For some reason, the output of the following doesn't contain any information about the replicas:

json_ob = '{"collection": "/seq/16006", "data_object": "16006_5.cram", "replicate": [{"checksum": "b92764c24d3346231fd8ef9fdb599df3", "number": 0, "valid": true}, {"checksum": "b92764c24d3346231fd8ef9fdb599df3", "number": 2, "valid": true}]}'
print("Converted json: %s" % convert_json_to_baton_objs(json_ob))

OUTPUT:

[<<class 'baton.models.DataObject'> object at 140404288519248: { _access_controls: None, metadata: None, path: /seq/16006/16006_5.cram, replicas: None }>]

[colin-nolan]

The first issue is with the example. The string assigned to json_ob is not valid baton JSON: baton uses the property replicates, not replicate (I think the property should be replicas but I digress...).

Once that has been corrected for however, there is a problem with the baton Python library as it assumes that timestamp information is given if along with the replica information:
https://github.com/wtsi-hgi/python-baton-wrapper/blob/a97af16b1435c8693c48aa6dfcc889e6c916f933/baton/_baton/json.py#L195
i.e. it is expecting baton-list --replicate --timestamp to be used.

The reason why timestamp information is being required here is because baton uses a questionable representation of replicas, in which their information is not contained in a single object: wtsi-npg/baton#146.

I have put an issue in for this on the baton wrapper:
wtsi-hgi/python-baton-wrapper#38

[colin-nolan]

The issue with the baton wrapper has been fixed :).