update import logic to update OmicsProcessing record

[aclum]

The import automation should make a DataObject record and add is to has_output on the NucelotideSequencing record. The NucelotideSequencing record will be part of the import csv file. I believe nmdc_automation/import_automation/activity_mapper.py is where this needs to be updated. It needs to do this instead of the current behavior which is to make a ReadQc record without an input data object.

We talked about doing this with a queries:run command since the NucelotideSequencing record will already exist.

When updating for this issue, also address:

• berkeley issue with DataObject records from import_automation #267
• import automation generating mongo keys for which values are None or an empty list #259

[ssarrafan]

@mbthornton-lbl @scanon @aclum can this one be closed this sprint?

[aclum]

Work has not started on this, moving to the next sprint. This will be worked on once #251 is done.

[ssarrafan]

251 is closed. PR being reviewed now. Hopefully it can be closed by Friday?