Add new command: annotate

[hrshdhgd]

Fixes #280

[matentzn]

Sorry meant to comment before, not Approve, just make sure you read the comments. Great job :)

[matentzn]

The problem with this is that if have have to creators in the metadata and want to add a third one.. it wont work. Would it make sense to make the method strictly additive for multi valued metadata? Maybe not. Do you have an opinion on this? Maybe it is correct the way it is..

[hrshdhgd]

Good catch! We will have to think about it. When is it additive and when is it replacement? Should there be a flag?

[hrshdhgd]

So what I have implemented now is if a slot to be annotated is multivalued , add new values to the list. But what if the entire slot value needs to be changed? How does the user indicate that?

Possible solutions:

• create a new method remove_annotation which does exactly the opposite of annotate? It seems inconvenient in my opinion.
• Have a keyword in params called remove which will be handled separately and would look like this:

params = {
            "mapping_set_id": ("http://w3id.org/my/mapping.sssom.tsv",),
            "mapping_set_version": ("2021-01-01",),
            "creator_id": ("orcid:2345"),
            "remove": { "creator_id": "orcid:1234" }
        }

Basically , remove will be a dict with key = slot to be edited and value will be the one to be removed.

• Have a --remove CLI option that lists the metadata that needs to be removed. The only allowed values here would be MULTIVALUED_SLOTS or maybe all slots)

[matentzn]

What about a boolean flag --replace-multivalued which defaults to false, and if it is true, it will remove any existing values from a multivalued value?

[hrshdhgd]

But what if the users want to retain some of the contents of the list and add new stuff? They'll have to type the ones they want again. If that's the case, the first solution would have worked and was a simple one too.

[hrshdhgd]

For now I've implemented replace_multivalued. I've added a TODO comment next to the click option. If we can think of a cleaner way to do this, we can always go back and improve the code.

[matentzn]

I think this is fine. good one :)

[matentzn]

This looks great! THANK you! The only tiny thing that is slightly unsatisfactory, is the fact that the sanitation of the kwars happens during annotate_file, but nothing keeps an API user to pass a broken "meta" dict into augment_metadata method.

[hrshdhgd]

Added a function are_params_slots that checks for slots in both annotate_file and augment_metadata