Missing actions in modifications_long.tsv

[bmeluch]

In rows where the attributes "expected_value" or "preferred_unit" are being modified, the "action" column is left blank. What modification is supposed to be happening here? @pkalita-lbl @turbomam do you remember what the intent was?

Examples https://github.com/microbiomedata/submission-schema/blob/0b9413915f63bd7fa9be70f32061db49dc422009/sheets_and_friends/tsv_in/modifications_long.tsv#L94

https://github.com/microbiomedata/submission-schema/blob/0b9413915f63bd7fa9be70f32061db49dc422009/sheets_and_friends/tsv_in/modifications_long.tsv#L222

[pkalita-lbl]

I don't know enough of the history here to know if that was intentional or not, but in actuality those rows currently do nothing.

The logs generated by sheets_and_friends as it processes the modifications_log.tsv file are quite noisy (noisy but also cryptic 🙃), but you can see here on line 3161 of the output of make all: https://github.com/microbiomedata/submission-schema/actions/runs/8827491751/job/24234818535#step:7:3162 It says it's processing the slot extreme_event, there is no action (nan), the target is expected_value and the value is date, string. The next line down (3162) says no action for nan indicating that it didn't do anything for that row (source).

Because there are no LinkML metamodel elements called expected_value or preferred_unit (unlike, say, range or description used in other rows), if I had to make a guess I would say those rows were maybe supposed to have the action replace_annotation (source).

So I think two valid paths forward are:

1. Add replace_annotation as the action to those rows
2. Remove the rows entirely

Maybe @turbomam could chime in on his preference

[turbomam]

Yeah, it looks like I was just confusing the capabilities of a couple of different pieces of software, like schemasheets, sheets_and_friends and yq. expected_value and preferred_unit are annotation keys, not LinkML features, like @pkalita-lbl said. Even if we did add those, I'm not sure they would show up in the Submission Portal interface. I'll look though that now.

[turbomam]

ammonium_nitrogen has an expected_value annotation of 'measurement value', but that doesn't show up when you double-click on the 'ammonium nitrogen' column header on a SoilInterface Submission Portal screen.

So I think that annotations aren't used in this project. I think we can just remove those TSV rows.

[turbomam]

There is a replace_annotation action in the sheets_and_friends action vocabulary, but I don't think we have used it in this repo.

[ssarrafan]

@turbomam @bmeluch not really sure if this is active or not? Can you please close or move to the next sprint or to the backlog?