moved most yq commands and comments

[turbomam]

No description provided.

[pkalita-lbl]

Having a .txt file of partial commands feels a bit ummm quirky to me. Why not a shell script with the commands to run, like

#!/usr/bin/env bash

file="$1"

# ...

yq -i '(.slots.[] | select(.domain == "Activity") | .domain ) = "NamedThing"' "$file"
yq -i '(.slots.[] | select(.domain == "Agent") | .domain ) = "NamedThing"' "$file"

# Or possibly even just pipe the output of one `yq` call into the next to avoid all the in-place file writing

# ...

And then invoke it in the Makefile like:

local/with_shuttles_yq.yaml: local/with_shuttles.yaml
    assets/yq-for-shuttles.sh $@

I think having 1. a file type (.sh) that any editor understands and 2. not having slightly cryptic loops in the Makefile will be more maintainable in the long run.

[mslarae13]

this is implemented to nmdc-schema for mixs classes. Uses the same method.

Some discussion & decision is needed here. Move to discussion