CLI interface to add/edit embedded annotations

[ptgolden]

We've been trying to speed up the mondo pipeline by replacing our use of sssom-py with sssom-java (#14 was a big part of this!). One of last things I've been trying to figure out is a way to add embedded annotations to a SSSOM file. sssom-py has an annotate command which accepts a series of flags covering all the standard SSSOM metadata (e.g. --mappings <mappings>, --creator_id <creator_id>, --mapping_tool <mapping_tool>. That doesn't really seem appropriate here.

Maybe this could work similar to the existing merging metadata feature, except that the metadata merged could come from a YAML file rather than a mapping set. Although it would be nice to annotate via command line parameters.

(Also, maybe this is already possible and I'm missing something!)

[gouttegd]

Maybe this could work similar to the existing merging metadata feature, except that the metadata merged could come from a YAML file rather than a mapping set.

This is exactly how it can be done. :) Use the --output-metadata option to specify the YAML file from which to get the metadata to use for the output set.

(Not to be confused with --metadata-output, which instructs the command to write the metadata to a separate file. Apologies for the poorly chosen option names!)

Although it would be nice to annotate via command line parameters.

I agree. Not keen on adding one option for every single metadata slot, but a single option taking a key-value pair (e.g. --annotate "mapping_tool=my mapping tool"), to be repeated as many times as needed, would be nice indeed.

[ptgolden]

Ah! Thank you. You were spot on-- I was getting it confused with the --metadata-output option.

[gouttegd]

The next version will have a --annotate NAME=VALUE option to assign metadata from the command line without having to use an intermediate file.