Print summary without output

Hi All,

Is there a way to override the verbose flag so the results always print to the terminal?

Specifically, I have an artifact that I’d like to pull about 5 lines of information out of automagically :sparkles: and print to the command line.

I’d prefer not to write a visualizer because (a) it’s intimidating and (b) I’m so close to something workable and I think it will add another couple weeks. I also find it really useful, essentially secondary help documentation and pulling it into a visualizer is just inconvenient :/.

However, you can’t register a function that doesn’t have any outputs, so it may just be disallowed.

Thanks,
Justine

Hey @jwdebelius, sounds like you’re getting close, woot!

Unfortunately we don’t have any kind of option to support this (mostly because that behavior presents challenges in an interface-agnostic world).

One option is to define Yet-Another-Type-And-Format (:tm:) and a transformer from that format -> qiime2.Metadata, then you get a “viz for free” by running this new output through metadata tabulate.

You might not need a new format, either, especially if you have defined a new format as part of your work. You could potentially just add this “metadata” as part of a directory format. We do something similar in q2-types:

Its a little hard to follow what is going on there because there is some inheritance, but basically we just tack on a few extra file formats into the Directory Format and call it a day.

It all kinda depends though, so let’s keep the discussion rolling!

Hi @thermokarst,

I’m writing documentation and Ive gotten it to run reasonably well, so next is the bigger integration test, and then… :crossed_fingers:.

It works with metadata tabulate, so that’s not an issue. (I have defined so many new transformers… I think Im testing 16 RN?)

I just want to be able to pull out 4 specific parameters to print to the … somewhere. Because this set of comamnds probably prefers to be run on a server. It’s possibly on my macbook with 2 cores, but its relatively slow :woman_shrugging: .

Because the values have to match an arbitrary set of upstream values and its assumed you’re getting a pre-formatted set. At the moment I’ll just recommend checking the provenance for the values and maybe re-visit making it more flexible in. the future.

So, if there was some magic that would, like, let me do something like qiime tools import --show-importable-types but accept an additional argument to print it would have been nice.

Best,
Justine