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NCATS-Tangerine / beacon-aggregator

A web service that operates over the Beacon network to provide a single software interface over the all the Beacons
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Create a simple command line client #86

Closed cmungall closed 5 years ago

cmungall commented 5 years ago

This would be useful for ad-hoc exploration. The swagger UI is nice but involves a lot of cut paste.

I am thinking something very simple, no-frills

e.g

kba concept $conceptId

not sure how best to deal with async. The CLI could simply be blocking.

$ kba concept $conceptId
Response: queryId 1234
$ kba ping
Response: last queryId = 1234
No results yet
$ kba ping
Response: last queryId = 1234
One result from foo-beacon
{....}
RichardBruskiewich commented 5 years ago

Lance did start a discussion with me about this. This seems to be a 2 step development activity:

  1. Code a clean (python) wrapper library accessing KBA. Such a library would also facilitate Jupyter notebook (hence, workflow integration) of knowledge beacon.s
  2. Code a CLI using that library.
cmungall commented 5 years ago

I see you swagger codegenned the main KB API

You could also omit 1, direct coding via the requests library and passing in parameters as dicts is often fine. YMMV

RichardBruskiewich commented 5 years ago

@cmungall yes, @lhannest started working on a generic beacon wrapper here. Lance, where do we sit with that (in this repo's code base)?

lhannest commented 5 years ago

@RichardBruskiewich It's finished and ready for use. Maybe a CLI should be added to it as well? It's pretty easy with the click library.

But yes, I think this is a good idea. I would make the aggregator CLI client blocking, but show a progress bar.

RichardBruskiewich commented 5 years ago

progress bar helpful, like the download kind of progress bars (hard to figure out, though, what to provide as a metric of progress in the software....) Maybe, add an optional "timeout" parameter, in case one wants to abort. Also, time taken for a KBA query is probably a function of page size requested (sometimes, page number too?)

cmungall commented 5 years ago

+1

On 9 Nov 2018, at 8:32, Lance Hannestad wrote:

@RichardBruskiewich It's finished and ready for use. Maybe a CLI should be added to it as well? It's pretty easy with the click library.

But yes, I think this is a good idea. I would make the aggregator client blocking, but show a progress bar.

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lhannest commented 5 years ago

https://pypi.org/project/kba/

https://github.com/NCATS-Tangerine/beacon-aggregator-client#command-line-interface