contexts parameter as a list of str

[antgonza]

It would be nice if all methods that require a context could match that requirement and receive a list of str vs just a str.

• Single context:

  
  ? redbiom.fetch.taxon_descendents
  Signature: redbiom.fetch.taxon_descendents(context, taxon, get=None)
  Docstring:
  Get tips associated with a taxon

Parameters

context : str The context to operate in taxon : str The taxon to search for get : function, optional A get method

- List of contexts: Help says that it gets multiple context but when testing passing a list or looping over it and passing individual contexts yield different results

? redbiom.util.ids_from Signature: redbiom.util.ids_from(it, exact, axis, contexts) Docstring: Grab samples from an iterable of IDs

Parameters

it : iteraable of str The IDs to search for exact : boolean If True, compute the intersection of results per context. If False, compute the union of results per context. axis : {'feature', 'sample'} The axis to operate over. contexts : list of str The contexts to search in

[wasade]

I disagree, this would complicate the API as consumers of the methods would then need to disentangle what identifiers are associated with the respective context. I'm not finding any instance of the redbiom codebase that utilizes list of context either...

@antgonza: "List of contexts: Help says that it gets multiple context but when testing passing a list or looping over it and passing individual contexts yield different results" -> that sounds surprising, do you have an example?

[antgonza]

• "testing passing a list": just did a few tests and could reproduce; should have added the examples to be sure ... anyway
• "disentangle identifiers associated with context": That makes sense, however, there are some cases that we don't care about that relationship (like in the code in Qiita) and the reason that you pass a list, and if the users cares they can pass a str or single element list.

[wasade]

What's being proposed is a change to a very large portion of the API. This will require a substantial and likely complex pull request. The motivation for this request is to remove simple for loops in Qiita. Is that assessment accurate?

I'm unable to reproduce the problem eluded too (see below). Would it be possible to provide an example of the problem encountered?

>>> import redbiom.fetch
>>> import redbiom.util
>>> context_a = 'Deblur-Illumina-16S-V1-2-150nt-780653'
>>> context_b = 'Deblur-Illumina-16S-V45-100nt-fbc5b2'
>>> context_a_sample_ids = redbiom.fetch.samples_in_context(context_a, unambiguous=True)
>>> context_b_sample_ids = redbiom.fetch.samples_in_context(context_b, unambiguous=True)
>>> observed_a = redbiom.util.ids_from(context_a_sample_ids, False, 'sample', [context_a])
>>> observed_b = redbiom.util.ids_from(context_b_sample_ids, False, 'sample', [context_b])
>>> observed_combined = redbiom.util.ids_from(context_a_sample_ids | context_b_sample_ids, False, 'sample', [context_a, context_b])
>>> assert (observed_a | observed_b) == observed_combined

[wasade]

I'm going to close this as I believe the for loop satisfies the need.