WIP: Closing out a few issues

biocore / redbiom

Sample search by metadata and features

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WIP: Closing out a few issues #122

Closed wasade closed 1 year ago

wasade commented 1 year ago

Closing out a few issues

fixes #119
fixes #117
fixes #116
fixes #43
fixes #44
fixes #46
fixes #52
fixes #50
fixes #41

We also introduce a performance improvement which reduces runtime for fetching the EMP500 (qiita study 13114) by over 50%. These gains are achieved by (a) avoiding taxonomy lookup for ASVs and (b) doubling buffer sizes for key calls to reduce HTTP requests. We did not observe further reductions in runtime by increasing buffers further.

wasade commented 1 year ago

...to demonstrate #117:

$ export context=Deblur_2021.09-Illumina-16S-V4-150nt-ac8c0b
$ redbiom fetch samples --context $context --output samples.biom 11896.A2.raw
$