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add cloud storage support for annotations #2512

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merged 1 commit into from
Apr 21, 2022

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bkmartinjr
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@bkmartinjr bkmartinjr commented Apr 14, 2022

This PR is a re-codification of #2501, resolving a number of issues with that PR. Many thanks to @arogozhnikov for the idea and draft PR.

Reviewers:
Functional: @seve
Readability: @seve


Changes

  • Port gene set and label annotation read/write routes to use DataLocator and the underlying fsspec package.
  • In support of this, add a couple of new API surfaces to DataLocator
  • Incorporate a couple of minor bug fixes noted in the original PR (eg, missing argument in annotations.py:write_gene_sets())
  • Reformatting to current conventions

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codecov bot commented Apr 14, 2022

Codecov Report

Merging #2512 (ea6a4b9) into main (002c9a5) will increase coverage by 0.02%.
The diff coverage is 50.94%.

@@            Coverage Diff             @@
##             main    #2512      +/-   ##
==========================================
+ Coverage   71.61%   71.64%   +0.02%     
==========================================
  Files          94       94              
  Lines        6454     6464      +10     
  Branches      739      738       -1     
==========================================
+ Hits         4622     4631       +9     
- Misses       1756     1757       +1     
  Partials       76       76              
Flag Coverage Δ
frontend 71.64% <50.94%> (+0.02%) ⬆️
javascript 71.64% <50.94%> (+0.02%) ⬆️
smokeTest ?
smokeTestAnnotations ?
unitTest 71.64% <50.94%> (+0.02%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
server/common/annotations/annotations.py 63.82% <ø> (ø)
server/common/annotations/local_file_csv.py 51.41% <47.91%> (+1.41%) ⬆️
server/common/utils/data_locator.py 70.00% <80.00%> (+1.46%) ⬆️

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@bkmartinjr bkmartinjr requested a review from seve April 14, 2022 01:07
@bkmartinjr bkmartinjr marked this pull request as ready for review April 14, 2022 01:10
@bkmartinjr bkmartinjr merged commit de44739 into main Apr 21, 2022
@bkmartinjr bkmartinjr deleted the bkmartinjr/annotations-locator branch April 21, 2022 01:18
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2 participants