Replace snapshot and remove workaround (#5229) #5313

nadove-ucsc · 2023-06-13T23:04:40Z

Connected issues: #5229

Followup PR to remove the initial workaround

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nadove-ucsc · 2023-06-13T23:09:39Z

Operator: only anvilprod needs a https://github.com/DataBiosphere/azul/labels/reindex for this PR

coveralls · 2023-06-13T23:24:32Z

coverage: 83.872% (-0.005%) from 83.877% when pulling efdec9f on issues/nadove-ucsc/5229-update-snapshot into 37bcbc2 on develop.

codecov · 2023-06-13T23:28:13Z

Codecov Report

Merging #5313 (efdec9f) into develop (37bcbc2) will decrease coverage by 0.01%.
The diff coverage is 0.00%.

@@             Coverage Diff             @@
##           develop    #5313      +/-   ##
===========================================
- Coverage    83.85%   83.85%   -0.01%     
===========================================
  Files          152      152              
  Lines        18539    18540       +1     
===========================================
  Hits         15546    15546              
- Misses        2993     2994       +1

Impacted Files	Coverage Δ
test/integration_test.py	`0.00% <0.00%> (ø)`

hannes-ucsc · 2023-06-15T05:21:39Z

test/integration_test.py

-                    # false positives in the current snapshots
-                    # (https://github.com/DataBiosphere/azul/issues/5229)
+                    is_supplementary = one(set.union(*(
+                        set(always_iterable(file['is_supplementary']))


Why are the inner sets needed? Wouldn't set(chain.from_iterable(… be a better choice here?

deployments/anvilprod/environment.py

hannes-ucsc

This comment is easy to miss. It would be better to roll it into the checklist.

nadove-ucsc · 2023-06-16T01:18:15Z

Second fixup addresses a failure that occurred with a primary bundle that lacked any files.

hannes-ucsc

Considering this and this, I think we may need to slow down a bit and prioritize the stability of our main deployments and the reliability of our tests.

test/integration_test.py

nadove-ucsc added the reindex:dev [process] PR requires reindexing dev label Jun 13, 2023

github-actions bot added the orange [process] Done by the Azul team label Jun 13, 2023

nadove-ucsc force-pushed the issues/nadove-ucsc/5229-update-snapshot branch from e780e73 to 014fc17 Compare June 13, 2023 23:54

hannes-ucsc mentioned this pull request Jun 14, 2023

Orphaned files in AnVIL snapshots #4654

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nadove-ucsc requested a review from achave11-ucsc June 14, 2023 01:36

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achave11-ucsc marked this pull request as ready for review June 14, 2023 16:40

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nadove-ucsc dismissed achave11-ucsc’s stale review via 36db500 June 15, 2023 23:36

nadove-ucsc force-pushed the issues/nadove-ucsc/5229-update-snapshot branch from 014fc17 to 36db500 Compare June 15, 2023 23:36

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hannes-ucsc added 2 reviews [process] Lead requested changes twice and removed 1 review [process] Lead requested changes once labels Jun 16, 2023

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nadove-ucsc force-pushed the issues/nadove-ucsc/5229-update-snapshot branch from e6edf7f to 8afa8c5 Compare June 16, 2023 01:53

nadove-ucsc mentioned this pull request Jun 19, 2023

Fix: IT subtests manifest and repository_files fail due to lack of files (#5168) #5305

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nadove-ucsc force-pushed the issues/nadove-ucsc/5229-update-snapshot branch 2 times, most recently from 965a71c to 61334da Compare June 20, 2023 22:00

nadove-ucsc requested a review from hannes-ucsc June 20, 2023 22:28

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hannes-ucsc force-pushed the issues/nadove-ucsc/5229-update-snapshot branch from 61334da to 0229c61 Compare June 21, 2023 02:47

hannes-ucsc approved these changes Jun 21, 2023

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hannes-ucsc assigned achave11-ucsc and unassigned hannes-ucsc Jun 21, 2023

[r] Replace snapshot and remove workaround (#5229)

efdec9f

achave11-ucsc force-pushed the issues/nadove-ucsc/5229-update-snapshot branch from 0229c61 to efdec9f Compare June 21, 2023 15:24

achave11-ucsc added the sandbox [process] Resolution is being verified in sandbox deployment label Jun 21, 2023

achave11-ucsc merged commit f1330a3 into develop Jun 21, 2023

achave11-ucsc deleted the issues/nadove-ucsc/5229-update-snapshot branch June 21, 2023 21:56

achave11-ucsc removed their assignment Jun 21, 2023

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Replace snapshot and remove workaround (#5229) #5313

Replace snapshot and remove workaround (#5229) #5313

nadove-ucsc commented Jun 13, 2023 •

edited by achave11-ucsc

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hannes-ucsc Jun 15, 2023

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Replace snapshot and remove workaround (#5229) #5313

Replace snapshot and remove workaround (#5229) #5313

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nadove-ucsc commented Jun 13, 2023 • edited by achave11-ucsc Loading

Checklist

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Author (reindex, API changes)

Author (chains)

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Author (operator tasks)

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Author (before every review)

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nadove-ucsc commented Jun 13, 2023

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nadove-ucsc commented Jun 13, 2023 •

edited by achave11-ucsc

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