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take us up through expected auto RDS updates #4391

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merged 7 commits into from Aug 9, 2021

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denis-yuen
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@denis-yuen denis-yuen commented Aug 5, 2021

this is newer than what aws rds is running (11.10) , companion to #4388

this maintains performance as seen with 11.8 and with JDBC 42.2.19 but this is with JDBC 42.2.23

Note that "Auto minor version upgrade" is on and will automatically take us to 11.12 at some point anyway

pgjdbc/pgjdbc#2180 explains the pain we ran into with JDBC 42.2.21 but doesn't explain the full problem with postgres 12/13

background benchmarking at https://app.slack.com/archives/CEGMXHBHT/p1628280502020200

@denis-yuen denis-yuen self-assigned this Aug 5, 2021
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codecov bot commented Aug 5, 2021

Codecov Report

Merging #4391 (5cde15d) into develop (3bef9b1) will increase coverage by 0.03%.
The diff coverage is n/a.

Impacted file tree graph

@@              Coverage Diff              @@
##             develop    #4391      +/-   ##
=============================================
+ Coverage      69.12%   69.16%   +0.03%     
  Complexity      3661     3661              
=============================================
  Files            266      266              
  Lines          15096    15096              
  Branches        1647     1647              
=============================================
+ Hits           10435    10441       +6     
+ Misses          3890     3884       -6     
  Partials         771      771              
Flag Coverage Δ
integrationtests 57.45% <ø> (ø)
languageparsingtests 0.58% <ø> (ø)
toolintegrationtests 30.39% <ø> (ø)
workflowintegrationtests 42.86% <ø> (+0.03%) ⬆️

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

Impacted Files Coverage Δ
...re/webservice/helpers/BitBucketSourceCodeRepo.java 82.92% <0.00%> (+3.65%) ⬆️

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denis-yuen commented Aug 5, 2021

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 374.108 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.433 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.764 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.058 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 27.407 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 31.867 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 35.897 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 21.589 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 32.491 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 36.593 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 26.647 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.476 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.993 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.156 s
[INFO] Running io.dockstore.webservice.ServiceIT

Weird, 11.12 is halfway better than develop but worse than 11.8
I hope we're not dealing with two issues

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[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 348.652 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.94 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.25 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.295 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.455 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.863 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 33.477 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 20.31 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.345 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 33.566 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.948 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 21.268 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.207 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.734 s

11.10
sigh

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denis-yuen commented Aug 5, 2021

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 357.133 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 25.532 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 22.917 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.726 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 28.022 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 32.592 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 34.383 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 20.936 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 30.647 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 33.66 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 24.127 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 21.509 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.188 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 23.752 s
[INFO] Running io.dockstore.webservice.ServiceIT

11.9

FFS

with JDBC 23

[INFO] Tests run: 13, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 160.501 s - in io.dockstore.webservice.WebhookIT
[INFO] testGithubDirDockstoreYml(io.dockstore.webservice.WebhookIT)  Time elapsed: 11.03 s
[INFO] testTestParameterPaths(io.dockstore.webservice.WebhookIT)  Time elapsed: 8.678 s
[INFO] testDescriptorChange(io.dockstore.webservice.WebhookIT)  Time elapsed: 9.156 s
[INFO] testTools(io.dockstore.webservice.WebhookIT)  Time elapsed: 11.865 s
[INFO] testGitHubReleaseNoWorkflowOnDockstore(io.dockstore.webservice.WebhookIT)  Time elapsed: 14.579 s
[INFO] testWorkflowMigration(io.dockstore.webservice.WebhookIT)  Time elapsed: 19.857 s
[INFO] testGitHubReleaseNoWorkflowOnDockstoreNoUser(io.dockstore.webservice.WebhookIT)  Time elapsed: 7.4 s
[INFO] testDockstoreYmlFilters(io.dockstore.webservice.WebhookIT)  Time elapsed: 15.959 s
[INFO] testDockstoreYmlAuthors(io.dockstore.webservice.WebhookIT)  Time elapsed: 18.282 s
[INFO] testInvalidDockstoreYmlFiles(io.dockstore.webservice.WebhookIT)  Time elapsed: 11.212 s
[INFO] testManualRefreshWorkflowWithGitHubApp(io.dockstore.webservice.WebhookIT)  Time elapsed: 8.154 s
[INFO] testDockstoreYmlPublish(io.dockstore.webservice.WebhookIT)  Time elapsed: 9.066 s
[INFO] testDeleteDefaultWorkflowVersion(io.dockstore.webservice.WebhookIT)  Time elapsed: 9.073 s

@denis-yuen denis-yuen changed the title test postgres newer postgres 11 as well take us up through expected auto RDS updates Aug 6, 2021
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think bitbucket is having issues (workflow-integration-tests)

@denis-yuen denis-yuen marked this pull request as ready for review August 6, 2021 20:10
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We'll need to reset dev back to 11.x. PG probably doesn't allow that; we may need to just spin up a new instance of RDS.

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sonarcloud bot commented Aug 6, 2021

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
0.0% 0.0% Duplication

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We'll need to reset dev back to 11.x. PG probably doesn't allow that; we may need to just spin up a new instance of RDS.

Depends on whether we figure this out and are still stuck on postgres 11 when dockstore 1.12 comes out.

One known unknown, is the testing slowdown actually seen in real life on AWS RDS or is https://ucsc-cgl.atlassian.net/browse/DOCK-1854 just due to the jdbc driver problem?

@denis-yuen denis-yuen merged commit 6f701da into develop Aug 9, 2021
@denis-yuen denis-yuen deleted the feature/what_about_newer_11 branch August 9, 2021 15:33
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One known unknown, is the testing slowdown actually seen in real life on AWS RDS or is https://ucsc-cgl.atlassian.net/browse/DOCK-1854 just due to the jdbc driver problem?

#4347 was only seen locally. I think the verification of #4338 shows there was no regression in prod.

I'll try #4347 again using these changes to see if it fixes it.

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4 participants