8000 Feature/junit5 by denis-yuen · Pull Request #214 · dockstore/dockstore-cli · GitHub
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Merged
merged 27 commits into from
Jan 24, 2023
Merged

Feature/junit5 #214

merged 27 commits into from
Jan 24, 2023

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denis-yuen
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@denis-yuen denis-yuen commented Jan 10, 2023

Description
CLI version of the chain of PRs that ended with dockstore/dockstore#5301

There are still a couple tests that use PowerMock (seems dead, doesn't support Java 17 or JUnit 5, generally bad practice) that are more involved and will require a spin-offf PR before junit4 can be banned from the CLI as well. Also some tests for cwl launching.

One obnoxious test took forever, a reminder to check your assumptions. It was deterministically running differently on CircleCI as opposed to locally, but changing whether it failed and passed on unrelated changes. Looks like the plugin directory was being downloaded and/or cached, but only when some random tests (probably in completely other classes) had run before the test in question, whether due to distribution by the parallel tests script or some oddity due to CircleCI caching.

This is a long way of saying, check your assumptions about tests and how they're isolated from one another. Is the filesystem reset, have stdout and stderr been reset, etc. Oy.

Review Instructions
Number of tests should be the same (or more) before/after this PR
Hmmm, right now at time of comment, it looks like we go from 391 (insights) to 402 (manual count, may need wait for 24 hours for insights to update)

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-5133

Security
None known
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@denis-yuen denis-yuen self-assigned this Jan 10, 2023
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codecov bot commented Jan 10, 2023

Codecov Report

Base: 69.15% // Head: 69.44% // Increases project coverage by +0.29% 🎉

Coverage data is based on head (84497a2) compared to base (9a62930).
Patch coverage: 0.00% of modified lines in pull request are covered.

Additional details and impacted files
@@              Coverage Diff              @@
##             develop     #214      +/-   ##
=============================================
+ Coverage      69.15%   69.44%   +0.29%     
- Complexity      1022     1047      +25     
=============================================
  Files             46       47       +1     
  Lines           5936     5937       +1     
  Branches         776      776              
=============================================
+ Hits            4105     4123      +18     
+ Misses          1498     1493       -5     
+ Partials         333      321      -12     
Flag Coverage Δ
bitbuckettests 10.03% <0.00%> (-0.01%) ⬇️
confidentialtooltests 53.81% <0.00%> (+0.39%) ⬆️
confidentialworkflowtests 28.53% <0.00%> (+0.09%) ⬆️
nonconfidentialtests 32.97% <0.00%> (+0.12%) ⬆️
singularitytests 16.92% <0.00%> (-0.01%) ⬇️
unittests 8.03% <0.00%> (-0.01%) ⬇️

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

Impacted Files Coverage Δ
...o/dockstore/client/cli/nested/SingularityTest.java 0.00% <0.00%> (ø)
.../dockstore/client/cli/nested/CromwellLauncher.java 76.92% <0.00%> (-1.71%) ⬇️
.../src/main/java/io/dockstore/client/cli/Client.java 48.75% <0.00%> (-0.25%) ⬇️
...in/java/io/github/collaboratory/cwl/CWLClient.java 80.24% <0.00%> (+0.17%) ⬆️
...ain/java/io/dockstore/common/FileProvisioning.java 70.55% <0.00%> (+0.30%) ⬆️
...io/dockstore/client/cli/nested/WorkflowClient.java 74.04% <0.00%> (+0.45%) ⬆️
...ckstore/client/cli/nested/AbstractEntryClient.java 74.00% <0.00%> (+0.59%) ⬆️
...ava/io/dockstore/client/cli/nested/ToolClient.java 72.52% <0.00%> (+0.66%) ⬆️
.../java/io/dockstore/client/cli/ArgumentUtility.java 79.54% <0.00%> (+3.78%) ⬆️

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@denis-yuen denis-yuen marked this pull request as ready for review January 19, 2023 23:31
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SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 39 Code Smells

0.0% 0.0% Coverage
0.0% 0.0% Duplication

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Looks good!

Out of curiosity, a lot of methods/classes changed from public to package access, what was the reason?

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Looks good!

Out of curiosity, a lot of methods/classes changed from public to package access, what was the reason?

Junit 5 added the ability to use package access. junit-team/junit-framework#679
Sonar Cloud/Codacy suggested it plus since we never/rarely(?) export tests and use them from a different package, it seemed appropriate.

@denis-yuen denis-yuen merged commit b99cb40 into develop Jan 24, 2023
@denis-yuen denis-yuen deleted the feature/junit5 branch January 24, 2023 19:33
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