8000 update snakemake plugin by denis-yuen · Pull Request #6107 · dockstore/dockstore · GitHub
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update snakemake plugin #6107

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Merged
merged 1 commit into from
May 2, 2025
Merged

update snakemake plugin #6107

merged 1 commit into from
May 2, 2025

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denis-yuen
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@denis-yuen denis-yuen commented May 2, 2025 •
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Description
Update Snakemake plugin

Review Instructions
n/a could login to the docker image and root around for the binary but seems overkill

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-7131

Security and Privacy

None

Please make sure that you've checked the following before submitting your pull request. Thanks!

  • Check that you pass the basic style checks and unit tests by running mvn clean install
  • Ensure that the PR targets the correct branch. Check the milestone or fix version of the ticket.
  • Follow the existing JPA patterns for queries, using named parameters, to avoid SQL injection
  • If you are changing dependencies, check the Snyk status check or the dashboard to ensure you are not introducing new high/critical vulnerabilities
  • Assume that inputs to the API can be malicious, and sanitize and/or check for Denial of Service type values, e.g., massive sizes
  • Do not serve user-uploaded binary images through the Dockstore API
  • Ensure that endpoints that only allow privileged access enforce that with the @RolesAllowed annotation
  • Do not create cookies, although this may change in the future
  • If this PR is for a user-facing feature, create and link a documentation ticket for this feature (usually in the same milestone as the linked issue). Style points if you create a documentation PR directly and link that instead.

@denis-yuen denis-yuen self-assigned this May 2, 2025
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codecov bot commented May 2, 2025 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.19%. Comparing base (46de46a) to head (1f6164f).
Report is 2 commits behind head on release/1.17.0.

Additional details and impacted files 
@@                 Coverage Diff                  @@
##             release/1.17.0    #6107      +/-   ##
====================================================
- Coverage             74.23%   74.19%   -0.04%     
+ Complexity             5663     5660       -3     
====================================================
  Files                   389      389              
  Lines                 20328    20328              
  Branches               2100     2100              
====================================================
- Hits                  15090    15082       -8     
- Misses                 4236     4244       +8     
  Partials               1002     1002
Flag Coverage Δ
bitbuckettests 25.94% <ø> (ø)
hoverflytests 27.62% <ø> (ø)
integrationtests 56.09% <ø> (ø)
languageparsingtests 10.82% <ø> (ø)
localstacktests 21.34% <ø> (ø)
regressionintegrationtests ?
toolintegrationtests 29.90% <ø> (ø)
unit-tests_and_non-confidential-tests 26.30% <ø> (ø)
workflowintegrationtests 37.36% <ø> (ø)

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@sonarqubecloud SonarQubeCloud
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sonarqubecloud bot commented May 2, 2025

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

@denis-yuen denis-yuen requested review from a team, kathy-t and svonworl and removed request for a team May 2, 2025 15:39
@denis-yuen denis-yuen marked this pull request as ready for review May 2, 2025 15:39
@denis-yuen denis-yuen merged commit f3fbaad into release/1.17.0 May 2, 2025
23 of 24 checks passed
@denis-yuen denis-yuen deleted the update_snakemake_plugin branch May 2, 2025 17:33
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@kathy-t kathy-t kathy-t approved these changes

@svonworl svonworl svonworl approved these changes

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@denis-yuen denis-yuen

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@denis-yuen @kathy-t @svonworl
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