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SMK app log tweak based on qa testing #6099

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Merged
merged 1 commit into from
Apr 21, 2025
Merged

SMK app log tweak based on qa testing #6099

merged 1 commit into from
Apr 21, 2025

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denis-yuen
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@denis-yuen denis-yuen commented Apr 17, 2025 •
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Description
Quick typo fix based on review of Snakemake preview functioning on qa

Review Instructions
Add a workflow where the subclass is wrong in the .dockstore.yml;

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-7016

Security and Privacy

If there are any concerns that require extra attention from the security team, highlight them here and check the box when complete.

  • Security and Privacy assessed

e.g. Does this change...

  • Any user data we collect, or data location?
  • Access control, authentication or authorization?
  • Encryption features?

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
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  • 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 Apr 17, 2025
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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 changed the title Tweaks based on qa testing SMK app log tweak based on qa testing Apr 17, 2025
@denis-yuen denis-yuen requested review from a team, kathy-t, hyunnaye and svonworl and removed request for a team April 17, 2025 17:27
@denis-yuen denis-yuen marked this pull request as ready for review April 17, 2025 17:44
kathy-t
kathy-t approved these changes Apr 17, 2025
View reviewed changes
dockstore-common/src/main/java/io/dockstore/common/yaml/YamlWorkflow.java
@@ -69,7 +69,7 @@ public void setName(final String name) {
}

@NotNull
@ValidDescriptorLanguage(entryType = EntryType.WORKFLOW, message = "must be a supported descriptor language (\"CWL\", \"WDL\", \"GALAXY\", or \"NFL\")")
@ValidDescriptorLanguage(entryType = EntryType.WORKFLOW, message = "must be a supported descriptor language (\"CWL\", \"WDL\", \"GALAXY\", \"SMK\", or \"NFL\")")
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There may already be a ticket for this, but we should adjust our .dockstore.yml templates as well https://docs.dockstore.org/en/stable/assets/templates/workflows/workflows.html#simple-generic-template-for-a-workflow and on the github app landing page https://qa.dockstore.org/github-landing-page?entryType=WORKFLOW

@denis-yuen denis-yuen merged commit bf018b1 into develop Apr 21, 2025
24 checks passed
@denis-yuen denis-yuen deleted the feature/smk_qa_testing branch April 21, 2025 14:26
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codecov bot commented Apr 21, 2025

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 74.24%. Comparing base (8094a60) to head (e28bb1c).
Report is 3 commits behind head on develop.

Additional details and impacted files 
@@            Coverage Diff             @@
##             develop    #6099   +/-   ##
==========================================
  Coverage      74.24%   74.24%           
  Complexity      5663     5663           
==========================================
  Files            389      389           
  Lines          20343    20343           
  Branches        2103     2103           
==========================================
  Hits           15104    15104           
  Misses          4237     4237           
  Partials        1002     1002
Flag Coverage Δ
bitbuckettests 26.01% <ø> (-0.01%) ⬇️
hoverflytests 27.66% <ø> (ø)
integrationtests 56.06% <ø> (ø)
languageparsingtests 10.81% <ø> (ø)
localstacktests 21.32% <ø> (ø)
toolintegrationtests 29.88% <ø> (ø)
unit-tests_and_non-confidential-tests 26.27% <ø> (ø)
workflowintegrationtests 37.50% <ø> (ø)

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Reviewers

@kathy-t kathy-t kathy-t approved these changes

@svonworl svonworl svonworl approved these changes

@hyunnaye hyunnaye Awaiting requested review from hyunnaye hyunnaye was automatically assigned from dockstore/dockstore

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@denis-yuen denis-yuen

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3 participants
@denis-yuen @kathy-t @svonworl
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