8000 lgtm migration by denis-yuen · Pull Request #5244 · dockstore/dockstore · GitHub
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lgtm migration #5244

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Merged
merged 3 commits into from
Nov 22, 2022
Merged

lgtm migration #5244

merged 3 commits into from
Nov 22, 2022

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denis-yuen
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@denis-yuen denis-yuen commented Nov 17, 2022 •
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Description
Enable CodeQL check (replacement for LGTM)
https://github.blog/2022-08-15-the-next-step-for-lgtm-com-github-code-scanning/

Will disable LGTM integration from the web console on merge

Review Instructions
See that recent builds have LGTM migrated checks
They should show up in https://github.com/dockstore/dockstore/security/code-scanning

Issue
https://ucsc-cgl.atlassian.net/browse/SEAB-3011

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 Nov 17, 2022
@denis-yuen denis-yuen changed the title Create codeql.yml lgtm migration Nov 17, 2022
@denis-yuen denis-yuen marked this pull request as ready for review November 17, 2022 16:20
@denis-yuen denis-yuen requested review from david4096, a team, coverbeck and hyunnaye and removed request for a team November 17, 2022 16:20
@sonarqubecloud
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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
No Duplication information No Duplication information

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codecov bot commented Nov 17, 2022 •
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Codecov Report

Base: 73.31% // Head: 72.58% // Decreases project coverage by -0.72% ⚠️

Coverage data is based on head (7f094e1) compared to base (7fcab72).
Patch coverage: 71.91% of modified lines in pull request are covered.

❗ Current head 7f094e1 differs from pull request most recent head d1e1867. Consider uploading reports for the commit d1e1867 to get more accurate results

Additional details and impacted files 
@@              Coverage Diff              @@
##             develop    #5244      +/-   ##
=============================================
- Coverage      73.31%   72.58%   -0.73%     
- Complexity      4337     4349      +12     
=============================================
  Files            287      292       +5     
  Lines          16690    16709      +19     
  Branches        1835     1838       +3     
=============================================
- Hits           12236    12128     -108     
- Misses          3586     3699     +113     
- Partials         868      882      +14
Flag Coverage Δ
bitbuckettests 28.26% <9.88%> (-0.16%) ⬇️
integrationtests 57.88% <58.65%> (+0.14%) ⬆️
languageparsingtests 10.85% <1.12%> (-0.04%) ⬇️
toolintegrationtests 23.50% <8.98%> (-6.96%) ⬇️
unit-tests_and_non-confidential-tests 26.90% <41.12%> (+0.13%) ⬆️
workflowintegrationtests 40.46% <35.95%> (-0.45%) ⬇️

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

Impacted Files Coverage Δ
.../io/dockstore/common/yaml/AbstractYamlService.java 46.25% <ø> (ø)
...main/java/io/dockstore/common/yaml/YamlAuthor.java 100.00% <ø> (ø)
...in/java/io/dockstore/common/yaml/YamlWorkflow.java 100.00% <ø> (ø)
...aml/constraints/AuthorHasNameOrOrcidValidator.java 100.00% <ø> (ø)
...ore/webservice/DockstoreWebserviceApplication.java 81.37% <ø> (+14.04%) ⬆️
...e/webservice/DockstoreWebserviceConfiguration.java 39.51% <0.00%> (-0.28%) ⬇️
...c/main/java/io/dockstore/webservice/core/Tool.java 88.46% <ø> (ø)
...c/main/java/io/dockstore/webservice/core/User.java 76.03% <ø> (ø)
...in/java/io/dockstore/webservice/core/Workflow.java 85.88% <ø> (ø)
...kstore/webservice/helpers/ZipSourceFileHelper.java 60.43% <ø> (ø)
... and 54 more

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This was referenced Nov 17, 2022
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@denis-yuen denis-yuen requested a review from kathy-t November 21, 2022 22:42
@denis-yuen denis-yuen merged commit 61861c1 into develop Nov 22, 2022
@denis-yuen denis-yuen deleted the feature/lgtm_migration branch November 22, 2022 15:12
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Reviewers

@coverbeck coverbeck coverbeck approved these changes

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

@david4096 david4096 Awaiting requested review from david4096

@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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@denis-yuen @coverbeck @kathy-t
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