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chore(deps): bump the minor group across 1 directory with 3 updates#6621
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dependabot/gradle/backend/minor-afd980b8f5

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@dependabot dependabot Bot commented on behalf of github Jun 4, 2026 •
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Bumps the minor group with 3 updates in the /backend directory: software.amazon.awssdk:s3, org.jetbrains.kotlin.jvm and org.jetbrains.kotlin.plugin.spring.

Updates software.amazon.awssdk:s3 from 2.45.1 to 2.46.12

Updates org.jetbrains.kotlin.jvm from 2.3.21 to 2.4.0

Release notes

Sourced from org.jetbrains.kotlin.jvm's releases.

Kotlin 2.4.0

Changelog

Analysis API

  • KT-83867 OVERLOAD_RESOLUTION_AMBIGUITY false positive with assertEquals in IJ repo
  • KT-83723 [Analysis API] Enable experimental KDoc resolver by default
  • KT-83388 Analysis API: properly support KMP in KotlinPackageProvider
  • KT-65683 Analysis API: Dangling file session creation causes a computeIfAbsent contract violation

Analysis API. Code Compilation

  • KT-78946 Evaluation of variable with local class in type parameter leads to InventNamesForLocalClasses exception

Analysis API. FIR

  • KT-68260 K2 AA: InvalidFirElementTypeException “For CALLABLE_REFERENCE_EXPRESSION with text ::lam1, unexpected element of type: no element found” with illegal callable reference call
  • KT-70896 AA: False positive deprecation warning with override of built-in method in JDK mapped class
  • KT-84711 K2 IDE sometimes loses FIR plugin-generated declarations after file changes
  • KT-84625 Analysis API: collectDesignationPath fails for nested classes inside plugin-generated top-level classes
  • KT-84596 Improve K2 Jooq completion performance
  • KT-84525 KaValueParameterSymbol#getHasSynthesizedName returns false for FirDeclarationOrigin.SubstitutionOverride.DeclarationSite
  • KT-83546 Kotlin analysis reach ClsCustomNavigationPolicy
  • KT-84259 Move CommonDefaultImportsProvider to the frontend independent module
  • KT-82945 Analysis API: KotlinIllegalArgumentExceptionWithAttachments: Expected FirResolvedTypeRef with ConeKotlinType but was FirUserTypeRefImpl
  • KT-71135 AA: exception from sealed inheritors checker when analyzeCopy

Analysis API. Infrastructure

Fixes

  • KT-83905 Analysis API: Improve UX with test data
  • KT-84913 Extract compiler classes used by the PSI & Analysis API to a separate module
  • KT-64986 Analysis API: Implement Analysis API tests for different KMP Platforms
  • KT-84776 The test data manager misses the redundancy check in the update mode
  • KT-84962 The test data manager misses -ea flag
  • KT-84388 Preserve the EOF status in the test data manager to avoid extra changes
  • KT-84362 Analysis API tests produce many warnings due to "not yet loaded registry"
  • KT-84279 Test Data Manager fails on a clean build
  • KT-83913 Exclude compiler-based Analysis API tests from Git tracking
  • KT-80379 Extract per-module test generators for AA tests
  • KT-84120 Move CLI modules out of kotlin-compiler-fe10-for-ide
  • KT-83200 Track external dependencies of the Analysis API modules

Analysis API. Light Classes

  • KT-82434 Light classes should prefer enum entries to properties
  • KT-84200 SLC: return type is not boxed for delegated methods with generic original method
  • KT-72451 "CCE: class PsiPrimitiveType cannot be cast to class PsiClassType" with same-named enum class and typealias

... (truncated)

Changelog

Sourced from org.jetbrains.kotlin.jvm's changelog.

2.4.0

Analysis API

  • KT-83867 OVERLOAD_RESOLUTION_AMBIGUITY false positive with assertEquals in IJ repo
  • KT-83723 [Analysis API] Enable experimental KDoc resolver by default
  • KT-83388 Analysis API: properly support KMP in KotlinPackageProvider
  • KT-65683 Analysis API: Dangling file session creation causes a computeIfAbsent contract violation

Analysis API. Code Compilation

  • KT-78946 Evaluation of variable with local class in type parameter leads to InventNamesForLocalClasses exception

Analysis API. FIR

  • KT-68260 K2 AA: InvalidFirElementTypeException “For CALLABLE_REFERENCE_EXPRESSION with text ::lam1, unexpected element of type: no element found” with illegal callable reference call
  • KT-70896 AA: False positive deprecation warning with override of built-in method in JDK mapped class
  • KT-84711 K2 IDE sometimes loses FIR plugin-generated declarations after file changes
  • KT-84625 Analysis API: collectDesignationPath fails for nested classes inside plugin-generated top-level classes
  • KT-84596 Improve K2 Jooq completion performance
  • KT-84525 KaValueParameterSymbol#getHasSynthesizedName returns false for FirDeclarationOrigin.SubstitutionOverride.DeclarationSite
  • KT-83546 Kotlin analysis reach ClsCustomNavigationPolicy
  • KT-84259 Move CommonDefaultImportsProvider to the frontend independent module
  • KT-82945 Analysis API: KotlinIllegalArgumentExceptionWithAttachments: Expected FirResolvedTypeRef with ConeKotlinType but was FirUserTypeRefImpl
  • KT-71135 AA: exception from sealed inheritors checker when analyzeCopy

Analysis API. Infrastructure

Fixes

  • KT-83905 Analysis API: Improve UX with test data
  • KT-84913 Extract compiler classes used by the PSI & Analysis API to a separate module
  • KT-64986 Analysis API: Implement Analysis API tests for different KMP Platforms
  • KT-84776 The test data manager misses the redundancy check in the update mode
  • KT-84962 The test data manager misses -ea flag
  • KT-84388 Preserve the EOF status in the test data manager to avoid extra changes
  • KT-84362 Analysis API tests produce many warnings due to "not yet loaded registry"
  • KT-84279 Test Data Manager fails on a clean build
  • KT-83913 Exclude compiler-based Analysis API tests from Git tracking
  • KT-80379 Extract per-module test generators for AA tests
  • KT-84120 Move CLI modules out of kotlin-compiler-fe10-for-ide
  • KT-83200 Track external dependencies of the Analysis API modules

Analysis API. Light Classes

  • KT-82434 Light classes should prefer enum entries to properties
  • KT-84200 SLC: return type is not boxed for delegated methods with generic original method
  • KT-72451 "CCE: class PsiPrimitiveType cannot be cast to class PsiClassType" with same-named enum class and typealias

Analysis API. PSI

... (truncated)

Commits
  • add726c Add ChangeLog for 2.4.0-RC2
  • 69a4a81 [Wasm] Add binaryen per-file arguments
  • 8907c63 [KGP] Suppress duplicate compiler warning output when --warning-mode=all is a...
  • f9bef12 [KGP] Add failing test for duplicate compiler warning output via Problems API
  • 7fe49c2 KT-86268: Use 2.4.0 toolchain for abiValidation with older CVs
  • 13d25e2 KT-86268: Regression test added
  • f7d1a76 [JKlib] Fix JAR deserializer configuration.
  • 5cec663 [JKlib] Wire up JvmBuiltInClassDescriptorFactory
  • ef14611 Make the default stability of non-final classes Unknown instead of Stable
  • d76473a [Gradle] Fix GeneralNativeIT.shouldAllowToOverrideDownloadUrl test failures
  • Additional commits viewable in compare view

Updates org.jetbrains.kotlin.plugin.spring from 2.3.21 to 2.4.0

Release notes

Sourced from org.jetbrains.kotlin.plugin.spring's releases.

Kotlin 2.4.0

Changelog

Analysis API

  • KT-83867 OVERLOAD_RESOLUTION_AMBIGUITY false positive with assertEquals in IJ repo
  • KT-83723 [Analysis API] Enable experimental KDoc resolver by default
  • KT-83388 Analysis API: properly support KMP in KotlinPackageProvider
  • KT-65683 Analysis API: Dangling file session creation causes a computeIfAbsent contract violation

Analysis API. Code Compilation

  • KT-78946 Evaluation of variable with local class in type parameter leads to InventNamesForLocalClasses exception

Analysis API. FIR

  • KT-68260 K2 AA: InvalidFirElementTypeException “For CALLABLE_REFERENCE_EXPRESSION with text ::lam1, unexpected element of type: no element found” with illegal callable reference call
  • KT-70896 AA: False positive deprecation warning with override of built-in method in JDK mapped class
  • KT-84711 K2 IDE sometimes loses FIR plugin-generated declarations after file changes
  • KT-84625 Analysis API: collectDesignationPath fails for nested classes inside plugin-generated top-level classes
  • KT-84596 Improve K2 Jooq completion performance
  • KT-84525 KaValueParameterSymbol#getHasSynthesizedName returns false for FirDeclarationOrigin.SubstitutionOverride.DeclarationSite
  • KT-83546 Kotlin analysis reach ClsCustomNavigationPolicy
  • KT-84259 Move CommonDefaultImportsProvider to the frontend independent module
  • KT-82945 Analysis API: KotlinIllegalArgumentExceptionWithAttachments: Expected FirResolvedTypeRef with ConeKotlinType but was FirUserTypeRefImpl
  • KT-71135 AA: exception from sealed inheritors checker when analyzeCopy

Analysis API. Infrastructure

Fixes

  • KT-83905 Analysis API: Improve UX with test data
  • KT-84913 Extract compiler classes used by the PSI & Analysis API to a separate module
  • KT-64986 Analysis API: Implement Analysis API tests for different KMP Platforms
  • KT-84776 The test data manager misses the redundancy check in the update mode
  • KT-84962 The test data manager misses -ea flag
  • KT-84388 Preserve the EOF status in the test data manager to avoid extra changes
  • KT-84362 Analysis API tests produce many warnings due to "not yet loaded registry"
  • KT-84279 Test Data Manager fails on a clean build
  • KT-83913 Exclude compiler-based Analysis API tests from Git tracking
  • KT-80379 Extract per-module test generators for AA tests
  • KT-84120 Move CLI modules out of kotlin-compiler-fe10-for-ide
  • KT-83200 Track external dependencies of the Analysis API modules

Analysis API. Light Classes

  • KT-82434 Light classes should prefer enum entries to properties
  • KT-84200 SLC: return type is not boxed for delegated methods with generic original method
  • KT-72451 "CCE: class PsiPrimitiveType cannot be cast to class PsiClassType" with same-named enum class and typealias

... (truncated)

Changelog

Sourced from org.jetbrains.kotlin.plugin.spring's changelog.

2.4.0

Analysis API

  • KT-83867 OVERLOAD_RESOLUTION_AMBIGUITY false positive with assertEquals in IJ repo
  • KT-83723 [Analysis API] Enable experimental KDoc resolver by default
  • KT-83388 Analysis API: properly support KMP in KotlinPackageProvider
  • KT-65683 Analysis API: Dangling file session creation causes a computeIfAbsent contract violation

Analysis API. Code Compilation

  • KT-78946 Evaluation of variable with local class in type parameter leads to InventNamesForLocalClasses exception

Analysis API. FIR

  • KT-68260 K2 AA: InvalidFirElementTypeException “For CALLABLE_REFERENCE_EXPRESSION with text ::lam1, unexpected element of type: no element found” with illegal callable reference call
  • KT-70896 AA: False positive deprecation warning with override of built-in method in JDK mapped class
  • KT-84711 K2 IDE sometimes loses FIR plugin-generated declarations after file changes
  • KT-84625 Analysis API: collectDesignationPath fails for nested classes inside plugin-generated top-level classes
  • KT-84596 Improve K2 Jooq completion performance
  • KT-84525 KaValueParameterSymbol#getHasSynthesizedName returns false for FirDeclarationOrigin.SubstitutionOverride.DeclarationSite
  • KT-83546 Kotlin analysis reach ClsCustomNavigationPolicy
  • KT-84259 Move CommonDefaultImportsProvider to the frontend independent module
  • KT-82945 Analysis API: KotlinIllegalArgumentExceptionWithAttachments: Expected FirResolvedTypeRef with ConeKotlinType but was FirUserTypeRefImpl
  • KT-71135 AA: exception from sealed inheritors checker when analyzeCopy

Analysis API. Infrastructure

Fixes

  • KT-83905 Analysis API: Improve UX with test data
  • KT-84913 Extract compiler classes used by the PSI & Analysis API to a separate module
  • KT-64986 Analysis API: Implement Analysis API tests for different KMP Platforms
  • KT-84776 The test data manager misses the redundancy check in the update mode
  • KT-84962 The test data manager misses -ea flag
  • KT-84388 Preserve the EOF status in the test data manager to avoid extra changes
  • KT-84362 Analysis API tests produce many warnings due to "not yet loaded registry"
  • KT-84279 Test Data Manager fails on a clean build
  • KT-83913 Exclude compiler-based Analysis API tests from Git tracking
  • KT-80379 Extract per-module test generators for AA tests
  • KT-84120 Move CLI modules out of kotlin-compiler-fe10-for-ide
  • KT-83200 Track external dependencies of the Analysis API modules

Analysis API. Light Classes

  • KT-82434 Light classes should prefer enum entries to properties
  • KT-84200 SLC: return type is not boxed for delegated methods with generic original method
  • KT-72451 "CCE: class PsiPrimitiveType cannot be cast to class PsiClassType" with same-named enum class and typealias

Analysis API. PSI

... (truncated)

Commits
  • add726c Add ChangeLog for 2.4.0-RC2
  • 69a4a81 [Wasm] Add binaryen per-file arguments
  • 8907c63 [KGP] Suppress duplicate compiler warning output when --warning-mode=all is a...
  • f9bef12 [KGP] Add failing test for duplicate compiler warning output via Problems API
  • 7fe49c2 KT-86268: Use 2.4.0 toolchain for abiValidation with older CVs
  • 13d25e2 KT-86268: Regression test added
  • f7d1a76 [JKlib] Fix JAR deserializer configuration.
  • 5cec663 [JKlib] Wire up JvmBuiltInClassDescriptorFactory
  • ef14611 Make the default stability of non-final classes Unknown instead of Stable
  • d76473a [Gradle] Fix GeneralNativeIT.shouldAllowToOverrideDownloadUrl test failures
  • Additional commits viewable in compare view

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@dependabot dependabot Bot added dependencies Pull requests that update a dependency file java Pull requests that update Java code labels Jun 4, 2026
@anna-parker

anna-parker commented Jun 5, 2026

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@claude help me understand why the [CodeQL Advanced / Analyze (java-kotlin) (pull_request)](https://github.com/loculus-project/loculus/actions/runs/26926906143/job/79520330607?pr=6621)Failing after 1m action failed but the backend built well and all integration tests work - do I need to update that action?

@claude

claude Bot commented Jun 5, 2026 •
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Claude finished @anna-parker's task in 58s —— View job

CodeQL Failure Analysis

  • Gather context
  • Check CodeQL workflow file
  • Investigate the failure reason
  • Provide explanation

The failure is not a problem with your workflow file — it's a known compatibility limitation of CodeQL's Kotlin extractor.

The exact error from the logs:

Caused by: com.semmle.extractor.java.interceptors.KotlinInterceptor$KotlinVersionTooRecentError: 
Kotlin version 2.4.0 is too recent. CodeQL currently supports versions below 2.3.30

Why the build/tests pass but CodeQL fails

The backend build and integration tests use the real Kotlin compiler, which compiles 2.4.0 just fine. The CodeQL java-kotlin extractor works differently — it intercepts the Kotlin compilation process to build its analysis database, and its own Kotlin interceptor only supports up to Kotlin 2.3.x (specifically below 2.3.30). Kotlin 2.4.0 is beyond that threshold, so the CodeQL instrumented build fails even though the normal build succeeds.

Do you need to update the action?

The workflow itself (.github/workflows/codeql.yml) uses github/codeql-action@v4, which is the current major version. Updating the action version alone won't fix this — the fix needs to come from GitHub releasing a new CodeQL extractor build that supports Kotlin 2.4.0.

Options

  1. Wait for CodeQL to release Kotlin 2.4.0 support (the most likely path — GitHub typically adds support for new Kotlin versions within weeks of release).

  2. Hold off on merging this PR until CodeQL support arrives, if CodeQL coverage for the backend is important to you right now.

  3. Proceed anyway — CodeQL will still analyze JavaScript/TypeScript and Python successfully; you'll just have a gap in Java/Kotlin analysis until support catches up. The build and tests are green, so the Kotlin upgrade itself is fine.

This is a common pattern with Kotlin major version bumps (e.g. the same thing happened with the 2.0 → 2.1 transition) and CodeQL support typically follows within a few weeks.

@anna-parker

anna-parker commented Jun 5, 2026

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ok then lets just wait a week or so for this!

@dependabot dependabot Bot force-pushed the dependabot/gradle/backend/minor-afd980b8f5 branch 2 times, most recently from 90764d2 to b8a191c Compare June 16, 2026 08:02
@dependabot
chore(deps): bump the minor group across 1 directory with 3 updates
fe1635f 
Bumps the minor group with 3 updates in the /backend directory: software.amazon.awssdk:s3, [org.jetbrains.kotlin.jvm](https://github.com/JetBrains/kotlin) and [org.jetbrains.kotlin.plugin.spring](https://github.com/JetBrains/kotlin).


Updates `software.amazon.awssdk:s3` from 2.45.1 to 2.46.12

Updates `org.jetbrains.kotlin.jvm` from 2.3.21 to 2.4.0
- [Release notes](https://github.com/JetBrains/kotlin/releases)
- [Changelog](https://github.com/JetBrains/kotlin/blob/master/ChangeLog.md)
- [Commits](JetBrains/kotlin@v2.3.21...v2.4.0)

Updates `org.jetbrains.kotlin.plugin.spring` from 2.3.21 to 2.4.0
- [Release notes](https://github.com/JetBrains/kotlin/releases)
- [Changelog](https://github.com/JetBrains/kotlin/blob/master/ChangeLog.md)
- [Commits](JetBrains/kotlin@v2.3.21...v2.4.0)

---
updated-dependencies:
- dependency-name: org.jetbrains.kotlin.jvm
  dependency-version: 2.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
- dependency-name: org.jetbrains.kotlin.plugin.spring
  dependency-version: 2.4.0
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
- dependency-name: software.amazon.awssdk:s3
  dependency-version: 2.46.3
  dependency-type: direct:production
  update-type: version-update:semver-minor
  dependency-group: minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot force-pushed the dependabot/gradle/backend/minor-afd980b8f5 branch from b8a191c to fe1635f Compare June 17, 2026 18:16
@dependabot @github

dependabot Bot commented on behalf of github Jun 24, 2026

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Looks like these dependencies are updatable in another way, so this is no longer needed.

@dependabot dependabot Bot closed this Jun 24, 2026
@dependabot dependabot Bot deleted the dependabot/gradle/backend/minor-afd980b8f5 branch June 24, 2026 18:14
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@anna-parker