chore(deps): bump the patch group in /backend with 4 updates by dependabot[bot] · Pull Request #4790 · loculus-project/loculus

dependabot · 2025-08-01T11:55:46Z

Bumps the patch group in /backend with 4 updates: org.apache.commons:commons-csv, org.flywaydb:flyway-database-postgresql, software.amazon.awssdk:s3 and org.springframework.boot.

Updates org.apache.commons:commons-csv from 1.14.0 to 1.14.1

Changelog

Sourced from org.apache.commons:commons-csv's changelog.

Apache Commons CSV 1.14.1 Release Notes

The Apache Commons CSV team is pleased to announce the release of Apache Commons CSV 1.14.1.

This document contains the release notes for the 1.14.1 version of Apache Commons CSV. Commons CSV reads and writes files in Comma Separated Value (CSV) format variations.

Commons CSV requires at least Java 8.

The Apache Commons CSV library provides a simple interface for reading and writing CSV files of various types.

This is a feature and maintenance release. Java 8 or later is required.

Changes in this version include:

Fixed Bugs
CSV-318: CSVPrinter.printRecord(Stream) hangs if given a parallel stream. Thanks to Joseph Shraibman, Gary Gregory.

CSV-318: CSVPrinter now uses an internal lock instead of synchronized methods. Thanks to Joseph Shraibman, Gary Gregory.
      org.apache.commons.csv.CSVPrinter.printRecords(ResultSet) now writes one record at a time using a lock. Thanks to Gary Gregory.
Changes
      Bump org.apache.commons:commons-parent from 81 to 85 [#542](https://github.com/apache/commons-csv/issues/542). Thanks to Gary Gregory, Dependabot.
      Bump commons-io:commons-io from 2.18.0 to 2.20.0. Thanks to Gary Gregory.
      Bump com.opencsv:opencsv from 5.10 to 5.11.2 [#545](https://github.com/apache/commons-csv/issues/545), [#551](https://github.com/apache/commons-csv/issues/551), [#553](https://github.com/apache/commons-csv/issues/553). Thanks to Gary Gregory, Dependabot.
      Bump org.apache.commons:commons-lang3 from 3.17.0 to 3.18.0 [#556](https://github.com/apache/commons-csv/issues/556). Thanks to Gary Gregory, Dependabot.
      Bump commons-codec:commons-codec from 1.18.0 to 1.19.0. Thanks to Gary Gregory.
Historical list of changes: https://commons.apache.org/proper/commons-csv/changes.html

For complete information on Apache Commons CSV, including instructions on how to submit bug reports, patches, or suggestions for improvement, see the Apache Commons CSV website:

https://commons.apache.org/proper/commons-csv/

Download page: https://commons.apache.org/proper/commons-csv/download_csv.cgi

Have fun! -Apache Commons CSV team

Commits

e14ef86 Ignore macOS file
d8724bf Prepare for the release candidate 1.14.1 RC1
b76971c Prepare for the next release candidate
b66814e Merge pull request #557 from apache/dependabot/github_actions/github/codeql-a...
9c95e92 Bump github/codeql-action from 3.29.2 to 3.29.4
1fb3716 Bump commons-codec:commons-codec from 1.18.0 to 1.19.0
7b72c50 Merge some string literals
9658373 Update the GitHub pull request template for AI
67192a9 Bump commons-io:commons-io from 2.19.0 to 2.20.0
59164c8 Bump com.opencsv:opencsv from 5.11.1 to 5.11.2 #553
Additional commits viewable in compare view

Updates org.flywaydb:flyway-database-postgresql from 11.10.3 to 11.10.5

Updates software.amazon.awssdk:s3 from 2.32.5 to 2.32.13

Updates org.springframework.boot from 3.5.3 to 3.5.4

Release notes

Sourced from org.springframework.boot's releases.

v3.5.4

🐞 Bug Fixes

LambdaSafe.withFilter is not public #46474

Executable JAR application class encounters performance issues when used with Palo Alto Network Cortex XDR agent #46402

Runtime dependencies are missing from aotCompileClasspath and aotTestCompileClasspath when using Kotlin #46398

Additional fields for structured JSON logging incompatible with nested ecs logging in 3.5.x #46351

Change in DefaultErrorAttributes alters the shape of API validation error responses #46260

jdbc.connections.active and jdbc.connections.idle metrics are not available when using Hikari in a native image #46225

developmentOnly and testAndDevelopmentOnly dependencies may prevent implementation dependencies from being included in the uber-jar #46205

Hash calculation for uber archive entries that require unpacking is inefficient #46203

Permissions are applied inconsistently when building uber archives with Gradle #46194

Environment variables using legacy dash format can no longer be bound #46184

EmbeddedWebServerFactoryCustomizerAutoConfiguration fails when undertow-core is on the classpath and undertow-servlet is not #46180

Executable JAR application class encounters performance issues #46177

Executable JAR application class encounters performance issues #46176

Setting spring.reactor.context-propagation has no effect when lazy initialization is enabled #46174

Setting spring.netty.leak-detection has no effect when lazy initialization is enabled #46170

SslInfo does not use its Clock when checking certificate validity #46011

📔 Documentation

Fix description of spring.batch.job.enabled #46247

Fix broken Kotlin examples in reference documentation #46168

Add Logback Access Reactor Netty to community starters #46060

🔨 Dependency Upgrades

Upgrade to ActiveMQ 6.1.7 #46373

Upgrade to Caffeine 3.2.2 #46432

Upgrade to Couchbase Client 3.8.2 #46460

Upgrade to GraphQL Java 24.1 #46395

Upgrade to Groovy 4.0.28 #46516

Upgrade to Hibernate 6.6.22.Final #46492

Upgrade to HikariCP 6.3.1 #46493

Upgrade to Infinispan 15.2.5.Final #46461

Upgrade to Jackson Bom 2.19.2 #46494

Upgrade to Jetty 12.0.23 #46375

Upgrade to MariaDB 3.5.4 #46376

Upgrade to Maven Invoker Plugin 3.9.1 #46377

Upgrade to Micrometer 1.15.2 #46280

Upgrade to Micrometer Tracing 1.5.2 #46281

Upgrade to MSSQL JDBC 12.10.1.jre11 #46378

Upgrade to MySQL 9.3.0 #46371

Upgrade to Neo4j Java Driver 5.28.9 #46434

Upgrade to Netty 4.1.123.Final #46435

Upgrade to Prometheus Client 1.3.10 #46379

Upgrade to Reactor Bom 2024.0.8 #46282

Upgrade to RxJava3 3.1.11 #46380

Upgrade to Spring AMQP 3.2.6 #46283

... (truncated)

Commits

925f9bc Release v3.5.4
d82fb35 Merge branch '3.4.x' into 3.5.x
4b6064f Next development version (v3.4.9-SNAPSHOT)
a39c8f0 Merge branch '3.4.x' into 3.5.x
99d53de Upgrade to Spring Integration 6.5.1
1b4aad5 Upgrade to Groovy 4.0.28
3f0f79b Upgrade to Spring Integration 6.4.6
ff8443c Upgrade to Groovy 4.0.28
aed8550 Merge branch '3.4.x' into 3.5.x
5406976 Apply commercial input consistently
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Bumps the patch group in /backend with 4 updates: [org.apache.commons:commons-csv](https://github.com/apache/commons-csv), org.flywaydb:flyway-database-postgresql, software.amazon.awssdk:s3 and [org.springframework.boot](https://github.com/spring-projects/spring-boot). Updates `org.apache.commons:commons-csv` from 1.14.0 to 1.14.1 - [Changelog](https://github.com/apache/commons-csv/blob/master/RELEASE-NOTES.txt) - [Commits](apache/commons-csv@rel/commons-csv-1.14.0...rel/commons-csv-1.14.1) Updates `org.flywaydb:flyway-database-postgresql` from 11.10.3 to 11.10.5 Updates `software.amazon.awssdk:s3` from 2.32.5 to 2.32.13 Updates `org.springframework.boot` from 3.5.3 to 3.5.4 - [Release notes](https://github.com/spring-projects/spring-boot/releases) - [Commits](spring-projects/spring-boot@v3.5.3...v3.5.4) --- updated-dependencies: - dependency-name: org.apache.commons:commons-csv dependency-version: 1.14.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: patch - dependency-name: org.flywaydb:flyway-database-postgresql dependency-version: 11.10.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: patch - dependency-name: software.amazon.awssdk:s3 dependency-version: 2.32.13 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: patch - dependency-name: org.springframework.boot dependency-version: 3.5.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: patch ... Signed-off-by: dependabot[bot] <support@github.com>

dependabot Bot added dependencies Pull requests that update a dependency file java Pull requests that update Java code labels Aug 1, 2025

dependabot Bot force-pushed the dependabot/gradle/backend/patch-adb4554a15 branch from 1a43a0a to 4606541 Compare August 4, 2025 20:49

anna-parker approved these changes Aug 5, 2025

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anna-parker merged commit 3ec8092 into main Aug 5, 2025
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anna-parker deleted the dependabot/gradle/backend/patch-adb4554a15 branch August 5, 2025 09:35

This was referenced Aug 6, 2025

Update Loculus version to 28aeaf pathoplexus/pathoplexus#599

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Update Loculus version to 496daa pathoplexus/pathoplexus#604

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pathoplexus-bot mentioned this pull request Aug 18, 2025

Update Loculus version to 803b5e pathoplexus/pathoplexus#609

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chore(deps): bump the patch group in /backend with 4 updates#4790

chore(deps): bump the patch group in /backend with 4 updates#4790
anna-parker merged 1 commit into
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dependabot Bot commented on behalf of github Aug 1, 2025 •

edited by loculus-bot

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Apache Commons CSV 1.14.1 Release Notes

Fixed Bugs

Changes

v3.5.4

🐞 Bug Fixes

📔 Documentation

🔨 Dependency Upgrades

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dependabot Bot commented on behalf of github Aug 1, 2025 •

edited by loculus-bot

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