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Merged
KochTobi merged 1 commit into from
Jan 13, 2026
Merged

Upgrade dependencies #1366

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29 changes: 24 additions & 5 deletions datamanager-app/pom.xml
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Expand Up @@ -83,10 +83,34 @@
<groupId>com.vaadin</groupId>
<!-- Replace artifactId with vaadin-core to use only free components -->
<artifactId>vaadin</artifactId>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-fileupload2-core</artifactId>
</dependency>
<dependency>
<groupId>com.vaadin</groupId>
<artifactId>vaadin-spring-boot-starter</artifactId>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-fileupload2-core</artifactId>
</exclusion>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.springframework.boot</groupId>
Expand Down Expand Up @@ -172,11 +196,6 @@
<artifactId>spring-boot-starter-test</artifactId>
<scope>test</scope>
</dependency>
<dependency>
<groupId>com.vaadin</groupId>
<artifactId>vaadin-testbench</artifactId>
<scope>test</scope>
</dependency>
<!-- Include JUnit 4 support for TestBench and others -->
<dependency>
<groupId>org.junit.vintage</groupId>
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2 changes: 0 additions & 2 deletions ...ager-app/src/main/java/life/qbic/datamanager/configuration/FinancingDatasourceConfig.java
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Expand Up @@ -4,7 +4,6 @@
import java.util.Map;
import java.util.Objects;
import javax.sql.DataSource;
import org.apache.commons.dbcp2.BasicDataSource;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.boot.autoconfigure.jdbc.DataSourceProperties;
Expand Down Expand Up @@ -55,7 +54,6 @@ public DataSourceProperties dataSourceProperties() {
public DataSource dataSource() {
return dataSourceProperties()
.initializeDataSourceBuilder()
.type(BasicDataSource.class)
.build();
}

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2 changes: 1 addition & 1 deletion datamanager-app/src/main/resources/application.properties
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Expand Up @@ -48,7 +48,7 @@ spring.jpa.database=mysql
spring.jpa.show-sql=false
spring.jpa.properties.hibernate.format_sql=false
# In case you want to access the H2 database (if you use one)
spring.h2.console.enabled=true
spring.h2.console.enabled=false
# Set explicitly to false to close a session on request finish
# https://www.baeldung.com/spring-open-session-in-view.
spring.jpa.open-in-view=false
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82 changes: 71 additions & 11 deletions datamanager-bom/pom.xml
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Expand Up @@ -11,14 +11,16 @@
<description>Bill of Materials for DataManager artifacts</description>

<properties>
<vaadin.version>24.4.13</vaadin.version>
<apache.poi.version>5.5.1</apache.poi.version>
<jackson.version>2.18.3</jackson.version>
<jakarta.persistence.version>3.2.0</jakarta.persistence.version>
<logback.version>1.5.24</logback.version>
<maven.compiler.source>21</maven.compiler.source>
<maven.compiler.target>21</maven.compiler.target>
<jakarta.persistence.version>3.2.0</jakarta.persistence.version>
<jackson.version>2.18.3</jackson.version>
<sonar.projectKey>qbicsoftware_data-manager-app</sonar.projectKey>
<sonar.organization>qbicsoftware</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
<sonar.organization>qbicsoftware</sonar.organization>
<sonar.projectKey>qbicsoftware_data-manager-app</sonar.projectKey>
<vaadin.version>24.4.13</vaadin.version>
</properties>

<distributionManagement>
Expand Down Expand Up @@ -129,10 +131,31 @@
<type>pom</type>
<scope>import</scope>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-fileupload2-core</artifactId>
<version>2.0.0-M4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.20.0</version>
</dependency>
<dependency>
<groupId>org.apache.activemq</groupId>
<artifactId>artemis-jakarta-server</artifactId>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
<version>2.43.0</version> <!-- version 2.44 is signed differently-->
</dependency>
<dependency>
<groupId>com.sun.mail</groupId>
<artifactId>jakarta.mail</artifactId>
<version>2.0.1</version>
<version>2.0.2</version>
</dependency>
<dependency>
<groupId>org.spockframework</groupId>
Expand Down Expand Up @@ -190,12 +213,12 @@
<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
<version>2.19.0</version>
<version>2.20.0</version>
</dependency>
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi</artifactId>
<version>5.4.0</version>
<version>${apache.poi.version}</version>
</dependency>
<dependency>
<groupId>com.fasterxml.jackson.core</groupId>
Expand All @@ -205,7 +228,13 @@
<dependency>
<groupId>org.apache.poi</groupId>
<artifactId>poi-ooxml</artifactId>
<version>5.4.0</version>
<version>${apache.poi.version}</version>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.javacrumbs.shedlock</groupId>
Expand All @@ -227,17 +256,48 @@
<dependency>
<groupId>org.docx4j</groupId>
<artifactId>docx4j-JAXB-ReferenceImpl</artifactId>
<version>11.5.3</version>
<version>11.5.9</version>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-lang3/3.20.0 -->
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
<version>3.20.0</version>
</dependency>
<dependency>
<groupId>edu.kit.datamanager</groupId>
<artifactId>ro-crate-java</artifactId>
<version>1.1.1</version>
<exclusions>
<exclusion>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
</exclusion>
</exclusions>
</dependency>

<dependency>
<groupId>commons-beanutils</groupId>
<artifactId>commons-beanutils</artifactId>
<version>1.11.0</version>
</dependency>

<dependency>
<groupId>org.docx4j</groupId>
<artifactId>docx4j-core</artifactId>
<version>11.5.0</version>
<version>11.5.9</version>
<exclusions>
<exclusion>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.glassfish.jaxb</groupId>
Expand Down
1 change: 0 additions & 1 deletion identity-infrastructure/pom.xml
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Expand Up @@ -24,7 +24,6 @@
<dependency>
<groupId>org.apache.activemq</groupId>
<artifactId>artemis-jakarta-server</artifactId>
<version>2.41.0</version>
</dependency>

</dependencies>
Expand Down
8 changes: 4 additions & 4 deletions logging/pom.xml
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Expand Up @@ -15,23 +15,23 @@
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-api</artifactId>
<version>2.0.16</version>
<version>2.0.17</version>
</dependency>
<dependency>
<groupId>org.slf4j</groupId>
<artifactId>slf4j-simple</artifactId>
<version>2.0.16</version>
<version>2.0.17</version>
</dependency>
<!-- https://mvnrepository.com/artifact/ch.qos.logback/logback-core -->
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.5.12</version>
<version>${logback.version}</version>
</dependency>
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-core</artifactId>
<version>1.5.16</version>
<version>${logback.version}</version>
</dependency>
</dependencies>
</dependencyManagement>
Expand Down
7 changes: 3 additions & 4 deletions pgp-keys-override.list
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Expand Up @@ -67,7 +67,7 @@ io.opencensus:*:* = 0x600EA202B1EC682F4A788E5AAC7A514BC9F9BB7
xerces:xercesImpl:* = 0x6CB87B18A453990EAC9453F87D713008CC07E9AD # xercesImpl. [oai_citation:12‡Untitled.txt](file-service://file-1UbSKN5j1vX3Pe1FvyAMhb)

# Sigstore (your own plugin/libs)
dev.sigstore:*:* = 0x2C02310024BAAE4B34976FFEAC74A3385D0E3252 # sigstore-maven-plugin / sigstore-java. [oai_citation:13‡Untitled.txt](file-service://file-1UbSKN5j1vX3Pe1FvyAMhb)
dev.sigstore:*:* = 0x300b49c14dfa7e0ad9d8515400e008229f5daf37 # sigstore-maven-plugin / sigstore-java. [oai_citation:13‡Untitled.txt](file-service://file-1UbSKN5j1vX3Pe1FvyAMhb)

# Misc seen in log
io.github.hakky54:sslcontext-kickstart:* = 0xE5138A8E9F2E7E42D38B14D99AEE152CDCCEBFCB # sslcontext-kickstart. [oai_citation:14‡Untitled.txt](file-service://file-1UbSKN5j1vX3Pe1FvyAMhb)
Expand Down Expand Up @@ -106,7 +106,6 @@ org.hibernate.orm:*:* = 0x1452F35849B50750F6A3BBB4B54011358B352F85
# --- Apache ActiveMQ Artemis (many modules in your log) ---
org.apache.activemq:*:* = 0x28417C95E8906D108392822354A43F3254868410


# --- JGroups (unsigned in Maven Central) ---
org.jgroups:jgroups:* = noSig
org.jgroups:jgroups:*:pom = noSig
Expand Down Expand Up @@ -225,8 +224,8 @@ org.jboss.forge.roaster:roaster-jdt:2.29.0.Final:pom = 0x001A438334F162E6AFB27F3
# Misc seen in the log
io.methvin:directory-watcher:0.18.0 = 0xAEE8A343247713A5A198640D4D1670765EF90EAB
io.methvin:directory-watcher:0.18.0:pom = 0xAEE8A343247713A5A198640D4D1670765EF90EAB
org.mariadb.jdbc:mariadb-java-client:3.5.6 = 0x4C470FFFEFC4D3DC59778655CE1A3DD5E3C94F49
org.mariadb.jdbc:mariadb-java-client:3.5.6:pom = 0x4C470FFFEFC4D3DC59778655CE1A3DD5E3C94F49
org.mariadb.jdbc:mariadb-java-client:3.5.7 = 0x4C470FFFEFC4D3DC59778655CE1A3DD5E3C94F49
org.mariadb.jdbc:mariadb-java-client:3.5.7:pom = 0x4C470FFFEFC4D3DC59778655CE1A3DD5E3C94F49
com.helger.commons:ph-commons:11.1.5 = 0x670BE7D076A0C89F5F07625AE57428DA9E879E7D
com.helger.commons:ph-commons:11.1.5:pom = 0x670BE7D076A0C89F5F07625AE57428DA9E879E7D
org.tomlj:tomlj:1.0.0 = 0x80F6D6B0D90C6747753344CAB5A9E81B565E89E0
Expand Down
29 changes: 17 additions & 12 deletions pom.xml
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Expand Up @@ -36,24 +36,29 @@
</modules>
<packaging>pom</packaging>


<parent>
<!-- https://mvnrepository.com/artifact/org.springframework.boot/spring-boot-starter-parent -->
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.5.9</version>
</parent>


<properties>
<apache.poi.version>5.5.1</apache.poi.version>
<jackson.version>2.18.3</jackson.version>
<jakarta.persistence.version>3.2.0</jakarta.persistence.version>
<java.version>21</java.version>
<vaadin.version>24.4.13</vaadin.version>
<logback.version>1.5.24</logback.version>
<maven.compiler.source>21</maven.compiler.source>
<maven.compiler.target>21</maven.compiler.target>
<jakarta.persistence.version>3.2.0</jakarta.persistence.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<jackson.version>2.18.3</jackson.version>
<sonar.projectKey>qbicsoftware_data-manager-app</sonar.projectKey>
<sonar.organization>qbicsoftware</sonar.organization>
<sonar.host.url>https://sonarcloud.io</sonar.host.url>
<sonar.organization>qbicsoftware</sonar.organization>
<sonar.projectKey>qbicsoftware_data-manager-app</sonar.projectKey>
<vaadin.version>24.4.13</vaadin.version>
</properties>

<parent>
<groupId>org.springframework.boot</groupId>
<artifactId>spring-boot-starter-parent</artifactId>
<version>3.5.6</version>
</parent>

<repositories>
<!-- The order of definitions matters. Explicitly defining central here to make sure it has the highest priority. -->
Expand Down Expand Up @@ -243,7 +248,7 @@
<plugin>
<groupId>dev.sigstore</groupId>
<artifactId>sigstore-maven-plugin</artifactId>
<version>1.3.0</version>
<version>2.0.0</version>
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@sven1103 sven1103 Jan 13, 2026

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Since this is a major version jump, can you verify that the build of sigstore files works still properly?

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@KochTobi KochTobi Jan 13, 2026 •
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Yes Sigstore files were created. .pom.sigstore.json and .jar.sigstore.json

<executions>
<execution>
<id>sigstore-sign</id>
Expand Down
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