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Updated pom to fix libraries #1250

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Merged
oblodgett merged 1 commit into from
Mar 4, 2025
Merged

Updated pom to fix libraries #1250

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21 changes: 16 additions & 5 deletions agr_api/pom.xml
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@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<parent>
Expand Down Expand Up @@ -28,6 +29,17 @@
<version>0.9.4</version>
</dependency>

<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-core</artifactId>
<version>2.20.0</version>
</dependency>

<dependency>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-api</artifactId>
</dependency>

<dependency>
<groupId>commons-io</groupId>
<artifactId>commons-io</artifactId>
Expand All @@ -41,7 +53,6 @@
<artifactId>commons-collections4</artifactId>
<version>4.4</version>
</dependency>

<!-- https://mvnrepository.com/artifact/commons-collections/commons-collections -->
<dependency>
<groupId>commons-collections</groupId>
Expand Down Expand Up @@ -88,10 +99,11 @@
</dependency>

<dependency>
<groupId>org.alliancegenome</groupId>
<groupId>${project.groupId}</groupId>
<artifactId>agr_java_core</artifactId>
<version>${revision}</version>
<version>${project.version}</version>
</dependency>

<dependency>
<groupId>org.hamcrest</groupId>
<artifactId>hamcrest-all</artifactId>
Expand All @@ -116,7 +128,6 @@
<build>
<finalName>${project.artifactId}</finalName>
<plugins>

<plugin>
<groupId>${quarkus.platform.group-id}</groupId>
<artifactId>quarkus-maven-plugin</artifactId>
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2 changes: 1 addition & 1 deletion agr_api/src/main/resources/application.properties.defaults
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Expand Up @@ -5,4 +5,4 @@ quarkus.http.root-path=/
quarkus.http.non-application-root-path=/
quarkus.swagger-ui.always-include=true
quarkus.swagger-ui.doc-expansion=none
quarkus.health.openapi.included=true
#quarkus.health.openapi.included=true
6 changes: 4 additions & 2 deletions agr_api_tester/pom.xml
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@@ -1,5 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>

<parent>
Expand All @@ -18,10 +19,11 @@

<dependencies>
<dependency>
<groupId>org.alliancegenome</groupId>
<groupId>${project.groupId}</groupId>
<artifactId>agr_api</artifactId>
<version>${project.version}</version>
</dependency>

</dependencies>

<build>
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2 changes: 1 addition & 1 deletion agr_cacher/pom.xml
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Expand Up @@ -17,7 +17,7 @@
</properties>
<dependencies>
<dependency>
<groupId>org.alliancegenome</groupId>
<groupId>${project.groupId}</groupId>
<artifactId>agr_java_core</artifactId>
<version>${project.version}</version>
</dependency>
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2 changes: 1 addition & 1 deletion agr_elasticsearch_util/pom.xml
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Expand Up @@ -17,7 +17,7 @@
</properties>
<dependencies>
<dependency>
<groupId>org.alliancegenome</groupId>
<groupId>${project.groupId}</groupId>
<artifactId>agr_java_core</artifactId>
<version>${project.version}</version>
</dependency>
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1 change: 1 addition & 0 deletions agr_indexer/.gitignore
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Expand Up @@ -3,3 +3,4 @@ target
.classpath
.project
/bin/
data
20 changes: 1 addition & 19 deletions agr_indexer/pom.xml
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Expand Up @@ -15,7 +15,7 @@
</properties>
<dependencies>
<dependency>
<groupId>org.alliancegenome</groupId>
<groupId>${project.groupId}</groupId>
<artifactId>agr_java_core</artifactId>
<version>${project.version}</version>
</dependency>
Expand Down Expand Up @@ -53,24 +53,6 @@
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.1</version>
<configuration>
<doclint>all,-html,-syntax,-accessibility,-missing</doclint>
<failOnError>false</failOnError>
<quiet>true</quiet>
</configuration>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
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2 changes: 1 addition & 1 deletion agr_intermine_data_extractor/pom.xml
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Expand Up @@ -20,7 +20,7 @@

<dependencies>
<dependency>
<groupId>org.alliancegenome</groupId>
<groupId>${project.groupId}</groupId>
<artifactId>agr_java_core</artifactId>
<version>${project.version}</version>
</dependency>
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18 changes: 0 additions & 18 deletions agr_java_core/pom.xml
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Expand Up @@ -163,24 +163,6 @@
</archive>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
<version>3.0.1</version>
<configuration>
<doclint>all,-html,-syntax,-accessibility,-missing</doclint>
<failOnError>false</failOnError>
<quiet>true</quiet>
</configuration>
<executions>
<execution>
<id>attach-javadocs</id>
<goals>
<goal>jar</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<groupId>io.smallrye</groupId>
<artifactId>jandex-maven-plugin</artifactId>
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2 changes: 1 addition & 1 deletion agr_variant_indexer/pom.xml
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Expand Up @@ -33,7 +33,7 @@
<artifactId>jackson-dataformat-yaml</artifactId>
</dependency>
<dependency>
<groupId>org.alliancegenome</groupId>
<groupId>${project.groupId}</groupId>
<artifactId>agr_java_core</artifactId>
<version>${project.version}</version>
</dependency>
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4 changes: 2 additions & 2 deletions pom.xml
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Expand Up @@ -22,8 +22,8 @@
<properties>
<maven.compiler.source>17</maven.compiler.source>
<maven.compiler.target>17</maven.compiler.target>
<revision>7.2.0</revision>
<quarkus.version>3.4.2</quarkus.version>
<revision>8.1.0</revision>
<quarkus.version>3.13.3</quarkus.version>
<infinispan.version>14.0.25.Final</infinispan.version>
<maven-checkstyle-plugin.version>3.3.1</maven-checkstyle-plugin.version>
<checkstyle.version>10.17.0</checkstyle.version>
Expand Down
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