From 8094a4f6916aa4a2082549d4aba2a46993d3cddc Mon Sep 17 00:00:00 2001
From: Olin Blodgett <nilo@nilosplace.net>
Date: Mon, 3 Mar 2025 18:21:15 -0500
Subject: [PATCH] Updated pom to fix libraries

---
 agr_api/pom.xml                               | 21 ++++++++++++++-----
 .../resources/application.properties.defaults |  2 +-
 agr_api_tester/pom.xml                        |  6 ++++--
 agr_cacher/pom.xml                            |  2 +-
 agr_elasticsearch_util/pom.xml                |  2 +-
 agr_indexer/.gitignore                        |  1 +
 agr_indexer/pom.xml                           | 20 +-----------------
 agr_intermine_data_extractor/pom.xml          |  2 +-
 agr_java_core/pom.xml                         | 18 ----------------
 agr_variant_indexer/pom.xml                   |  2 +-
 pom.xml                                       |  4 ++--
 11 files changed, 29 insertions(+), 51 deletions(-)

diff --git a/agr_api/pom.xml b/agr_api/pom.xml
index a1898e832..a177dfb1d 100644
--- a/agr_api/pom.xml
+++ b/agr_api/pom.xml
@@ -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>
@@ -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>
@@ -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>
@@ -88,10 +99,11 @@
 		</dependency>
 
 		<dependency>
-			<groupId>org.alliancegenome</groupId>
+			<groupId>${project.groupId}</groupId>
 			<artifactId>agr_java_core</artifactId>
-			<version>${revision}</version>
+			<version>${project.version}</version>
 		</dependency>
+
 		<dependency>
 			<groupId>org.hamcrest</groupId>
 			<artifactId>hamcrest-all</artifactId>
@@ -116,7 +128,6 @@
 	<build>
 		<finalName>${project.artifactId}</finalName>
 		<plugins>
-
 			<plugin>
 				<groupId>${quarkus.platform.group-id}</groupId>
 				<artifactId>quarkus-maven-plugin</artifactId>
diff --git a/agr_api/src/main/resources/application.properties.defaults b/agr_api/src/main/resources/application.properties.defaults
index 3cd1bf941..a0311cc27 100644
--- a/agr_api/src/main/resources/application.properties.defaults
+++ b/agr_api/src/main/resources/application.properties.defaults
@@ -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
diff --git a/agr_api_tester/pom.xml b/agr_api_tester/pom.xml
index f521cf9fd..6dd3ee8e9 100644
--- a/agr_api_tester/pom.xml
+++ b/agr_api_tester/pom.xml
@@ -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>
@@ -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>
diff --git a/agr_cacher/pom.xml b/agr_cacher/pom.xml
index 47e7f27db..ac9e80167 100644
--- a/agr_cacher/pom.xml
+++ b/agr_cacher/pom.xml
@@ -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>
diff --git a/agr_elasticsearch_util/pom.xml b/agr_elasticsearch_util/pom.xml
index 0f4b04596..e34fcdd27 100644
--- a/agr_elasticsearch_util/pom.xml
+++ b/agr_elasticsearch_util/pom.xml
@@ -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>
diff --git a/agr_indexer/.gitignore b/agr_indexer/.gitignore
index 97aebbb1c..ae96766f0 100644
--- a/agr_indexer/.gitignore
+++ b/agr_indexer/.gitignore
@@ -3,3 +3,4 @@ target
 .classpath
 .project
 /bin/
+data
diff --git a/agr_indexer/pom.xml b/agr_indexer/pom.xml
index f53de768b..9e6ecf2ba 100644
--- a/agr_indexer/pom.xml
+++ b/agr_indexer/pom.xml
@@ -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>
@@ -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>
diff --git a/agr_intermine_data_extractor/pom.xml b/agr_intermine_data_extractor/pom.xml
index 783d2a7fa..e787240c7 100644
--- a/agr_intermine_data_extractor/pom.xml
+++ b/agr_intermine_data_extractor/pom.xml
@@ -20,7 +20,7 @@
 
 	<dependencies>
 		<dependency>
-			<groupId>org.alliancegenome</groupId>
+			<groupId>${project.groupId}</groupId>
 			<artifactId>agr_java_core</artifactId>
 			<version>${project.version}</version>
 		</dependency>
diff --git a/agr_java_core/pom.xml b/agr_java_core/pom.xml
index c8fb3d746..7b11f5856 100644
--- a/agr_java_core/pom.xml
+++ b/agr_java_core/pom.xml
@@ -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>
diff --git a/agr_variant_indexer/pom.xml b/agr_variant_indexer/pom.xml
index a7903e79c..2a6b3a131 100644
--- a/agr_variant_indexer/pom.xml
+++ b/agr_variant_indexer/pom.xml
@@ -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>
diff --git a/pom.xml b/pom.xml
index 7df6b67b9..7ed1fb7d4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -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>