From 818635cb8d02b02c1d83cd4fb8f3f89fff0c69fe Mon Sep 17 00:00:00 2001
From: gcolon021 <gcolon021@gmail.com>
Date: Wed, 4 Oct 2023 18:01:25 -0400
Subject: [PATCH] [ALS-5000] Update maven compiler plugin to latest

Maven compiler plugin has a dependency on log4j.
---
 pic-sure-resources/pom.xml | 169 +++++++-------
 pom.xml                    | 446 ++++++++++++++++++-------------------
 2 files changed, 307 insertions(+), 308 deletions(-)

diff --git a/pic-sure-resources/pom.xml b/pic-sure-resources/pom.xml
index 96b01ea0..2770f877 100644
--- a/pic-sure-resources/pom.xml
+++ b/pic-sure-resources/pom.xml
@@ -1,87 +1,86 @@
 <?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">
-	<modelVersion>4.0.0</modelVersion>
-	<parent>
-		<artifactId>pic-sure-api</artifactId>
-		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
-		<version>2.1.0-SNAPSHOT</version>
-	</parent>
-	<artifactId>pic-sure-resources</artifactId>
-	<packaging>pom</packaging>
-	<name>pic-sure-resources</name>
-	<modules>
-		<module>pic-sure-resource-api</module>
-		<module>pic-sure-ga4gh-dos</module>
-		<module>pic-sure-hsapi-resource</module>
-		<module>pic-sure-passthrough-resource</module>
-		<module>pic-sure-aggregate-data-sharing-resource</module>
-		<module>pic-sure-visualization-resource</module>
-	</modules>
-	<dependencies>
-		<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>slf4j-api</artifactId>			
-		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>slf4j-jdk14</artifactId>
-			<version>1.7.32</version>
-		</dependency>
-	</dependencies>
-	<build>
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-war-plugin</artifactId>
-					<configuration>
-						<attachClasses>true</attachClasses>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-compiler-plugin</artifactId>
-					<configuration>
-						<source>9</source>
-						<target>9</target>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-dependency-plugin</artifactId>
-					<executions>
-						<execution>
-							<id>retrieve-mysql-driver</id>
-							<phase>generate-sources</phase>
-							<goals>
-								<goal>copy</goal>
-							</goals>
-							<inherited>false</inherited>
-							<configuration>
-								<artifactItems>
-									<artifactItem>
-										<groupId>com.mysql</groupId>
-										<artifactId>mysql-connector-j</artifactId>
-										<version>8.0.32</version>
-										<type>jar</type>
-										<overWrite>true</overWrite>
-										<outputDirectory>${project.build.directory}/modules/system/layers/base/com/sql/mysql/main/</outputDirectory>
-									</artifactItem>
-								</artifactItems>
-							</configuration>
-						</execution>
-					</executions>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-war-plugin</artifactId>
-					<configuration>
-						<failOnMissingWebXml>false</failOnMissingWebXml>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-	</build>
+<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>
+    <artifactId>pic-sure-api</artifactId>
+    <groupId>edu.harvard.hms.dbmi.avillach</groupId>
+    <version>2.1.0-SNAPSHOT</version>
+  </parent>
+  <artifactId>pic-sure-resources</artifactId>
+  <packaging>pom</packaging>
+  <name>pic-sure-resources</name>
+  <modules>
+    <module>pic-sure-resource-api</module>
+    <module>pic-sure-ga4gh-dos</module>
+    <module>pic-sure-hsapi-resource</module>
+    <module>pic-sure-passthrough-resource</module>
+    <module>pic-sure-aggregate-data-sharing-resource</module>
+    <module>pic-sure-visualization-resource</module>
+  </modules>
+  <dependencies>
+    <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
+    <dependency>
+      <groupId>org.slf4j</groupId>
+      <artifactId>slf4j-api</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.slf4j</groupId>
+      <artifactId>slf4j-jdk14</artifactId>
+      <version>1.7.32</version>
+    </dependency>
+  </dependencies>
+  <build>
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-war-plugin</artifactId>
+          <configuration>
+            <attachClasses>true</attachClasses>
+          </configuration>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-compiler-plugin</artifactId>
+          <configuration>
+            <source>9</source>
+            <target>9</target>
+          </configuration>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-dependency-plugin</artifactId>
+          <executions>
+            <execution>
+              <id>retrieve-mysql-driver</id>
+              <phase>generate-sources</phase>
+              <goals>
+                <goal>copy</goal>
+              </goals>
+              <inherited>false</inherited>
+              <configuration>
+                <artifactItems>
+                  <artifactItem>
+                    <groupId>com.mysql</groupId>
+                    <artifactId>mysql-connector-j</artifactId>
+                    <version>8.0.32</version>
+                    <type>jar</type>
+                    <overWrite>true</overWrite>
+                    <outputDirectory>${project.build.directory}/modules/system/layers/base/com/sql/mysql/main/</outputDirectory>
+                  </artifactItem>
+                </artifactItems>
+              </configuration>
+            </execution>
+          </executions>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-war-plugin</artifactId>
+          <configuration>
+            <failOnMissingWebXml>false</failOnMissingWebXml>
+          </configuration>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+  </build>
 </project>
diff --git a/pom.xml b/pom.xml
index 62972ca9..48c0b29c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1,232 +1,232 @@
-<?xml version="1.0" encoding="UTF-8"?> 
+<?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">
-	<modelVersion>4.0.0</modelVersion>
-	<groupId>edu.harvard.hms.dbmi.avillach</groupId>
-	<artifactId>pic-sure-api</artifactId>
-	<version>2.1.0-SNAPSHOT</version>
-	<packaging>pom</packaging>
-	<name>pic-sure-api</name>
-	<modules>
-		<module>pic-sure-api-war</module>
-		<module>pic-sure-api-data</module>
-		<module>pic-sure-resources</module>
-		<module>pic-sure-util</module>
-	</modules>
-	<repositories>
-		<repository>
-			<id>github</id>
-			<url>https://maven.pkg.github.com/hms-dbmi/pic-sure</url>
-			<snapshots>
-				<enabled>true</enabled>
-			</snapshots>
-		</repository>
-	</repositories>
-	<properties>
-		<jackson.version>2.10.5</jackson.version>		
-	</properties>
-	<build>
-		<pluginManagement>
-			<plugins>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.8.0</version>
-					<configuration>
-						<release>11</release>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-war-plugin</artifactId>
-					<version>3.2.0</version>
-					<configuration>
-						<failOnMissingWebXml>false</failOnMissingWebXml>
-					</configuration>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-surefire-plugin</artifactId>
-					<version>2.22.0</version>
-					<configuration>
-						<argLine>
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>edu.harvard.hms.dbmi.avillach</groupId>
+  <artifactId>pic-sure-api</artifactId>
+  <version>2.1.0-SNAPSHOT</version>
+  <packaging>pom</packaging>
+  <name>pic-sure-api</name>
+  <modules>
+    <module>pic-sure-api-war</module>
+    <module>pic-sure-api-data</module>
+    <module>pic-sure-resources</module>
+    <module>pic-sure-util</module>
+  </modules>
+  <repositories>
+    <repository>
+      <id>github</id>
+      <url>https://maven.pkg.github.com/hms-dbmi/pic-sure</url>
+      <snapshots>
+        <enabled>true</enabled>
+      </snapshots>
+    </repository>
+  </repositories>
+  <properties>
+    <jackson.version>2.10.5</jackson.version>
+  </properties>
+  <build>
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-compiler-plugin</artifactId>
+          <version>3.11.0</version>
+          <configuration>
+            <release>11</release>
+          </configuration>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-war-plugin</artifactId>
+          <version>3.2.0</version>
+          <configuration>
+            <failOnMissingWebXml>false</failOnMissingWebXml>
+          </configuration>
+        </plugin>
+        <plugin>
+          <groupId>org.apache.maven.plugins</groupId>
+          <artifactId>maven-surefire-plugin</artifactId>
+          <version>2.22.0</version>
+          <configuration>
+            <argLine>
 							--illegal-access=permit
 						</argLine>
-					</configuration>
-				</plugin>
-			</plugins>
-		</pluginManagement>
-	</build>
-	<dependencies>
-		<dependency>
-			<groupId>junit</groupId>
-			<artifactId>junit</artifactId>
-			<version>4.13.1</version>
-			<scope>test</scope>
-		</dependency>
-	</dependencies>
-	<dependencyManagement>
-		<dependencies>
-			<dependency>
-				<groupId>com.fasterxml.jackson.core</groupId>
-				<artifactId>jackson-core</artifactId>
-				<version>${jackson.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>com.fasterxml.jackson.core</groupId>
-				<artifactId>jackson-databind</artifactId>
-				<version>2.10.5.1</version>
-			</dependency>
-			<dependency>
-				<groupId>com.fasterxml.jackson.core</groupId>
-				<artifactId>jackson-annotations</artifactId>
-				<version>${jackson.version}</version>
-			</dependency>
-			<dependency>
-				<groupId>io.jsonwebtoken</groupId>
-				<artifactId>jjwt</artifactId>
-				<version>0.9.0</version>
-			</dependency>
-			<dependency>
-				<groupId>javax</groupId>
-				<artifactId>javaee-api</artifactId>
-				<version>8.0</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>javax.xml.bind</groupId>
-				<artifactId>jaxb-api</artifactId>
-				<version>2.3.0</version>
-			</dependency>
-			<dependency>
-				<groupId>com.sun.xml.bind</groupId>
-				<artifactId>jaxb-core</artifactId>
-				<version>2.3.0</version>
-			</dependency>
-			<dependency>
-				<groupId>com.sun.xml.bind</groupId>
-				<artifactId>jaxb-impl</artifactId>
-				<version>2.3.0</version>
-			</dependency>
-            <!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-core -->
-            <dependency>
-				<groupId>org.hibernate.javax.persistence</groupId>
-				<artifactId>hibernate-jpa-2.1-api</artifactId>
-				<version>1.0.2.Final</version>
-				<scope>provided</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.hibernate</groupId>
-				<artifactId>hibernate-annotations</artifactId>
-				<version>3.5.6-Final</version>
-				<scope>provided</scope>
-				<exclusions>
-					<exclusion>
-						<groupId>org.hibernate.javax.persistence</groupId>
-						<artifactId>hibernate-jpa-2.0-api</artifactId>
-					</exclusion>
-				</exclusions>
-			</dependency>
-			<!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
-				<dependency>
-				<groupId>org.slf4j</groupId>
-				<artifactId>slf4j-api</artifactId>
-				<version>1.7.25</version>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.commons</groupId>
-				<artifactId>commons-lang3</artifactId>
-				<version>3.7</version>
-				<scope>compile</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.slf4j</groupId>
-				<artifactId>slf4j-log4j12</artifactId>
-				<version>1.7.25</version>
-				<scope>test</scope>
-			</dependency>
+          </configuration>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+  </build>
+  <dependencies>
+    <dependency>
+      <groupId>junit</groupId>
+      <artifactId>junit</artifactId>
+      <version>4.13.1</version>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+  <dependencyManagement>
+    <dependencies>
+      <dependency>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-core</artifactId>
+        <version>${jackson.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-databind</artifactId>
+        <version>2.10.5.1</version>
+      </dependency>
+      <dependency>
+        <groupId>com.fasterxml.jackson.core</groupId>
+        <artifactId>jackson-annotations</artifactId>
+        <version>${jackson.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>io.jsonwebtoken</groupId>
+        <artifactId>jjwt</artifactId>
+        <version>0.9.0</version>
+      </dependency>
+      <dependency>
+        <groupId>javax</groupId>
+        <artifactId>javaee-api</artifactId>
+        <version>8.0</version>
+        <scope>provided</scope>
+      </dependency>
+      <dependency>
+        <groupId>javax.xml.bind</groupId>
+        <artifactId>jaxb-api</artifactId>
+        <version>2.3.0</version>
+      </dependency>
+      <dependency>
+        <groupId>com.sun.xml.bind</groupId>
+        <artifactId>jaxb-core</artifactId>
+        <version>2.3.0</version>
+      </dependency>
+      <dependency>
+        <groupId>com.sun.xml.bind</groupId>
+        <artifactId>jaxb-impl</artifactId>
+        <version>2.3.0</version>
+      </dependency>
+      <!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-core -->
+      <dependency>
+        <groupId>org.hibernate.javax.persistence</groupId>
+        <artifactId>hibernate-jpa-2.1-api</artifactId>
+        <version>1.0.2.Final</version>
+        <scope>provided</scope>
+      </dependency>
+      <dependency>
+        <groupId>org.hibernate</groupId>
+        <artifactId>hibernate-annotations</artifactId>
+        <version>3.5.6-Final</version>
+        <scope>provided</scope>
+        <exclusions>
+          <exclusion>
+            <groupId>org.hibernate.javax.persistence</groupId>
+            <artifactId>hibernate-jpa-2.0-api</artifactId>
+          </exclusion>
+        </exclusions>
+      </dependency>
+      <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api -->
+      <dependency>
+        <groupId>org.slf4j</groupId>
+        <artifactId>slf4j-api</artifactId>
+        <version>1.7.25</version>
+      </dependency>
+      <dependency>
+        <groupId>org.apache.commons</groupId>
+        <artifactId>commons-lang3</artifactId>
+        <version>3.7</version>
+        <scope>compile</scope>
+      </dependency>
+      <dependency>
+        <groupId>org.slf4j</groupId>
+        <artifactId>slf4j-log4j12</artifactId>
+        <version>1.7.25</version>
+        <scope>test</scope>
+      </dependency>
 
-			<!--  Removed log4j 1.2.7 and adding log4j-core -->
-			<dependency>
-					<groupId>org.apache.logging.log4j</groupId>
-					<artifactId>log4j-core</artifactId>
-					<version>2.18.0</version>
-			</dependency>
+      <!--  Removed log4j 1.2.7 and adding log4j-core -->
+      <dependency>
+        <groupId>org.apache.logging.log4j</groupId>
+        <artifactId>log4j-core</artifactId>
+        <version>2.18.0</version>
+      </dependency>
 
-			<!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-core -->
-			<dependency>
-				<groupId>org.hibernate</groupId>
-				<artifactId>hibernate-core</artifactId>
-				<version>3.5.6-Final</version>
-				<scope>provided</scope>
-			</dependency>
+      <!-- https://mvnrepository.com/artifact/org.hibernate/hibernate-core -->
+      <dependency>
+        <groupId>org.hibernate</groupId>
+        <artifactId>hibernate-core</artifactId>
+        <version>3.5.6-Final</version>
+        <scope>provided</scope>
+      </dependency>
 
-			<dependency>
-				<groupId>org.apache.httpcomponents</groupId>
-				<artifactId>httpcore</artifactId>
-				<version>4.4.4</version>
-			</dependency>
-			<dependency>
-				<groupId>org.apache.httpcomponents</groupId>
-				<artifactId>httpclient</artifactId>
-				<version>4.5.13</version>
-			</dependency>
-			<dependency>
-				<groupId>commons-io</groupId>
-				<artifactId>commons-io</artifactId>
-				<version>2.7</version>
-			</dependency>
-			<dependency>
-				<groupId>com.github.tomakehurst</groupId>
-				<artifactId>wiremock-standalone</artifactId>
-				<version>2.14.0</version>
-				<scope>test</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.glassfish.jersey.core</groupId>
-				<artifactId>jersey-common</artifactId>
-				<version>2.26</version>
-				<scope>test</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.jboss.resteasy</groupId>
-				<artifactId>resteasy-jaxb-provider</artifactId>
-				<version>3.15.1</version>
-			</dependency>
-			<dependency>
-				<groupId>org.mockito</groupId>
-				<artifactId>mockito-core</artifactId>
-				<version>2.23.4</version>
-				<scope>test</scope>
-			</dependency>
-			<dependency>
-				<groupId>org.jboss.resteasy</groupId>
-				<artifactId>resteasy-jackson2-provider</artifactId>
-				<version>3.15.6.Final</version>
-			</dependency>
+      <dependency>
+        <groupId>org.apache.httpcomponents</groupId>
+        <artifactId>httpcore</artifactId>
+        <version>4.4.4</version>
+      </dependency>
+      <dependency>
+        <groupId>org.apache.httpcomponents</groupId>
+        <artifactId>httpclient</artifactId>
+        <version>4.5.13</version>
+      </dependency>
+      <dependency>
+        <groupId>commons-io</groupId>
+        <artifactId>commons-io</artifactId>
+        <version>2.7</version>
+      </dependency>
+      <dependency>
+        <groupId>com.github.tomakehurst</groupId>
+        <artifactId>wiremock-standalone</artifactId>
+        <version>2.14.0</version>
+        <scope>test</scope>
+      </dependency>
+      <dependency>
+        <groupId>org.glassfish.jersey.core</groupId>
+        <artifactId>jersey-common</artifactId>
+        <version>2.26</version>
+        <scope>test</scope>
+      </dependency>
+      <dependency>
+        <groupId>org.jboss.resteasy</groupId>
+        <artifactId>resteasy-jaxb-provider</artifactId>
+        <version>3.15.1</version>
+      </dependency>
+      <dependency>
+        <groupId>org.mockito</groupId>
+        <artifactId>mockito-core</artifactId>
+        <version>2.23.4</version>
+        <scope>test</scope>
+      </dependency>
+      <dependency>
+        <groupId>org.jboss.resteasy</groupId>
+        <artifactId>resteasy-jackson2-provider</artifactId>
+        <version>3.15.6.Final</version>
+      </dependency>
 
-			<dependency>
-				<groupId>io.swagger.core.v3</groupId>
-				<artifactId>swagger-jaxrs2</artifactId>
-				<version>2.2.7</version>
-			</dependency>
-			<dependency>
-				<groupId>io.swagger.core.v3</groupId>
-				<artifactId>swagger-jaxrs2-servlet-initializer-v2</artifactId>
-				<version>2.2.7</version>
-			</dependency>
-			<dependency>
-				<groupId>io.swagger.core.v3</groupId>
-				<artifactId>swagger-annotations</artifactId>
-				<version>2.2.8</version>
-			</dependency>
-		</dependencies>
-	</dependencyManagement>
-	<distributionManagement>
-		<repository>
-			<id>github</id>
-			<name>GitHub HMS-DBMI Apache Maven Packages</name>
-			<url>https://maven.pkg.github.com/hms-dbmi/pic-sure</url>
-		</repository>
-	</distributionManagement>
+      <dependency>
+        <groupId>io.swagger.core.v3</groupId>
+        <artifactId>swagger-jaxrs2</artifactId>
+        <version>2.2.7</version>
+      </dependency>
+      <dependency>
+        <groupId>io.swagger.core.v3</groupId>
+        <artifactId>swagger-jaxrs2-servlet-initializer-v2</artifactId>
+        <version>2.2.7</version>
+      </dependency>
+      <dependency>
+        <groupId>io.swagger.core.v3</groupId>
+        <artifactId>swagger-annotations</artifactId>
+        <version>2.2.8</version>
+      </dependency>
+    </dependencies>
+  </dependencyManagement>
+  <distributionManagement>
+    <repository>
+      <id>github</id>
+      <name>GitHub HMS-DBMI Apache Maven Packages</name>
+      <url>https://maven.pkg.github.com/hms-dbmi/pic-sure</url>
+    </repository>
+  </distributionManagement>
 </project>