From 7b6bce628246f7654ea4b9a9bdf1414dc53b9b78 Mon Sep 17 00:00:00 2001
From: Tadgh <garygrantgraham@gmail.com>
Date: Mon, 9 Dec 2024 22:44:20 -0800
Subject: [PATCH] Plugin cleanup (#6545)

* wip remove old maven

* remove mvn 2 dep, bump plugin-api and plugin-annotations

* import maven core

* Remove weird collections import

* wip

* Bump license plugin, versions plugin, and jacoco plugin. Remove coveralls

* Bump shade, antrun, errorprone

* Fix errorprone warning about duplicate branches in XMLUtil

* Fix errorprone warning about duplicate branches in SctHandlerRelationship

* Exclude docs snippets

* Remove old-intellij

* Add profile for errorprone, completely remove ROOT profile

* move errorprone into a profile

* license

* reset pom version

* spotless

* Reinstate errorprone

* self review

* revert migration move

* Reversion of DO_NOTHING

---------

Co-authored-by: tadgh <garygraham@smiledigitalhealth.com>
---
 .../main/java/ca/uhn/fhir/util/XmlUtil.java   |   6 +-
 hapi-fhir-dist/pom.xml                        |   2 +-
 .../term/snomedct/SctHandlerRelationship.java |   4 -
 hapi-tinder-plugin/pom.xml                    |  31 +--
 .../uhn/fhir/tinder/model/BaseRootType.java   |   2 +-
 pom.xml                                       | 192 +++++++-----------
 6 files changed, 76 insertions(+), 161 deletions(-)

diff --git a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/XmlUtil.java b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/XmlUtil.java
index f49de276065..867af919470 100644
--- a/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/XmlUtil.java
+++ b/hapi-fhir-base/src/main/java/ca/uhn/fhir/util/XmlUtil.java
@@ -1678,11 +1678,7 @@ public class XmlUtil {
 			XMLEventWriter ew = XmlUtil.createXmlFragmentWriter(w);
 
 			for (XMLEvent next : theEvents) {
-				if (next.isCharacters()) {
-					ew.add(next);
-				} else {
-					ew.add(next);
-				}
+				ew.add(next);
 			}
 			ew.close();
 			return w.toString();
diff --git a/hapi-fhir-dist/pom.xml b/hapi-fhir-dist/pom.xml
index 8ffce201dd0..c2aac03bba4 100644
--- a/hapi-fhir-dist/pom.xml
+++ b/hapi-fhir-dist/pom.xml
@@ -265,7 +265,7 @@
 				<plugins>
 					<plugin>
 						<artifactId>maven-assembly-plugin</artifactId>
-						<version>${maven_assembly_plugin_version}</version>
+						<version>${maven-assembly-plugin-version}</version>
 						<executions>
 							<execution>
 								<phase>package</phase>
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/snomedct/SctHandlerRelationship.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/snomedct/SctHandlerRelationship.java
index 7fd1838f62c..9de4c3927d7 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/snomedct/SctHandlerRelationship.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/term/snomedct/SctHandlerRelationship.java
@@ -92,10 +92,6 @@ public final class SctHandlerRelationship implements IZipContentsHandlerCsv {
 						}
 					}
 				}
-			} else if (ignoredTypes.contains(typeConcept.getDisplay())) {
-				// ignore
-			} else {
-				// ourLog.warn("Unknown relationship type: {}/{}", typeId, typeConcept.getDisplay());
 			}
 		}
 	}
diff --git a/hapi-tinder-plugin/pom.xml b/hapi-tinder-plugin/pom.xml
index ed97670654c..05c3fdd10cb 100644
--- a/hapi-tinder-plugin/pom.xml
+++ b/hapi-tinder-plugin/pom.xml
@@ -41,10 +41,10 @@
 		</dependency>
 		<!--
 		Because Tinder is a part of the HAPI FHIR build process (it generates
-		a bunch of the actual HAPI structure code), but also uses HAPI FHIR 
+		a bunch of the actual HAPI structure code), but also uses HAPI FHIR
 		in order to run (e.g. to load ValueSet resources), we keep the dependencies
 		for the structures
-		a version behind the main library. This is weird, but it works. 
+		a version behind the main library. This is weird, but it works.
 		-->
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
@@ -163,23 +163,8 @@
 		<!-- Maven -->
 		<dependency>
 			<groupId>org.apache.maven</groupId>
-			<artifactId>maven-project</artifactId>
-			<!--
-		<exclusions>
-			<exclusion>
-				<groupId>org.codehaus.plexus</groupId>
-				<artifactId>plexus-utils</artifactId>
-			</exclusion>
-			<exclusion>
-				<groupId>org.apache.maven</groupId>
-				<artifactId>maven-model</artifactId>
-			</exclusion>
-			<exclusion>
-				<groupId>org.apache.maven</groupId>
-				<artifactId>maven-artifact</artifactId>
-			</exclusion>
-		</exclusions>
-		-->
+			<artifactId>maven-core</artifactId>
+		<version>3.9.9</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.maven</groupId>
@@ -190,14 +175,6 @@
 			<groupId>org.apache.maven.plugin-tools</groupId>
 			<artifactId>maven-plugin-annotations</artifactId>
 			<scope>provided</scope>
-			<!--
-            <exclusions>
-				<exclusion>
-					<groupId>org.apache.maven</groupId>
-					<artifactId>maven-artifact</artifactId>
-				</exclusion>
-			</exclusions>
-			-->
 		</dependency>
 
 		<!-- Ant tasks -->
diff --git a/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/BaseRootType.java b/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/BaseRootType.java
index a7afd8c9f8c..3c193feebc7 100644
--- a/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/BaseRootType.java
+++ b/hapi-tinder-plugin/src/main/java/ca/uhn/fhir/tinder/model/BaseRootType.java
@@ -1,9 +1,9 @@
 package ca.uhn.fhir.tinder.model;
 
 import ca.uhn.fhir.tinder.model.SearchParameter.Include;
-import edu.emory.mathcs.backport.java.util.Collections;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.List;
 
 public abstract class BaseRootType extends BaseElement {
diff --git a/pom.xml b/pom.xml
index d56db2046d3..0e12614c049 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1015,7 +1015,7 @@
 		<commons_io_version>2.17.0</commons_io_version>
 		<commons_lang3_version>3.17.0</commons_lang3_version>
 		<com_jamesmurty_utils_version>1.2</com_jamesmurty_utils_version>
-		<error_prone_core_version>2.23.0</error_prone_core_version>
+		<error_prone_core_version>2.36.0</error_prone_core_version>
 		<mockito_version>5.8.0</mockito_version>
 		<nullaway_version>0.7.9</nullaway_version>
 		<guava_version>33.2.1-jre</guava_version>
@@ -1045,6 +1045,8 @@
 		<jackson_databind_version>2.18.1</jackson_databind_version>
 		<httpclient5_version>5.4.1</httpclient5_version>
 		<httpcore5_version>5.3.1</httpcore5_version>
+		<jackson_version>2.17.1</jackson_version>
+		<jackson_databind_version>2.17.1</jackson_databind_version>
 		<maven_assembly_plugin_version>3.3.0</maven_assembly_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
 		<okhttp_version>4.12.0</okhttp_version>
@@ -1069,7 +1071,6 @@
 		<log4j_to_slf4j_version>2.24.1</log4j_to_slf4j_version>
 		<spring_version>6.1.14</spring_version>
 		<spring_data_bom_version>2024.0.5</spring_data_bom_version>
-		<spring_batch_version>4.3.10</spring_batch_version>
 		<spring_boot_version>3.3.5</spring_boot_version>
 		<spring_retry_version>2.0.10</spring_retry_version>
 		<json_path_version>2.9.0</json_path_version>
@@ -1095,10 +1096,19 @@
 		<maven.compiler.testSource>17</maven.compiler.testSource>
 		<maven.compiler.testTarget>17</maven.compiler.testTarget>
 		<maven.compiler.testRelease>17</maven.compiler.testRelease>
-		<maven_checkstyle_version>3.4.0</maven_checkstyle_version>
 
 		<!-- Jacoco -->
 		<argLine></argLine>
+
+		<!-- Plugin Versioning -->
+		<maven-resources-plugin-version>3.3.0</maven-resources-plugin-version>
+		<buildnumber-maven-plugin-version>3.2.1</buildnumber-maven-plugin-version>
+		<jacoco-maven-plugin-version>0.8.12</jacoco-maven-plugin-version>
+		<maven-assembly-plugin-version>3.3.0</maven-assembly-plugin-version>
+		<maven-license-plugin-version>2.5.0</maven-license-plugin-version>
+		<maven-enforcer-plugin-version>3.5.0</maven-enforcer-plugin-version>
+		<maven-checkstyle-version>3.4.0</maven-checkstyle-version>
+
 	</properties>
 
 	<dependencyManagement>
@@ -1676,21 +1686,16 @@
 				<artifactId>wagon-scm</artifactId>
 				<version>3.4.3</version>
 			</dependency>
-			<dependency>
-				<groupId>org.apache.maven</groupId>
-				<artifactId>maven-project</artifactId>
-				<version>2.2.1</version>
-			</dependency>
 			<dependency>
 				<groupId>org.apache.maven</groupId>
 				<artifactId>maven-plugin-api</artifactId>
-				<version>3.8.6</version>
+				<version>3.9.9</version>
 				<scope>provided</scope>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.maven.plugin-tools</groupId>
 				<artifactId>maven-plugin-annotations</artifactId>
-				<version>3.9.0</version>
+				<version>3.14.0</version>
 			</dependency>
 			<dependency>
 				<groupId>org.apache.poi</groupId>
@@ -2442,7 +2447,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-resources-plugin</artifactId>
-					<version>3.3.0</version>
+					<version>${maven-resources-plugin-version}</version>
 				</plugin>
 				<plugin>
 					<groupId>org.springframework.boot</groupId>
@@ -2462,7 +2467,7 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-assembly-plugin</artifactId>
-					<version>${maven_assembly_plugin_version}</version>
+					<version>${maven-assembly-plugin-version}</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.felix</groupId>
@@ -2472,37 +2477,38 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-antrun-plugin</artifactId>
-					<version>3.0.0</version>
-				</plugin>
-				<plugin>
-					<groupId>org.apache.maven.plugins</groupId>
-					<artifactId>maven-clean-plugin</artifactId>
 					<version>3.1.0</version>
 				</plugin>
+				<plugin>
+					<groupId>org.apache.maven.plugins</groupId>
+					<artifactId>maven-clean-plugin</artifactId>
+					<version>3.4.0</version>
+				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-compiler-plugin</artifactId>
-					<version>3.11.0</version>
+					<version>3.13.0</version>
 					<configuration>
-						<forceJavacCompilerUse>true</forceJavacCompilerUse>
 						<encoding>UTF-8</encoding>
 						<fork>true</fork>
 						<meminitial>500m</meminitial>
 						<maxmem>2000m</maxmem>
-						<compilerArgs>
-							<arg>-XDcompilePolicy=simple</arg>
-							<arg>-Xplugin:ErrorProne -Xep:MissingSummary:OFF -Xep:JavaUtilDate:OFF -XepExcludedPaths:.*/src/test/java/.*</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.main=ALL-UNNAMED</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.model=ALL-UNNAMED</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.processing=ALL-UNNAMED</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED</arg>
-							<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED</arg>
-							<arg>-J--add-opens=jdk.compiler/com.sun.tools.javac.code=ALL-UNNAMED</arg>
-							<arg>-J--add-opens=jdk.compiler/com.sun.tools.javac.comp=ALL-UNNAMED</arg>
-						</compilerArgs>
+						<forceLegacyJavacApi>true</forceLegacyJavacApi>
+							<compilerArgs>
+								<arg>-XDcompilePolicy=simple</arg>
+								<arg>--should-stop=ifError=FLOW</arg>
+								<arg>-Xplugin:ErrorProne -Xep:MissingSummary:OFF -Xep:JavaUtilDate:OFF -XepExcludedPaths:.*/src/test/java/.*|.*/hapi-fhir-docs/src/main/java/.*</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.api=ALL-UNNAMED</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.file=ALL-UNNAMED</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.main=ALL-UNNAMED</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.model=ALL-UNNAMED</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.parser=ALL-UNNAMED</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.processing=ALL-UNNAMED</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.tree=ALL-UNNAMED</arg>
+								<arg>-J--add-exports=jdk.compiler/com.sun.tools.javac.util=ALL-UNNAMED</arg>
+								<arg>-J--add-opens=jdk.compiler/com.sun.tools.javac.code=ALL-UNNAMED</arg>
+								<arg>-J--add-opens=jdk.compiler/com.sun.tools.javac.comp=ALL-UNNAMED</arg>
+							</compilerArgs>
 						<annotationProcessorPaths>
 							<path>
 								<groupId>com.google.errorprone</groupId>
@@ -2567,12 +2573,12 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-shade-plugin</artifactId>
-					<version>2.4.3</version>
+					<version>3.6.0</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-source-plugin</artifactId>
-					<version>3.2.1</version>
+					<version>3.3.1</version>
 				</plugin>
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
@@ -2598,30 +2604,22 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-war-plugin</artifactId>
-					<version>3.3.2</version>
+					<version>3.4.0</version>
 				</plugin>
 				<plugin>
 					<groupId>org.codehaus.mojo</groupId>
 					<artifactId>build-helper-maven-plugin</artifactId>
-					<version>3.2.0</version>
+					<version>3.6.0</version>
 				</plugin>
 				<plugin>
 					<groupId>org.codehaus.mojo</groupId>
 					<artifactId>buildnumber-maven-plugin</artifactId>
-					<version>3.0.0</version>
-				</plugin>
-				<plugin>
-					<groupId>org.codehaus.mojo</groupId>
-					<artifactId>cobertura-maven-plugin</artifactId>
-					<version>2.7</version>
-					<configuration>
-						<skip>true</skip>
-					</configuration>
+					<version>${buildnumber-maven-plugin-version}</version>
 				</plugin>
 				<plugin>
 					<groupId>org.codehaus.mojo</groupId>
 					<artifactId>license-maven-plugin</artifactId>
-					<version>2.0.0</version>
+					<version>${maven-license-plugin-version}</version>
 					<configuration>
 						<verbose>true</verbose>
 						<addSvnKeyWords>false</addSvnKeyWords>
@@ -2631,7 +2629,7 @@
 				<plugin>
 					<groupId>org.codehaus.mojo</groupId>
 					<artifactId>versions-maven-plugin</artifactId>
-					<version>2.8.1</version>
+					<version>2.18.0</version>
 					<configuration>
 						<processDependencyManagementTransitive>false</processDependencyManagementTransitive>
 					</configuration>
@@ -2646,19 +2644,10 @@
 					<artifactId>maven-changes-plugin</artifactId>
 					<version>${maven_changes_version}</version>
 				</plugin>
-				<plugin>
-					<groupId>org.eluder.coveralls</groupId>
-					<artifactId>coveralls-maven-plugin</artifactId>
-					<version>4.3.0</version>
-					<configuration>
-						<coberturaReports>
-						</coberturaReports>
-					</configuration>
-				</plugin>
 				<plugin>
 					<groupId>org.jacoco</groupId>
 					<artifactId>jacoco-maven-plugin</artifactId>
-					<version>0.8.9</version>
+					<version>${jacoco-maven-plugin-version}</version>
 					<configuration>
 						<excludes>
 							<exclude>ca/uhn/fhir/model/dstu2/**/*.class</exclude>
@@ -2743,12 +2732,12 @@
 				<plugin>
 					<groupId>org.apache.maven.plugins</groupId>
 					<artifactId>maven-install-plugin</artifactId>
-					<version>2.5.2</version>
+					<version>3.1.3</version>
 				</plugin>
 				<plugin>
 					<groupId>org.codehaus.mojo</groupId>
 					<artifactId>animal-sniffer-maven-plugin</artifactId>
-					<version>1.23</version>
+					<version>1.24</version>
 					<configuration>
 						<signature>
 							<groupId>net.sf.androidscents.signature</groupId>
@@ -2773,12 +2762,12 @@
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-checkstyle-plugin</artifactId>
 				<inherited>true</inherited>
-				<version>${maven_checkstyle_version}</version>
+				<version>${maven-checkstyle-version}</version>
 			</plugin>
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-enforcer-plugin</artifactId>
-				<version>3.3.0</version>
+				<version>${maven-enforcer-plugin-version}</version>
 				<executions>
 					<execution>
 						<id>enforce-maven</id>
@@ -3165,21 +3154,6 @@
 				</plugins>
 			</build>
 		</profile>
-		<profile>
-			<id>ROOT</id>
-			<reporting>
-				<plugins>
-				</plugins>
-			</reporting>
-			<modules>
-			</modules>
-			<build>
-				<plugins>
-					<!-- <plugin> <artifactId>maven-assembly-plugin</artifactId> <version>${maven_assembly_plugin_version}</version> <executions> <execution> <phase>package</phase> <goals> <goal>single</goal> </goals>
-						<configuration> <attach>false</attach> <descriptors> <descriptor>${project.basedir}/src/assembly/hapi-fhir-sample-projects.xml</descriptor> </descriptors> </configuration> </execution> </executions> </plugin> -->
-				</plugins>
-			</build>
-		</profile>
 		<profile>
 			<id>JACOCO</id>
 			<build>
@@ -3223,16 +3197,16 @@
 							</execution>
 						</executions>
 					</plugin>
-					<!--					<plugin>-->
-					<!--						<groupId>org.apache.maven.plugins</groupId>-->
-					<!--						<artifactId>maven-checkstyle-plugin</artifactId>-->
-					<!--						<executions>-->
-					<!--							<execution>-->
-					<!--								<id>hapi-single-module-checkstyle</id>-->
-					<!--								<phase>none</phase>-->
-					<!--							</execution>-->
-					<!--						</executions>-->
-					<!--					</plugin>-->
+						<plugin>
+							<groupId>org.apache.maven.plugins</groupId>
+							<artifactId>maven-checkstyle-plugin</artifactId>
+							<executions>
+								<execution>
+									<id>hapi-single-module-checkstyle</id>
+									<phase>none</phase>
+								</execution>
+							</executions>
+						</plugin>
 				</plugins>
 			</build>
 		</profile>
@@ -3284,48 +3258,20 @@
 							</execution>
 						</executions>
 					</plugin>
-					<!--					<plugin>-->
-					<!--						<groupId>org.apache.maven.plugins</groupId>-->
-					<!--						<artifactId>maven-checkstyle-plugin</artifactId>-->
-					<!--						<executions>-->
-					<!--							<execution>-->
-					<!--								<id>validate</id>-->
-					<!--								<phase>none</phase>-->
-					<!--							</execution>-->
-					<!--						</executions>-->
-					<!--					</plugin>-->
-				</plugins>
-			</build>
-		</profile>
-
-		<!--
-		This profile is basically here to work around an IJ bug where the
-		<testSource> tag is ignored in IJ's compiler. See:
-		https://youtrack.jetbrains.com/issue/IDEA-85478
-		IntelliJ 2023.1 now supports this, so we removed the activation.
-		But if you want to run an older IntelliJ, activate the old-intellij profile in the Maven tab.
-		-->
-		<profile>
-			<id>old-intellij</id>
-			<activation>
-				<activeByDefault>false</activeByDefault>
-			</activation>
-			<build>
-				<plugins>
 					<plugin>
 						<groupId>org.apache.maven.plugins</groupId>
-						<artifactId>maven-compiler-plugin</artifactId>
-						<configuration>
-							<source>17</source>
-							<target>17</target>
-							<release>17</release>
-							<testSource>17</testSource>
-							<testTarget>17</testTarget>
-						</configuration>
+						<artifactId>maven-checkstyle-plugin</artifactId>
+						<executions>
+							<execution>
+								<id>validate</id>
+								<phase>none</phase>
+							</execution>
+						</executions>
 					</plugin>
 				</plugins>
 			</build>
 		</profile>
+
 		<profile>
 			<id>ossrh-repo</id>
 			<activation>