From feff73473610b49bd4fc9492fab8c8e1933b3174 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 22 Jan 2021 11:24:23 -0500
Subject: [PATCH] Bump jaxb-runtime from 2.3.1 to 3.0.0 (#2289)

* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Bump jaxb-runtime from 2.3.1 to 3.0.0

Bumps jaxb-runtime from 2.3.1 to 3.0.0.

Signed-off-by: dependabot[bot] <support@github.com>

* Add jakarta bindings

* Dependency cleanup

* More depndency cleanup

* Work on deps

* Replace transaction annotation

* Cleanup

* Another fix

* Build fix

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: jamesagnew <jamesagnew@gmail.com>
---
 hapi-deployable-pom/pom.xml                   | 12 ++---
 hapi-fhir-cli/hapi-fhir-cli-api/pom.xml       |  8 ---
 hapi-fhir-jpaserver-api/pom.xml               | 50 ++++++-------------
 hapi-fhir-jpaserver-base/pom.xml              | 45 -----------------
 .../search/HapiLuceneAnalysisConfigurer.java  |  2 -
 hapi-fhir-jpaserver-model/pom.xml             | 16 +++---
 hapi-fhir-structures-dstu2.1/pom.xml          | 10 ----
 hapi-fhir-structures-dstu2/pom.xml            | 10 ----
 hapi-fhir-structures-dstu3/pom.xml            | 38 --------------
 hapi-fhir-structures-hl7org-dstu2/pom.xml     | 10 ----
 hapi-fhir-structures-r4/pom.xml               | 10 ----
 hapi-fhir-validation/pom.xml                  | 10 ----
 pom.xml                                       | 10 +---
 13 files changed, 26 insertions(+), 205 deletions(-)

diff --git a/hapi-deployable-pom/pom.xml b/hapi-deployable-pom/pom.xml
index 2781a057c6f..4b57d899174 100644
--- a/hapi-deployable-pom/pom.xml
+++ b/hapi-deployable-pom/pom.xml
@@ -99,14 +99,6 @@
 							<groupId>javax.mail</groupId>
 							<artifactId>javax.mail-api</artifactId>
 						</dependency>
-						<dependency>
-							<groupId>javax.activation</groupId>
-							<artifactId>javax.activation-api</artifactId>
-						</dependency>
-						<dependency>
-							<groupId>com.helger</groupId>
-							<artifactId>ph-schematron</artifactId>
-						</dependency>
 						<dependency>
 							<groupId>commons-logging</groupId>
 							<artifactId>commons-logging</artifactId>
@@ -151,6 +143,10 @@
 							<groupId>net.bytebuddy</groupId>
 							<artifactId>byte-buddy</artifactId>
 						</dependency>
+						<dependency>
+							<groupId>javax.xml.bind</groupId>
+							<artifactId>jaxb-api</artifactId>
+						</dependency>
 						<dependency>
 							<groupId>com.sun.xml.bind</groupId>
 							<artifactId>jaxb-impl</artifactId>
diff --git a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
index 1d373e7221d..6fb9e4b6835 100644
--- a/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
+++ b/hapi-fhir-cli/hapi-fhir-cli-api/pom.xml
@@ -224,14 +224,6 @@
 			<groupId>javax.xml.bind</groupId>
 			<artifactId>jaxb-api</artifactId>
 		</dependency>
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-core</artifactId>-->
-		<!--</dependency>-->
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-impl</artifactId>-->
-		<!--</dependency>-->
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
diff --git a/hapi-fhir-jpaserver-api/pom.xml b/hapi-fhir-jpaserver-api/pom.xml
index 843ebfd672a..07c7e0c1bfe 100644
--- a/hapi-fhir-jpaserver-api/pom.xml
+++ b/hapi-fhir-jpaserver-api/pom.xml
@@ -56,37 +56,15 @@
 			<artifactId>hapi-fhir-structures-hl7org-dstu2</artifactId>
 			<version>${project.version}</version>
 		</dependency>
-        <dependency>
-            <groupId>ca.uhn.hapi.fhir</groupId>
-            <artifactId>hapi-fhir-jpaserver-model</artifactId>
-            <version>${project.version}</version>
-        </dependency>
-        <dependency>
-            <groupId>ca.uhn.hapi.fhir</groupId>
-            <artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
-            <version>${project.version}</version>
-        </dependency>
 		<dependency>
-			<groupId>org.hibernate</groupId>
-			<artifactId>hibernate-core</artifactId>
-			<exclusions>
-				<exclusion>
-					<artifactId>xml-apis</artifactId>
-					<groupId>xml-apis</groupId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.jboss.spec.javax.transaction</groupId>
-					<artifactId>jboss-transaction-api_1.2_spec</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>javax.activation</groupId>
-					<artifactId>activation</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>javax.activation</groupId>
-					<artifactId>javax.activation-api</artifactId>
-				</exclusion>
-			</exclusions>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-model</artifactId>
+			<version>${project.version}</version>
+		</dependency>
+		<dependency>
+			<groupId>ca.uhn.hapi.fhir</groupId>
+			<artifactId>hapi-fhir-jpaserver-searchparam</artifactId>
+			<version>${project.version}</version>
 		</dependency>
 		<dependency>
 			<groupId>org.hibernate.search</groupId>
@@ -137,13 +115,13 @@
 			<artifactId>javax.annotation-api</artifactId>
 		</dependency>
 
-        <dependency>
-            <groupId>javax.servlet</groupId>
-            <artifactId>javax.servlet-api</artifactId>
-            <scope>provided</scope>
-        </dependency>
+		<dependency>
+			<groupId>javax.servlet</groupId>
+			<artifactId>javax.servlet-api</artifactId>
+			<scope>provided</scope>
+		</dependency>
 
-        <!-- test dependencies -->
+		<!-- test dependencies -->
 		<dependency>
 			<groupId>ch.qos.logback</groupId>
 			<artifactId>logback-classic</artifactId>
diff --git a/hapi-fhir-jpaserver-base/pom.xml b/hapi-fhir-jpaserver-base/pom.xml
index 4322697f967..f012a3ff2e1 100644
--- a/hapi-fhir-jpaserver-base/pom.xml
+++ b/hapi-fhir-jpaserver-base/pom.xml
@@ -373,43 +373,13 @@
 		</dependency>
 
 		<!-- Hibernate -->
-		<dependency>
-			<groupId>org.hibernate</groupId>
-			<artifactId>hibernate-core</artifactId>
-			<exclusions>
-				<exclusion>
-					<artifactId>xml-apis</artifactId>
-					<groupId>xml-apis</groupId>
-				</exclusion>
-				<exclusion>
-					<groupId>javax.activation</groupId>
-					<artifactId>javax.activation-api</artifactId>
-				</exclusion>
-				<!--<exclusion>-->
-				<!--<groupId>org.jboss.spec.javax.transaction</groupId>-->
-				<!--<artifactId>jboss-transaction-api_1.2_spec</artifactId>-->
-				<!--</exclusion>-->
-			</exclusions>
-		</dependency>
 		<dependency>
 			<groupId>org.hibernate</groupId>
 			<artifactId>hibernate-entitymanager</artifactId>
-			<exclusions>
-				<exclusion>
-					<groupId>org.jboss.spec.javax.transaction</groupId>
-					<artifactId>jboss-transaction-api_1.2_spec</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.hibernate</groupId>
 			<artifactId>hibernate-java8</artifactId>
-			<exclusions>
-				<exclusion>
-					<groupId>org.jboss.spec.javax.transaction</groupId>
-					<artifactId>jboss-transaction-api_1.2_spec</artifactId>
-				</exclusion>
-			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.hibernate</groupId>
@@ -435,11 +405,6 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-		<dependency>
-			<groupId>com.sun.activation</groupId>
-			<artifactId>javax.activation</artifactId>
-			<version>1.2.0</version>
-		</dependency>
 		<dependency>
 			<groupId>javax.mail</groupId>
 			<artifactId>javax.mail-api</artifactId>
@@ -715,16 +680,6 @@
 						<artifactId>jaxb-runtime</artifactId>
 						<version>${jaxb_runtime_version}</version>
 					</dependency>
-					<!--<dependency>-->
-					<!--<groupId>com.sun.xml.bind</groupId>-->
-					<!--<artifactId>jaxb-core</artifactId>-->
-					<!--<version>${jaxb_core_version}</version>-->
-					<!--</dependency>-->
-					<!--<dependency>-->
-					<!--<groupId>com.sun.xml.bind</groupId>-->
-					<!--<artifactId>jaxb-impl</artifactId>-->
-					<!--<version>${jaxb_core_version}</version>-->
-					<!--</dependency>-->
 				</dependencies>
 			</plugin>
 			<plugin>
diff --git a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/HapiLuceneAnalysisConfigurer.java b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/HapiLuceneAnalysisConfigurer.java
index 5e2ac24acda..63be4acab22 100644
--- a/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/HapiLuceneAnalysisConfigurer.java
+++ b/hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/search/HapiLuceneAnalysisConfigurer.java
@@ -20,7 +20,6 @@ package ca.uhn.fhir.jpa.search;
  * #L%
  */
 
-import com.sun.xml.bind.api.impl.NameConverter;
 import org.apache.lucene.analysis.core.KeywordTokenizerFactory;
 import org.apache.lucene.analysis.core.LowerCaseFilterFactory;
 import org.apache.lucene.analysis.core.StopFilterFactory;
@@ -35,7 +34,6 @@ import org.apache.lucene.analysis.standard.StandardTokenizerFactory;
 import org.hibernate.search.backend.lucene.analysis.LuceneAnalysisConfigurationContext;
 import org.hibernate.search.backend.lucene.analysis.LuceneAnalysisConfigurer;
 import org.springframework.stereotype.Component;
-import org.springframework.stereotype.Service;
 
 /**
  * Factory for defining the analysers.
diff --git a/hapi-fhir-jpaserver-model/pom.xml b/hapi-fhir-jpaserver-model/pom.xml
index a33574e8ccf..20f587e4ab0 100644
--- a/hapi-fhir-jpaserver-model/pom.xml
+++ b/hapi-fhir-jpaserver-model/pom.xml
@@ -12,16 +12,16 @@
 	<artifactId>hapi-fhir-jpaserver-model</artifactId>
 	<packaging>jar</packaging>
 
-	<name>HAPI FHIR Model</name>
+	<name>HAPI FHIR JPA Model</name>
 
 	<dependencies>
-	
+
 		<!--  FHIR  -->
 		<dependency>
-    		<groupId>org.fhir</groupId>
-    		<artifactId>ucum</artifactId>
-    	</dependency>
-	
+			<groupId>org.fhir</groupId>
+			<artifactId>ucum</artifactId>
+		</dependency>
+
 		<dependency>
 			<groupId>ca.uhn.hapi.fhir</groupId>
 			<artifactId>hapi-fhir-base</artifactId>
@@ -71,10 +71,6 @@
 					<artifactId>xml-apis</artifactId>
 					<groupId>xml-apis</groupId>
 				</exclusion>
-				<exclusion>
-					<groupId>org.jboss.spec.javax.transaction</groupId>
-					<artifactId>jboss-transaction-api_1.2_spec</artifactId>
-				</exclusion>
 				<exclusion>
 					<groupId>javax.activation</groupId>
 					<artifactId>activation</artifactId>
diff --git a/hapi-fhir-structures-dstu2.1/pom.xml b/hapi-fhir-structures-dstu2.1/pom.xml
index 8ab6ce22d2e..7b99ba1e215 100644
--- a/hapi-fhir-structures-dstu2.1/pom.xml
+++ b/hapi-fhir-structures-dstu2.1/pom.xml
@@ -235,16 +235,6 @@
 			<artifactId>jaxb-api</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-core</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-impl</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
diff --git a/hapi-fhir-structures-dstu2/pom.xml b/hapi-fhir-structures-dstu2/pom.xml
index b8873469e41..e33032dd929 100644
--- a/hapi-fhir-structures-dstu2/pom.xml
+++ b/hapi-fhir-structures-dstu2/pom.xml
@@ -125,16 +125,6 @@
 			<artifactId>jaxb-api</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-core</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-impl</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
diff --git a/hapi-fhir-structures-dstu3/pom.xml b/hapi-fhir-structures-dstu3/pom.xml
index 90d3d27520a..477963a6cdd 100644
--- a/hapi-fhir-structures-dstu3/pom.xml
+++ b/hapi-fhir-structures-dstu3/pom.xml
@@ -197,23 +197,6 @@
 			<optional>true</optional>
 		</dependency>
 
-		<!--
-		<dependency>
-			<groupId>xpp3</groupId>
-			<artifactId>xpp3_min</artifactId>
-			<version>1.1.4c</version>
-			<optional>true</optional>
-		</dependency>
-		-->
-
-		<!--
-		<dependency>
-			<groupId>net.sf.saxon</groupId>
-			<artifactId>Saxon-HE</artifactId>
-			<version>9.6.0-4</version>
-		</dependency>
-		-->
-
 		<!-- Used by the validator -->
 		<dependency>
 			<groupId>com.github.ben-manes.caffeine</groupId>
@@ -292,27 +275,6 @@
 			<artifactId>javax.activation-api</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<dependency>
-			<groupId>javax.xml.bind</groupId>
-			<artifactId>jaxb-api</artifactId>
-			<scope>test</scope>
-		</dependency>
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-core</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-impl</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
-		<dependency>
-			<groupId>org.glassfish.jaxb</groupId>
-			<artifactId>jaxb-runtime</artifactId>
-			<scope>test</scope>
-		</dependency>
-
 
 		<!-- UNIT TEST DEPENDENCIES -->
 		<dependency>
diff --git a/hapi-fhir-structures-hl7org-dstu2/pom.xml b/hapi-fhir-structures-hl7org-dstu2/pom.xml
index 61c226a13de..f60c3d14611 100644
--- a/hapi-fhir-structures-hl7org-dstu2/pom.xml
+++ b/hapi-fhir-structures-hl7org-dstu2/pom.xml
@@ -176,16 +176,6 @@
 			<artifactId>jaxb-api</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-core</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-impl</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
diff --git a/hapi-fhir-structures-r4/pom.xml b/hapi-fhir-structures-r4/pom.xml
index efa1c54d01f..cfecffc5da3 100644
--- a/hapi-fhir-structures-r4/pom.xml
+++ b/hapi-fhir-structures-r4/pom.xml
@@ -245,16 +245,6 @@
 			<artifactId>jaxb-api</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-core</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-impl</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
diff --git a/hapi-fhir-validation/pom.xml b/hapi-fhir-validation/pom.xml
index f4f609cda83..6122a2d5224 100644
--- a/hapi-fhir-validation/pom.xml
+++ b/hapi-fhir-validation/pom.xml
@@ -268,16 +268,6 @@
 			<artifactId>jaxb-api</artifactId>
 			<scope>test</scope>
 		</dependency>
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-core</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
-		<!--<dependency>-->
-			<!--<groupId>com.sun.xml.bind</groupId>-->
-			<!--<artifactId>jaxb-impl</artifactId>-->
-			<!--<scope>test</scope>-->
-		<!--</dependency>-->
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
diff --git a/pom.xml b/pom.xml
index f38a6af45b0..efc9b20b587 100644
--- a/pom.xml
+++ b/pom.xml
@@ -746,7 +746,7 @@
 		<jaxb_bundle_version>2.2.11_1</jaxb_bundle_version>
 		<jaxb_api_version>2.3.1</jaxb_api_version>
 		<jaxb_core_version>2.3.0.1</jaxb_core_version>
-		<jaxb_runtime_version>2.3.1</jaxb_runtime_version>
+		<jaxb_runtime_version>3.0.0</jaxb_runtime_version>
 		<jena_version>3.16.0</jena_version>
 		<jersey_version>3.0.0</jersey_version>
 		<!-- 9.4.17 seems to have issues -->
@@ -892,12 +892,6 @@
 				<groupId>com.helger</groupId>
 				<artifactId>ph-schematron</artifactId>
 				<version>${ph_schematron_version}</version>
-				<exclusions>
-					<exclusion>
-						<groupId>jakarta.xml.bind</groupId>
-						<artifactId>jakarta.xml.bind-api</artifactId>
-               </exclusion>
-				</exclusions>
 			</dependency>
 			<dependency>
 				<groupId>com.helger</groupId>
@@ -917,7 +911,7 @@
 			<dependency>
 				<groupId>com.sun.activation</groupId>
 				<artifactId>jakarta.activation</artifactId>
-				<version>1.2.1</version>
+				<version>2.0.0</version>
 			</dependency>
 			<dependency>
 				<groupId>com.sun.mail</groupId>