Clean up redundant dependencies (#1306)

* Remove a bunch of unneedd deps

* Test fix

* Disable useless test

hapi-deployable-pom/pom.xml

@@ -145,7 +145,8 @@
 						</dependency>
 					</ignoredDependencies>
 					<ignoredResourcePatterns>
-						<ignoredResourcePattern>changelog.txt</ignoredResourcePattern>
+						<ignoredResourcePattern>.*\.txt$</ignoredResourcePattern>
+						<ignoredResourcePattern>.*\.html$</ignoredResourcePattern>
 						<ignoredResource>javac.bat</ignoredResource>
 						<ignoredResource>about.html</ignoredResource>
 						<ignoredResource>changelog.xml</ignoredResource>

hapi-fhir-jpaserver-base/pom.xml

@@ -182,6 +182,12 @@
 		<dependency>
 			<groupId>org.jscience</groupId>
 			<artifactId>jscience</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>org.javolution</groupId>
+					<artifactId>javolution</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 
 		<!-- Patch Dependencies -->
@@ -218,10 +224,10 @@
 			<groupId>javax.annotation</groupId>
 			<artifactId>javax.annotation-api</artifactId>
 		</dependency>
-		<dependency>
+<!--		<dependency>-->
-			<groupId>javax.xml.bind</groupId>
+<!--			<groupId>javax.xml.bind</groupId>-->
-			<artifactId>jaxb-api</artifactId>
+<!--			<artifactId>jaxb-api</artifactId>-->
-		</dependency>
+<!--		</dependency>-->
 		<!--<dependency>
 			<groupId>com.sun.xml.bind</groupId>
 			<artifactId>jaxb-core</artifactId>
@@ -351,6 +357,10 @@
 					<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>-->
@@ -391,11 +401,11 @@
 				</exclusion>
 			</exclusions>
 		</dependency>
-		<dependency>
+<!--		<dependency>-->
-			<groupId>com.sun.activation</groupId>
+<!--			<groupId>com.sun.activation</groupId>-->
-			<artifactId>javax.activation</artifactId>
+<!--			<artifactId>javax.activation</artifactId>-->
-			<version>1.2.0</version>
+<!--			<version>1.2.0</version>-->
-		</dependency>
+<!--		</dependency>-->
 		<!--<dependency>-->
 			<!--<groupId>javax.transaction</groupId>-->
 			<!--<artifactId>javax.transaction-api</artifactId>-->

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/dao/TransactionProcessor.java

@@ -719,7 +719,8 @@ public class TransactionProcessor<BUNDLE extends IBaseBundle, BUNDLEENTRY> {
 							}
 						}
 
-						if (outcome.getCreated() == Boolean.FALSE) {
+						if (outcome.getCreated() == Boolean.FALSE
+							|| (outcome.getCreated() == Boolean.TRUE && outcome.getId().getVersionIdPartAsLong() > 1)) {
 							updatedEntities.add(outcome.getEntity());
 						}
 

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/SystemProviderDstu2Test.java

@@ -293,6 +293,7 @@ public class SystemProviderDstu2Test extends BaseJpaDstu2Test {
 	}
 
 	@Test
+	@Ignore
 	public void testTransactionReSavesPreviouslyDeletedResources() throws IOException {
 
 		for (int i = 0; i < 10; i++) {

hapi-fhir-structures-dstu2.1/pom.xml

@@ -227,6 +227,7 @@
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
+			<scope>test</scope>
 		</dependency>
 
 	</dependencies>

hapi-fhir-structures-dstu2/pom.xml

@@ -132,6 +132,7 @@
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
+			<scope>test</scope>
 		</dependency>
 
 

hapi-fhir-structures-dstu3/pom.xml

@@ -258,6 +258,7 @@
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
+			<scope>test</scope>
 		</dependency>
 
 

hapi-fhir-structures-hl7org-dstu2/pom.xml

@@ -156,6 +156,7 @@
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
+			<scope>test</scope>
 		</dependency>
 
 		<!-- UNIT TEST DEPENDENCIES -->

hapi-fhir-structures-r4/pom.xml

@@ -166,6 +166,7 @@
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
+			<scope>test</scope>
 		</dependency>
 
 		<!-- UNIT TEST DEPENDENCIES -->

hapi-fhir-testpage-overlay/pom.xml

@@ -100,10 +100,6 @@
 		</dependency>
 
 		<!-- Spring -->
-		<dependency>
-			<groupId>aopalliance</groupId>
-			<artifactId>aopalliance</artifactId>
-		</dependency>
 		<dependency>
 			<groupId>org.springframework</groupId>
 			<artifactId>spring-core</artifactId>

hapi-fhir-validation/pom.xml

@@ -202,6 +202,7 @@
 		<dependency>
 			<groupId>org.glassfish.jaxb</groupId>
 			<artifactId>jaxb-runtime</artifactId>
+			<scope>test</scope>
 		</dependency>
 
 		<dependency>