Work on codecov integration

hapi-fhir-jacoco/pom.xml

@@ -318,6 +318,7 @@
 								<fileSet implementation="org.apache.maven.shared.model.fileset.FileSet">
 									<directory>${basedir}/..</directory>
 									<includes>
+										<!--
 										<include>hapi-fhir-base/target/jacoco.exec</include>
 										<include>hapi-fhir-client/target/jacoco.exec</include>
 										<include>hapi-fhir-server/target/jacoco.exec</include>
@@ -326,13 +327,16 @@
 										<include>hapi-fhir-structures-hl7org-dstu2/target/jacoco.exec</include>
 										<include>hapi-fhir-structures-dstu3/target/jacoco.exec</include>
 										<include>hapi-fhir-structures-r4/target/jacoco.exec</include>
+										-->
 										<include>hapi-fhir-jpaserver-model/target/jacoco.exec</include>
 										<include>hapi-fhir-jpaserver-searchparam/target/jacoco.exec</include>
 										<include>hapi-fhir-jpaserver-subscription/target/jacoco.exec</include>
 										<include>hapi-fhir-jpaserver-base/target/jacoco.exec</include>
+										<!--
 										<include>hapi-fhir-client-okhttp/target/jacoco.exec</include>
 										<include>hapi-fhir-android/target/jacoco.exec</include>
 										<include>hapi-fhir-validation/target/jacoco.exec</include>
+										-->
 									</includes>
 								</fileSet>
 							</fileSets>
@@ -351,6 +355,7 @@
 					</execution>
 				</executions>
 			</plugin>
+			<!--
 			<plugin>
 				<groupId>org.eluder.coveralls</groupId>
 				<artifactId>coveralls-maven-plugin</artifactId>
@@ -381,7 +386,8 @@
 						<version>2.3.0</version>
 					</dependency>
 				</dependencies>
-			</plugin>
+				</plugin>
+				-->
 			<plugin>
 				<groupId>org.codehaus.mojo</groupId>
 				<artifactId>build-helper-maven-plugin</artifactId>
@@ -394,9 +400,11 @@
 						</goals>
 						<configuration>
 							<sources>
+								<!--
 								<source>../hapi-fhir-base/src/main/java</source>
 								<source>../hapi-fhir-client/src/main/java</source>
 								<source>../hapi-fhir-server/src/main/java</source>
+								-->
 								<source>../hapi-fhir-jpaserver-model/src/main/java</source>
 								<source>../hapi-fhir-jpaserver-searchparam/src/main/java</source>
 								<source>../hapi-fhir-jpaserver-subscription/src/main/java</source>
@@ -424,9 +432,11 @@
 		<resources>
 		</resources>
 		<testResources>
+			<!--
 			<testResource>
 				<directory>../hapi-fhir-base/src/test/resources</directory>
 			</testResource>
+			-->
 			<testResource>
 				<directory>../hapi-fhir-jpaserver-model/src/test/resources</directory>
 			</testResource>
@@ -439,6 +449,7 @@
 			<testResource>
 				<directory>../hapi-fhir-jpaserver-base/src/test/resources</directory>
 			</testResource>
+			<!--
 			<testResource>
 				<directory>../hapi-fhir-structures-dstu/src/test/resources</directory>
 			</testResource>
@@ -454,6 +465,7 @@
 			<testResource>
 				<directory>../hapi-fhir-client-okhttp/src/test/resources</directory>
 			</testResource>
+			-->
 		</testResources>
 	</build>
 	<reporting>

hapi-fhir-jpaserver-base/pom.xml

@@ -660,14 +660,6 @@
 				<groupId>org.jacoco</groupId>
 				<artifactId>jacoco-maven-plugin</artifactId>
 				<configuration>
-					<classFolders>
-						<classFolder>${basedir}/target/classes</classFolder>
-						<classFolder>${basedir}../hapi-fhir-base/target/classes</classFolder>
-					</classFolders>
-					<sourceFolders>
-						<sourceFolder>${basedir}/src/main/java</sourceFolder>
-						<sourceFolder>${basedir}/../hapi-fhir-base/src/main/java</sourceFolder>
-					</sourceFolders>
 					<dumpOnExit>true</dumpOnExit>
 				</configuration>
 				<executions>
@@ -677,6 +669,17 @@
 							<goal>prepare-agent</goal>
 						</goals>
 					</execution>
+					<execution>
+                  <id>post-integration-test</id>
+                  <phase>install</phase>
+                  <goals>
+                     <goal>report</goal>
+                  </goals>
+                  <configuration>
+                     <dataFile>${project.build.directory}/jacoco.exec</dataFile>
+                     <outputDirectory>${project.reporting.outputDirectory}/jacoco-report</outputDirectory>
+                  </configuration>
+               </execution>
 				</executions>
 			</plugin>
 			<plugin>

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/dao/r4/FhirResourceDaoR4SearchPageExpiryTest.java

@@ -324,7 +324,7 @@ public class FhirResourceDaoR4SearchPageExpiryTest extends BaseJpaR4Test {
 			}
 		});
 
-		DatabaseSearchCacheSvcImpl.setNowForUnitTests(search3timestamp.get() + 1100);
+		DatabaseSearchCacheSvcImpl.setNowForUnitTests(search3timestamp.get() + 2100);
 
 		myStaleSearchDeletingSvc.pollForStaleSearchesAndDeleteThem();
 		newTxTemplate().execute(new TransactionCallbackWithoutResult() {

pom.xml

@@ -607,7 +607,7 @@
 		<httpcore_version>4.4.11</httpcore_version>
 		<httpclient_version>4.5.9</httpclient_version>
 		<jackson_version>2.9.9</jackson_version>
-		<jackson_databind_version>2.9.9.1</jackson_databind_version>
+		<jackson_databind_version>2.9.10</jackson_databind_version>
 		<maven_assembly_plugin_version>3.1.0</maven_assembly_plugin_version>
 		<maven_license_plugin_version>1.8</maven_license_plugin_version>
 		<resteasy_version>4.0.0.Beta3</resteasy_version>

src/changes/changes.xml

@@ -13,6 +13,7 @@
 				<![CDATA[
 				<ul>
 					<li>Hibernate Core (Core): 5.4.2.Final -&gt; 5.4.4.Final</li>
+					<li>Jackson Databind (JPA): 2.9.9 -&gt; 2.9.10 (CVE-2019-16335, CVE-2019-14540)</li>
 				</ul>
 				]]>
 			</action>