Merge remote-tracking branch 'remotes/origin/master' into ks-20191119-scheduler

hapi-fhir-cli/hapi-fhir-cli-api/src/test/java/ca/uhn/fhir/cli/HapiFlywayMigrateDatabaseCommandTest.java

@@ -81,7 +81,7 @@ public class HapiFlywayMigrateDatabaseCommandTest {
 	@Test
 	public void testMigrateFrom340_NoFlyway() throws IOException, SQLException {
 
-		File location = getLocation("migrator_h2_test_340_current");
+		File location = getLocation("migrator_h2_test_340_current_noflyway");
 
 		String url = "jdbc:h2:" + location.getAbsolutePath() + ";create=true";
 		DriverTypeEnum.ConnectionProperties connectionProperties = DriverTypeEnum.H2_EMBEDDED.newConnectionProperties(url, "", "");

hapi-fhir-docs/pom.xml

@@ -82,11 +82,6 @@
 			<artifactId>jdom2</artifactId>
 			<version>2.0.6</version>
 		</dependency>
-		<dependency>
-			<groupId>org.slf4j</groupId>
-			<artifactId>slf4j-simple</artifactId>
-			<version>1.7.28</version>
-		</dependency>
 		<!-- Needed for JEE/Servlet support -->
 		<dependency>
 			<groupId>javax.servlet</groupId>

hapi-fhir-jpaserver-base/src/main/java/ca/uhn/fhir/jpa/delete/DeleteConflictList.java

@@ -24,12 +24,17 @@ import ca.uhn.fhir.jpa.util.DeleteConflict;
 import org.apache.commons.lang3.Validate;
 import org.hl7.fhir.instance.model.api.IIdType;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Set;
 import java.util.function.Predicate;
 
 public class DeleteConflictList implements Iterable<DeleteConflict> {
 	private final List<DeleteConflict> myList = new ArrayList<>();
 	private final Set<String> myResourceIdsMarkedForDeletion;
+	private int myRemoveModCount;
 
 	/**
 	 * Constructor
@@ -69,11 +74,38 @@ public class DeleteConflictList implements Iterable<DeleteConflict> {
 
 	@Override
 	public Iterator<DeleteConflict> iterator() {
-		return myList.iterator();
+		// Note that handlers may add items to this list, so we're using a special iterator
+		// that is ok with this. Only removals from the list should trigger a concurrent modification
+		// issue
+		return new Iterator<DeleteConflict>() {
+
+			private final int myOriginalRemoveModCont = myRemoveModCount;
+			private int myNextIndex = 0;
+
+			@Override
+			public boolean hasNext() {
+				checkForCoModification();
+				return myNextIndex < myList.size();
+			}
+
+			@Override
+			public DeleteConflict next() {
+				checkForCoModification();
+				return myList.get(myNextIndex++);
+			}
+
+			private void checkForCoModification() {
+				Validate.isTrue(myOriginalRemoveModCont == myRemoveModCount);
+			}
+		};
 	}
 
 	public boolean removeIf(Predicate<DeleteConflict> theFilter) {
-		return myList.removeIf(theFilter);
+		boolean retVal = myList.removeIf(theFilter);
+		if (retVal) {
+			myRemoveModCount++;
+		}
+		return retVal;
 	}
 
 	public void addAll(DeleteConflictList theNewConflicts) {

hapi-fhir-jpaserver-base/src/test/java/ca/uhn/fhir/jpa/provider/r4/CascadingDeleteInterceptorR4Test.java

@@ -64,6 +64,10 @@ public class CascadingDeleteInterceptorR4Test extends BaseResourceProviderR4Test
 		e.setSubject(new Reference(myPatientId));
 		myEncounterId = ourClient.create().resource(e).execute().getId().toUnqualifiedVersionless();
 
+		CarePlan cp = new CarePlan();
+		cp.setEncounter(new Reference(myEncounterId));
+		ourClient.create().resource(cp).execute();
+
 		Observation o = new Observation();
 		o.setStatus(Observation.ObservationStatus.FINAL);
 		o.setSubject( new Reference(myPatientId));

hapi-fhir-jpaserver-migrate/pom.xml

@@ -101,6 +101,22 @@
 		</pluginManagement>
 
 		<plugins>
+			<plugin>
+				<groupId>org.jacoco</groupId>
+				<artifactId>jacoco-maven-plugin</artifactId>
+				<configuration>
+					<dumpOnExit>true</dumpOnExit>
+				</configuration>
+				<executions>
+					<execution>
+						<id>default-prepare-agent</id>
+						<goals>
+							<goal>prepare-agent</goal>
+						</goals>
+					</execution>
+				</executions>
+			</plugin>
+
 			<!-- Tell Maven which Java source version you want to use -->
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/BaseMigrator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
 import org.flywaydb.core.api.MigrationInfoService;
 

hapi-fhir-jpaserver-migrate/src/main/java/ca/uhn/fhir/jpa/migrate/BruteForceMigrator.java

@@ -1,5 +1,25 @@
 package ca.uhn.fhir.jpa.migrate;
 
+/*-
+ * #%L
+ * HAPI FHIR JPA Server - Migration
+ * %%
+ * Copyright (C) 2014 - 2019 University Health Network
+ * %%
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ * #L%
+ */
+
 import ca.uhn.fhir.jpa.migrate.taskdef.BaseTask;
 import ca.uhn.fhir.rest.server.exceptions.InternalErrorException;
 import org.flywaydb.core.api.MigrationInfoService;

src/changes/changes.xml

@@ -50,6 +50,10 @@
 				ValueSet Precalculation sometimes failed on Oracle DBs due to an invalid SQL function. This
 				has been corrected.
 			</action>
+			<action type="fix">
+				A ConcurrentModificationException was sometimes thrown when performing a cascading delete.
+				This has been corrected.
+			</action>
 		</release>
 		<release version="4.1.0" date="2019-11-13" description="Jitterbug">
 			<action type="add">